Sequencing and Genomic Characterization of the first Monkeypox Virus in Ningxia,China
A molecular tracing platform for the monkeypox virus was established by high-throughput sequencing and bioinformatics analysis.It was created to provide technical support for the prevention and control of monkeypox outbreaks in Ningxia,China.The DNA of the first positive sample of nucleic acids from the monkeypox virus was used as a template to construct an amplicon sequencing library for ultrasensitive capture of the whole genome.High-throughput sequencing was based on the Nextseq 2000 sequencing platform from Illumina.After sequence splicing,the online tools of Nextclade were used to analyze variations in the nucleotides,genome lineage typing,and traceability of the virus.Bioinformatics analysis was undertaken on the sequence and structure of the A35R protein of the neutralizing antibody.Ct values of the target gene F3L in oropharyngeal swabs and pustule fluid were 33.6 and 17.8,respectively,indicating a higher virus load in pustule fluid compared with oropharyngeal swabs.Whole-genome sequences were obtained from samples of pustule fluid with an average sequencing depth of 2,306× and genome coverage of 99.12％.The sequences belonged to type C.1 of clade Ⅱb(West African branch)and contained 84 nucleotide-mutation sites,resulting in 36 amino-acid mutations.Analyses of phylogenetic trees showed that the sequences were closely related to EPI-ISL_18059183 submitted by Yunnan Province in China(sampled on 28 June 2023)and recent strains circulating in Japan.The Ningxia sequence carried three unique nucleotide-mutation sites(C94049T,C142797T,C174897T)in addition to sharing 81 nucleotide-mutation sites with these sequences.Homology modeling using SWISS MODEL revealed high similarity between the globular domain of A35R protein and that of A33R protein of the cowpox virus.The whole-genome sequence of the monkeypox virus was obtained from pustule fluid,and had a total length of 197,209 bp.A technical platform for mutations and molecular tracing of the monkeypox virus was also established.
万方数据
维普
