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Volume 27, Number 5—May 2021
Research Letter

Novel Mutation of SARS-CoV-2, Vietnam, July 2020

Hoang Vu Mai Phuong1, Trinh Son Tung1, Ung Thi Hong Trang, Nguyen Le Khanh Hang, Nguyen Vu Son, Pham thi Hien, Le thi Thanh, Vuong Duc Cuong, Ton That Thanh, Nguyen thi Thanh Nhan, Tran Nhu Duong, Ngu Duy Nghia, Tran Anh Tu, Marc Choisy, Maia A. Rabaa, H. Rogier van Doorn, Dang Duc Anh, and Le Quynh MaiComments to Author 
Author affiliations: National Institute of Hygiene and Epidemiology, Hanoi, Vietnam (H.V.M. Phuong, U.T.H. Trang, N.L.K. Hang, N.V. Son, P. thi Hien, L. thi Thanh, V.D. Cuong, T.N. Duong, N.D. Nghia, T.A. Tu, D.D. Anh, L.Q. Mai); Oxford University Clinical Research Unit, Hanoi (T.S. Tung, H.R. van Doorn); Centre for Disease Control and Prevention, Danang, Vietnam (T.T. Thanh, N. thi T. Nhan); Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam (M. Choisy, M.A. Rabaa); University of Oxford, Oxford, UK (M. Choisy, M.A. Rabaa, H.R. van Doorn)

Main Article

Figure

Maximum likelihood phylogenetic trees of SARS-CoV-2 B.1.1 lineage sequences globally and sequences from Danang, Vietnam. A) Global maximum-likelihood phylogenetic tree of SARS-CoV-2 B.1.1 lineage. The phylogeny was inferred with the general time-reversible plus frequencies model using 1,000 bootstrap replicates. Red dots represent viruses from the Danang cluster. The outer ring shows lineage as determined using Pangolin (https://github.com/cov-lineages/pangolin/releases/tag/v2.3.0), and the inner ring shows the geographic location of collection. B) Maximum-likelihood phylogenetic tree built from 26 Danang-related SARS-CoV-2 sequences (represented by DN plus a 3-digit number); the Wuhan strain genome (GenBank accession no. NC_045512.2) is an outgroup. Columns to the right show the nucleotide variation in 3 locations on the SARS-CoV-2 genome that define phylogenetic clusters in the Danang cluster with their origin, the location the patients were found, and the cluster of the sequence. The ModelFinder Plus option Hasegawa-Kishino-Yano substitution model, including modelling of amino acid frequencies was the best model for these samples. Scale bar indicates substitutions per site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure. Maximum likelihood phylogenetic trees of SARS-CoV-2 B.1.1 lineage sequences globally and sequences from Danang, Vietnam. A) Global maximum-likelihood phylogenetic tree of SARS-CoV-2 B.1.1 lineage. The phylogeny was inferred with the general time-reversible plus frequencies model using 1,000 bootstrap replicates. Red dots represent viruses from the Danang cluster. The outer ring shows lineage as determined using Pangolin (https://github.com/cov-lineages/pangolin/releases/tag/v2.3.0), and the inner ring shows the geographic location of collection. B) Maximum-likelihood phylogenetic tree built from 26 Danang-related SARS-CoV-2 sequences (represented by DN plus a 3-digit number); the Wuhan strain genome (GenBank accession no. NC_045512.2) is an outgroup. Columns to the right show the nucleotide variation in 3 locations on the SARS-CoV-2 genome that define phylogenetic clusters in the Danang cluster with their origin, the location the patients were found, and the cluster of the sequence. The ModelFinder Plus option Hasegawa-Kishino-Yano substitution model, including modelling of amino acid frequencies was the best model for these samples. Scale bar indicates substitutions per site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Main Article

1These authors equally contributed to this work.

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