Genomic surveillance of emerging SARS-CoV-2 Omicron variations in Tianjin Municipality, China 2022  

作　　者：Xin Gao Ming Zou Yue Lei Zhaolin Tan Zhichao Zhuang Baolu Zheng Aiping Yu Yanzhen Han Xiaohui Lu Xiaochang Liu Ying Wang Yuan Wang Liru Guo Guangwen Liu Wen Li Yang Liu Likun Lv Peiyong Ning Xiaoyan Li 

机构地区：[1]Tianjin Centers for Disease Control and Prevention,Tianjin 300011,China [2]Tianjin Key Laboratory of Pathogenic Microbiologyof Infectious Disease,Tianjin Centers for Disease Controland Prevention,Tianjin 300011,China

出　　处：《Biosafety and Health》2024年第2期61-69,共9页生物安全与健康（英文）

基　　金：funded by the National Key Research and Development Program of China(No.2023YFC3041500);a key project of the Tianjin Municipal Health Commission(No.MS20014);Tianjin Municipal Health Commission Project(No.TJWJ2022ZD010);Tianjin Municipal Administration for Technology Project(No.20JCZDJC00130);Tianjin Key Medical Discipline(Specialty)Construction Project(No.TJYXZDXK-050A).

摘　　要：The coronavirus disease 2019(COvID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has severely impacted public health.In 2022,the Omicron variant of SARS-CoV-2 rapidly became the dominant circulating variant in the local COVID-19 outbreaks in Tianjin Municipality,China.To gain a deeper understanding of the genetic variations of the Omicron variant in Tianjin,specimens from indi-viduals who tested positive for SARS-CoV-2 between December 2021 and November 2022 were used for virus whole genome sequencing and phylogenetic analysis.A total of 1,674 high-quality Omicron sequences were obtained,consisting of 1,339 sequences from local cases belonging to 20 Phylogenetic Assignment of Named Global Outbreak(PANGO)lineages and 335 sequences from imported cases belonging to 70 lineages.Tianjin experienced five waves of local outbreaks,accompanied by multiple substitutions among subvariants,ranging from the initial BA.1.1 lineage to the subsequent BA.2,BF.7,and BA.5.2 lineages.The evolutionary rate of local strains,estimated to be 28.999 substitutions per year,and the evolutionary rate of imported strains,estimated to be 24.946 substitutions per year,were lower than that of the strains circulating globally.The addi-tional substitutions and deletions of local strains have been used to identify and disrupt the virus transmission chains.The subvariants such as BA.5.2.48,BA.5.2.49,BF.7.14,and XBB.1 circulating in the fifth epidemic wave presented criterial immune escape mutations including S:R346T,S:L452R and S:F486V.It is essential to implement genomic surveillance strategies to investigate further the development of genomic mutation char-acteristics in the SARS-CoV-2 variant.This ongoing monitoring will contribute to a better understanding of the virus's genetic changes and aid in effective control measures.

关 键 词：Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) Coronavirus disease 2019(COVID-19) Omicron variant Whole genome sequencing(WGS) 

分 类 号：R511[医药卫生—内科学] R181.8[医药卫生—临床医学]