Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7

Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7 | 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 Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7 Shaolei Ren, Liang Xue, Junshan Gao, Weicheng Cai, Peng Lin This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4236232/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 5 You are reading this latest preprint version Abstract A significant foodborne pathogen that causes acute gastroenteritis worldwide is sapovirus. Currently, there have been reports of certain recombinant strains of sapovirus, and the genetic diversity of this virus is continuously increasing. In this study, sapovirus nucleotide sequences with entire VP1 and NS6-7 regions were obtained from GenBank, and phylogenetic analysis and genetic distance calculations were performed to investigate the genetic diversity of the VP1 and NS6-7 regions of this virus. In addition to the 19 known genogroups, a small number of sequences were discovered to be beyond the range of known genogroups and were temporarily divided (Bat NA1-Bat NA3). This was based on the genetic diversity of the entire VP1 region. Based on the VP1 region, 38 key reference sequences were also suggested. Furthermore, for 33 sequences for which the genotyping tool mistyped, the genotype and genogroup information were modified. We also attempted to categorize sapovirus based on the genetic diversity of the nucleotide sequences of NS6-7 region. Phylogenetically, 17 P (polymerase)-groups (GI.P-GIII.P, GV.P-GVIII.P, GX.P-GXIX.P) and one tentative (GNA1.P) were identified based on the genetic diversity of nucleotide sequences in the entire NS6-7 region, and 35 related reference sequences were also suggested. Nine recombinant sequences, including six recombinant genotypes (GI.1[P4], GI.2[P1], GII.4[P1], GII.4[PNA1], GII.6[P2], and GV.5[P3]), were identified by genetic diversity differences between VP1 and NS6-7 of sapovirus. With this approach, sapovirus recombination events may be effectively characterized. Sapovirus Genetic diversity Reference sequences Recombination Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Full Text Additional Declarations Tables 1-3 are available in the Supplementary Files section. Supplementary Files Table1.docx Table2.docx Table3.docx Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Major Revision - English Corrections 29 May, 2024 Reviewers agreed at journal 17 Apr, 2024 Reviewers invited by journal 15 Apr, 2024 Editor assigned by journal 09 Apr, 2024 First submitted to journal 08 Apr, 2024 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board 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-4236232","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":291427432,"identity":"517a686b-b0ba-4020-8770-d1f113e24bb0","order_by":0,"name":"Shaolei Ren","email":"","orcid":"","institution":"Bohai University","correspondingAuthor":false,"prefix":"","firstName":"Shaolei","middleName":"","lastName":"Ren","suffix":""},{"id":291427433,"identity":"e2a5708d-e233-40df-899c-48accfdef2b4","order_by":1,"name":"Liang Xue","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAxklEQVRIiWNgGAWjYLACxgYgwczA+IB4DVAtzAYkamFgYJMgSr18+xnzx4U7bOTM2XnMKt6UMcjzix3Ar8XgTI5h88wzacaWzWxpN+ecYzCcOTuBgBYJHsNm3rbDiRsOMx+7zdvGkGBwm4AW+RkQLfUbDjO2FROlheEGREuCAdAWZqK0GJxJK5w9sy3NcMNhtmTJOeckCPtFvv3whs+FbTbyBufPGH54U2Yjzy9NyGEMoEiEAR4iowZFC3E6RsEoGAWjYGQBAO5IP16lXAFlAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-9131-8377","institution":"Guangdong Academy of Science Institute of Microbiology","correspondingAuthor":true,"prefix":"","firstName":"Liang","middleName":"","lastName":"Xue","suffix":""},{"id":291427434,"identity":"69618a98-555d-4141-8ff7-26aa6baeca78","order_by":2,"name":"Junshan Gao","email":"","orcid":"","institution":"Guangdong Academy of Science Institute of Microbiology","correspondingAuthor":false,"prefix":"","firstName":"Junshan","middleName":"","lastName":"Gao","suffix":""},{"id":291427435,"identity":"9c99c1f2-41b3-4808-9b04-37775defdc4c","order_by":3,"name":"Weicheng Cai","email":"","orcid":"","institution":"Guangdong Academy of Science Institute of Microbiology","correspondingAuthor":false,"prefix":"","firstName":"Weicheng","middleName":"","lastName":"Cai","suffix":""},{"id":291427436,"identity":"caab0de2-ca54-4bf1-8d0a-390d9a820c5c","order_by":4,"name":"Peng Lin","email":"","orcid":"","institution":"Bohai University","correspondingAuthor":false,"prefix":"","firstName":"Peng","middleName":"","lastName":"Lin","suffix":""}],"badges":[],"createdAt":"2024-04-08 11:55:11","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4236232/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4236232/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":54881187,"identity":"8d5b851f-e9d3-4e40-b17b-ed6e88fdceb6","added_by":"auto","created_at":"2024-04-18 04:46:28","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":248562,"visible":true,"origin":"","legend":"\u003cp\u003ePairwise distance distribution histograms of sapovirus VP1 nucleotide sequences\u003c/p\u003e","description":"","filename":"Fig.1.