Genetic characteristics and nucleic acid detection results of SARS-CoV-2 in 2297 clinical samples

ABSTRACT

Objective To analyze the genomics characteristics and nucleic acid detection results of the severe Acute respiratory syndrome coronavirus 2（SARS-CoV-2） in 2 297 clinical samples collected in January and February, 2020 in Laboratory of Microbiology of Changsha Municipal Center for Disease Control and Prevention. Methods Viral RNA of throat swabs or respiratory tract specimens of coronavirus disease 2019（COVID-19） suspected cases from January 19, 2020 to February 29, 2020 was extracted and SARS-CoV-2 nucleic acid was detected by real-time reverse transcription polymerase chain reaction.The full length genome of SARS-CoV-2 in positive samples was enriched by using viral genome capture kit and sequenced on Illumina MiSeq platform.The raw reads were mapped and aligned with SPAdes software v 3.13.0.Reference SARS-CoV-2 sequences were obtained from GISAID（https//www.gisaid.org） andviral genetic evolution and antigen variation were analyzed. Results A total of 215 SARS-Co V2-nucleic acid positive samples were identified from 2 297 clinical samples.Among the SARS-Co V2-positive samples, 110 were males and 105 were from females.The male to female ratio was 1.05∶1.The highest positive rate was among 40-<60 years old people（11.35%） and the lowest positive rate was in children under 6 years old（5.49%）.The peak of newly confirmed cases was in the 5 th week（January 26 to February 1, 2020） and then decreased.There was no newly positive case after February 25, 2020.Five SARS-Co V2-whole genome sequences were obtained and there were 4 to 6 nucleotide mutations compared to the Wuhan reference strain, and the homology was more than 99.90%.Most mutations occurred only once except C8782 T and T28144 C, indicating random mutations.Phylogenetic analysis revealed that the 5 sequences belonged to the L/B or S/A lineages and were highly homologous with strains prevalent in other provinces of China at the same time. Conclusions With the quick nucleic acid tests and quarantine measures, the SARS-Co V2-positive cases in Changsha began to decline after a 2-week increasing period, and there was no new confirmed cases 6 weeks later.The genomes of SARS-Co V-2 prevalent in Changsha are highly homology with the Wuhan strains in the early 2020 and no obvious mutation is found in the local pandemic period. Reset