Weijia Zhang

This study investigates the codon usage characteristics of Japanese encephalitis virus (JEV) genotype 5 (G5). Based on 339 complete JEV genome sequences, we systematically compared the codon usage patterns of G5 with other genotypes (G1–G4) using a multi-faceted approach, including evolutionary analysis, nucleotide composition, Relative Synonymous Codon Usage (RSCU), Principal Component Analysis (PCA), Effective Number of Codons Plot analysis (ENC-Plot), Parity Rule 2 analysis (PR2), Neutrality plot analysis, dinucleotide abundance analysis and Codon Adaptation Index analysis (CAI). The results indicate that G5 forms a distinct evolutionary branch, with both its overall GC content (50%) and GC content at the third codon position (GC3, 53%) being lower than those of other genotypes. RSCU analysis revealed a preferential use of A/U-ended codons in G5, indicating a trend towards reduced GC3 usage. ENC analysis demonstrated a stronger codon usage bias in G5 (mean ENC = 54.2). Furthermore, ENC-plot, PR2, and neutrality plot analyses collectively suggested that G5 is subject to stronger natural selection pressure. Analysis of dinucleotide abundance showed a significant increase in CA values in G5, while CAI analysis indicated higher translational efficiency in human hosts compared to Culex mosquito hosts. Our findings suggest that G5 JEV, potentially through reduced Cytosine-phosphate-Guanine (CpG) usage and optimized codon preference, may enhance its capabilities for immune evasion and host adaptation, and could possess the potential for efficient replication in humans or other mammalian hosts. This research provides crucial theoretical insights into the molecular evolutionary mechanisms of G5 JEV and informs related vaccine development.

Wuxiang virus (WUXV) is the first sandfly-borne Phlebovirus isolated from Phlebotomus chinensis collected in China and has been established as a consistent viral presence in the local sandfly populations of both Wuxiang County and Yangquan City. However, its distribution in the Shanxi Province remains unclear. In this study, three novel WUXV strains were isolated from sandflies collected from Jiexiu City, Shanxi Province, China, in 2022. Subsequently, whole-genome sequences of these novel strains were generated using next-generation sequencing. The open reading frame (ORF) sequences of the WUXV strains from the three locations were subjected to gene analysis. Phylogenetic analysis revealed that WUXV belongs to two distinct clades with geographical differences. Strains from Wuxiang County and Yangquan City belonged to clade 1, whereas strains from Jiexiu City belonged to clade 2. Reassortment and recombination analyses indicated no gene reassortment or recombination between the two clades. However, four reassortments or recombination events could be detected in clade 1 strains. By aligning the amino acid sequences, eighty-seven mutation sites were identified between the two clades, with seventeen, sixty, nine, and one site(s) in the proteins RdRp, M, NSs, and N, respectively. Additionally, selection pressure analysis identified 17 positively selected sites across the entire genome of WUXV, with two, thirteen, one, and one site(s) in the proteins RdRp, M, NSs, and N, respectively. Notably, sites M-312 and M-340 in the M segment not only represented mutation sites but also showed positive selective pressure effects. These findings highlight the need for continuous nationwide surveillance of WUXV.

In recent years, numerous viruses have been identified from ticks, and some have been linked to clinical cases of emerging tick-borne diseases. Chinese northeast frontier is tick infested. However, there is a notable lack of systematic monitoring efforts to assess the viral composition in the area, leaving the ecological landscape of viruses carried by ticks not clear enough. Between April and June 2017, 7101 ticks were collected to perform virus surveillance on the China–North Korea border, specifically in Tonghua, Baishan, and Yanbian. A total of 2127 Ixodes persulcatus were identified. Further investigation revealed the diversity of tick-borne viruses by transcriptome sequencing of Ixodes persulcatus. All ticks tested negative for tick-borne encephalitis virus. Transcriptome sequencing expanded 121 genomic sequence data of 12 different virus species from Ixodes persulcatus. Notably, a new segmented flavivirus, named Baishan Forest Tick Virus, were identified, closely related to Alongshan virus and Harz mountain virus. Therefore, this new virus may pose a potential threat to humans. Furthermore, the study revealed the existence of seven emerging tick-borne viruses dating back to 2017. These previously identified viruses included Mudanjiang phlebovirus, Onega tick phlebovirus, Sara tick phlebovirus, Yichun mivirus, and three unnamed viruses (one belonging to the Peribunyaviridae family and the other two belonging to the Phenuiviridae family). The existence of these emerging tick-borne viruses in tick samples collected in 2017 suggests that their history may extend further than previously recognized. This study provides invaluable insights into the virome of Ixodes persulcatus in the China–North Korea border region, enhancing our ongoing efforts to manage the risks associated with tick-borne viruses.

Background Japanese encephalitis (JE) is a vaccine-preventable mosquito-borne disease caused by infection with the Japanese encephalitis virus (JEV). G1, G3 and G5 JEV have been isolated in China, but the dominant genotype circulating in Chinese coastal areas remains unknown. Besides, the emergence of G5 JEV infection case in South Korea suggests a risk of G5 JEV transmission in epidemic areas. We search for G5 JEV infected case and try to understand which genotype of JEV was more relative to human Japanese encephalitis in coastal provinces of China. Methods In this study, we collected serum specimens of JE cases in three coastal provinces of China (Guangdong, Zhejiang and Shandong Province) from 2018 to 2020 and conducted JEV cross-neutralization test against genotype 1, 3 and 5 JEV. In the same serum specimen, if one neutralization antibody titer had a 4-fold difference with the other two, the case was considered infected by that genotype of JEV. Results The acute serum specimens of clinical reported JE cases were obtained for laboratory confirming from hospitals in Shandong (92 cases), Zhejiang (192 cases) and Guangdong (77 cases) of China from 2018 to 2020. 70 of total 361 serum specimens were laboratory confirmed JEV infection. 2 cases were confirmed infected by genotype 1 JEV, 32 cases were by genotype 3 JEV and 2 was by genotype 5 JEV. Conclusions The investigation found that there were genotype 1, 3 and 5 JEV infections in JE cases in coastal area of China from 2018 to 2020. Genotype 3 was the main infection genotype among JE cases who have the definite infection genotype, and the infection case caused by genotype 5 JEV was confirmed serologically in China.

Kadipiro virus (KDV) belongs to the Reoviridae family, which consists of segmented, non-enveloped, double-stranded RNA viruses. It has previously been isolated from Culex, Anopheles, Armigeres and Aedes mosquitoes in Indonesia and China. Here, we describe the isolation and characterization of SDKL1625 from Anopheles sinensis mosquitoes in Shandong province, China. In this study, we isolated Kadipiro virus in Aedes albopictus C6/36 cell culture and the complete genome sequencing was made by next generation sequencing. We isolated and characterized a Kadipiro virus from Anopheles sinensis mosquitoes in 2016 in Shandong province, China. Nucleotide and amino acid homology analysis of SDKL1625 showed higher levels of sequence identity with QTM27331 (Odonata, China, 2016) than with JKT-7075 (Culex fuscocephalus, Indonesia, 1981). The SDKL1625 has 86–97% amino acid identity with the JKT-7075, 88–99% amino acid identity with the QTM27331. Among the 12 fragments, VP1, VP2, VP4, VP6, VP7, VP9 and VP12 showed high amino acid identity (> 90%) and VP5 showed the lowest identity (86% and 88%). This is the first identification of KDV from mosquito in China. Virus morphology and genome organization were also determined, which will further enrich our understanding of the molecular biological characteristics of KDV and seadornaviruses.