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Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021

OBJECTIVE: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the G...

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Autores principales: LIANG, Dan, WANG, Tao, LI, Jiao Jiao, GUAN, Da Wei, ZHANG, Guan Ting, LIANG, Yu Feng, LI, An An, HONG, Wen Shan, WANG, Li, CHEN, Meng Lin, DENG, Xiao Ling, CHEN, Feng Juan, PAN, Xing Fei, JIA, Hong Ling, LEI, Chun Liang, KE, Chang Wen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Editorial Board of Biomedical and Environmental Sciences. Published by Elsevier (Singapore) Pte Ltd. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9187330/
https://www.ncbi.nlm.nih.gov/pubmed/35676810
http://dx.doi.org/10.3967/bes2022.055
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author LIANG, Dan
WANG, Tao
LI, Jiao Jiao
GUAN, Da Wei
ZHANG, Guan Ting
LIANG, Yu Feng
LI, An An
HONG, Wen Shan
WANG, Li
CHEN, Meng Lin
DENG, Xiao Ling
CHEN, Feng Juan
PAN, Xing Fei
JIA, Hong Ling
LEI, Chun Liang
KE, Chang Wen
author_facet LIANG, Dan
WANG, Tao
LI, Jiao Jiao
GUAN, Da Wei
ZHANG, Guan Ting
LIANG, Yu Feng
LI, An An
HONG, Wen Shan
WANG, Li
CHEN, Meng Lin
DENG, Xiao Ling
CHEN, Feng Juan
PAN, Xing Fei
JIA, Hong Ling
LEI, Chun Liang
KE, Chang Wen
author_sort LIANG, Dan
collection PubMed
description OBJECTIVE: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated. METHODS: In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants. RESULTS: We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations. CONCLUSION: These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China.
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spelling pubmed-91873302022-06-13 Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021 LIANG, Dan WANG, Tao LI, Jiao Jiao GUAN, Da Wei ZHANG, Guan Ting LIANG, Yu Feng LI, An An HONG, Wen Shan WANG, Li CHEN, Meng Lin DENG, Xiao Ling CHEN, Feng Juan PAN, Xing Fei JIA, Hong Ling LEI, Chun Liang KE, Chang Wen Biomed Environ Sci Original Article OBJECTIVE: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated. METHODS: In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants. RESULTS: We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations. CONCLUSION: These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China. The Editorial Board of Biomedical and Environmental Sciences. Published by Elsevier (Singapore) Pte Ltd. 2022-05 2022-06-10 /pmc/articles/PMC9187330/ /pubmed/35676810 http://dx.doi.org/10.3967/bes2022.055 Text en © 2022 The Editorial Board of Biomedical and Environmental Sciences Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Original Article
LIANG, Dan
WANG, Tao
LI, Jiao Jiao
GUAN, Da Wei
ZHANG, Guan Ting
LIANG, Yu Feng
LI, An An
HONG, Wen Shan
WANG, Li
CHEN, Meng Lin
DENG, Xiao Ling
CHEN, Feng Juan
PAN, Xing Fei
JIA, Hong Ling
LEI, Chun Liang
KE, Chang Wen
Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title_full Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title_fullStr Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title_full_unstemmed Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title_short Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 – May 2021
title_sort genomic epidemiology of imported cases of covid-19 in guangdong province, china, october 2020 – may 2021
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9187330/
https://www.ncbi.nlm.nih.gov/pubmed/35676810
http://dx.doi.org/10.3967/bes2022.055
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