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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-03-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.851323/full |
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| author | Ning Zhao Nan Zhou Huafeng Fan Jie Ding Xingyu Xu Xiaoqing Dong Xiaoxiao Dong Dandan Xu Xiaoyu Min Yan Yu Hongjin Gong Lingfeng Mao Min He |
| author_facet | Ning Zhao Nan Zhou Huafeng Fan Jie Ding Xingyu Xu Xiaoqing Dong Xiaoxiao Dong Dandan Xu Xiaoyu Min Yan Yu Hongjin Gong Lingfeng Mao Min He |
| author_sort | Ning Zhao |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T14:15:37Z |
| format | Article |
| id | doaj.art-2a45c98f8b2245bdb928822edac60fb4 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T14:15:37Z |
| publishDate | 2022-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-2a45c98f8b2245bdb928822edac60fb42022-12-21T23:42:19ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-03-011310.3389/fmicb.2022.851323851323Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, ChinaNing Zhao0Nan Zhou1Huafeng Fan2Jie Ding3Xingyu Xu4Xiaoqing Dong5Xiaoxiao Dong6Dandan Xu7Xiaoyu Min8Yan Yu9Hongjin Gong10Lingfeng Mao11Min He12Microbiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaHangzhou Baocheng Biotechnology Co., Ltd., Hangzhou, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaHangzhou Baocheng Biotechnology Co., Ltd., Hangzhou, ChinaMicrobiology Laboratory, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, ChinaCoronavirus 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.https://www.frontiersin.org/articles/10.3389/fmicb.2022.851323/fullSARS-CoV-2genomesvariantphylogenyevolution |
| spellingShingle | Ning Zhao Nan Zhou Huafeng Fan Jie Ding Xingyu Xu Xiaoqing Dong Xiaoxiao Dong Dandan Xu Xiaoyu Min Yan Yu Hongjin Gong Lingfeng Mao Min He Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China Frontiers in Microbiology SARS-CoV-2 genomes variant phylogeny evolution |
| 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 | SARS-CoV-2 genomes variant phylogeny evolution |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.851323/full |
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