Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

Abstract

Background

As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens.

Results

This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006–2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations.

Conclusions

These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40168-020-00965-z.

Contributors

Zhiqiang Wu: [e-mail]

Qi Jin:

ORCID: http://orcid.org/0000-0002-3586-6344

[e-mail]

Journal

Journal ID (nlm-ta): Microbiome

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: BioMed Central (London )

ISSN (Electronic): 2049-2618

Publication date (Electronic): 21 January 2021

Publication date PMC-release: 21 January 2021

Publication date Collection: 2021

Volume: 9

Affiliations

[1 ]GRID grid.506261.6, ISNI 0000 0001 0706 7839, NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, , Chinese Academy of Medical Sciences & Peking Union Medical College, ; Beijing, PR China

[2 ]GRID grid.506261.6, ISNI 0000 0001 0706 7839, Key Laboratory of Respiratory Disease Pathogenomics, , Chinese Academy of Medical Sciences & Peking Union Medical College, ; Beijing, PR China

[3 ]GRID grid.420826.a, ISNI 0000 0004 0409 4702, EcoHealth Alliance, ; New York, NY USA

[4 ]Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Vietnam

[5 ]GRID grid.269823.4, ISNI 0000 0001 2164 6888, Wildlife Conservation Society, Health Program, ; Bronx, NY USA

[6 ]GRID grid.9723.f, ISNI 0000 0001 0944 049X, Faculty of Veterinary Technology, , Kasetsart University, ; Bangkok, Thailand

[7 ]GRID grid.10223.32, ISNI 0000 0004 1937 0490, Faculty of Tropical Medicine, , Mahidol University, ; Bangkok, Thailand

[8 ]GlaxoSmithKline Vaccines, Singapore City, Singapore

[9 ]GRID grid.418537.c, Virology Unit, , Institut Pasteur in Cambodia, ; Phnom Penh, Cambodia

[10 ]GRID grid.464500.3, ISNI 0000 0004 1758 1139, Yunnan Institute of Parasitic Diseases, ; Pu’er, PR China

[11 ]GRID grid.17063.33, ISNI 0000 0001 2157 2938, Department of Laboratory Medicine and Pathobiology, , University of Toronto, ; Toronto, Canada

Article

Publisher ID: 965

DOI: 10.1186/s40168-020-00965-z

PMC ID: 7818139

SO-VID: 0253c1da-49c5-456d-b1d0-fa24cdc019d8

Copyright statement: © The Author(s) 2021

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 81772228

Award Recipient : Zhiqiang Wu

Funded by: Mega-projects of Science Research for the thirteenth Five-Year Plan (CN)

Award ID: 2018ZX10101001

Award Recipient : Zhiqiang Wu

Funded by: CAMS Innovation Fund for Medical Sciences

Award ID: 2016-I2M-1-014 and 2017-I2M-B&R-12

Award Recipient : Zhiqiang Wu

Categories

Subject: Research

Custom metadata

issue-copyright-statement © The Author(s) 2021