关键词: 猴痘病毒, 高通量测序, 基因组特征, 单核苷酸多态性

Abstract: Objective To analyze the full genome sequences of the monkeypox virus in 23 cases from Jiangsu Province from June to September 2023 and to study their molecular evolutionary characteristics. Method Samples such as oropharyngeal swabs, vesicle fluid, and vesicle exudate swabs from monkeypox cases were collected for viral nucleic acid detection by Real-time PCR. Amplicon sequencing technology was used to capture the full genome of the monkeypox virus in the samples. Finally, next-generation sequencing was performed by the MiniSeq high-throughput sequencer to analyze the virus evolution and mutation of the sequence. Result The average sequencing depth of the 23 samples ranged from 907.3× to 11 578.58×, and the coverage (sequencing depth ≥10×) was between 95.5% and 99.94%. Phylogenetic analysis showed that the viruses belonged to the MPXV Ⅱb C.1 (2023) lineage, which belonged to the same clade as sequences from Japan, Korea, Portugal, and China at the same time, and were distributed in three cluster clusters. Single nucleotide polymorphism (SNPs) analysis identified a total of 60 SNPs, including 59 base substitutions and one base deletion, with 26 non-synonymous mutations affecting host immune regulation, membrane protein, and viral transcriptional regulation functions. Among the 26 non-synonymous mutations, 25 SNPs were apolipoprotein B mRNA-editing catalytic polypeptide-like 3 (APOBEC3-like) mutations, and six shared mutations in 23 samples were all APOBEC3-like mutations. Samples 23010 and 23011 differed by only one mutation site at C177833T, and C76450T and G80405A were found exclusively in these two samples. Conclusion The 23 cases of monkeypox virus in Jiangsu Province from June to September 2023 were all of the Ⅱb evolutionary branch C.1 (2023) lineage, and the virus source was imported from multiple sources. Genome-wide surveillance and research of the monkeypox virus should be carried out on an ongoing basis, closely following the source of the virus and the evolution of the variants after local transmission.

Key words: Monkeypox virus, High-throughput sequencing, Gene characterization, Single nucleotide polymorphism