Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

Autor: Petrone ME; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA. mary.petrone@yale.edu., Rothman JE; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Breban MI; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Ott IM; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Russell A; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA., Lasek-Nesselquist E; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA., Badr H; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA., Kelly K; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA., Omerza G; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA., Renzette N; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA., Watkins AE; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Kalinich CC; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Alpert T; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Brito AF; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Earnest R; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Tikhonova IR; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA., Castaldi C; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA., Kelly JP; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA., Shudt M; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA., Plitnick J; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA., Schneider E; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA., Murphy S; Murphy Medical Associates, Greenwich, CT, 06830, USA., Neal C; Murphy Medical Associates, Greenwich, CT, 06830, USA., Laszlo E; Murphy Medical Associates, Greenwich, CT, 06830, USA., Altajar A; Murphy Medical Associates, Greenwich, CT, 06830, USA., Pearson C; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA., Muyombwe A; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA., Downing R; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA., Razeq J; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA., Niccolai L; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Wilson MS; Yale Health Center, Yale University, New Haven, CT, 06510, USA., Anderson ML; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Wang J; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA., Liu C; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA., Hui P; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA., Mane S; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA., Taylor BP; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA., Hanage WP; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA., Landry ML; Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA., Peaper DR; Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA., Bilguvar K; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA.; Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA., Fauver JR; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Vogels CBF; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., Gardner LM; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA., Pitzer VE; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA., St George K; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA., Adams MD; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA., Grubaugh ND; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA. nathan.grubaugh@yale.edu.; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06510, USA. nathan.grubaugh@yale.edu.
Jazyk: angličtina
Zdroj: Communications biology [Commun Biol] 2022 May 11; Vol. 5 (1), pp. 439. Date of Electronic Publication: 2022 May 11.
DOI: 10.1038/s42003-022-03347-3
Abstrakt: SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (R t ) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the R t of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19.
(© 2022. The Author(s).)
Databáze: MEDLINE
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