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Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.
Petrone, Mary E; Rothman, Jessica E; Breban, Mallery I; Ott, Isabel M; Russell, Alexis; Lasek-Nesselquist, Erica; Badr, Hamada; Kelly, Kevin; Omerza, Greg; Renzette, Nicholas; Watkins, Anne E; Kalinich, Chaney C; Alpert, Tara; Brito, Anderson F; Earnest, Rebecca; Tikhonova, Irina R; Castaldi, Christopher; Kelly, John P; Shudt, Matthew; Plitnick, Jonathan; Schneider, Erasmus; Murphy, Steven; Neal, Caleb; Laszlo, Eva; Altajar, Ahmad; Pearson, Claire; Muyombwe, Anthony; Downing, Randy; Razeq, Jafar; Niccolai, Linda; Wilson, Madeline S; Anderson, Margaret L; Wang, Jianhui; Liu, Chen; Hui, Pei; Mane, Shrikant; Taylor, Bradford P; Hanage, William P; Landry, Marie L; Peaper, David R; Bilguvar, Kaya; Fauver, Joseph R; Vogels, Chantal B F; Gardner, Lauren M; Pitzer, Virginia E; St George, Kirsten; Adams, Mark D; Grubaugh, Nathan D.
  • 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.
  • Badr H; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA.
  • Kelly K; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, 21218, MD, 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; The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, 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; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
  • Castaldi C; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA.
  • Kelly JP; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, 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.
  • Schneider E; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.
  • Murphy S; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA.
  • Neal C; Wadsworth Center, New York State Department of Health, Albany, NY, 12208, USA.
  • Laszlo E; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12222, USA.
  • Altajar A; Murphy Medical Associates, Greenwich, CT, 06830, USA.
  • Pearson C; Murphy Medical Associates, Greenwich, CT, 06830, USA.
  • Muyombwe A; Murphy Medical Associates, Greenwich, CT, 06830, USA.
  • Downing R; Murphy Medical Associates, Greenwich, CT, 06830, USA.
  • Razeq J; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA.
  • Niccolai L; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA.
  • Wilson MS; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA.
  • Anderson ML; Connecticut State Department of Public Health, Rocky Hill, CT, 06067, USA.
  • Wang J; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
  • Liu C; Yale Health Center, Yale University, New Haven, CT, 06510, USA.
  • Hui P; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
  • Mane S; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • Taylor BP; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • Hanage WP; Department of Pathology, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • Landry ML; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA.
  • Peaper DR; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
  • Bilguvar K; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA.
  • Fauver JR; Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • Vogels CBF; Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • Gardner LM; Yale Center for Genome Analysis, Yale University, New Haven, CT, 06510, USA.
  • Pitzer VE; Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA.
  • St George K; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
  • Adams MD; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
  • Grubaugh ND; Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA.
Commun Biol ; 5(1): 439, 2022 05 11.
Article in English | MEDLINE | ID: covidwho-1839575
ABSTRACT
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 (Rt) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the Rt 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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Commun Biol Year: 2022 Document Type: Article Affiliation country: S42003-022-03347-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: Commun Biol Year: 2022 Document Type: Article Affiliation country: S42003-022-03347-3