Genomic characteristics of SARS-CoV-2 from an outbreak in inbound flight
10.3760/cma.j.cn112866-20221014-00211
- VernacularTitle:一起入境航班关联新冠肺炎聚集性疫情病毒全基因组特征分析
- Author:
Wei DUAN
1
;
Dong WANG
;
Zhaomin FENG
;
Fu LI
;
Shujuan CUI
;
Bing LYU
;
Zhichao LIANG
;
Daitao ZHANG
;
Peng YANG
;
Quanyi WANG
;
Yang PAN
Author Information
1. 北京市疾病预防控制中心，北京 100013
- Keywords:
Severe acute respiratory syndrome coronavirus 2;
Genome;
Viral load;
Phylogenetic analysis;
Variation
- From:
Chinese Journal of Experimental and Clinical Virology
2023;37(2):140-145
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the genomic characteristics and variations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) derived from an outbreak in inbound flight in Aug, 2022 in Beijing, and provide reference data for disease prevention and control and risk assessment.Methods:Fifty respiratory tract specimens from all cases in this outbreak were collected. The digital PCR (ddPCR) was used to determine the viral loads of the specimens. The full genome of the viruses were sequenced by Next-generation sequencing. Then analuses were performed on the genetic identity, variations and phylogenesis.Results:The median of viral loads in all 50 samples were 5.57×10 4 copies/ml and 5.85×10 4 copies/ml, for ORF1ab gene and N gene, respectively. A total of 46 SARS-CoV-2 genomes were obtained, which all belonged to Omicron/BA.5. Two genome clusters were observed, involving 21 and 7 cases, with a nucleotide sequence identities of 99.993% and 99.997%, respectively. Conclusions:The studied outbreak was composed of two main clusters and other individual cases with Omicron/BA.5 virus overseas.