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/a16ebc96e8b6ce0505705f57.png"},{"id":54880682,"identity":"66c0438d-5581-4e99-b227-ed8deaba18eb","added_by":"auto","created_at":"2024-04-18 04:38:27","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1061755,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic trees of sapoviruses based on complete VP1 nucleotide sequences. The entry number and assigned genogroup and genotype are indicated. The Manchester strain (Hu/Manchester/93/UK; GenBank accession no. X86560) was selected as the root of the phylogenetic tree. The same genogroup sequences are marked with the same color background, and the corrected sequence is marked with a special format, with the wrong genotype inside the vertical line and the correct genotype outside the vertical line\u003c/p\u003e","description":"","filename":"Fig.2.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/1a02cc835f9f016fb1cf7364.png"},{"id":54880688,"identity":"869cc5e2-a119-4343-897d-1fb916978847","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":92494,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic trees of sapoviruses based on complete VP1 reference nucleotide sequences. The number of entries into the sequences and the genotype represented are labelled. The Manchester strain (Hu/Manchester/93/UK; GenBank accession no. X86560) was selected as the root of the phylogenetic tree. The scale represents the number of nucleotide substitutions per site\u003c/p\u003e","description":"","filename":"Fig.3.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/6167cf87742b0d9f20f33476.png"},{"id":54880687,"identity":"3896b1a5-ec22-41ee-90b0-3819894ad78c","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":302271,"visible":true,"origin":"","legend":"\u003cp\u003ePairwise distance distribution histograms of sapovirus NS6-7 nucleotide sequences\u003c/p\u003e","description":"","filename":"Fig.4.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/83539a3895866c3fbdd8dfd3.png"},{"id":54880690,"identity":"7cf76425-c085-4fef-96f4-7486dff1e890","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":729970,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic trees of sapoviruses based on complete NS6-7 nucleotide sequences. The entry number and assigned genogroup and genotype are indicated. The Manchester strain (Hu/Manchester/93/UK; GenBank accession no. X86560) was selected as the root of the phylogenetic tree. The same genogroup sequences are marked with the same color background\u003c/p\u003e","description":"","filename":"Fig.5.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/d18a731018f1a0b3518a0093.png"},{"id":54880684,"identity":"aee19dbe-176f-4028-ab0d-86b3a06af8a2","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":89264,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic trees of sapoviruses based on complete NS6-7 reference nucleotide sequences. The number of entries into the sequences and the genotype represented are labelled. The Manchester strain (Hu/Manchester/93/UK; GenBank accession no. X86560) was selected as the root of the phylogenetic tree. The scale represents the number of nucleotide substitutions per site\u003c/p\u003e","description":"","filename":"Fig.6.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/c98a0fe223638d536b974d93.png"},{"id":54880691,"identity":"9589c54b-f92d-4ca9-99df-0f467f84ae4f","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":6528198,"visible":true,"origin":"","legend":"\u003cp\u003eRecombination analysis of sapovirus sequences: (a) GI.1[P4]-MN794208, (b) GI.2[P1]-GQ261222, (c) GII.4[P1]-AB522397, (d) GII.4[P1]-KX274477, (e) GII.4[P1]-MG012446, (f)GII.4[P1]-MZ488271, (g) GII.4[PNA1]-MN794218, (h) GII.6[P2]-MH933793, (i) GV.5[P3]-LC215885. The similarity of the recombinant sequence to the nucleotide sequence is represented by the y-axis. The nucleotide locations are displayed on the X-axis. The recombinant prediction sites were those that shared similarities with both the recombinant strains and the two sapovirus parental strains with