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BMC genomics2023; 24(1); 568; doi: 10.1186/s12864-023-09646-1

Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau.

Abstract: Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. Results: By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. Conclusions: This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.
© 2023. BioMed Central Ltd., part of Springer Nature.
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Publication Date: 2023-09-25 PubMed ID: 37749507PubMed Central: PMC10521573DOI: 10.1186/s12864-023-09646-1Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigates the diversity and composition of viral communities found in herbivorous mammals in the Northwest Plateau region using metagenomic analysis.
  • It identifies various DNA and RNA viruses within different host species and evaluates their potential implications for animal and human health.

Background and Objective

  • Mammals can act as hosts for a wide array of infectious viruses, making the study of their viral communities important for understanding disease ecology and potential zoonotic threats.
  • The Northwest Plateau region had limited data regarding the viral populations in herbivorous mammals prior to this study.
  • This research aimed to characterize and compare the viral diversity present in seven herbivorous mammalian species across two sampling areas, Wuwei and Jinchang, in Gansu Province.

Methods

  • Samples from seven species of herbivorous mammals were collected in two distinct areas of the Northwest Plateau.
  • Virus metagenomics was employed, involving:
    • Library construction from viral nucleic acids extracted from the samples.
    • Next-generation sequencing (NGS) to obtain viral sequence data.
    • Bioinformatic classification of sequence reads (contigs and singlets) into viral families based on sequence similarity.
  • Phylogenetic analyses were performed on viral marker genes to explore genetic diversity and evolutionary relationships among identified viruses.

Key Findings

  • A total of 24 viral families were classified from the sequence data derived from the herbivorous mammals.
  • The viral community compositions in the two geographic areas (Wuwei and Jinchang) were relatively similar, indicating ecological stability across locations.
  • Across the seven animal species studied, the majority of viral reads were from single-stranded DNA (ssDNA) viruses, predominantly CRESS-DNA viruses (circular Rep-encoding single-stranded DNA viruses).
  • Phylogenetics showed high genetic diversity among CRESS-DNA viruses and microviruses (bacteriophages infecting bacteria).
  • RNA viruses identified included nodaviruses, pepper mild mottle viruses, and picornaviruses:
    • CRESS-DNA viruses and nodaviruses are typically associated with plants and insects, implying that their presence in mammals is likely linked to the herbivorous diet.
    • Microviruses infect bacteria and were also detected, suggesting a link to gut bacterial communities within the host animals.
    • Two notable picornaviruses were detected:
      • One from red deer exhibited close similarity to human hepatitis A virus, raising questions about potential cross-species viral transmission or common ancestry.
      • Another from wild horse appears to represent a potentially novel species within the Picornaviridae family, expanding known viral diversity.

Conclusions and Implications

  • This study provides a comprehensive profile of the viral communities present in herbivorous mammals from the Northwest Plateau, revealing both diversity and compositional stability across regions and species.
  • The identification of plant- and insect-associated viruses points to dietary origins influencing viral presence in these mammals.
  • Detection of picornaviruses related to human pathogens highlights the importance of monitoring wildlife for viruses that may pose zoonotic risks.
  • Findings expand scientific understanding of potential pathogenic viruses in herbivorous mammals, contributing valuable knowledge for veterinary and public health surveillance in this ecologically unique region.

Cite This Article

APA
Pan J, Ji L, Wu H, Wang X, Wang Y, Wu Y, Yang S, Shen Q, Liu Y, Zhang W, Zhang K, Shan T. (2023). Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau. BMC Genomics, 24(1), 568. https://doi.org/10.1186/s12864-023-09646-1

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 24
Issue: 1
Pages: 568
PII: 568

Researcher Affiliations

Pan, Jiamin
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Ji, Likai
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Wu, Haisheng
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Wang, Xiaochun
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Wang, Yan
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Wu, Yan
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Yang, Shixing
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Shen, Quan
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Liu, Yuwei
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
Zhang, Wen
  • Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China. z0216wen@yahoo.com.
Zhang, Keshan
  • State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China. vetzks009@163.com.
Shan, Tongling
  • Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China. shantongling@shvri.ac.cn.

MeSH Terms

  • Animals
  • Humans
  • Deer
  • Phylogeny
  • Brassicaceae
  • Vegetables
  • Cloning, Molecular

Grant Funding

  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No.2022YFC2603801 / National Key Research and Development Programs of China
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
  • No. 20220817004 / Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents

Conflict of Interest Statement

The authors declare no competing interests.

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