Effects of sample processing modes on high-throughput sequencing of coronavirus whole genome
10.3760/cma.j.cn112309-20191011-00322
- VernacularTitle:不同样本测序前处理方案对冠状病毒基因组高通量测序结果的影响
- Author:
Jing CHEN
1
;
Yawei ZHANG
;
Peihua NIU
;
Rojian LU
;
Na ZHU
;
Hang FAN
;
Wenjie TAN
Author Information
1. 温州医科大学检验医学院 生命科学学院，检验医学教育部重点实验室，浙江省医学遗传学重点实验室，医学病毒学研究所 325035
- From:
Chinese Journal of Microbiology and Immunology
2020;40(2):103-109
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To study the effects of different pre-sequencing sample processing modes on the results of whole genome sequencing with high-throughput sequencing (HTS) by taking the largest RNA virus (human coronavirus, HCoV) as the representative.Methods:Cell-cultured human coronavirus HCoV-OC43 strains were used as the representative samples and divided into different groups based on pre-sequencing processing modes as follows: untreated group, DNase and RNase treatment before nucleic acid extraction group, DNase treatment after nucleic acid extraction group, and DNase and RNase treatment before nucleic acid extraction and DNase treatment after nucleic acid extraction group. Nucleic acid samples of each group were analyzed by direct RNA sequencing (without amplification) and DNA sequencing after sequence independent single primer amplification (SISPA), respectively.Results:No significant difference in viral genome coverage rates was observed between different groups. The highest genome coverage and sequencing accuracy were obtained in DNase treatment after nucleic acid extraction group by direct RNA sequencing, and the ratio of viral reads and the sequencing depth of each locus were effectively improved by SISPA amplification.Conclusions:This study provided an optimized technical strategy for whole genome sequencing of RNA viruses such as coronavirus.
