Molecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries

Molecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries | 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 Molecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries Pierre Teodosio Felix, Robson da Silva Ramos, Sara da Silva Nascimento, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-76869/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 Although some Countries in South America have implemented laboratory and patient management protocols for the new coronavirus, the lack of access to basic sanitation and hygiene measures, as well as the lack of drugs and vaccines, has significantly interfered with the epidemiological mechanics of the virus, emphasizing its implications. Therefore, trying to understand the evolutionary aspects of the virus, emerges as another strategy that can help in the most varied measures of prophylaxis. In this work, we evaluated the levels of genetic diversity in 38 complete Genomes of SARS-CoV-2 from six countries in South America, using specific methodologies for paired F ST , AMOVA, mismatch, demographic and spatial expansions, molecular diversity and for the time of evolutionary divergence. The analyses showed non-significant evolutionary divergences within and between the six countries, as well as a significant similarity to the time of genetic evolutionary divergence between all populations. Thus, it seems safe to affirm that we will find similar results for the other Countries of South America, reducing speculation about the existence of rapid and silent mutations that, although there are as we have shown in this work, do not increase, until this moment, the genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and drugs in general. Bioinformatics Mathematical and Theoretical Biology Population Genetics SARS-CoV-2 COVID-19 Coronavirus Phylogeny AMOVA Bioinformatics South America Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Full Text Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the latest manuscript can be downloaded and accessed as a PDF. 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. 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-76869","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":2289575,"identity":"a59b5622-2773-4fda-bc81-e63f8873c9ca","order_by":0,"name":"Pierre Teodosio Felix","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABFUlEQVRIie2RMUsDMRTHX3iQLrlmjQjXr/DKgefhl+lRqEsHQSgFpd4hZCp11cEP4eZYCVyX0C/Q5cBZOOjioGI8EJe709EhP8gb/uSX95IAeDz/EaxrCH0EVgIo4HXgKnUrEXAEpL8p8K24beon6FDiHhb7+ZxC3hNHF8HjcbqSpoRqZiA+XDcqyTUf31lLEUc+2QVWpVpNiN1uDSSrUaNCRkQs12+pRix2gVaRG48w0AbINg9GRu5Z/kFXGpk+rxW5qfC9UxHI8oxG3HVxh6uQw5Sc3q64u0QsK2iokY8P7r8UNT17Wm5PRbJseTFpnll2SQMp7bB60QsxuNk8lK+zkzAWLYM1pmu3WoRfv9jj8Xg8jk/Zk0s4iRySSgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-9159-7206","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Pierre","middleName":"Teodosio","lastName":"Felix","suffix":""},{"id":2289576,"identity":"dde17470-2862-41f3-8364-f76b742d8da5","order_by":1,"name":"Robson da Silva Ramos","email":"","orcid":"https://orcid.org/0000-0002-9935-2633","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Robson","middleName":"da Silva","lastName":"Ramos","suffix":""},{"id":2289577,"identity":"4f1a0b09-eb92-46c6-bbcb-f273a0340b34","order_by":2,"name":"Sara da Silva Nascimento","email":"","orcid":"https://orcid.org/0000-0002-0090-2456","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Sara","middleName":"da Silva","lastName":"Nascimento","suffix":""},{"id":2289578,"identity":"d1575eb4-f949-42b1-99f7-22871f510463","order_by":3,"name":"Willams Felipe Ferreira Silva","email":"","orcid":"https://orcid.org/0000-0001-8210-8442","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Willams","middleName":"Felipe Ferreira","lastName":"Silva","suffix":""},{"id":2289579,"identity":"e0eac837-3708-46ef-b44e-530b94daa10c","order_by":4,"name":"Maria Dara Pereira da Silva","email":"","orcid":"","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Maria","middleName":"Dara Pereira da","lastName":"Silva","suffix":""},{"id":2289580,"identity":"5b2e4f7a-fe1f-4cc4-8b3e-427b9b3d32be","order_by":5,"name":"Bianca Sarah Ferreira dos Santos","email":"","orcid":"https://orcid.org/0000-0002-2674-0053","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Bianca","middleName":"Sarah Ferreira dos","lastName":"Santos","suffix":""},{"id":2289581,"identity":"e5654077-ad01-4dbd-a048-6ebe68f189f7","order_by":6,"name":"Cícero Batista do Nascimento Filho","email":"","orcid":"https://orcid.org/0000-0002-2356-770X","institution":"Laboratory of Population Genetics and Computational Evolutionary Biology - 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The evolutionary history was inferred using the maximum likelihood method and the 3-parameter Tamura model [1]. The tree with the highest probability of logging (-1366.35) is shown. The percentage of trees in which the associated dollar sums group together is shown next to the branches. The initial trees for heuristic research were obtained automatically by applying the Join-Join and BioNJ algorithms to an array of distances in estimated pairs using the Tamura 3 parameter model and then selecting the topology with a higher log probability value. This analysis involved 38 nucleotide sequences. The evolutionary analyses were performed in MEGA X","description":"","filename":"Fig2.png","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/Fig2.png"},{"id":2437840,"identity":"3ed1d481-574e-4724-91e4-ad32e4c14cdf","added_by":"auto","created_at":"2020-09-16 17:10:10","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":42491,"visible":true,"origin":"","legend":"Matrix of paired differences between the populations studied: between the groups; within the groups; and Nei distance for the complete genome sequences of SARS-CoV-2 from six countries in South America.","description":"","filename":"Fig3.png","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/Fig3.png"},{"id":2437841,"identity":"297ce164-91ff-4d1c-a3e1-3e34cd4d07d3","added_by":"auto","created_at":"2020-09-16 