Whole genome sequencing of SARS-CoV-2 isolated in Guangdong Province and factors influencing the sequencing
10.3760/cma.j.cn112309-20200216-00065
- VernacularTitle:广东省新型冠状病毒全基因组序列测定及其影响因素分析
- Author:
Lijun LIANG
1
;
Bosheng LI
;
Zhe LIU
;
Zhencui LI
;
Qianfang GUO
;
Yingchao SONG
;
Xue ZHUANG
;
Lirong ZOU
;
Jianxiang YU
;
Jie WU
Author Information
1. 广东省疾病预防控制中心，广东省新发传染病病原学检测技术研究中心，广东省病原微生物种质资源保藏与利用重点实验室，广东省病原微生物监测与应急检测重点学科，WHO合作培训中心，广州 511430
- From:
Chinese Journal of Microbiology and Immunology
2020;40(3):174-177
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To obtain the genome sequences of SARS-CoV-2 in respiratory specimens in Guangdong Province with next-generation sequencing (NGS) and analyze the factors influencing sequencing.Methods:Eight upper and lower respiratory tract specimens were collected from patients with SARS-CoV-2 infection in Guangdong Province in January 2020. RNA library construction was used to obtain the genome sequences of SARS-CoV-2. A bio-informatics software package (CLC Genomics Workbench 12.0) was used to analyze and compare the genomic sequences.Results:Five SARS-CoV-2 genome sequences were obtained from the eight specimens and two were obtained from lower respiratory tract specimens. The nucleotide homology to SARS-CoV-2 was 97.74%-99.90%. The Ct values were lower, while the sequencing depth, coverage, relative abundance and genome integrity were higher in sequencing the SARS-CoV-2 in lower respiratory tract specimens.Conclusions:The low Ct value of SARS-CoV-2 in the samples was good for sequencing.
