Whole genome sequencing and analysis of 2019 novel coronavirus imported from a freighter in Fujian province, China
10.3760/cma.j.cn112866-2022-0121-00012
- VernacularTitle:福建省一起经货轮输入的新冠肺炎病毒全基因组测序分析
- Author:
Qi LIN
1
;
Zhimiao HUANG
;
Zehui CHEN
;
Xiaohong ZENG
;
Wei CHEN
;
Yingxiang ZHENG
;
Yuwei WENG
Author Information
1. 福建省疾病预防控制中心 福建省人兽共患病研究重点实验室，福州 350012
- Keywords:
2019 novel coronavirus;
Delta variant;
High-throughput sequencing;
Variation characteristics;
Whole genome
- From:
Chinese Journal of Experimental and Clinical Virology
2022;36(2):121-127
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To investigate the whole genome characteristics and mutation of imported 2019-nCoV and trace potential source at the genomics level, the viral genomes from the specimens of a cluster of COVID-19 cases which were imported from a freighter were directly sequenced and determined by high-throughput sequencing technology and bioinformatics analysis.Methods:Throat swab specimens from the 8 confirmed cases of COVID-19 from the same freighter were collected to perform the whole genome sequencing for 2019-nCoV using the targeted genome amplification, combined with Ion S5 next-generation sequencing (NGS) technology. Varieties of online virus analysis platforms was used to classify the viruses and analyze mutation sites in the whole genome. Phylogenetic analysis software was used to construct a phylogenetic tree for the viruses, combined with the epidemiological data of the case, to speculate about the source of the viruses.Results:Eight complete genome sequences of 2019-nCoV was successfully obtained. The complete genomes of the viruses were 29, 822-29, 865 bp in length, with the average sequencing depth of 11 928×-33 588× and the coverage of 99.73%-99.87%; the result of Pangolin classification showed that all the eight 2019-nCoV genomes belong to VOC/Delta (B.1.617.2) lineage. The result of whole genome mutation analysis showed that compared with the Wuhan reference strain, the median number of nucleotide mutations in the eight 2019-nCoV genome sequences was 35 (31 to 38), and the median number of amino acid mutations was 26 (24-28); the mutation sites were distributed in 8 gene coding regions (ORF1a, ORF1b, S, ORF3a, M, ORF7a, ORF8, N). Further analysis revealed that eight 2019-nCoV genomes contained 23 characteristic mutation sites belonging to the Delta (B.1.617.2·AY.2) variants of 2019-nCoV. Since the mutation sites among the eight 2019-nCoV genomes were not completely overlapped, and the epidemiological survey report showed that the freighter stopped at multiple ports and had personnel alternation, it was speculated that the clustered COVID-19 cases might have different origins. Phylogenetic analysis showed that all the eight 2019-nCoV genomes were on the AY.2 sub-lineage of the B. 1.617.2 lineage. This result was consistent with the result of Pangolin classification and mutation analysis.Conclusions:In this study, 8 whole genome sequences of Delta variants were obtained through NGS technology from the clustered COVID-19 cases which were imported from a freighter. The sequencing method and analysis result in this study could provide reference for the 2019-nCoV mutation analysis and tracing the source of the COVID-19 cases for the prevention and control of the COVID-19 epidemic.
