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Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a pandemic and is threatening human health globally. The rapid genome sequencing and bioinformatic analysis of SARS-CoV-2 have become a helpful tool in the battle against the COVID...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8969601/ https://www.ncbi.nlm.nih.gov/pubmed/35369437 http://dx.doi.org/10.3389/fmicb.2022.851323 |
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author | Zhao, Ning Zhou, Nan Fan, Huafeng Ding, Jie Xu, Xingyu Dong, Xiaoqing Dong, Xiaoxiao Xu, Dandan Min, Xiaoyu Yu, Yan Gong, Hongjin Mao, Lingfeng He, Min |
author_facet | Zhao, Ning Zhou, Nan Fan, Huafeng Ding, Jie Xu, Xingyu Dong, Xiaoqing Dong, Xiaoxiao Xu, Dandan Min, Xiaoyu Yu, Yan Gong, Hongjin Mao, Lingfeng He, Min |
author_sort | Zhao, Ning |
collection | PubMed |
description | Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a pandemic and is threatening human health globally. The rapid genome sequencing and bioinformatic analysis of SARS-CoV-2 have become a helpful tool in the battle against the COVID-19. Here, we report the genetic characteristics, variations and phylogenetic analysis of SARS-CoV-2 sequenced from 42 clinical specimens. The complete genomes sequencing of SARS-CoV-2 were performed using Oxford Nanopore sequencing. All genomes accumulated mutations compared to the Wuhan-Hu-1 (GenBank Accession No: MN908947.3). Our data of the 42 whole genomes revealed 16 different lineages. The B.1.1 lineage was the most frequent, and 5, 2, 2, 3, and 1 sequences were classified as lineages of B.1.1.7, B.1.351, P.1, B.1.617.2, and C.37, respectively. A total of 328 nucleotide mutation sites were found in 42 genomes, among which A23403G mutation (D614G amino acid change in the spike protein) was the most common substitution. The phylogenetic trees of 42 SARS-CoV-2 sequences and GISAID-available SARS-CoV-2 sequences were constructed and its taxonomic status was supported. These results will provide scientific basis for tracing the source and prevention and control of SARS-CoV-2 imported from abroad in Nanjing, China. |
format | Online Article Text |
id | pubmed-8969601 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-89696012022-04-01 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China Zhao, Ning Zhou, Nan Fan, Huafeng Ding, Jie Xu, Xingyu Dong, Xiaoqing Dong, Xiaoxiao Xu, Dandan Min, Xiaoyu Yu, Yan Gong, Hongjin Mao, Lingfeng He, Min Front Microbiol Microbiology Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a pandemic and is threatening human health globally. The rapid genome sequencing and bioinformatic analysis of SARS-CoV-2 have become a helpful tool in the battle against the COVID-19. Here, we report the genetic characteristics, variations and phylogenetic analysis of SARS-CoV-2 sequenced from 42 clinical specimens. The complete genomes sequencing of SARS-CoV-2 were performed using Oxford Nanopore sequencing. All genomes accumulated mutations compared to the Wuhan-Hu-1 (GenBank Accession No: MN908947.3). Our data of the 42 whole genomes revealed 16 different lineages. The B.1.1 lineage was the most frequent, and 5, 2, 2, 3, and 1 sequences were classified as lineages of B.1.1.7, B.1.351, P.1, B.1.617.2, and C.37, respectively. A total of 328 nucleotide mutation sites were found in 42 genomes, among which A23403G mutation (D614G amino acid change in the spike protein) was the most common substitution. The phylogenetic trees of 42 SARS-CoV-2 sequences and GISAID-available SARS-CoV-2 sequences were constructed and its taxonomic status was supported. These results will provide scientific basis for tracing the source and prevention and control of SARS-CoV-2 imported from abroad in Nanjing, China. Frontiers Media S.A. 2022-03-17 /pmc/articles/PMC8969601/ /pubmed/35369437 http://dx.doi.org/10.3389/fmicb.2022.851323 Text en Copyright © 2022 Zhao, Zhou, Fan, Ding, Xu, Dong, Dong, Xu, Min, Yu, Gong, Mao and He. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Zhao, Ning Zhou, Nan Fan, Huafeng Ding, Jie Xu, Xingyu Dong, Xiaoqing Dong, Xiaoxiao Xu, Dandan Min, Xiaoyu Yu, Yan Gong, Hongjin Mao, Lingfeng He, Min Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title | Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title_full | Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title_fullStr | Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title_full_unstemmed | Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title_short | Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China |
title_sort | mutations and phylogenetic analyses of sars-cov-2 among imported covid-19 from abroad in nanjing, china |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8969601/ https://www.ncbi.nlm.nih.gov/pubmed/35369437 http://dx.doi.org/10.3389/fmicb.2022.851323 |
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