Genetic characteristics of mpox virus from the first mpox case in Sichuan

Objective To analyze the genetic characteristics of the mpox virus (MPXV) isolated from the first mpox case in Sichuan.

Methods Oropharyngeal swab and skin lesion swab were collected from the case to extract MPXV nucleic acid for real-time polymerase chain reaction (PCR) test. After confirmed the positive PCR results, nanopore sequencing was used to sequence the whole genome of MPXV. Minimap2 (v2.18-r1015), Medaka (v1.8.0) and Snpeff (v4.3.1) were used to analyze sequence data. Nextclade (https://clades.nextstrain.org/) was used for the genotype identification. IQ-TREE (v2.1.2) was used to construct phylogenetic tree.

Results The oropharyngeal swab and skin lesion swab collected from the case were positive for MPXV tested by three real-time PCR kits. The cycle threshold (Ct) value of the skin lesion swab was lower than that of the oropharyngeal swab by three real-time PCR kits. Whole genome sequencing analysis revealed that the MPXV strain from this case belonged to lineage B.1.3 in clade IIb. Phylogenetic analysis showed that the strain was homologous to those identified in the United States, Japan, and Zhejiang province of China with nucleotide similarity between 99.98% and 99.99%. The strain shared the highest nucleotide similarity (99.99%) with the strain from Zhejiang. Compared to the reference genome (NC_063383.1). The strain carried 70 nucleotide substitutions.

Conclusion The genetic characteristics of MPXV detected in Sichuan were similar to those detected in other areas of China. It is vital to strengthen surveillance for the genetic characteristics of MPXV for the timely detection of new variants.