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. 2021 Apr;41(2):228-235.
doi: 10.1007/s11596-021-2340-3. Epub 2021 Apr 20.

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China

Bai-Sheng Li #  1   2 , Zhen-Cui Li #  1   2 , Yao Hu #  1   2 , Li-Jun Liang  1   2 , Li-Rong Zou  1   2 , Qian-Fang Guo  1   2 , Zhong-Hua Zheng  1   2 , Jian-Xiang Yu  1   2 , Tie Song  1   2 , Jie Wu  3   4   5
Affiliations

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province, China

Bai-Sheng Li et al. Curr Med Sci. 2021 Apr.

Abstract

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.

Keywords: genomic evolution; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); spike protein.

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