Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

Abstract

Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42–82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.

Comparison of viral communities in the blood, feces and various tissues of wild brown rats (Rattus norvegicus)

“…A total of 28 new PBV strains were obtained from fecal samples of wild Rattus norvegicus , indicating that Rattus norvegicus is one of the critical wildlife reservoirs for PBV. Two studies on the diversity of RNA viruses in wild animals in the plateau region of western China showed that a large number of segmented PBVs and a small number of unsegmented PBVs were found in the feces of Tibetan rats and Himalayan zoko rats, which were generally consistent with PBVs in woodchuck [ 49 , 50 ]. Most PBVs in this experiment were grouped with known genotypes but clustered with other animals.…”

Viral diversity in wild and urban rodents of Yunnan Province, China

“…Our work on viral diversity differs from previous investigations due to distinct study approaches [ 4 , 37 ]. While metagenomics and metatranscriptomics have previously characterized rodent virome at organ level, much remains to be understood regarding the diversity of zoonotic viruses at species and habitat levels [ 35 , 38 ]. This knowledge gap underscores the complexity of host-virus interactions in Yunnan rodent populations, with unique viral profiles across species and organs, with spleen samples consistently exhibiting high mammal viral diversity.…”

Chemical Pretreatments and Anaerobic Digestion Shape the Virome and Functional Microbiome in Fecal Sludge

“…Putative virus contigs were compared with the NT database by using BLAST, and the result of the best hit with e ≤ 10 −5 was selected for species annotation. 39 The viruses were annotated with contig percentages at the family and species levels. The reads per kilobase per million mapped reads (RPKM) for each virus contig were calculated.…”

“…Putative virus sequences with a similarity of <80% were searched in the virus NT and NR databases by using BLASTN (version 2.9.0+; ) and BLASTX (version 2.9.0+; ). Putative virus contigs were compared with the NT database by using BLAST, and the result of the best hit with e ≤ 10 –5 was selected for species annotation . The viruses were annotated with contig percentages at the family and species levels.…”