RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

Genomic characterization of Rocahepevirus ratti hepatitis E virus genotype C1 in Yunnan province of China

The Rocahepevirus ratti hepatitis E virus genotype C1 (HEV-C1) has been documented to infect humans. However, the understanding of HEV-C1 remains constrained. This study aims to determine the prevalence and genomic characteristics of HEV-C1 in small animals in Yunnan province of southwestern China. A total of 444 liver tissues were collected from animals covering the orders Rodentia, Soricomorpha, Scandentia and Erinaceomorpha in three regions in Yunnan. Then Paslahepevirus balayani and Rocahepevirus were examined using RT-qPCR. The detection rate of Rocahepevirus was 12.95 % (36/278) in animals of order Rodentia, with 14.77 % (35/237) in Rattus tanezumi and 33.33 % (1/3) in Niviventer fulvescens. No Paslahepevirus balayani was detected. Additionally, two full-length Rocahepevirus sequences (MSE-17 and LHK-54) and thirty-three partial ORF1 sequences were amplified and determined to be HEV-C1. MSE-17 and LHK-54 shared moderate nucleotide identity (78.9 %-80.3 %) with HEV-C1 isolated in rats and humans. The HEV-C1 isolated from Niviventer fulvescens demonstrated a 100 % nucleotide identity with that from Rattus tanezumi. The rat HEV-C1 sequences isolated in our study and other Asian HEV-C1 sequences were phylogenetically distant from those isolated in North America and Europe. Furthermore, the two full-length sequences isolated in our study had less amino acid substitutions in the motifs of RNA-dependent RNA polymerase domain (F204L and L238F), compared with other Asian sequences. In summary, HEV-C1 commonly spreads in rats in Yunnan province of China. Our findings suggest a spatially associated phylogeny, and potential cross-species transmission of HEV-C1.

Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures

Introduction

Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown.

Methods

In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures.

Results

In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome.

Discussion

Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

ICTV Virus Taxonomy Profile: Lispiviridae 2023

Members of the family Lispiviridae are viruses with negative-sense RNA genomes of 6.5-15.5 kb that have mainly been found in arthropods and nematodes. The genomes of lispivirids contain several open reading frames, typically encoding a nucleoprotein (N), a glycoprotein (G), and a large protein (L) including an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Lispiviridae, which is available at ictv.global/report/lispiviridae.

Transcriptome mining of RNA viruses (family Totiviridae ) in Eimeria necatrix and Eimeria stiedai

Coccidian protozoa from the genus Eimeria are widespread parasites of vertebrates, causing serious disease (coccidiosis) and economic loss most notably in poultry. Several species of Eimeria are themselves infected with small RNA viruses assigned to the family Totiviridae . In this study, the sequences of two such viruses were newly determined, one of which represents the first complete protein-coding sequence of a virus from E. necatrix , an important pathogen of chickens, and the other of which is from E. stiedai , an important pathogen of rabbits. Sequence features of the newly identified viruses, compared with those of ones reported previously, provide several insights. Phylogenetic analyses suggest that these eimerian viruses constitute a well-demarcated clade, probably deserving of recognition as a distinct genus.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance

Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.