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dc.contributor.authorObermeyer, Fritz
dc.contributor.authorJankowiak, Martin
dc.contributor.authorBarkas, Nikolaos
dc.contributor.authorSchaffner, Stephen F
dc.contributor.authorPyle, Jesse D.
dc.contributor.authorYurkovetskiy, Lonya
dc.contributor.authorBosso, Matteo
dc.contributor.authorPark, Daniel J.
dc.contributor.authorBabadi, Mehrtash
dc.contributor.authorMacInnis, Bronwyn L.
dc.contributor.authorLuban, Jeremy
dc.contributor.authorSabeti, Pardis C.
dc.contributor.authorLemieux, Jacob E.
dc.date2022-08-11T08:08:34.000
dc.date.accessioned2022-08-23T15:59:43Z
dc.date.available2022-08-23T15:59:43Z
dc.date.issued2022-02-16
dc.date.submitted2022-05-26
dc.identifier.citation<p>Obermeyer F, Jankowiak M, Barkas N, Schaffner SF, Pyle JD, Yurkovetskiy L, Bosso M, Park DJ, Babadi M, MacInnis BL, Luban J, Sabeti PC, Lemieux JE. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. medRxiv [Preprint]. 2022 Feb 16:2021.09.07.21263228. doi: 10.1101/2021.09.07.21263228. Update in: Science. 2022 May 24;:abm1208. PMID: 35194619; PMCID: PMC8863165. <a href="https://doi.org/10.1101/2021.09.07.21263228" target="_blank" title="view preprint in medrxiv">Link to preprint on medRxiv.</a></p>
dc.identifier.doi10.1101/2021.09.07.21263228
dc.identifier.pmid35194619
dc.identifier.urihttp://hdl.handle.net/20.500.14038/30735
dc.description<p>This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.</p>
dc.description.abstractRepeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization.
dc.language.isoen_US
dc.relation<p>Now published in <em>Science</em> doi: <a href="https://doi.org/10.1126/science.abm1208" target="_blank">10.1126/science.abm1208</a></p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/35194619/" target="_blank" title="view preprint in PubMed">View preprint in PubMed</a></p>
dc.rightsThe copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nd/4.0/
dc.subjectEpidemiology
dc.subjectSARS-CoV-2 variants
dc.subjectmutations
dc.subjectviral lineages
dc.subjectfitness
dc.subjectEpidemiology
dc.subjectGenetics and Genomics
dc.subjectImmunology and Infectious Disease
dc.subjectInfectious Disease
dc.subjectMicrobiology
dc.subjectVirus Diseases
dc.titleAnalysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness [preprint]
dc.typePreprint
dc.source.journaltitlemedRxiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=3239&amp;context=faculty_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/2206
dc.identifier.contextkey29379126
refterms.dateFOA2022-08-23T15:59:43Z
html.description.abstract<p>Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR<sub>0</sub>, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR<sub>0</sub> to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR<sub>0</sub> forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization.</p>
dc.identifier.submissionpathfaculty_pubs/2206
dc.contributor.departmentProgram in Molecular Medicine


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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Except where otherwise noted, this item's license is described as The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.