distinct genotypes\u003c/p\u003e","description":"","filename":"Fig.7.png","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/8d338b12a79895e2686643f7.png"},{"id":54881612,"identity":"5167a996-a9f6-4fad-8561-bcca497e3802","added_by":"auto","created_at":"2024-04-18 04:54:41","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1875871,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1_covered_a4e86f0c-d5b4-4574-ae6a-96b06a237151.pdf"},{"id":54881186,"identity":"53184ad1-f01d-49ef-9808-4443afffc497","added_by":"auto","created_at":"2024-04-18 04:46:27","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":18570,"visible":true,"origin":"","legend":"","description":"","filename":"Table1.docx","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/862c66a5d2acdf076ac5fd04.docx"},{"id":54880685,"identity":"1e31d78e-6950-46fb-b490-abb6ccdd2223","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":21000,"visible":true,"origin":"","legend":"","description":"","filename":"Table2.docx","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/c2a481cb8cd24f426548e076.docx"},{"id":54880689,"identity":"abe100b9-93a6-4ca2-8bfa-28b31c69b159","added_by":"auto","created_at":"2024-04-18 04:38:28","extension":"docx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":21279,"visible":true,"origin":"","legend":"","description":"","filename":"Table3.docx","url":"https://assets-eu.researchsquare.com/files/rs-4236232/v1/d49540341fb756d553bbe1f1.docx"}],"financialInterests":"\u003cp\u003eTables 1-3 are available in the Supplementary Files section.\u003c/p\u003e","formattedTitle":"Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Sapovirus, Genetic diversity, Reference sequences, Recombination","lastPublishedDoi":"10.21203/rs.3.rs-4236232/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4236232/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"A significant foodborne pathogen that causes acute gastroenteritis worldwide is sapovirus. Currently, there have been reports of certain recombinant strains of sapovirus, and the genetic diversity of this virus is continuously increasing. In this study, sapovirus nucleotide sequences with entire VP1 and NS6-7 regions were obtained from GenBank, and phylogenetic analysis and genetic distance calculations were performed to investigate the genetic diversity of the VP1 and NS6-7 regions of this virus. In addition to the 19 known genogroups, a small number of sequences were discovered to be beyond the range of known genogroups and were temporarily divided (Bat NA1-Bat NA3). This was based on the genetic diversity of the entire VP1 region. Based on the VP1 region, 38 key reference sequences were also suggested. Furthermore, for 33 sequences for which the genotyping tool mistyped, the genotype and genogroup information were modified. We also attempted to categorize sapovirus based on the genetic diversity of the nucleotide sequences of NS6-7 region. Phylogenetically, 17 P (polymerase)-groups (GI.P-GIII.P, GV.P-GVIII.P, GX.P-GXIX.P) and one tentative (GNA1.P) were identified based on the genetic diversity of nucleotide sequences in the entire NS6-7 region, and 35 related reference sequences were also suggested. Nine recombinant sequences, including six recombinant genotypes (GI.1[P4], GI.2[P1], GII.4[P1], GII.4[PNA1], GII.6[P2], and GV.5[P3]), were identified by genetic diversity differences between VP1 and NS6-7 of sapovirus. With this approach, sapovirus recombination events may be effectively characterized.","manuscriptTitle":"Comparative analysis of sapovirus genetic diversity based on VP1 and NS6-7","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-04-18 04:38:23","doi":"10.21203/rs.3.rs-4236232/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major Revision - English Corrections","date":"2024-05-29T15:00:02+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2024-04-17T23:56:28+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-04-15T13:46:56+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-04-09T05:48:38+00:00","index":"","fulltext":""},{"type":"submitted","content":"Archives of Virology","date":"2024-04-08T07:54:45+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"69928efe-7f06-4bc8-a1ab-1ba0f2c2f1b9","owner":[],"postedDate":"April 18th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2024-05-29T19:01:28+00:00","versionOfRecord":[],"versionCreatedAt":"2024-04-18 04:38:23","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4236232","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4236232","identity":"rs-4236232","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}