Neural replicators analysis of human papillomaviruses

Neural replicators analysis of human papillomaviruses | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Neural replicators analysis of human papillomaviruses Alexandr Alexandrovich Ezhov This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1847539/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract An analysis of complete human papillomavirus genomes using neural replicators is presented. When studying the shape of replicator tables, which reflect the ability of neural networks of different sizes to generate self-reproducing descendants, as well as the structures of the patterns transmitted by them, it was found that this information reliably distinguishes between two subgenera of human papillomaviruses of the genus Alpha, where one subgenus consists of Alpha-2 and Alpha-4 species belonging to warts, and the second subgenus, other species related to diseases of the mucosa, in particular, to cervical cancer. The genera Beta and Gamma are also reliably distinguished from the genus Alpha, in particular, by a different form of transmitted patterns. More interestingly, the genus Nu seems to be a good fit as a type of subgenus containing both Alpha-2 and Alpha-4 species, a fact that has not previously been revealed by conventional analysis based on DNA sequence alignment and genome similarity assessment. In addition, analysis of the patterns transmitted by the replicator network clearly distinguishes porcupine sigma papillomavirus EdPV1 from human Nu, as well as from any other human papillomavirus, which calls into question the well-known argument for horizontal gene transfer between humans and other types of papillomavirus hosts. Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Introduction The use of artificial neural replicators for the analysis of nucleotide sequences of viroid RNA was presented in [ 1 ]. The main idea of ​​the approach was an attempt to differentiate classes of viroids according to their " pathogens ". These virtual pathogens can replicate using the information contained in the viral sequences. As candidates for the role of such artificial pathogens, artificial neural replicators were used in [ 1 ]. In this work, a specific representations of nucleotide sequences were introduced using two incomplete binary codes and it was found that the self-reproduction of neuronal replicators differs in the corresponding two cases. It also turned out that in many cases the patterns transmitted by neural replicators - fuzzy motifs - can have interesting symmetry and contain useful information for further analysis. Here we present the results of the analysis of the genome sequences of both RNA and DNA viruses, with a focus on double-stranded human papillomaviruses. We start with a brief overview of neural replicator analysis (NRA), then briefly touch on the features of replicator tables (RT) for viral genome sequences of different sizes, and devote the main part of the article to the analysis of more than 200 types of human papillomavirus. In conclusion, a discussion of the results obtained is presented. Neural Replicators Analysis The basic artificial neural network model used in Neural Replicators Analysis (NRA) is the self-reproducible neural network (neural replicator) [ 1 , 3 , 4 ]. This model includes the mechanism of synchronously changing threshold of all neurons having binary states x i (+ 1 or − 1) in the standard Hopfield network [ 2 ]. The remarkable phenomena observed in such a system [ 1 , 3 , 4 ] is that in a chain of networks after few steps of transmission a special network arises in a chain which transmit further just those patterns which it learned from its neighbor . So, this network produces its exact copy , or is self-reproducible. The self-reproducible networks are absolutely transparent ones − they show as quasi attractors all learned patterns during the cycle of threshold growth. The model [ 1 ] suggests that neurons take binary values. Though many generalizations of this model permit to avoid this restriction just such code scheme was used for genomic analysis in a previous paper [ 1 ]. In this paper non-traditional representation of nucleotide sequences was used. Instead of four-letter genetic code two binary code schemes to represent these sequences were introduced. The first code (called WS code) combines the Watson-Crick pairs (AT) and (CG) and presents them as a weak (AT) pair encoded by “–1” and a strong (CG) pair encoded by “+1”. The second keto-amino (KM) code combines a wobble pair (TG) encoded with “+1” and a less stable (AC) pair encoded with “–1”. These two incomplete codes were used to construct sets of networks of different sizes K starting from 3 with the Hebbian interconnections calculated with the use of patterns generated by sliding the nucleotide sequence consisting of N nucleotides with a window having a length K. N resulting patterns (note, that their number does not depend on K ) are used to form the Hebbian matrices of interconnections of the two parent fully connected Hopfield networks (for WS and KM coded patterns, correspondingly). For a sliding window of the same size the source parent network can generate a nontrivial replicator with a non-empty set of the patterns for transmission, or non-replicating network with empty set of patterns for transmission. This last network cannot generate descendants or, in other words, cannot breed. The last situation is rather common for some virus types, but, in general, RTs of viruses have non-trivial form. In [ 1 ] it was demonstrated that despite a wide range of RT forms some reasonable approximate categorization of two viroid families can be derived. Other interesting phenomenon is connected to the replicator transmitted patterns - fuzzy motifs . It was shown [ 1 ] that patterns transmitted by replicators contain additional information and often have interesting symmetries and periodicities [ 1 ]. In this paper it is demonstrated that these symmetries can be useful for differentiation of human papillomaviruses genera. Really in this case the sets of WS-coded transmitted patterns simplify to single pattern for the network of maximal size (the replicators of large sizes do not exist) and the analysis of this set becomes easily interpreted. More details about the different additional results of the application of NRA to the study of rather short viroid genomes are presented in [ 1 ]. Application To Virus Genomes Obviously, the approach proposed in [ 1 ] and applied to the analysis of viroids can also be applied to virus genomes. Hepatitis delta virus (HDV) has the smallest DNA genome, closely resembling the RNA genome of viroids [ 5 ], and its replicator table has a form typical of viroids, as well as a small genome, such as that of narnaviruses or mitoviruses (see Fig. 1 ). The replicator tables of other hepatitis viruses have different shapes, but, as we will further see, the RTs of hepatitis A, C, and E viruses have fairly common forms for viruses with modest and large genomes. The main feature of these viruses is that they do not have replicators generated on KM, encoded DNA or RNA sequences (Fig. 2 ). Let us pay attention to the RT of the hepatitis E virus (Fig. 2 E). It also lacks replicators when its RNA sequence is represented by the WS code. For hepatitis A and C, these replicators exist, but only up to a certain maximum size of the neural network: five for hepatitis A and eight for hepatitis C. Also for hepatitis A, there are all replicators of smaller network dimensions (starting from 3). We will call such RTs monotonic. In contrast, for the hepatitis C virus, there is no replicator for network size 6. We will call corresponding RTs nonmonotonic and will further use asterisks to mark corresponding virus data. Further we can forget about right columns of RT and use only maximal size of replicators corresponding to WS code for the analysis. It can be seemed that this information is rather poor, in particular, if we take into account that RT for the virus SARS 2 isolate 2019-nCoV (WHU01 29881 bp ssRNA(+)) is the same as the RT for hepatitis A. But in such a case we can use additional information related to the patterns which use replicator networks for information transmission. For example, for hepatitis A replicators of the size 5 are built on only one pattern: 11–111, while for SARS virus on two patterns: 11–111 and − 11 − 1 -11. As we will see the forms of RT and forms of patterns can give us interesting information about virus genomes similarities and also about their divergence. Analysis Of Human Papillomaviruses Here, we apply the approach described above to the analysis of human papillomavirus (HPV) genomic sequences. HPVs are small, non-enveloped, double-stranded DNA viruses belonging to the Papillomaviridae family. This family was designated as a separate family, Papillomaviridae, in the 7th ICTV report [ 6 ]. The taxonomy of these viruses is usually based on the study of the nucleotide sequences of the main viral capsid protein L1 [ 7 ]. HPV types belonging to different genera share less than 60% similarity within the main capsid protein L1 sequence of the genome. Different types of viruses within the genus have 60 to 70% similarity. The new HPV type has less than 90% similarity to any other HPV type. The papillomavirus nomenclature at the species level and above is determined by the papillomavirus study group of the International Committee on Taxonomy of Viruses [ 8 ]. Human papillomaviruses are classified into 5 genera - Alpha, Beta, Gamma, Mu and Nu, containing many species and types: the number of these types increases linearly with time for the beta genus and extremely rapidly for the gamma genus - the rate of detection of HPV types increases, mainly as the result of metagenomic sequencing [ 9 ]. Here we use species and types taxonomy data provided in [ 10 ] and the relevant NCBI and GenBank references are provided in the Materials section. Instead of RTs, which in this case do not have replicators for CM-encoded sequences for a genome size of about 8000, we will use a convenient visualization of the situation, showing only replicators with WS-code. Next, we will use colors to mark the maximum size of the N max replicator neural network generated using the WS-encoded genome sequence. Thus, the situation of the absence of replicators will be marked in black, the presence of only a replicator of size 3 in purple, the presence of a maximum size 4 in blue, the maximum size 5 in light blue, the maximum size 6 in green, the maximum size 7 in yellow, the maximum size 8 in orange and the maximum size 9 in red (see Fig. 3 ). It turns out that this set of colors is sufficient to characterize all replicators of maximum size for all types of human papillomaviruses studied. We will also use one or two asterisks to denote cases with non-monotonic sets of replicators (up to one maximum size), when a replicator does not exist for one or two smaller sizes, respectively. We start with the genus Alpha papillomavirus and present the results of their study on Fig. 3 . Alpha papillomaviruses Standard characteristics of this genus is that “Alpha HPVs preferentially infect the anogenital and oral mucosa, causing both malignant and benign neoplasms. Cutaneous lesions have also been observed”. [ 11 ]. One of the oncological disease connected with Alpha genus is the cervical cancer (note, however, that HPV belonging to Beta and Gamma genera are also considered as carcinogenic cofactors of cervical cancer [ 12 ]). There are some interesting observations that can be seen in this picture. Firstly, the Alpha-2 and Alpha-4 species, which have a large size of replicators (up to 9), differ significantly from other species of the Alpha papillomavirus genus. It is noteworthy that, unlike the types of other species, it is the types of these two species that cause the formation of skin warts (as we found in [ 7 ] “The genus alpha also includes a few cutaneous HPV types (HPV2, 3, 7, 10, 27, 28, and 57), which cause common and plantar warts " In addition, most types of high oncogenic risk (HR) are characterized by the absence of replicators (black boxes). Thus, using NRA, we can recognize a clear division of the genus Alpha into two subgenera, which was not obtained by a method based on the study of the similarity of the nucleotide sequences of the main capsid protein L1 [ 7 ]. More information can be obtained by considering patterns which are transmitted by replicators of maximal size. In all cases they transmit single patterns which for all types of species Alpha-2, Alpha-4 and also Alpha-3 are periodic with period equals to 2 (see Fig. 4 ). With only one very interesting exception (which will be further discussed) such periodic transmitted patterns are typical only to the Alpha papillomavirus genus. However, for species Alpha-14 non-periodic patterns are transmitted by replicator of the size 5. In order to clarify the situation with Alpha-14 let us consider the Beta genus of human papillomavirus. Beta papillomaviruses Beta HPVs cause only skin lesions and exist in a latent form in the general population, but are activated under conditions of immunosuppression [ 11 ]. Beta HPV types under the influence of certain cofactors can also trigger a malignant process. Recent studies point to the role of human papillomavirus Beta types and HPV-associated inflammation in the development of squamous cell skin cancer (the second most common non-melanoma skin cancer after basal cell carcinoma). But Beta HPV infection appears to play an important role in initiating carcinogenesis, but not in tumor progression [ 13 ]. NRA shows that the "coloristic" of Beta papillomaviruses (Fig. 5 ) differs from what we observe for Alpha papillomaviruses (Fig. 3 ). It is characterized by a predominance of replicators with a maximum size of 5 (blue boxes), a lack of larger replicators (such as those of Alpha-2 and Alpha-4), and a small number of types without replicators at all (Fig. 5 ). Even more remarkable, all 5-neuron replicators transmit a single pattern that is identical to the non-periodic pattern of HPV90 and HPV106 types Alpha-14 (Fig. 3 ). So, in terms of neural replicator analysis, should species Alpha-14 be moved to the genus Beta or other genera? We can clarify this by looking at the genera Gamma and Mu (we realize that this analysis is rather rough and does not claim to draw any solid conclusions). We also note that Beta-1 is the only genus of human papillomaviruses containing types HPV8, HPV47, HPV99, which have transmitted patterns of length 4, and type HPV8 has a complex set of such patterns, including not one, but four members. This type, along with HPV5, HPV20 (Beta-1), HPV17 (Beta-2) and especially HPV28 (Alpha-2), also unique among all human papillomaviruses. It has a pattern length of 6 and is associated with a high risk of developing squamous cell skin cancer [ 13 ]. Gamma papillomaviruses The Gamma papillomavirus genus is highly diverse, but most healthy adults chronically shed Gamma virions from apparently healthy skin surfaces. Recent metagenomic studies have nearly doubled the number of known Gamma HPV types [ 14 ]. While the Beta papillomavirus genus is related to epidermodysplasia verruciforma, patients with the WHIM syndrome (warts, hypogammaglobulinemia, infections, myelokathexis) have been found to be uniquely susceptible to Gamma HPV- associated skin warts. Neural replicator analysis of Gamma papillomaviruses shows that they share some properties with Beta papillomaviruses, but also differ from them. Like Beta papillomaviruses, their types can form replicators with a maximum length of up to 5. More importantly, the only kind of non-periodic transmission pattern is the same as that of Beta papillomaviruses. The number of species of Gamma papillomaviruses is large and, as can be seen from Fig. 6 , the proportion of Gamma papillomaviruses that do not generate neural replicators (black boxes) exceeds 60%, while for Beta papillomaviruses this figure is about 11%. Thus, we can assume that Alpha-14 papillomaviruses species are more similar to Beta, and not to Gamma human papillomaviruses. Mu papillomaviruses Mu papillomaviruses are among the HPV types associated with cutaneous disease. The HPV1 type is responsible for about 30% cases of common warts [ 15 ]. The results obtained for Mu human papillomaviruses show, that they are similar to those for Beta and Gamma papillomaviruses (see Fig. 7 left): the type HPV63 has the same non-periodic transmitted pattern as for the Beta and Gamma genera. Nu papillomaviruses The most interesting result of NRA was obtained for Nu (HPV41) human papillomavirus. Initially, this virus was isolated from a facial wart, but subsequently its DNA was found in some skin carcinomas and precancerous keratoses [ 16 ]. The genomic sequence of this virus is most distantly related to all other types of human papillomaviruses, and HPV41 virus has been identified as the first type of new Nu genus. But NRA analysis shows that it is ideal for Alpha-2 specie because it has a maximal replicator size of 7 as well as the same periodic transmitted pattern (Fig. 7 right). The clinical manifestations of Nu virus infection are similar to those of the Alpha-2 species (although it also causes malignant skin lesions), so this result is not inconsistent with the characteristics of this genus. What is also interesting is that NRA may provide some additional information about the problem of virus transfer to another host, as well as the taxonomy of viruses. As the Van Doorslayer paper says [ 17 ]: “Because of the absence of cross-species infections, it is unlikely that horizontal gene transfer played any role in the evolution of the Papillomaviridae. In fact, a study specifically looking at the influence of horizontal gene transfer identified only a single potential cross-species transmission event. This event involved ancestors of a porcupine (EdPV1) and human (HPV41) papillomavirus [ 18 ]. These two viruses are the only members of a divergent genus (Nu papillomavirus); it will be of interest to see how the inclusion of more viruses in this genus will affect the conclusion of cross-species infection [ 17 ]”. In this situation, it was very interesting to use NRA to study the porcupine EdPV1 virus. It turned out that indeed it has a replicator of maximum size 6 (7 for HPV41), but the pattern transmitted by this replicator (3-periodic) differs significantly not only from the 2-period pattern of HPV41, but also from any pattern transmitted by the replicators of all papillomaviruses (see Fig. 7 right bottom). Thus, from the point of view of the NRA, the porcupine sigma virus EdPV1 cannot be combined with the HPV41 virus into one genus, nor can it be attached to any other genera of human papillomaviruses. Materials Below the data used in the study is presented: it contains the species name, type, NCBI and GenBank accession number and the length of the virus ssDNA are shown. Alpha papillomaviruses Alpha-1 HPV32 NC_001586.1 7961 bp Alpha-7 HPV18 LC636309 7857 bp HPV42 LR862086 7920 bp HPV39 LR862071 7833 bp Alpha-2 HPV3 X74462.1 7820 bp HPV45 EF202167.1 7849 bp HPV10 X74465 7919 bp HPV59 LR862080.1 7898 bp HPV28 U31783.1 7959 bp HPV68 GQ472851.1 7830 bp HPV29 U31784.1 7916 bp HPV70 U21941.1 7905 bp HPV77 Y15175 7887 bp HPV97 EF436229.1 7843 bp HPV78 AB793779 7805 bp Alpha-8 HPV7 MK463913 8037 bp HPV94 GU117628 7872 bp HPV40 X74478 7909 bp HPV117 GQ246950.1 7895 bp HPV43 LR861953 8007 bp HPV125 FN547152.2 7809 bp HPV91 AF419318.1 7966 bp HPV160 AB745694 7779 bp Alpha-9 HPV16 NC_001526.4 7906 bp Alpha-3 HPV61 U31793.1 7989 bp HPV31 LR862053 7878 bp HPV62 AY395706.1 8092 bp HPV33 M12732.1 7909 bp HPV72 X94164.1 7988 bp HPV35 M74117.1 7851 bp HPV81 AJ620209.1 8070 bp HPV52 LC373207.1 7906 bp HPV83 AF151983 8104 bp HPV58 LC376008 7824 bp HPV84 AF293960 7948 bp HPV67 D21208 7801 bp HPV86 AF349909 7983 bp Alpha-10 HPV6 AF092932 8012 bp HPV87 KU298941.1 7992 bp HPV11 HE574705 7933 bp HPV89 KU298945.1 8074 bp HPV13 X62843 7880 bp HPV102 DQ090083.1 8078bp HPV44 LR862067 7836 bp HPV114 GQ244463.1 8069 bp HPV74 LR862050 7902 bp Alpha-4 HPV2 MN605988.1 7859 bp Alpha-11 HPV34 KF436817 7788 bp HPV27 AB211993.1 7831 bp HPV73 LR862011 7716 bp HPV57 MK463925 7848 bp Alpha-13 HPV54 HPU37488 7759 bp Alpha-5 HPV26 NC_001583.1 7855 bp Alpha-14 HPV71 NC_039089 8017 bp HPV51 KF436884 7815 bp HPV90 NC_004104 8033 bp HPV69 KF436864.1 7705 bp HPV196 DQ080082 8035 bp HPV82 AB027021.1 7821 bp Alpha-6 HPV30 LR862000 7843 bp HPV53 NC_001593.1 7856 bp HPV56 LR862083 7866 bp HPV66 LC511686.1 7818 bp Beta papillomaviruses Beta-1 HPV5 JN211194 7746 bp HPV23 U31781.1 7324 bp HPV8 M12737.1 7654 bp HPV37 U31786.1 7421 bp HPV12 X74466.1 7673 bp HPV38 JN211196 7397 bp HPV14 X74467.1 7439 bp HPV80 Y15176.1 7427 bp HPV19 X74470.1 7685 bp HPV100 FM955839.1 7380 bp HPV20 U31778.1 7757 bp HPV104 FV955840 7386 bp HPV21 U31779.1 7779 bp HPV107 EF42222.1 7562 bp HPV24 U31782.1 7452 bp HPV110 EU410348.1 7423 bp HPV25 X74471.1 7713 bp HPV111 EU410349.1 7384 bp HPV36 U31785.1 7722 bp HPV113 FM955842.1 7412 bp HPV47 M32305.1 7726 bp HPV120 FN598907 7304 bp HPV93 AY382778 7450 bp HPV122 GQ845444.1 7397 bp HPV98 FM955837.2 7466 bp HPV145 HM999997 7375 bp HPV99 FM955838 7698 bp HPV151 FN77756 7386 bp HPV105 FM955841.1 7667 bp HPV159 HE963025 7443 bp HPV118 GQ246951.1 7597 bp HPV174 HF930491.1 7359 bp HPV124 GQ845446.1 7489 bp Beta-3 HPV49 NC_001591.1 7560 bp HPV143 HM999995 7715bp HPV75 Y15173.1 7537 bp HPV152 JF304768 7480 bp HPV76 Y15174 7549 bp Beta-2 HPV9 NC_001596.1 7434 bp HPV115 FJ947080.1 7476 bp HPV15 X74468.1 7412 bp Beta-4 HPV92 NC_004500.1 7461 bp HPV17 JN211195 7426 bp Beta-5 HPV96 NC_005134.2 7438 bp HPV22 U31780.1 7368 bp HPV150 FN677755.1 7336 bp Gamma papillomaviruses Gamma-1 HPV4 NC_001457.1 7353 bp Gamma-11 HPV126 NC_016157.1 7326 bp HPV65 X70829.1 7308 bp HPV136 NC_017994.1 7319 bp HPV95 AJ620210.1 7337 bp HPV140 NC_017996.1 7341 bp HPV158 KT698168.1 7192 bp HPV141 HM999993 7384 bp HPV173 KF006400.1 7297 bp HPV154 NC_021483.1 7286 bp HPV205 KT698167.1 7298 bp HPV169 JX413105.1 7252 bp Gamma-2 HPV48 NC_001690.1 7100 bp HPV171 KF006398.1 7261 bp HPV200 KP692114.1 7137 bp HPV202 KP692116.1 7344 bp Gamma-3 HPV50 NC_001691.1 7184 bp Gamma-12 HPV127 NC_014469.1 7181 bp Gamma-4 HPV60 NC_001693.1 7313 bp HPV132 NC_014955.1 7125 bp Gamma-5 HPV88 NC_010329.1 7326 bp HPV148 GU129016.1 7164 bp Gamma-6 HPV101 LR861930 7259 bp HPV157 KT698166.1 7154 bp HPV103 NC_008188.1 7263 bp HPV165 JX444072.1 7129 bp HP108 NC_012213.1 7149 bp HPV199 KJ913662.1 7184 bp Gamma-7 HPV109 NC_012485.1 7346 bp Gamma-13 HPV128 NC_014952.1 7259 bp HPV123 GQ845445.1 7329 bp HPV153 JN171845 7240 bp HPV134 NC_014956.1 7309 bp Gamma-14 HPV131 NC_014954.1 7182 bp HPV138 HM999990.1 7353 bp Gamma-15 HPV135 NC_017993.1 7293 bp HPV139 HM999991.1 7360 bp HPV146 HM999998 7265 bp HPV149 GU117629.1 7333 bp HPV179 NC_022095.1 7228 bp HPV155 JF906559.1 7352 bp Gamma-16 HPV137 NC_017995.1 7236 bp HPV170 JX413110.1 7417 bp Gamma-17 HPV144 NC_017997.1 7271 bp Gamma-8 HPV112 NC_012486.1 7227 bp Gamma-18 HPV175 NC_038524.1 7226 bp HPV119 GQ845441.1 7251 bp Gamma-19 HPV161 NC_038522.1 7238 bp HPV147 HM999996.1 7224 bp HPV162 JX413108.1 7214 bp HPV164 JX413106.1 7233 bp HPV166 NC_019023.1 7212 bp HPV168 KC862317.1 7204 bp Gamma-20 HPV163 NC_028125.1 7233 bp Gamma-9 HPV116 NC_013035.1 7184 bp Gamma-21 HPV167 NC_022892.1 7228 bp HPV129 