Whole-genome sequencing of SARS-CoV-2 variants isolated from imported cases in Sichuan Province from December 2022 to January 2023
10.3760/cma.j.cn112309-20240314-00090
- VernacularTitle:2022年12月—2023年1月四川省境外输入病例新型冠状病毒全基因组特征分析
- Author:
Huiping YANG
1
;
Yan PAN
;
Lyubo TIAN
;
Yu KUANG
;
Lei ZHANG
;
Lihui WANG
;
Linlin ZHOU
;
Ming PAN
Author Information
1. 四川省疾病预防控制中心微生物检验所，成都 610041
- Keywords:
SARS-CoV-2;
Imported cases;
Whole genome
- From:
Chinese Journal of Microbiology and Immunology
2024;44(7):601-607
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the distribution and genomic characteristics of SARS-CoV-2 variants isolated from imported cases of COVID-19 in Sichuan Province from December 2022 to January 2023.Methods:This study selected 108 nasal and throat swab samples with fluorescence threshold (Ct)≤32 that were collected from imported COVID-19 cases in Sichuan Province from December 2022 to January 2023. Targeted amplification and Illumina NextSeq? 2000 system were used for whole-genome sequencing. Nextclade and Pangolin online platforms were used to determine the virus genotypes and analyze the mutation loci. A phylogenetic tree was constructed using maximum likelihood.Results:A total of 55 SARS-CoV-2 whole genome sequences with coverage of >95% were obtained, and all of the strains were Omicron variants. Compared with the sequence of reference strain Wuhan-Hu-1, the median number of nucleotide mutation sites of 21L, 22B, 22D, 22E, and 22F genotypes were 93, 75, 92, 78, and 92, and the median number of amino acid mutation sites were 68, 53, 68, 69, and 65, respectively. From December 2022 to January 2023, the predominant circulating SARS-CoV-2 variants from imported cases in Sichuan Province were BA.5.2 (10.91%, 6/55), XBB.1.1 (9.10%, 5/55), BF.7.14 (7.23%, 4/55), and BQ.1.1 (7.23%, 4/55).Conclusions:The distribution of SARS-CoV-2 variants can reflect the global epidemic trend to a certain extent. However, it is different from the distribution of local circulating variants in the Chinese mainland. The XXB variants with transmission advantages can be detected in large numbers of inbound travelers before becoming the predominant circulating strains in the Chinese mainland.
