Mutational Analysis of SARS-CoV-2 Genomes in Key Cities of China

Mutational Analysis of SARS-CoV-2 Genomes in Key Cities of China | 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 Mutational Analysis of SARS-CoV-2 Genomes in Key Cities of China Qiwei Cui, Jeffrey Zheng This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-72695/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract From December 2019, SARS-CoV-2 induced pneumonia broke out in Wuhan and then spread rapidly from multiple resources to other provinces and other cities in China. In this paper, genomes collected in four Chinese cities: Wuhan, Guangzhou, Shanghai, Hangzhou were analyzed as the A1 module of the MAS. Starting from the virus gene sequence itself, multiple probability statistics are applied to extract characteristics from virus genomes. Variations of genomes can be compared and visualized in such conditions. It is interesting to see various similar and different properties visualized under various groups after transformations. In this way, key mutation characteristics could be observed and this type of results is helpful for further scientific researches on COVID-19 applications. Epigenetics & Genomics Computational Biology Materials Theory and Modeling variation measurement variation projection genome visualization comparison Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 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 2 posted You are reading this latest preprint version Show more versions 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-72695","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":2185722,"identity":"9c1fbf23-c375-4ebd-86c8-292410d81107","order_by":0,"name":"Qiwei Cui","email":"","orcid":"","institution":"Yunnan University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Qiwei","middleName":"","lastName":"Cui","suffix":""},{"id":2185723,"identity":"7cf53d69-826f-49aa-8407-de3bc0227929","order_by":1,"name":"Jeffrey Zheng","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABAUlEQVRIiWNgGAWjYJACAzDJDsQJDDYMDBJEapFgYAZrSSNOCwNcCwPDYcJa+Nt7DxTz/LKr42dmPvziQc35xP7ZzQcfMNTYROM0/cy5BGPevmQJyWa2NIuEY7cTZ9w5lmzAcCwttwGXPyRyDIx5e5glDA7zmBkkNtxObLiRYybB2HCYkJZ6CXuIlnOJ84nSwvPjsIQBM4/xg8SGA4kbCGmROHPGwHBuw3HJGYfZ0hgSjiUbb7yRlmyQgMcv/O09ZgZv/lTz87c3H/74o8ZOdt6N5IMPPtTY4NQCBGwGjG0QBihGHMEqE3ArBwHmBwx/IIwPQMIev+JRMApGwSgYiQAAlbVaa02SHDwAAAAASUVORK5CYII=","orcid":"","institution":"Yunnan University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Jeffrey","middleName":"","lastName":"Zheng","suffix":""}],"badges":[],"createdAt":"2020-09-05 08:40:48","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":true,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false,"coiExplicitlySet":false},"doi":"10.21203/rs.3.rs-72695/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-72695/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":4824421,"identity":"66ef106c-349f-4ae1-af75-48881590c0ad","added_by":"auto","created_at":"2021-01-08 22:07:11","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":92614,"visible":true,"origin":"","legend":"From left to right: variation projection map of Wuhan and Guangzhou","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/fa054e072517a1b0ec778b23.png"},{"id":4824422,"identity":"93bfbae3-f868-4e7d-874f-28c78351be90","added_by":"auto","created_at":"2021-01-08 22:07:11","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":110021,"visible":true,"origin":"","legend":"From left to right: variation projection map of Hangzhou and Shanghai","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/f5b979d8da2d3f47bb3377cf.png"},{"id":4824454,"identity":"a35273b7-9b38-4b07-8045-286b76d41bbb","added_by":"auto","created_at":"2021-01-08 22:10:12","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":133527,"visible":true,"origin":"","legend":"Sequence comparison of multiple genes detected in Wuhan and Guangzhou","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/1b408968abcbe150a6a30a3d.png"},{"id":4824423,"identity":"56934982-b8bd-41f4-8f22-f5b5b8744f3f","added_by":"auto","created_at":"2021-01-08 22:07:11","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":225437,"visible":true,"origin":"","legend":"Sequence comparison of multiple genes detected in Hangzhou and Shanghai","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/20622c2cd9d6ca00f8e7674b.png"},{"id":4824570,"identity":"d7b9cb8c-b827-42d5-8422-925f629da225","added_by":"auto","created_at":"2021-01-08 22:13:12","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":171404,"visible":true,"origin":"","legend":"Comparison of gene sequences between Wuhan and Guangzhou, Wuhan and\nHangzhou","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/be59fa84d48d107fb8788eb7.png"},{"id":4824430,"identity":"1f7a3b4f-52e9-48ad-9d1c-1449058503a1","added_by":"auto","created_at":"2021-01-08 22:07:12","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":111254,"visible":true,"origin":"","legend":"Comparison of gene sequences between Wuhan and Shanghai, Guangzhou\nand