NC_014953.1 7219 bp Gamma-22 HPV172 NC_038523.1 7203 bp Gamma-10 HPV121 NC_014185.1 7342 bp Gamma-23 HPV156 NC_033781.1 7329 bp HPV130 GU117630.1 7388 bp Gamma-24 HPV178 NC_023891.1 7314 bp HPV133 GU117633.1 7358 bp HPV197 KM085343 7278 bp HPV142 HM999994.1 7374 bp Gamma-25 HPV184 NC_038914.1 7324 bp HPV180 KC108722.1 7356 bp Gamma-27 HPV207 MK645900.1 7247 bp Mu, Nu and Sigma papillomaviruses Mu-1 HPV1 NC_001356.1 7815 bp Mu-2 HPV63 NC_001458.1 7348 bp Mu-3 HPV204 NC_038525.1 7227 bp Nu HPV41 NC_001354.1 7614 bp Sigma EdPV-1 NC_006951.1 7428 bp Discussion While recognizing the limitations of the NRA, we nevertheless believe that its application to human papillomaviruses may provide further insight into the problem of virus taxonomy, or at least provide some additional features such as the form of RT, as well as the form of transmission patterns that may be added to the characteristics of viruses, especially when performing polythetic classification. It has been shown here that this approach can be used to isolate the Alpha human papillomavirus species responsible for the formation of warts and to hypothesize the similarity of the genus Nu with this subgenus of the genus Alpha, as well as the dissimilarity between Nu of the human papillomavirus and the Sigma porcupine virus. The advantages of NRA are associated with the ability to process complete genomes without the need to know their structure, as well as without alignment [ 19 ] of nucleotide sequences of different types of viruses. We hope that NRA can indeed be a useful element in the studies of the virus genome, and the considered case of human papillomavirus is more interesting than the case of viroids [ 1 ]. Perhaps the main advantage of NRA will not be in the ordering of virus types, but rather in the classification of genera. Indeed, such a feature of transmitted patterns as their periodicity can be considered suitable for monothetic classification, but the existence of types that do not have replicators makes this difficult. On the other hand, the absence of replicators and the proportion of such “dead” non-replicating networks in the genus can be considered as a feature for the polythetic classification [ 20 ] of genera (for example, as in the case of differentiation of Beta and Gamma papillomaviruses in this work). The hard question for the NRA's approach is "Why does it work?" also requires future research. The general understanding is that neural networks allow for non-linear data transformation, which proves to be very useful in many applications, including data categorization, classification, and pattern recognition. In addition, being complex systems, they have emergent properties and exhibit emergent patterns—for example, the fine-grained patterns transmitted by replicators. In any case, the world of known viral genomes is so large that there is a large field for future research on the application of NRA and the “artificial pathogen” (neural replicator) model of genomic sequences and for the assessment of their usefulness. Declarations Acknowledgments I am very grateful to Professor Marc H. V. van Regenmortel for his interest to our attempts to apply neural replicators to genome analysis and also to Professor Eörs Szathmáry for his interest to our model of neural self-reproducible networks. Compliance with ethical standards Conflict of interest The author declares that he has no conflict of interest. Ethical approval This research did not contain studies involving human participants or animals by the author. References Ezhov AA (2020) Can artificial neural replicators be useful for studying RNA replicators? Arch Virol 165(11):2513–2529 Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. 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Mol Biol Evol 27(6):1301–1314 Shen-Gunther J, Cai H, Zhang H, Wang Y (2019) Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. Front Genet 10:489 Van Regenmortel MHV (2019) Solving the species problem in viral taxonomy: recommendations on non–Latinized binomial species names and on abandoning attempts to assign metagenomic viral sequences to species taxa. Arch Virol 164:2223–2229 Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About In Review Editorial Policies Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-1847539","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":121205186,"identity":"1bd4a8ee-8bda-44f1-84a4-5ca79bcb357a","order_by":0,"name":"Alexandr Alexandrovich Ezhov","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAr0lEQVRIiWNgGAWjYFACHiCuYGBgY2BsYEggXssZA5CWxgbitTC2GYBYQGuIAfz8Zw8+5p33J59Purn9wQOGe4kE9Uk2nEs25t1mYNkmcxDksGLCWgwO9phJztxmYMAmkQjSkkBYi/1hHqCWOaRoMWDjMZP42ECKFokzPMYGH44Zg7XMSDBIMCaohb//jOGDhBo5A/kZ6Q8+/qhIkCWoBd2dJKofBaNgFIyCUYAdAACWQjfBH6HaLwAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-7208-0623","institution":"Troickij institut innovacionnyh i termoadernyh issledovanij","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Alexandr","middleName":"Alexandrovich","lastName":"Ezhov","suffix":""}],"badges":[],"createdAt":"2022-07-11 16:55:34","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1847539/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1847539/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":24211258,"identity":"99c480a6-dc9c-423b-9607-094258f2b673","added_by":"auto","created_at":"2022-07-22 17:22:10","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":27137,"visible":true,"origin":"","legend":"\u003cp\u003eThe examples of Replicator Tables of viruses with short genome sequencies are characterized by different forms of RT where both WS and also KM coded sequencies generate self-reproducible neural networks – replicators (gray boxes). The absence of replicators is illustrated by blue boxes.\u0026nbsp;\u0026nbsp;1) \u003cem\u003eHepatitis delta virus\u003c/em\u003e genomic RNA,\u0026nbsp;GenBank: D01075.1M, 1682 bp,\u0026nbsp;2) \u003cem\u003eSaccharomyces 23S RNA narnavirus\u003c/em\u003e NC_004050\u0026nbsp;2891 bp, \u0026nbsp;3)\u0026nbsp;\u003cem\u003eFusarium poae narnavirus 1\u003c/em\u003e NCBI Reference Sequence: NC_030865, 2297 bp, 4) \u003cem\u003eOphiostoma mitovirus 5\u003c/em\u003e NC_004053.1 2474 bp 5)\u0026nbsp;\u003cem\u003eBinucleate Rhizoctonia mitovirus K1 isolate\u003c/em\u003e NC_027921.1 2794 bp\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/69c87d9e54964cd64abffedc.png"},{"id":24211260,"identity":"c2dade31-8924-4970-a599-540613639bf7","added_by":"auto","created_at":"2022-07-22 17:22:10","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":33294,"visible":true,"origin":"","legend":"\u003cp\u003eReplicator tables of hepatitis viruses. With the exception of delta viruses (D), all other viruses (A,B,C,E) are characterized by the absence of replicators built using KM-encoded genomic sequences (only blue boxes in the right columns). A)\u0026nbsp;\u003cem\u003eHepatitis A isolate p16\u0026nbsp;virus\u003c/em\u003e genomic RNA,\u0026nbsp;GenBank: KP879217.1, 7476 bp,\u0026nbsp;B) \u003cem\u003eHepatitis B virus isolate MT,\u003c/em\u003e\u0026nbsp;GenBank: KC492739.1,\u0026nbsp;3215 bp,\u0026nbsp;С)\u0026nbsp;\u003cem\u003eHepatitis С virus genotype 1,\u003c/em\u003e NCBI Reference Sequence: NC_004102, 9646 bp, D) \u003cem\u003eHepatitis delta virus\u003c/em\u003e genomic RNA,\u0026nbsp;GenBank: D01075.1M, 1682 bp,\u0026nbsp;\u0026nbsp;E) \u003cem\u003eHepatitis E virus, \u003c/em\u003eNC_001434, 7176 bp.\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/4e16423d35d7360485d77b78.png"},{"id":24210663,"identity":"0c672883-d1f6-4d6f-a199-8f96cda523d7","added_by":"auto","created_at":"2022-07-22 17:17:10","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":92122,"visible":true,"origin":"","legend":"\u003cp\u003eThe maximal size of replicators for different species and types of the genus Alpha of human papillomaviruses. The sets of replicator patterns of the types HPV77, HPV78, HPV72 and HPV106 are non-monotonic (replicator of one of the size lower than the maximal size does not exist – corresponding colored boxes are marked by the asterisk)\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/e66d8aa2269b7eceb6205a2a.png"},{"id":24211628,"identity":"35bb0c89-6d07-43f8-8ed2-87e3130669fa","added_by":"auto","created_at":"2022-07-22 17:27:10","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":68744,"visible":true,"origin":"","legend":"\u003cp\u003eThe single patterns transmitted with replicator networks of maximal size are presented. Neuron states (pattern binary components) are represented by black (state equals to –1) or white (+1) circles. \u0026nbsp;Transmitted patterns corresponding to the Alpha-2,3,4 species are periodic with period equals to 2 (note, that patterns of HPV27 and HPV57 are complementary – shifted by one position). On contrary, the pattern transmitted by replicators corresponding to types HPV90 and HPV106 belonging to\u0026nbsp;Alpha-14 is not periodic.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/1b5335a74bf7df64ca17a27c.png"},{"id":24210666,"identity":"2501941d-03a7-4a16-8b28-922a8d4a744d","added_by":"auto","created_at":"2022-07-22 17:17:10","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":77565,"visible":true,"origin":"","legend":"\u003cp\u003eThe maximum size of replicators for different species and types of the genus Beta human papillomavirus. The sets of many replicator patterns are non-monotonic: one (one asterisk) or two (two asterisks) replicators of length less than the maximum do not exist. Pay attention to a small part of virus types for which there are no replicators (black boxes).\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/0095e972f4b39e7a62180c85.png"},{"id":24210667,"identity":"af8bdc67-d6f5-4f3c-99cb-6ba404fcfcdc","added_by":"auto","created_at":"2022-07-22 17:17:10","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":110154,"visible":true,"origin":"","legend":"\u003cp\u003eThe maximal size of replicators for different species and types of the Gamma genus of human papillomaviruses. The sets of some replicator patterns are non-monotonic, with one (one asterisk) or two (two asterisks) less than maximum replicators missing. Pay attention to most of the types of viruses for which there are no replicators (black boxes).\u003c/p\u003e","description":"","filename":"floatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/34fdfe26933455a41713fa9f.png"},{"id":24210669,"identity":"88d28bb8-3812-4572-ad16-de8c54878519","added_by":"auto","created_at":"2022-07-22 17:17:10","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":52584,"visible":true,"origin":"","legend":"\u003cp\u003eMaximum size of replicators for different species and genus types Mu (top left) and Nu (top right) of human papillomavirus and porcupine papillomavirus EdPV1 (bottom right). The patterns transmitted by replicators are presented. The pattern of the EdPv1 virus differs both from the 2-period pattern of human papillomavirus Nu (and Alpha genus) and from the aperiodic pattern of the Mu, Beta and Gamma genera.