Complete genome sequencing and traceability analysis of SARS-CoV-2 in Binhai New Area, Tianjin / 中华微生物学和免疫学杂志

ABSTRACT

Objective:To analyze the whole genome traceability and variation analysis of SARS-CoV-2 in local COVID-19 outbreaks in Binhai New Area, Tianjin.Methods:The whole-genome high-throughput sequencing was performed on throat swab samples collected from one local asymptomatic infected person and five confirmed cases of COVID-19 in Binhai New Area of Tianjin from November 7 to December 5, 2020. The sequencing data were assembled by De novo. MAFFT v7.0 multiple sequence alignment program and MEGA X software were used to compare the above data and construct phylogenetic tree (Neighbor-joining method).Results:The genetic similarity between the sequences of 6 SARS-CoV-2 strains and Wuhan reference sequence (Wuhan-Hu-1) was greater than 99.9%. Two of six strains were genetically identical, conform to the L-Lineage European Branch Ⅱ.1(America Branch)/B.1; The other four strains had the same genes and were in line with the characteristics of L-Lineage European Branch Ⅰ/B.1.1.These six strains belonged to different evolutionary branches and two different transmission chains. There were 18 nucleotide mutation sites in sequences of six SARS-CoV-2 strains, eight of which were synonymous mutation sites, nine of which were missense mutation sites, resulting in nine amino acid mutation sites, and important mutation sites of RDRP-P323L and S-D614G were found in all of the six samples.Conclusions:In this study, there were two COVID-19 outbreaks in Binhai New Area of Tianjin, and the sequences of six SARS-CoV-2 strains belonged to different evolutionary branches and two different transmission chains. It might come from porters′ contact with imported cold chain items contaminated with SARS-CoV-2 from different sources. All the sequences of six SARS-CoV-2 strains had P323L and D614G mutations, which indicated that the virus mutation and transmission ability were stronger. The surveillance of important employees of the cold chain in Tianjin and local and imported cases should be continuously strengthened.