Identification and Genomic Characterization of Two Novel Hepatoviruses in Shrews from Yunnan Province, China

• Published in: Viruses 2024-06, Vol.16 (6), p.969
• Main Authors: Tang, Yi, Zhao, Kai, Yin, Hong-Min, Yang, Li-Ping, Wu, Yue-Chun, Li, Feng-Yi, Yang, Ze, Lu, Hui-Xuan, Wang, Bo, Yang, Yin, Zhang, Yun-Zhi, Yang, Xing-Lou
• Format: Article
• Language: English
• Subjects: amplicon and QNome nanopore sequencing (A-QNS); Animals; Annealing; China - epidemiology; codon usage bias; Diagnosis; Epidemiology; Ethics; Genetic aspects; Genome, Viral; Genomes; Genomics - methods; Health aspects; Hepatitis A; Hepatitis A virus; hepatitis A virus (HAV); Hepatovirus; Hepatovirus (HepV); High-Throughput Nucleotide Sequencing; Host range; Marine mammals; Next-generation sequencing; next-generation sequencing (NGS); Nucleotide sequence; Phylogeny; Picornaviridae Infections - epidemiology; Picornaviridae Infections - veterinary; Picornaviridae Infections - virology; Protein structure; Proteins; RNA, Viral - genetics; Secondary structure; shrew; Shrews; Shrews - virology; Small mammals
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v16060969

Hepatitis A virus (HAV), a member of the genus ( HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew ( ) and long-tailed brown-toothed shrew ( ), respectively. Our sequence and phylogenetic analyses of EpMa-HAV and EpLe-HAV indicated that they belong to the species (HepV-I) clade II, also known as the Chinese shrew HepV clade. Notably, the codon usage bias pattern of novel shrew HepVs is consistent with that of previously identified Chinese shrew HepV. Furthermore, our structural analysis demonstrated that shrew HepVs differ from other mammalian HepVs in RNA secondary structure and exhibit variances in key protein sites. Overall, the discovery of two novel HepVs in shrews expands the host range of HepV and underscores the existence of genetically diverse animal homologs of human HAV within the genus HepV.