\u003c/p\u003e","description":"","filename":"floatimage7.png","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/0edd10b8bea049019247f251.png"},{"id":27341015,"identity":"778d8e87-468a-4e4c-8b8e-777ce2fe5357","added_by":"auto","created_at":"2022-10-04 19:53:32","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":968894,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1847539/v1/5cf4609c-f57c-400e-9bb6-752496e1e442.pdf"}],"financialInterests":"","formattedTitle":"Neural replicators analysis of human papillomaviruses","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe use of artificial neural replicators for the analysis of nucleotide sequences of viroid RNA was presented in [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. The main idea of ​​the approach was an attempt to differentiate classes of viroids according to their \"\u003cem\u003epathogens\u003c/em\u003e\". These virtual pathogens can replicate using the information contained in the viral sequences. As candidates for the role of such artificial pathogens, artificial neural replicators were used in [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. In this work, a specific representations of nucleotide sequences were introduced using two incomplete binary codes and it was found that the self-reproduction of neuronal replicators differs in the corresponding two cases. It also turned out that in many cases the patterns transmitted by neural replicators \u003cem\u003e- fuzzy motifs\u003c/em\u003e - can have interesting symmetry and contain useful information for further analysis.\u003c/p\u003e \u003cp\u003eHere we present the results of the analysis of the genome sequences of both RNA and DNA viruses, with a focus on double-stranded human papillomaviruses. We start with a brief overview of neural replicator analysis (NRA), then briefly touch on the features of replicator tables (RT) for viral genome sequences of different sizes, and devote the main part of the article to the analysis of more than 200 types of human papillomavirus. In conclusion, a discussion of the results obtained is presented.\u003c/p\u003e\n\u003ch2\u003eNeural Replicators Analysis\u003c/h2\u003e\n\u003cp\u003e \u003cdiv class=\"BlockQuote\"\u003e \u003cp\u003eThe basic artificial neural network model used in Neural Replicators Analysis (NRA) is the self-reproducible neural network (neural replicator) [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. This model includes the mechanism of synchronously changing threshold of all neurons having binary states x\u003csub\u003ei\u003c/sub\u003e (+\u0026thinsp;1 or \u0026minus;\u0026thinsp;1) in the standard Hopfield network [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. The remarkable phenomena observed in such a system [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e] is that in a chain of networks after few steps of transmission a special network arises in a chain which transmit further \u003cem\u003ejust those patterns which it learned from its neighbor\u003c/em\u003e. So, this network produces its \u003cem\u003eexact copy\u003c/em\u003e, or is self-reproducible. The self-reproducible networks are absolutely transparent ones\u0026thinsp;\u0026minus;\u0026thinsp;they show as quasi attractors all learned patterns during the cycle of threshold growth. The model [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e] suggests that neurons take binary values. Though many generalizations of this model permit to avoid this restriction just such code scheme was used for genomic analysis in a previous paper [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. In this paper \u003cem\u003enon-traditional representation\u003c/em\u003e of nucleotide sequences was used. Instead of four-letter genetic code \u003cem\u003etwo binary code schemes\u003c/em\u003e to represent these sequences were introduced. The first code (called WS code) combines the Watson-Crick pairs (AT) and (CG) and presents them as a weak (AT) pair encoded by \u0026ldquo;\u0026ndash;1\u0026rdquo; and a strong (CG) pair encoded by \u0026ldquo;+1\u0026rdquo;. The second keto-amino (KM) code combines a wobble pair (TG) encoded with \u0026ldquo;+1\u0026rdquo; and a less stable (AC) pair encoded with \u0026ldquo;\u0026ndash;1\u0026rdquo;. These two incomplete codes were used to construct sets of networks of different sizes \u003cem\u003eK\u003c/em\u003e starting from 3 with the Hebbian interconnections calculated with the use of patterns generated by sliding the nucleotide sequence consisting of \u003cem\u003eN\u003c/em\u003e nucleotides with a window having a length \u003cem\u003eK. N\u003c/em\u003e resulting patterns (note, that their number does not depend on \u003cem\u003eK\u003c/em\u003e) are used to form the Hebbian matrices of interconnections of the two parent fully connected Hopfield networks (for WS and KM coded patterns, correspondingly). For a sliding window of the same size the source parent network can generate a nontrivial replicator with a non-empty set of the patterns for transmission, or non-replicating network with empty set of patterns for transmission. This last network cannot generate descendants or, in other words, cannot breed. The last situation is rather common for some virus types, but, in general, RTs of viruses have non-trivial form. In [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e] it was demonstrated that despite a wide range of RT forms some reasonable approximate categorization of two viroid families can be derived. Other interesting phenomenon is connected to the replicator transmitted patterns - \u003cem\u003efuzzy motifs\u003c/em\u003e. It was shown [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e] that patterns transmitted by replicators contain additional information and often have interesting symmetries and periodicities [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. In this paper it is demonstrated that these symmetries can be useful for differentiation of human papillomaviruses genera. Really in this case the sets of WS-coded transmitted patterns simplify to single pattern for the network of maximal size (the replicators of large sizes do not exist) and the analysis of this set becomes easily interpreted. More details about the different additional results of the application of NRA to the study of rather short viroid genomes are presented in [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003c/p\u003e\n\u003ch2\u003eApplication To Virus Genomes\u003c/h2\u003e\n\u003cp\u003eObviously, the approach proposed in [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e] and applied to the analysis of viroids can also be applied to virus genomes. Hepatitis delta virus (HDV) has the smallest DNA genome, closely resembling the RNA genome of viroids [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e], and its replicator table has a form typical of viroids, as well as a small genome, such as that of narnaviruses or mitoviruses (see Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eThe replicator tables of other hepatitis viruses have different shapes, but, as we will further see, the RTs of hepatitis A, C, and E viruses have fairly common forms for viruses with modest and large genomes. The main feature of these viruses is that they do not have replicators generated on KM, encoded DNA or RNA sequences (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e\u003cp\u003eLet us pay attention to the RT of the hepatitis E virus (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eE). It also lacks replicators when its RNA sequence is represented by the WS code. For hepatitis A and C, these replicators exist, but only up to a certain maximum size of the neural network: five for hepatitis A and eight for hepatitis C. Also for hepatitis A, there are all replicators of smaller network dimensions (starting from 3). We will call such RTs monotonic. In contrast, for the hepatitis C virus, there is no replicator for network size 6. We will call corresponding RTs nonmonotonic and will further use asterisks to mark corresponding virus data.\u003c/p\u003e \u003cp\u003eFurther we can forget about right columns of RT and use only maximal size of replicators corresponding to WS code for the analysis. It can be seemed that this information is rather poor, in particular, if we take into account that RT for the virus SARS 2 isolate 2019-nCoV (WHU01 29881 bp ssRNA(+)) is the same as the RT for hepatitis A. But in such a case we can use additional information related to the patterns which use replicator networks for information transmission. For example, for hepatitis A replicators of the size 5 are built on only one pattern: 11\u0026ndash;111, while for SARS virus on two patterns: 11\u0026ndash;111 and \u0026minus;\u0026thinsp;11\u0026thinsp;\u0026minus;\u0026thinsp;1 -11. As we will see the forms of RT and forms of patterns can give us interesting information about virus genomes similarities and also about their divergence.\u003c/p\u003e\n\u003ch2\u003eAnalysis Of Human Papillomaviruses\u003c/h2\u003e\n\u003cp\u003eHere, we apply the approach described above to the analysis of human papillomavirus (HPV) genomic sequences. HPVs are small, non-enveloped, double-stranded DNA viruses belonging to the Papillomaviridae family. This family was designated as a separate family, Papillomaviridae, in the 7th ICTV report [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. The taxonomy of these viruses is usually based on the study of the nucleotide sequences of the main viral capsid protein L1 [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. HPV types belonging to different genera share less than 60% similarity within the main capsid protein L1 sequence of the genome. Different types of viruses within the genus have 60 to 70% similarity. The new HPV type has less than 90% similarity to any other HPV type. The papillomavirus nomenclature at the species level and above is determined by the papillomavirus study group of the International Committee on Taxonomy of Viruses [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. Human papillomaviruses are classified into 5 genera - Alpha, Beta, Gamma, Mu and Nu, containing many species and types: the number of these types increases linearly with time for the beta genus and extremely rapidly for the gamma genus - the rate of detection of HPV types increases, mainly as the result of metagenomic sequencing [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. Here we use species and types taxonomy data provided in [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e] and the relevant NCBI and GenBank references are provided in the \u003cspan refid=\"Sec10\" class=\"InternalRef\"\u003eMaterials\u003c/span\u003e section.\u003c/p\u003e \u003cp\u003eInstead of RTs, which in this case do not have replicators for CM-encoded sequences for a genome size of about 8000, we will use a convenient visualization of the situation, showing only replicators with WS-code. Next, we will use colors to mark the maximum size of the N\u003csub\u003emax\u003c/sub\u003e replicator neural network generated using the WS-encoded genome sequence. Thus, the situation of the absence of replicators will be marked in black, the presence of only a replicator of size 3 in purple, the presence of a maximum size 4 in blue, the maximum size 5 in light blue, the maximum size 6 in green, the maximum size 7 in yellow, the maximum size 8 in orange and the maximum size 9 in red (see Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). It turns out that this set of colors is sufficient to characterize all replicators of maximum size for all types of human papillomaviruses studied. We will also use one or two asterisks to denote cases with non-monotonic sets of replicators (up to one maximum size), when a replicator does not exist for one or two smaller sizes, respectively. We start with the genus Alpha papillomavirus and present the results of their study on Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e.\u003c/p\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eAlpha papillomaviruses\u003c/h2\u003e \u003cp\u003eStandard characteristics of this genus is that \u0026ldquo;Alpha HPVs preferentially infect the anogenital and oral mucosa, causing both malignant and benign neoplasms. Cutaneous lesions have also been observed\u0026rdquo;. [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. One of the oncological disease connected with Alpha genus is the cervical cancer (note, however, that HPV belonging to Beta and Gamma genera are also considered as carcinogenic cofactors of cervical cancer [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]).