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2 results on '"Barkas, N"'

1. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

Author

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, Obermeyer, F, Jankowiak, M, Barkas, N, Schaffner, SF, Pyle, JD, Yurkovetskiy, L, Bosso, M, Park, DJ, Babadi, M, MacInnis, BL, Luban, J, Sabeti, PC, and Lemieux, JE

Abstract

Repeated emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have 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 nonspike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.

Published
2022

2. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Author

Siddle, KJ, Krasilnikova, LA, Moreno, GK, Schaffner, SF, Vostok, J, Fitzgerald, NA, Lemieux, JE, Barkas, N, Loreth, C, Specht, I, Tomkins-Tinch, CH, Paull, JS, Schaeffer, B, Taylor, BP, Loftness, B, Johnson, H, Schubert, PL, Shephard, HM, Doucette, M, Fink, T, Lang, AS, Baez, S, Beauchamp, J, Hennigan, S, Buzby, E, Ash, S, Brown, J, Clancy, S, Cofsky, S, Gagne, L, Hall, J, Harrington, R, Gionet, GL, DeRuff, KC, Vodzak, ME, Adams, GC, Dobbins, ST, Slack, SD, Reilly, SK, Anderson, LM, Cipicchio, MC, DeFelice, MT, Grimsby, JL, Anderson, SE, Blumenstiel, BS, Meldrim, JC, Rooke, HM, Vicente, G, Smith, NL, Messer, KS, Reagan, FL, Mandese, ZM, Lee, MD, Ray, MC, Fisher, ME, Ulcena, MA, Nolet, CM, English, SE, Larkin, KL, Vernest, K, Chaluvadi, S, Arvidson, D, Melchiono, M, Covell, T, Harik, V, Brock-Fisher, T, Dunn, M, Kearns, A, Hanage, WP, Bernard, C, Philippakis, A, Lennon, NJ, Gabriel, SB, Gallagher, GR, Smole, S, Madoff, LC, Brown, CM, Park, DJ, MacInnis, BL, Sabeti, PC, Siddle, KJ, Krasilnikova, LA, Moreno, GK, Schaffner, SF, Vostok, J, Fitzgerald, NA, Lemieux, JE, Barkas, N, Loreth, C, Specht, I, Tomkins-Tinch, CH, Paull, JS, Schaeffer, B, Taylor, BP, Loftness, B, Johnson, H, Schubert, PL, Shephard, HM, Doucette, M, Fink, T, Lang, AS, Baez, S, Beauchamp, J, Hennigan, S, Buzby, E, Ash, S, Brown, J, Clancy, S, Cofsky, S, Gagne, L, Hall, J, Harrington, R, Gionet, GL, DeRuff, KC, Vodzak, ME, Adams, GC, Dobbins, ST, Slack, SD, Reilly, SK, Anderson, LM, Cipicchio, MC, DeFelice, MT, Grimsby, JL, Anderson, SE, Blumenstiel, BS, Meldrim, JC, Rooke, HM, Vicente, G, Smith, NL, Messer, KS, Reagan, FL, Mandese, ZM, Lee, MD, Ray, MC, Fisher, ME, Ulcena, MA, Nolet, CM, English, SE, Larkin, KL, Vernest, K, Chaluvadi, S, Arvidson, D, Melchiono, M, Covell, T, Harik, V, Brock-Fisher, T, Dunn, M, Kearns, A, Hanage, WP, Bernard, C, Philippakis, A, Lennon, NJ, Gabriel, SB, Gallagher, GR, Smole, S, Madoff, LC, Brown, CM, Park, DJ, MacInnis, BL, and Sabeti, PC

Abstract

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.

Published
2022

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