Identification of SARS-CoV-2 through combined 2nd and 3rd generation sequencing technology
10.3969/j.issn.1002-2694.2023.00.122
- VernacularTitle:联合二代和三代测序技术鉴定新冠病毒
- Author:
Qi LIN
1
;
Zhi-Miao HUANG
;
Zhi-Wei ZENG
;
Wei CHEN
;
Ming-Jian CHEN
;
Yu-Wei WENG
Author Information
1. 福建省人兽共患病研究重点实验室(福建省疾控预防控制中心),福州 350012
- Keywords:
SARS-CoV-2;
high-throughput sequencing;
BQ.1 lineage;
variation analysis
- From:
Chinese Journal of Zoonoses
2023;39(11):1053-1059
- CountryChina
- Language:Chinese
-
Abstract:
To rapidly and accurately identify novel SARS-CoV-2 variants,we used combined 2nd and 3rd generation sequen-cing technology to sequence and analyze the viral genomes of two specimens from SARS-CoV-2 infection cases imported into Fujian Province.Nanopore and Illumina techniques were used to perform whole genome sequencing of SARS-CoV-2.A pangolin system was used to determine the virus type.Evolutionary analysis software was used to construct the phylogenetic tree.Next-clade was used to analyze the whole genome variation,and estimate ACE2 receptor affinity and immune escape ability.Two complete genome sequences of SARS-CoV-2 were obtained from respiratory specimens from the two cases,with lengths of 29 665 bp and 29 682 bp.The average genome coverage were＞99.0％,and the virus typing results all indicated Omicron BQ.1 lineage.Phylogenetic analysis demonstrated that the two viruses were located in the same cluster of the Omicron BQ.1 line-age.On the basis of these findings and epidemiological data,we speculated that the two cases might have originated from the same infection.Variation analysis indicated that the two viruses shared all 77 mutation sites;except for S:A27S and S:24-26del,all were characteristic mutation sites of the BQ.1 lineage.The predicted ACE2 receptor affinity and immune escape abili-ty scores of the two viruses were both＞0.6,thus suggesting significant changes in their biological characteristics and requiring continuous monitoring and warning.The combined 2nd and 3rd generation sequencing technology was successfully applied to i-dentify the first BQ.1 lineage of the SARS-CoV-2 imported into Fujian Province,considering the timeliness and accuracy of whole genome sequencing,thus providing a technical reference for SARS-CoV-2 variant monitoring.
