SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021
, Mitali Mishra1
, Stephen Sameroff, Alexandra Petrosov, James Ng, Alper Gokden, Jane MaCauley, Komal Jain, Courtney Renken, James Tanu Duworko, Moses Badio, Wilhemina Jallah, Lisa Hensley, Thomas Briese, W. Ian Lipkin, and Nischay Mishra
Author affiliations: National Public Health Institute of Liberia, Monrovia, Liberia (B. Shobayo, J. MaCauley); Partnership for Research on Infectious Diseases in Liberia, Monrovia (B. Shobayo, C. Renken, J.T. Duworko, M. Badio, L. Hensley); Columbia University, New York, New York, USA (M. Mishra, S. Sameroff, A. Petrosov, J. Ng, A. Gokden, K. Jain, T. Briese, W.I. Lipkin, N. Mishra); National Institutes of Health, Bethesda, Maryland, USA (C. Renken, L. Hensley); Ministry of Health, Monrovia (W. Jallah)
Figure. Phylogenetic analysis of 77 nasopharyngeal swab samples collected during coronavirus disease case surge, Libera, March–July 2021, and reference sequences. We created a maximum-likelihood nucleotide phylogenetic tree of the complete polyprotein coding region by using MEGA X (https://www.megasoftware.net), with a bootstrap value of 100 and and used Tamura-Nei 93 (TN93) as a substitution model with a discrete gamma distribution (+G) for evolutionary rate; the rate variation model allowed some sites to be evolutionarily invariable (+I). Numbers along the branches are bootstrap values of 100 bootstrap resamplings. Teal indicates samples collected in March 2021; purple indicates samples collected in April 2021; pink indicates samples collected in May 2021; blue indicates samples collected in June 2021; orange indicates samples collected in July 2021; brown indicates variants of concern or variants of interest; black indicates other circulating variants; green indicates severe acute respiratory syndrome coronavirus 2 reference sequence and other early parental sequences from 2020.
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