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Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genom...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Huazhong University of Science and Technology
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056187/ https://www.ncbi.nlm.nih.gov/pubmed/33877539 http://dx.doi.org/10.1007/s11596-021-2340-3 |
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author | Li, Bai-sheng Li, Zhen-cui Hu, Yao Liang, Li-jun Zou, Li-rong Guo, Qian-fang Zheng, Zhong-hua Yu, Jian-xiang Song, Tie Wu, Jie |
author_facet | Li, Bai-sheng Li, Zhen-cui Hu, Yao Liang, Li-jun Zou, Li-rong Guo, Qian-fang Zheng, Zhong-hua Yu, Jian-xiang Song, Tie Wu, Jie |
author_sort | Li, Bai-sheng |
collection | PubMed |
description | Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks. |
format | Online Article Text |
id | pubmed-8056187 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Huazhong University of Science and Technology |
record_format | MEDLINE/PubMed |
spelling | pubmed-80561872021-04-20 Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China Li, Bai-sheng Li, Zhen-cui Hu, Yao Liang, Li-jun Zou, Li-rong Guo, Qian-fang Zheng, Zhong-hua Yu, Jian-xiang Song, Tie Wu, Jie Curr Med Sci Article Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks. Huazhong University of Science and Technology 2021-04-20 2021 /pmc/articles/PMC8056187/ /pubmed/33877539 http://dx.doi.org/10.1007/s11596-021-2340-3 Text en © Huazhong University of Science and Technology 2021 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Article Li, Bai-sheng Li, Zhen-cui Hu, Yao Liang, Li-jun Zou, Li-rong Guo, Qian-fang Zheng, Zhong-hua Yu, Jian-xiang Song, Tie Wu, Jie Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title | Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title_full | Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title_fullStr | Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title_full_unstemmed | Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title_short | Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China |
title_sort | genomic evolution and variation of sars-cov-2 in the early phase of covid-19 pandemic in guangdong province, china |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056187/ https://www.ncbi.nlm.nih.gov/pubmed/33877539 http://dx.doi.org/10.1007/s11596-021-2340-3 |
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