\u003c/p\u003e\u003cp\u003eThere are some interesting observations that can be seen in this picture. Firstly, the Alpha-2 and Alpha-4 species, which have a large size of replicators (up to 9), differ significantly from other species of the Alpha papillomavirus genus. It is noteworthy that, unlike the types of other species, it is the types of these two species that cause the formation of skin warts (as we found in [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e] \u0026ldquo;The genus alpha also includes a few cutaneous HPV types (HPV2, 3, 7, 10, 27, 28, and 57), which cause common and plantar warts \" In addition, most types of high oncogenic risk (HR) are characterized by the absence of replicators (black boxes). Thus, using NRA, we can recognize a clear division of the genus Alpha into two subgenera, which was not obtained by a method based on the study of the similarity of the nucleotide sequences of the main capsid protein L1 [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMore information can be obtained by considering patterns which are transmitted by replicators of maximal size. In all cases they transmit single patterns which for all types of species Alpha-2, Alpha-4 and also Alpha-3 are \u003cem\u003eperiodic\u003c/em\u003e with period equals to 2 (see Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). With only one very interesting exception (which will be further discussed) such periodic transmitted patterns are typical only to the Alpha papillomavirus genus. However, for species Alpha-14 non-periodic patterns are transmitted by replicator of the size 5. In order to clarify the situation with Alpha-14 let us consider the Beta genus of human papillomavirus.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003eBeta papillomaviruses\u003c/h2\u003e \u003cp\u003eBeta HPVs cause only skin lesions and exist in a latent form in the general population, but are activated under conditions of immunosuppression [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. Beta HPV types under the influence of certain cofactors can also trigger a malignant process. Recent studies point to the role of human papillomavirus Beta types and HPV-associated inflammation in the development of squamous cell skin cancer (the second most common non-melanoma skin cancer after basal cell carcinoma). But Beta HPV infection appears to play an important role in initiating carcinogenesis, but not in tumor progression [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. NRA shows that the \"coloristic\" of Beta papillomaviruses (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e) differs from what we observe for Alpha papillomaviruses (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). It is characterized by a predominance of replicators with a maximum size of 5 (blue boxes), a lack of larger replicators (such as those of Alpha-2 and Alpha-4), and a small number of types without replicators at all (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). Even more remarkable, all 5-neuron replicators transmit a single pattern that is \u003cem\u003eidentical\u003c/em\u003e to the non-periodic pattern of HPV90 and HPV106 types Alpha-14 (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). So, in terms of neural replicator analysis, should species Alpha-14 be moved to the genus Beta or other genera? We can clarify this by looking at the genera Gamma and Mu (we realize that this analysis is rather rough and does not claim to draw any solid conclusions). We also note that Beta-1 is the only genus of human papillomaviruses containing types HPV8, HPV47, HPV99, which have transmitted patterns of length 4, and type HPV8 has a complex set of such patterns, including not one, but four members. This type, along with HPV5, HPV20 (Beta-1), HPV17 (Beta-2) and especially HPV28 (Alpha-2), also unique among all human papillomaviruses. It has a pattern length of 6 and is associated with a high risk of developing squamous cell skin cancer [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003eGamma papillomaviruses\u003c/h2\u003e \u003cp\u003eThe Gamma papillomavirus genus is highly diverse, but most healthy adults chronically shed Gamma virions from apparently healthy skin surfaces. Recent metagenomic studies have nearly doubled the number of known Gamma HPV types [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. While the Beta papillomavirus genus is related to epidermodysplasia verruciforma, patients with the WHIM syndrome (warts, hypogammaglobulinemia, infections, myelokathexis) have been found to be uniquely susceptible to Gamma HPV- associated skin warts.\u003c/p\u003e \u003cp\u003eNeural replicator analysis of Gamma papillomaviruses shows that they share some properties with Beta papillomaviruses, but also differ from them. Like Beta papillomaviruses, their types can form replicators with a maximum length of up to 5. More importantly, the only kind of non-periodic transmission pattern is the same as that of Beta papillomaviruses. The number of species of Gamma papillomaviruses is large and, as can be seen from Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, the proportion of Gamma papillomaviruses that do not generate neural replicators (black boxes) exceeds 60%, while for Beta papillomaviruses this figure is about 11%. Thus, we can assume that Alpha-14 papillomaviruses species are more similar to Beta, and not to Gamma human papillomaviruses.\u003c/p\u003e\u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eMu papillomaviruses\u003c/h2\u003e \u003cp\u003eMu papillomaviruses are among the HPV types associated with cutaneous disease. The HPV1 type is responsible for about 30% cases of common warts [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. The results obtained for Mu human papillomaviruses show, that they are similar to those for Beta and Gamma papillomaviruses (see Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e left): the type HPV63 has the same non-periodic transmitted pattern as for the Beta and Gamma genera.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003eNu papillomaviruses\u003c/h2\u003e \u003cp\u003eThe most interesting result of NRA was obtained for Nu (HPV41) human papillomavirus. Initially, this virus was isolated from a facial wart, but subsequently its DNA was found in some skin carcinomas and precancerous keratoses [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. The genomic sequence of this virus is most distantly related to all other types of human papillomaviruses, and HPV41 virus has been identified as the first type of new Nu genus. But NRA analysis shows that it is ideal for Alpha-2 specie because it has a maximal replicator size of 7 as well as the same periodic transmitted pattern (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e right). The clinical manifestations of Nu virus infection are similar to those of the Alpha-2 species (although it also causes malignant skin lesions), so this result is not inconsistent with the characteristics of this genus. What is also interesting is that NRA may provide some additional information about the problem of virus transfer to another host, as well as the taxonomy of viruses. As the Van Doorslayer paper says [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]:\u003c/p\u003e \u003cp\u003e\u0026ldquo;Because of the absence of cross-species infections, it is unlikely that horizontal gene transfer played any role in the evolution of the Papillomaviridae. In fact, a study specifically looking at the influence of horizontal gene transfer identified only a single potential cross-species transmission event. This event involved ancestors of a porcupine (EdPV1) and human (HPV41) papillomavirus [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. These two viruses are the only members of a divergent genus (Nu papillomavirus); it will be of interest to see how the inclusion of more viruses in this genus will affect the conclusion of cross-species infection [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]\u0026rdquo;.\u003c/p\u003e \u003cp\u003eIn this situation, it was very interesting to use NRA to study the porcupine EdPV1 virus. It turned out that indeed it has a replicator of maximum size 6 (7 for HPV41), but the pattern transmitted by this replicator (3-periodic) differs significantly not only from the 2-period pattern of HPV41, but also from any pattern transmitted by the replicators of all papillomaviruses (see Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e right bottom). Thus, from the point of view of the NRA, the porcupine sigma virus EdPV1 cannot be combined with the HPV41 virus into one genus, nor can it be attached to any other genera of human papillomaviruses.\u003c/p\u003e \u003c/div\u003e"},{"header":"Materials","content":"\u003cp\u003eBelow the data used in the study is presented: it contains the species name, type, NCBI and GenBank accession number and the length of the virus ssDNA are shown.\u003c/p\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eAlpha papillomaviruses\u003c/h2\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Taba\" border=\"1\"\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eAlpha-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001586.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7961 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"6\" rowspan=\"7\"\u003e \u003cp\u003eAlpha-7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLC636309\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7857 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV42\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLR862086\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7920 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV39\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862071\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7833 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"9\" rowspan=\"10\"\u003e \u003cp\u003eAlpha-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX74462.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7820 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eEF202167.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7849 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX74465\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7919 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862080.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7898 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU31783.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7959 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eGQ472851.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7830 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU31784.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7916 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eU21941.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7905 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV77\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY15175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7887 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV97\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eEF436229.