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Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis
BACKGROUND: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier Ltd.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9949854/ https://www.ncbi.nlm.nih.gov/pubmed/36773619 http://dx.doi.org/10.1016/S0140-6736(23)00129-0 |
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author | Pan, Yang Wang, Liang Feng, Zhaomin Xu, Hui Li, Fu Shen, Ying Zhang, Daitao Liu, William J Gao, George F Wang, Quanyi |
author_facet | Pan, Yang Wang, Liang Feng, Zhaomin Xu, Hui Li, Fu Shen, Ying Zhang, Daitao Liu, William J Gao, George F Wang, Quanyi |
author_sort | Pan, Yang |
collection | PubMed |
description | BACKGROUND: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic. METHODS: We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study. FINDINGS: We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022. INTERPRETATION: The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility. FUNDING: National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences. TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section. |
format | Online Article Text |
id | pubmed-9949854 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier Ltd. |
record_format | MEDLINE/PubMed |
spelling | pubmed-99498542023-02-24 Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis Pan, Yang Wang, Liang Feng, Zhaomin Xu, Hui Li, Fu Shen, Ying Zhang, Daitao Liu, William J Gao, George F Wang, Quanyi Lancet Articles BACKGROUND: Due to the national dynamic zero-COVID strategy in China, there were no persistent local transmissions of SARS-CoV-2 in Beijing before December, 2022. However, imported cases have been frequently detected over the past 3 years. With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. Spatiotemporal analyses of recent viral genome sequences compared with that of global pooled and local data are crucial for the global response to the ongoing COVID-19 pandemic. METHODS: We routinely collected respiratory samples covering both imported and local cases in Beijing for the last 3 years (of which the present study pertains to samples collected between January and December, 2022), and then randomly selected samples for analysis. Next-generation sequencing was used to generate the SARS-CoV-2 genomes. Phylogenetic and population dynamic analyses were performed using high-quality complete sequences in this study. FINDINGS: We obtained a total of 2994 complete SARS-CoV-2 genome sequences in this study, among which 2881 were high quality and were used for further analysis. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages. Nevertheless, BA.5.2 and BF.7 are currently dominant in Beijing, accounting for 90% of local cases since Nov 14 (315 of 350 local cases sequenced in this study). The effective population size for both BA.5.2 and BF.7 in Beijing increased after Nov 14, 2022. INTERPRETATION: The co-circulation of BF.7 and BA.5.2 has been present in the current outbreak since Nov 14, 2022 in Beijing, and there is no evidence that novel variants emerged. Although our data were only from Beijing, the results could be considered a snapshot of China, due to the frequent population exchange and the presence of circulating strains with high transmissibility. FUNDING: National Key Research and Development Program of China and Strategic Priority Research Program of the Chinese Academy of Sciences. TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section. Elsevier Ltd. 2023 2023-02-08 /pmc/articles/PMC9949854/ /pubmed/36773619 http://dx.doi.org/10.1016/S0140-6736(23)00129-0 Text en © 2023 Elsevier Ltd. All rights reserved. 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 | Articles Pan, Yang Wang, Liang Feng, Zhaomin Xu, Hui Li, Fu Shen, Ying Zhang, Daitao Liu, William J Gao, George F Wang, Quanyi Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title | Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title_full | Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title_fullStr | Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title_full_unstemmed | Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title_short | Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis |
title_sort | characterisation of sars-cov-2 variants in beijing during 2022: an epidemiological and phylogenetic analysis |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9949854/ https://www.ncbi.nlm.nih.gov/pubmed/36773619 http://dx.doi.org/10.1016/S0140-6736(23)00129-0 |
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