Objective To analyze the genetic characteristics of the whole genome sequences of severe fever with thrombocytopenia syndrome virus (SFTSV) in Chuzhou and Anqing of Anhui province from 2021 to 2023 and provide evidence for the prevention and control of severe fever withthrombocytopenia syndrome(SFTS).

Methods A total of 55 SFTSV strains were collected in Chuzhou and Anqing during 2021−2023 for whole genome sequence amplification and analysis. The L, M and S segments of the strains were analyzed by software MEGA 7.01, DNASTAR 7.1 and RDP 4.101 to identify the genotype, sequence similarity, genetic recombination and selection pressure.

Results Genotype A, C, E, F and 3 reassortment forms were found in 55 SFTSV strains. The major genotypes in Chuzhou and Anqing were A and F, respectively. The similarities of L, M, and S segments of the strains ranged from 95.40% to 100.00%, 93.40% to 99.90%, and 94.20% to 100.00%, respectively. The viral RNA-dependent RNA polymerase (RdRp) , glycoprotein precursor (GP), nucleocapsid (NP) and nonstructural protein (NSs) amino acid sequence similarities were 99.20%–100.00%, 97.30%–100.00%, 98.80%–100.00%, and 96.60%–100.00%, respectively. Genetic recombination occurred in the S segment of 3 SFTSV strains. The ratios of substitution rates at non-synonymous versus synonymous sites of the RdRp, GP, NP and NSs were 0.05, 0.14, 0.03 and 0.13, respectively.

Conclusion Multiple genotypes of SFTSV were detected in Chuzhou and Anqing cities, indicating that it is necessary to strengthen the etiological surveillance for SFTS to provide basic data for the prevention and control of SFTS in Anhui province.