Shanghai","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/ec464ef6516a351317e5c2f2.png"},{"id":4824453,"identity":"ffa89924-f033-49a6-a5f4-ecf1fdeb6517","added_by":"auto","created_at":"2021-01-08 22:10:12","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":83940,"visible":true,"origin":"","legend":"Comparison of gene sequences between Wuhan and Shanghai","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/7f9a5ef0674da9a0b9198cd3.png"},{"id":4824455,"identity":"61a43ba1-2fc0-4893-81e8-c2b44ce0d7d3","added_by":"auto","created_at":"2021-01-08 22:10:12","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":98409,"visible":true,"origin":"","legend":"Comparison of gene sequences between Wuhan and Guangzhou","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/ba6081f424f6932e8f4a83ad.png"},{"id":4824424,"identity":"903d0cbb-e8e5-4dac-95ca-98569ce43a01","added_by":"auto","created_at":"2021-01-08 22:07:11","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":119636,"visible":true,"origin":"","legend":"Comparison of gene sequences between Wuhan and wuhan-hangzhou","description":"","filename":"9.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/93cab76f481b1c3e1b39ed2b.png"},{"id":4824429,"identity":"4969624d-4c40-4371-accb-20a668fd8735","added_by":"auto","created_at":"2021-01-08 22:07:12","extension":"png","order_by":10,"title":"Figure 10","display":"","copyAsset":false,"role":"figure","size":78893,"visible":true,"origin":"","legend":"Comparison of gene sequences between Guangzhou and Shanghai","description":"","filename":"10.png","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2/f656a5be6e5732232dd01a0a.png"},{"id":13572255,"identity":"54d7d0c5-cf46-4343-8ee4-877b5b53f8e4","added_by":"auto","created_at":"2021-09-17 03:50:50","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4970019,"visible":true,"origin":"","legend":"","description":"","filename":"Chapter13R.pdf","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2_covered.pdf"},{"id":13529757,"identity":"5669a7e1-991b-44ac-ae1c-5e9f53e476dd","added_by":"auto","created_at":"2021-09-17 01:05:44","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4974228,"visible":true,"origin":"","legend":"","description":"","filename":"Chapter13R.pdf","url":"https://assets-eu.researchsquare.com/files/rs-72695/v1_covered.pdf"},{"id":4824594,"identity":"62bf7148-d288-4045-b307-fdc22f8879ba","added_by":"auto","created_at":"2021-01-08 22:16:15","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3567926,"visible":true,"origin":"","legend":"","description":"","filename":"Chapter13R.pdf","url":"https://assets-eu.researchsquare.com/files/rs-72695/v2_stamped.pdf"}],"financialInterests":"","formattedTitle":"\u003cp\u003eMutational Analysis of SARS-CoV-2 Genomes in Key Cities of China\u003c/p\u003e","fulltext":[{"header":"Full Text","content":"Due to technical limitations, full-text HTML conversion of this manuscript could not be completed. However, the latest manuscript can be downloaded and \u003ca href='/article/rs-72695/latest.pdf' target='_blank'\u003e accessed as a PDF.\u003c/a\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"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":"variation measurement, variation projection, genome, visualization, comparison","lastPublishedDoi":"10.21203/rs.3.rs-72695/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-72695/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eFrom December 2019, SARS-CoV-2 induced pneumonia broke out in Wuhan and then spread rapidly from multiple resources to other provinces and other cities in China. In this paper, genomes collected in four Chinese cities: Wuhan, Guangzhou, Shanghai, Hangzhou were analyzed as the A1 module of the MAS. Starting from the virus gene sequence itself, multiple probability statistics are applied to extract characteristics from virus genomes. Variations of genomes can be compared and visualized in such conditions. It is interesting to see various similar and different properties visualized under various groups after transformations. In this way, key mutation characteristics could be observed and this type of results is helpful for further scientific researches on COVID-19 applications.\u003c/p\u003e","manuscriptTitle":"Mutational Analysis of SARS-CoV-2 Genomes in Key Cities of China","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2021-01-08 22:07:10","doi":"10.21203/rs.3.rs-72695/v2","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}},{"code":1,"date":"2020-09-09 22:23:10","doi":"10.21203/rs.3.rs-72695/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":"368c676e-76ba-480e-b7b3-58510a1f65db","owner":[],"postedDate":"January 8th, 2021","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":476186,"name":"Epigenetics \u0026 Genomics"},{"id":476187,"name":"Computational Biology"},{"id":476188,"name":"Materials Theory and Modeling"}],"tags":[],"updatedAt":"2020-09-09T22:23:10+00:00","versionOfRecord":[],"versionCreatedAt":"2021-01-08 22:07:10","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-72695","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-72695","identity":"rs-72695","version":["v2"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}