Objective:The objective of this study is to sequence whole genome of the rabies virus in the saliva specimen of a suspected rabies case with onset of rabies from a wildlife (hog badger) bite wound in Sichuan province, where the genetic variation characteristics of the virus was analyzed at the molecular level, so as to understand the prevalence and mutation of wildlife rabies virus in Sichuan province.Methods:Total viral RNA was extracted from the saliva specimen of the suspected rabies case. Then, rabies virus sequences were amplified using PCR with specific primers; the gene fragments obtained were sequenced, and the sequences obtained were spliced using biological software to obtain the whole genome sequence of the rabies virus strain. The genetic variation characteristics of the whole genome were analyzed.Results:The whole genome nucleotide sequence of a strain of rabies virus of hog badger origin (hereinafter referred to as SCR23-052) was obtained by sequencing, and NCBI online BLAST and comparison with several reference sequences showed that the composition and structure of the whole genome sequence of SCR23-052 conformed to the characteristics of the Lyssavirus under the Rhabdoviridae; the highest similarity in nucleotide and amino acid sequences in various gene regions was observed between SCR23-052 and the strains of Ningxia (J) and Chongqing (CQ92, 02050CHI). The sequence variability of SCR23-052 genome was significantly lower at the amino acid level than that at the nucleotide level, which indicated that most of the nucleotide variants in the protein-coding genes belonged to synonymous mutations. Phylogenetic analysis showed that SCR23-052 belonged to genotype V, which did not show any obvious mutation in the major antigenic site of the glycoprotein, underwent amino acid glycosylation at positions 56 and 338 by the online site prediction, and showed the least amino acid difference compared with the signal peptide sequence of the vaccine strain CTN181. The virus in this study has an A→T mutation at position 332 in the nucleoprotein major antigenic site with all reference vaccine strains, and an L→V mutation at position 379 in the B-cell epitope with the CTN181 vaccine strain. SCR23-052 was consistent with both genotype V reference strains at the nucleoprotein study site.Conclusions:The whole genome sequence of a wildlife strain of genotype V rabies virus of hog badger origin was obtained, which was different from that of the genotype I strain of rabies virus of dog origin that previously reported to be prevalent in Sichuan. The genome sequence of SCR23-052 differed from that of the reference vaccine strains to a varying degree, but the main virulence characteristics remained unaltered.

Objective:To detect and study the genetic evolution and biological characteristics of the first imported Zika virus (ZIKV) in a suspected case from Singapore to Sichuan Tianfu airport for inbound transfer on June 28, 2024, and so to provide reference for prevention and control of ZIKV disease.Methods:Serum sample was collected from the inbound transfer passenger, we detected ZIKV RNA using real-time RT-PCR method. The whole genome sequence was obtained through target next-generation sequencing (tNGS). CLC Genomics Workbench software was used for sequence analysis and splicing, and MEGA 7.0 software was used for phylogenetic tree construction.Results:Real-time RT-PCR result showed that the serum sample was positive. The phylogenetic tree which was constructed based on the whole genome sequence of ZIKV indicated the Sichuan strain was located on Asian lineage. Gene homology analysis showed that the homology between Sichuan strain and Asian, African strains ranged from 84.4%-98.6%. The Sichuan strain showed unique molecular features of 139S, 982V and 2634M.Conclusions:The ZIKV strain in Sichuan inbound transfer passenger in June 2024 belongs to the Asian lineage, which agrees with the epidemiological investigation outcome.

Objective:To detect and study the genetic evolution and biological characteristics of the first imported Zika virus (ZIKV) in a suspected case from Singapore to Sichuan Tianfu airport for inbound transfer on June 28, 2024, and so to provide reference for prevention and control of ZIKV disease.Methods:Serum sample was collected from the inbound transfer passenger, we detected ZIKV RNA using real-time RT-PCR method. The whole genome sequence was obtained through target next-generation sequencing (tNGS). CLC Genomics Workbench software was used for sequence analysis and splicing, and MEGA 7.0 software was used for phylogenetic tree construction.Results:Real-time RT-PCR result showed that the serum sample was positive. The phylogenetic tree which was constructed based on the whole genome sequence of ZIKV indicated the Sichuan strain was located on Asian lineage. Gene homology analysis showed that the homology between Sichuan strain and Asian, African strains ranged from 84.4%-98.6%. The Sichuan strain showed unique molecular features of 139S, 982V and 2634M.Conclusions:The ZIKV strain in Sichuan inbound transfer passenger in June 2024 belongs to the Asian lineage, which agrees with the epidemiological investigation outcome.

Objective:To analyze the molecular characteristics of E genes of imported dengue virus (DENV) in Sichuan province from 2012 to 2021, such as serotypes and genotypes, and so to provide the basis for virus traceability.Methods:DENV E genes of the 28 serum samples which were tested DENV positive by real time RT-qPCR from 2012 to 2021 in Sichuan province were amplified and sequenced by RT-PCR. Bioinformatics software Mega Align5.0 was used for the alignment analyses of nucleotide and deduced amino acid sequences, and bioinformatics software Mega7.0 was used to draw phylogenetic trees.Results:RT-PCR and sequencing indicated that 28 E genes of DENV were obtained. The serotypes and genotypes of DENV were revealed by homology and phylogenetic analysis based on E genes of DENV; 20 virus strains of Sichuan belonged to DENV serotype 1 (DENV-1), of which 16 virus strains were genotype I (G-I), 4 virus strains were genotype V (G-V); 7 virus strains belonged to DENV serotype 2 (DENV-2), of which 4 virus strains were G-I, 3 virus strains were genotype II (G-II); 1 virus strain belonged to DENV serotype 3 (DENV-3), G-I. The phylogenetic trees showed that Sichuan strains had more homology with strains of Southeast Asia and Guangdong province in China, that is consistent with the epidemiological data.Conclusions:In 2012 to 2021, the imported DENV in Sichuan province had 3 serotypes and multiple genotypes, and they were most likely transmitted from Southeast Asian countries.