17:10:10","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":169512,"visible":true,"origin":"","legend":"Comparison between the Demographic and Spatial Expansion of sequences of the complete genomes of SARS-CoV-2 from six countries in South America. (a and b) Graphs of demographic expansion and spatial expansion of haplotypes from Brazil, respectively; (c and d) Graphs of demographic expansion and spatial expansion of haplotypes from Venezuela, respectively. *Graphs Generated by the statistical package in R language using the output data of the Software Arlequin version 3.5.1.2","description":"","filename":"Fig4.png","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/Fig4.png"},{"id":2437842,"identity":"d3b2f9e2-833a-459c-a575-78afecb41e44","added_by":"auto","created_at":"2020-09-16 17:10:10","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":30287,"visible":true,"origin":"","legend":"Matrix of divergence time between the complete genomes of SARS-CoV-2 from six countries in South America. In evidence the high value τ present between the sequences of Brazil and Venezuela. * Generated by the statistical package in R language using the output data of the Software Arlequin version 3.5.1.2.","description":"","filename":"Fig5.png","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/Fig5.png"},{"id":2437843,"identity":"4e54c7ea-78c3-413e-b806-9eb588d433d7","added_by":"auto","created_at":"2020-09-16 17:10:10","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":61147,"visible":true,"origin":"","legend":"Graph of molecular diversity indices for the complete genomes of SARS-CoV-2 from six countries in South America. In the graph the values of θ: (θk) Relationship between the expected number of alllos (k) and the sample size; (θH) Expected homozygosity in a balanced relationship between drift and mutation; (θS) Relationship between the number of segregating sites (S), sample size (n) and non-recombinant sites; (θπ) Relationship between the average number of paired differences (π) and θ. * Generated by the statistical package in R language using the output data of the Arlequin software version 3.5.1.2.","description":"","filename":"Fig6.png","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/Fig6.png"},{"id":13530891,"identity":"69176146-1aa3-4fe0-a156-9ad1bcec1d3e","added_by":"auto","created_at":"2021-09-17 01:10:36","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1308748,"visible":true,"origin":"","legend":"","description":"","filename":"MolecularvarianceanalysisAMOVAandlevelsofgeneticdiversityofcompletegenomeofSARSCoV2virusfromofsixSouthAmericanCountries.pdf","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1_covered.pdf"},{"id":2437845,"identity":"e56d90d6-9bda-4501-9e46-fb23998156db","added_by":"auto","created_at":"2020-09-16 17:10:19","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":648734,"visible":true,"origin":"","legend":"","description":"","filename":"MolecularvarianceanalysisAMOVAandlevelsofgeneticdiversityofcompletegenomeofSARSCoV2virusfromofsixSouthAmericanCountries.pdf","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1_stamped.pdf"},{"id":2437844,"identity":"558adf6e-1356-4950-87ff-67ebd008f6b1","added_by":"auto","created_at":"2020-09-16 17:10:11","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":587337,"visible":true,"origin":"","legend":"","description":"","filename":"MolecularvarianceanalysisAMOVAandlevelsofgeneticdiversityofcompletegenomeofSARSCoV2virusfromofsixSouthAmericanCountries.pdf","url":"https://assets-eu.researchsquare.com/files/rs-76869/v1/MolecularvarianceanalysisAMOVAandlevelsofgeneticdiversityofcompletegenomeofSARSCoV2virusfromofsixSouthAmericanCountries.pdf"}],"financialInterests":"","formattedTitle":"\u003cp\u003eMolecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries\u003c/p\u003e","fulltext":[{"header":"Full Text","content":"Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. 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Therefore, trying to understand the evolutionary aspects of the virus, emerges as another strategy that can help in the most varied measures of prophylaxis. In this work, we evaluated the levels of genetic diversity in 38 complete Genomes of SARS-CoV-2 from six countries in South America, using specific methodologies for paired F\u003csub\u003eST\u003c/sub\u003e, AMOVA, mismatch, demographic and spatial expansions, molecular diversity and for the time of evolutionary divergence. The analyses showed non-significant evolutionary divergences within and between the six countries, as well as a significant similarity to the time of genetic evolutionary divergence between all populations. Thus, it seems safe to affirm that we will find similar results for the other Countries of South America, reducing speculation about the existence of rapid and silent mutations that, although there are as we have shown in this work, do not increase, until this moment, the genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and drugs in general.\u003c/p\u003e\u003cp\u003e\u003cbr\u003e\u003c/p\u003e","manuscriptTitle":"Molecular variance analysis (AMOVA) and levels of genetic diversity of complete genome of SARS-CoV-2 virus from of six South American Countries","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2020-09-16 17:10:08","doi":"10.21203/rs.3.rs-76869/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":"24243413-9017-4abd-9410-c1d2e668048a","owner":[],"postedDate":"September 16th, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":514048,"name":"Bioinformatics"},{"id":514049,"name":"Mathematical and Theoretical Biology"},{"id":514050,"name":"Population Genetics"}],"tags":[],"updatedAt":"2020-09-16T17:10:08+00:00","versionOfRecord":[],"versionCreatedAt":"2020-09-16 17:10:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-76869","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-76869","identity":"rs-76869","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}