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7843 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV78\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAB793779\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7805 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eAlpha-8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eMK463913\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8037 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV94\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGU117628\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7872 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eX74478\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7909 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV117\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGQ246950.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7895 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV43\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR861953\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8007 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV125\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eFN547152.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7809 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV91\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAF419318.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7966 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV160\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAB745694\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7779 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"6\" rowspan=\"7\"\u003e \u003cp\u003eAlpha-9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_001526.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7906 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"10\" rowspan=\"11\"\u003e \u003cp\u003eAlpha-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV61\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU31793.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7989 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862053\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7878 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAY395706.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8092 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV33\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eM12732.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7909 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX94164.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7988 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV35\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eM74117.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7851 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV81\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAJ620209.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8070 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV52\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLC373207.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7906 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV83\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAF151983\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8104 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLC376008\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7824 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV84\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAF293960\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7948 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eD21208\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7801 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV86\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAF349909\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7983 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"4\" rowspan=\"5\"\u003e \u003cp\u003eAlpha-10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eAF092932\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8012 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV87\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKU298941.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7992 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHE574705\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7933 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV89\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKU298945.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8074 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eX62843\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7880 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV102\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eDQ090083.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8078bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV44\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862067\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7836 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV114\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGQ244463.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8069 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV74\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862050\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7902 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eAlpha-4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMN605988.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7859 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eAlpha-11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKF436817\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7788 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAB211993.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7831 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLR862011\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7716 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMK463925\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7848 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAlpha-13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHPU37488\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7759 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eAlpha-5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001583.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7855 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eAlpha-14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_039089\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8017 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKF436884\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7815 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV90\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_004104\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8033 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV69\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKF436864.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7705 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV196\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDQ080082\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e8035 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV82\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAB027021.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7821 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"4\" morerows=\"4\" nameend=\"c8\" namest=\"c5\" rowspan=\"5\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eAlpha-6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLR862000\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7843 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV53\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001593.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7856 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV56\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLR862083\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7866 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV66\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLC511686.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7818 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eBeta papillomaviruses\u003c/h2\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Tabb\" border=\"1\"\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"18\" rowspan=\"19\"\u003e \u003cp\u003eBeta-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJN211194\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7746 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"15\" rowspan=\"16\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eU31781.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7324 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eM12737.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7654 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eU31786.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7421 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX74466.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7673 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eJN211196\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7397 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX74467.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7439 bp\u003c/p\u003e \u003c/td\u003e 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align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7713 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV111\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eEU410349.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7384 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV36\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU31785.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7722 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eFM955842.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7412 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV47\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eM32305.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7726 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV120\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eFN598907\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7304 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAY382778\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7450 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV122\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eGQ845444.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7397 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eFM955837.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7466 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV145\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHM999997\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7375 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV99\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e 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align=\"left\" colname=\"c5\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eBeta-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV49\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_001591.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7560 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV143\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHM999995\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7715bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV75\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eY15173.