Whole genome sequencing of SARS-CoV-2 from specimens of six cases of SARS-CoV-2 infection in Lianyungang City
Objective To directly determine and sequence the whole genome of SARS-CoV-2 from specimens of SARS-CoV-2 infection cases by high-throughput sequencing technology,and to analyze the genome characteristics and variation of SARS-CoV-2 and conduct molecular traceability.Methods The throat swab specimens from six confirmed cases of SARS-CoV-2 infection in different periods in Lianyungang City were selected to perform the whole genome sequencing for SARS-CoV-2 using the Illumina iSeq100 next-generation sequencing(NGS)technology.Many varieties of online virus variation analysis platforms were used to analyze the genome variation of SARS-CoV-2.The whole genome sequencing was performed by using phylogenetic analysis softwares like CLC and MEGA,and then we speculated about the source of SARS-CoV-2 combined with the epidemiological data of the cases.Results We successfully obtained the complete genome sequences of SARS-CoV-2 from six samples,and the complete genomes of SARS-CoV-2 were 29,873-29,903 bp in length,with the genome coverage of 91.0％-100.0％.Compared with the Wuhan/WH01/2019 reference strain,a total of 28,56,82,75,78 and 79 nucleotide mutation sites were detected,involving 19,40,62,52,56 and 57 amino acid mutations,with the nonsynonymous mutations covering 67.9％(19/28),71.4％(40/56),75.6％(62/82),69.3％(52/75),71.8％(56/78)and 72.1％(57/79)respectively.Phylogenetic analysis displayed that sample LYG20210406 belonged to clade B.1.351,sample LYG20210723 to clade AY.42,sample LYG20220312 to clade BA.2.3,sample LYG20220709 to clade BA.2.2.1,sample LYG20220825 to clade BA.2.76,and sample LYG20221006 to clade BA.5.2.Sample LYG20210406 showed a close connection with the epidemic strain in Philippines.The genome sequences of LYG20210723,LYG20220312,LYG20220709,LYG20220825 and LYG20221006 were closest to those of the SARS-CoV-2 strains prevalent internationally during the same period,which were consistent with the results of epidemiological surveys.Conclusion The next-generation sequencing method and data analysis process in this study can be applied to SARS-CoV-2 variation analysis and molecular traceability,and also have a good application prospect in municipal-level CDCs.Therefore,they are of great significance for prevention and control of the SARS-CoV-2 epidemic.
severe acute respiratory syndrome coronavirus 2whole genome characteristichigh-throughput sequencingphylogenetic analysis
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