Characteristics of full-genome sequence of four imported Omicron variants of SARS-CoV-2 in Changsha City
HUANG Zheng1, XU Ming-zhong1, OU Xin-hua1, XIANG Xing-yu2, ZHAN Zhi-fei2, YAO Dong1
1. Changsha Municipal Center for Disease Control and Prevention, Changsha, Hunan 410004, China; 2. Hunan Provincial Center for Disease Control and Prevention, Changsha, Hunan 410000, China
Abstract：Objective To analyze the characteristics and genetic variation based on full-genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from imported cases in Changsha City. Methods The high-throughput sequencing technology was used to perform whole genome sequencing of SARS-CoV-2 isolated in December 2021. Nucleotide sequences were compared, and phylogenetic analysis was conducted. Results Genome sequences of four SARS-CoV-2 strains were obtained in this research. The full length of genome sequences was 29,685 bp. Based on nucleotide sequences, homology comparison showed that four SARS-CoV-2 strains shared 99.6% and 99.9% similarity with Wuhan-Hu-1 reference strain (EPI_ISL_402125) and Omicron strain (EPI_ISL_8890653), respectively. Phylogenetic analysis revealed that the strains belonged to BA.1.1 branch which SARS-CoV-2 Omicron variants presented. The amino acid sequences revealed that four SARS-CoV-2 strains contained the mutation sites that had been reported in Omicron variants. We also found some novel substitution sites in ORF1ab amino acid sequences, including G5494S, K4346R, T5035I and E6945D, and R346K novel substitution in receptor-binding domain of S sequences. Conclusion The imported Omicron variants of SARS-CoV-2 in Changsha City contained all representative mutation sites that had been reported to increase the viral transmission and pathogenicity. We should continue to strengthen prophylactic measures against SARS-CoV-2.
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2022, Vol. 29 