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7537 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV152\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJF304768\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7480 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eY15174\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7549 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"3\" rowspan=\"4\"\u003e \u003cp\u003eBeta-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001596.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7434 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV115\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eFJ947080.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7476 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX74468.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7412 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eBeta-4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV92\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_004500.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7461 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJN211195\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7426 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eBeta-5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV96\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_005134.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7438 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU31780.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7368 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV150\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eFN677755.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7336 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eGamma papillomaviruses\u003c/h2\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Tabc\" border=\"1\"\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eGamma-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001457.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7353 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"7\" rowspan=\"8\"\u003e \u003cp\u003eGamma-11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV126\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_016157.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7326 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV65\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eX70829.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7308 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV136\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_017994.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7319 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV95\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAJ620210.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7337 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV140\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_017996.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7341 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV158\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKT698168.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7192 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV141\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHM999993\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7384 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV173\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKF006400.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7297 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV154\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_021483.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7286 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV205\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKT698167.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7298 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV169\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eJX413105.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7252 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eGamma-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001690.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7100 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV171\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKF006398.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7261 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV200\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKP692114.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7137 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV202\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKP692116.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7344 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGamma-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV50\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001691.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7184 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eGamma-12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV127\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_014469.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7181 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGamma-4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001693.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7313 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV132\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_014955.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7125 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGamma-5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV88\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_010329.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7326 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV148\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eGU129016.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7164 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eGamma-6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV101\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eLR861930\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7259 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV157\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKT698166.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7154 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV103\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_008188.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7263 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV165\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eJX444072.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7129 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHP108\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_012213.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7149 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV199\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKJ913662.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7184 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"7\" rowspan=\"8\"\u003e \u003cp\u003eGamma-7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV109\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_012485.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7346 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eGamma-13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV128\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_014952.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7259 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV123\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGQ845445.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7329 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV153\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eJN171845\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7240 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV134\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_014956.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7309 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_014954.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7182 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV138\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHM999990.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7353 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eGamma-15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV135\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_017993.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7293 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV139\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHM999991.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7360 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV146\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eHM999998\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7265 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV149\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGU117629.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7333 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV179\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_022095.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7228 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV155\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJF906559.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7352 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV137\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_017995.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7236 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV170\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJX413110.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7417 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV144\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_017997.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7271 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"4\" rowspan=\"5\"\u003e \u003cp\u003eGamma-8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV112\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_012486.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7227 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV175\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_038524.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7226 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV119\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGQ845441.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7251 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eGamma-19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV161\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_038522.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7238 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV147\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHM999996.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7224 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV162\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eJX413108.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7214 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV164\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eJX413106.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7233 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV166\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_019023.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7212 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV168\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKC862317.