Genomic analysis of a 2019-novel coronavirus (2019-nCoV) strain in the first COVID-19 patient found in Hangzhou
10.3760/cma.j.cn112150-20200217-00128
- VernacularTitle:杭州市首例新型冠状病毒肺炎病例病毒全基因组序列测定及分析
- Author:
Hua YU
1
;
Xuchu WANG
;
Jun LI
;
Xin QIAN
;
Xinfen YU
;
Zhou SUN
;
Junfang CHEN
;
Qingjun KAO
;
Haoqiu WANG
;
Jingcao PAN
Author Information
1. 杭州市疾病预防控制中心卫生检验中心 310021
- Keywords:
Genome;
2019-nCoV;
COVID-19
- From:
Chinese Journal of Preventive Medicine
2020;54(5):486-490
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To understand the viral genomic characteristics of a 2019-novel coronavirus (2019-nCoV) strain in the first COVID-19 patient found in Hangzhou, China.Methods:Viral RNA was extracted in throat swab and sputum sample of the patient and was performed real-time reverse transcription PCR detection and obtained viral genome by high-throughput sequencing method. Phylogenetic analysis was conducted using 29 2019-nCoV genomes and 30 β-coronavirus genomes deposited in NCBI GenBank. Fifteen genomes from Wuhan were grouped by mutation sites and others were identified by Wuhan's or specific mutation sites.Results:A 29 833 bp length genome of the first 2019-nCoV strain in Hangzhou was obtained, covering full length of the coding regions of coronavirus. Phylogenetic analysis showed that the genome was closest to the genome of a bat SARS-like coronavirus strain RaTG13 with an identity of 96.11% (28 666/29 826). Among the genes between two genomes, E genes were highly conserved (99.56%), while S genes had lowest identity (92.87%). The genome sequence similarities among 29 strains from China (Hangzhou, Wuhan, and Shenzhen), Japan, USA, and Finland, were all more than 99.9%; however, some single nucleotide polymorphisms were identified in some strains.Conclusion:The genome of Hangzhou 2019-nCoV strain was very close to the genomes of strains from other cities in China and overseas collected at early epidemic phase. The 2019-nCoV genome sequencing method used in this paper provides an useful tool for monitoring variation of viral genes.
