Whole genomic characteristics of Senecavirus A strain SVA/CH-GX01-2020

【Objective】To study the pathogenic characteristics and molecular epidemiological features of Senecavirus A（SVA）through in-depth analysis of the whole genome characteristics of the Guangxi isolated strain，which provided theoretical basis for the effective prevention of outbreaks and epidemics of the disease.【Method】The virus was isolated from the suspected clinical sample collected from Guangxi in 2020，and identified by RT-PCR detection and indirect immunofluorescence assay（IFA）. After segmental amplification and sequencing of SVA strain whole genome，the sequences were spliced using Lasergene 7.1. Then，the whole genome sequence of SVA isolate was compared with 55 representative SVA strains of different years at home and abroad using MegAlign，and a phylogenetic tree was constructed using MEGA 11.0.【Result】One SVA strain was isolated，identified，and named strain SVA/CH-GX01-2020. The genome of strain SVA/CH-GX01-2020 was 7250 bp in length and the open reading frame（ORF）encoded 2181 amino acid residues. Compared with 55 representative SVA strains from home and abroad in different years，the similarities of nucleotide sequence and deduced amino acid sequence between SVA/CH-GX01-2020 strain and the other strains from home and abroad were 93.3%-98.7% and 97.3%-99.6% respectively. Among them，the SVA/CH-GX01-2020 strain had the lowest genomic similarity with the American classical strains SVV-001 and ATCC PTA-5343. Genetic evolution analysis showed that SVA/CH-GX01-2020 strain had distant genetic relationship with SVV-001 strain and ATCC PTA-5343 strain from America，located in the same branch with most isolates from China，and was very closely related to the Guangxi isolate SVA/GX/CH/2018. Amino acid sequence analysis revealed that，compared with the American classical SVA strain SVV- 001，the first Chinese isolate CH-01-2015，and the Guangxi isolate SVA/GX/CH/2018，the amino acid mutation sites in the SVA/CH-GX01-2020 strain were mainly concentrated in non-structural protein 3D region，it was relatively conserved in the structural protein VP4 and non-structural protein 2A regions.【Conclusion】The SVA/CH-GX01-2020 strain has its own unique genetic variation characteristics. The SVA strains from different geographical areas show different degrees of genetic relationship，indicating genetic diversity of the clinical strains，so surveillances and epidemiological investigations should be strengthened.