Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province
- 1Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai China
- 2Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu China
Abstract
The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05231-0.
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BibTeX
@article{ying2026metagenomic,
title = {{Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province}},
author = {Kaiye Ying and Xiaofei Song and Jiaheng Chen and Yongshun Wang and Hailian Wu and Qi Zhang and Xiaoyan Yang and Wenxuan Peng and Haisheng Wu and Wen Zhang and Qingwen Zhang},
journal = {BMC Microbiology},
year = {2026},
month = jun,
doi = {10.1186/s12866-026-05231-0},
url = {https://doi.org/10.1186/s12866-026-05231-0},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province
AU - Kaiye Ying
AU - Xiaofei Song
AU - Jiaheng Chen
AU - Yongshun Wang
AU - Hailian Wu
AU - Qi Zhang
AU - Xiaoyan Yang
AU - Wenxuan Peng
AU - Haisheng Wu
AU - Wen Zhang
AU - Qingwen Zhang
PY - 2026
DA - 2026/06/10
JO - BMC Microbiology
DO - 10.1186/s12866-026-05231-0
UR - https://doi.org/10.1186/s12866-026-05231-0
AB - The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05231-0.
SN - 1471-2180
ER -