Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness [preprint]
Authors
Obermeyer, FritzJankowiak, Martin
Barkas, Nikolaos
Schaffner, Stephen F
Pyle, Jesse D.
Yurkovetskiy, Lonya
Bosso, Matteo
Park, Daniel J.
Babadi, Mehrtash
MacInnis, Bronwyn L.
Luban, Jeremy
Sabeti, Pardis C.
Lemieux, Jacob E.
UMass Chan Affiliations
Program in Molecular MedicineDocument Type
PreprintPublication Date
2022-02-16Keywords
EpidemiologySARS-CoV-2 variants
mutations
viral lineages
fitness
Epidemiology
Genetics and Genomics
Immunology and Infectious Disease
Infectious Disease
Microbiology
Virus Diseases
Metadata
Show full item recordAbstract
Repeated 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.Source
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. Link to preprint on medRxiv.
DOI
10.1101/2021.09.07.21263228Permanent Link to this Item
http://hdl.handle.net/20.500.14038/30735PubMed ID
35194619Notes
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.
Related Resources
Now published in Science doi: 10.1126/science.abm1208
Rights
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.Distribution License
http://creativecommons.org/licenses/by-nd/4.0/ae974a485f413a2113503eed53cd6c53
10.1101/2021.09.07.21263228
Scopus Count
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.