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7204 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV163\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_028125.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7233 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eGamma-9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV116\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_013035.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7184 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV167\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_022892.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7228 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV129\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_014953.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7219 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV172\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_038523.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7203 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"4\" rowspan=\"5\"\u003e \u003cp\u003eGamma-10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV121\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_014185.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7342 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV156\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_033781.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7329 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV130\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGU117630.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7388 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eGamma-24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV178\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_023891.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7314 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV133\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGU117633.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7358 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV197\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eKM085343\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7278 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV142\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eHM999994.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7374 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV184\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNC_038914.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7324 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV180\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eKC108722.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7356 bp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eGamma-27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHPV207\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eMK645900.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e7247 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eMu, Nu and Sigma papillomaviruses\u003c/h2\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Tabd\" border=\"1\"\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMu-1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001356.1\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7815 bp\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMu-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV63\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001458.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7348 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMu-3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV204\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_038525.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7227 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHPV41\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_001354.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7614 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSigma\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEdPV-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eNC_006951.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7428 bp\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eWhile recognizing the limitations of the NRA, we nevertheless believe that its application to human papillomaviruses may provide further insight into the problem of virus taxonomy, or at least provide some additional features such as the form of RT, as well as the form of transmission patterns that may be added to the characteristics of viruses, especially when performing polythetic classification. It has been shown here that this approach can be used to isolate the Alpha human papillomavirus species responsible for the formation of warts and to hypothesize the similarity of the genus Nu with this subgenus of the genus Alpha, as well as the dissimilarity between Nu of the human papillomavirus and the Sigma porcupine virus. The advantages of NRA are associated with the ability to process complete genomes without the need to know their structure, as well as without alignment [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e] of nucleotide sequences of different types of viruses. We hope that NRA can indeed be a useful element in the studies of the virus genome, and the considered case of human papillomavirus is more interesting than the case of viroids [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Perhaps the main advantage of NRA will not be in the ordering of virus types, but rather in the classification of genera. Indeed, such a feature of transmitted patterns as their periodicity can be considered suitable for monothetic classification, but the existence of types that do not have replicators makes this difficult. On the other hand, the absence of replicators and the proportion of such \u0026ldquo;dead\u0026rdquo; non-replicating networks in the genus can be considered as a feature for the polythetic classification [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e] of genera (for example, as in the case of differentiation of Beta and Gamma papillomaviruses in this work). The hard question for the NRA's approach is \"Why does it work?\" also requires future research. The general understanding is that neural networks allow for non-linear data transformation, which proves to be very useful in many applications, including data categorization, classification, and pattern recognition. In addition, being complex systems, they have emergent properties and exhibit emergent patterns\u0026mdash;for example, the fine-grained patterns transmitted by replicators. In any case, the world of known viral genomes is so large that there is a large field for future research on the application of NRA and the \u0026ldquo;artificial pathogen\u0026rdquo; (neural replicator) model of genomic sequences and for the assessment of their usefulness.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eI am very grateful to Professor Marc H. V. van Regenmortel for his interest to our attempts to apply neural replicators to genome analysis and also to Professor \u0026nbsp;E\u0026ouml;rs Szathm\u0026aacute;ry for his interest to our model of neural self-reproducible networks.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompliance with ethical standards\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe author declares that he has no conflict of interest.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical approval\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThis research did not contain studies involving human participants or animals by the author.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eEzhov AA (2020) Can artificial neural replicators be useful for studying RNA replicators? Arch Virol 165(11):2513\u0026ndash;2529\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. PNAS 79:2554\u0026ndash;2558\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEzhov AA, Vvedensky VL, Khromov AG, Knizhnikova LA (1991) Self-reproducible neural networks with synchronously changing neuronal threshold. In: Holden AV, Kryukov VI (eds) Neurocomputers and attention II: connectionism and neurocomputers. Manchester University Press, pp 523\u0026ndash;534\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEzhov AA, Khromov AG, Knizhnikova LA, Vvedensky VL (1991) Self-reproducible networks: classification, antagonistic rules and generalization. Neural Networks World 1:52\u0026ndash;57\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFlores 2012] Flores R, Ruiz-Ruiz S, Serra P (2012) Viroids and hepatitis delta virus. 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Virology 445:11\u0026ndash;20\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePocrupine 1] Shah SD, Doorbar J, Goldstein RA (2010) Analysis of Host\u0026ndash;Parasite Incongruence in Papillomavirus Evolution Using Importance Sampling. Mol Biol Evol 27(6):1301\u0026ndash;1314\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eShen-Gunther J, Cai H, Zhang H, Wang Y (2019) Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. Front Genet 10:489\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVan Regenmortel MHV (2019) Solving the species problem in viral taxonomy: recommendations on non\u0026ndash;Latinized binomial species names and on abandoning attempts to assign metagenomic viral sequences to species taxa. Arch Virol 164:2223\u0026ndash;2229\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-1847539/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1847539/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eAn analysis of complete human papillomavirus genomes using neural replicators is presented. When studying the shape of replicator tables, which reflect the ability of neural networks of different sizes to generate self-reproducing descendants, as well as the structures of the patterns transmitted by them, it was found that this information reliably distinguishes between two subgenera of human papillomaviruses of the genus Alpha, where one subgenus consists of Alpha-2 and Alpha-4 species belonging to warts, and the second subgenus, other species related to diseases of the mucosa, in particular, to cervical cancer. The genera Beta and Gamma are also reliably distinguished from the genus Alpha, in particular, by a different form of transmitted patterns. More interestingly, the genus Nu seems to be a good fit as a type of subgenus containing both Alpha-2 and Alpha-4 species, a fact that has not previously been revealed by conventional analysis based on DNA sequence alignment and genome similarity assessment. In addition, analysis of the patterns transmitted by the replicator network clearly distinguishes porcupine sigma papillomavirus EdPV1 from human Nu, as well as from any other human papillomavirus, which calls into question the well-known argument for horizontal gene transfer between humans and other types of papillomavirus hosts.\u003c/p\u003e","manuscriptTitle":"Neural replicators analysis of human papillomaviruses","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2022-07-22 17:17:08","doi":"10.21203/rs.3.rs-1847539/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"cb91906c-629b-4660-90eb-15ed8b16e087","owner":[],"postedDate":"July 22nd, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2022-10-04T19:53:21+00:00","versionOfRecord":[],"versionCreatedAt":"2022-07-22 17:17:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-1847539","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-1847539","identity":"rs-1847539","version":["v1"]},"buildId":"i_I_jhV-QviBjPLXJga9V","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}