Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia

Fuka Kikuchi; Keita Aoki; Satoshi D Ohdachi; Kimiyuki Tsuchiya; Masaharu Motokawa; Takamichi Jogahara; Nguyễn Trường Sơn; Saw Bawm; Kyaw San Lin; Thida Lay Thwe; Chandika D Gamage; Marie Claudine Ranorosoa; Hasmahzaiti Omar; Ibnu Maryanto; Hitoshi Suzuki; Keiko Tanaka-Taya; Shigeru Morikawa; Tetsuya Mizutani; Motoi Suzuki; Richard Yanagihara; Satoru Arai

doi:10.3389/fcimb.2020.00438

Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia

Front Cell Infect Microbiol. 2020 Aug 27:10:438. doi: 10.3389/fcimb.2020.00438. eCollection 2020.

Authors

Fuka Kikuchi^{1

2

3}, Keita Aoki², Satoshi D Ohdachi⁴, Kimiyuki Tsuchiya⁵, Masaharu Motokawa⁶, Takamichi Jogahara⁷, Nguyễn Trường Sơn^{8

9}, Saw Bawm¹⁰, Kyaw San Lin¹¹, Thida Lay Thwe¹², Chandika D Gamage¹³, Marie Claudine Ranorosoa¹⁴, Hasmahzaiti Omar¹⁵, Ibnu Maryanto¹⁶, Hitoshi Suzuki¹⁷, Keiko Tanaka-Taya¹, Shigeru Morikawa¹⁸, Tetsuya Mizutani³, Motoi Suzuki¹, Richard Yanagihara¹⁹, Satoru Arai¹

Affiliations

¹ Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.
² Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan.
³ Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan.
⁴ Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
⁵ Laboratory of Bioresources, Applied Biology Co., Ltd., Tokyo, Japan.
⁶ The Kyoto University Museum, Kyoto University, Kyoto, Japan.
⁷ Faculty of Law, Economics and Management, Okinawa University, Naha, Japan.
⁸ Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
⁹ Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
¹⁰ Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar.
¹¹ Department of Aquaculture and Aquatic Disease, University of Veterinary Science, Nay Pyi Taw, Myanmar.
¹² Department of Zoology, Yangon University of Distance Education, Yangon, Myanmar.
¹³ Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
¹⁴ Mention Foresterie et Environnement, Ecole Supérieur des Sciences Agronomiques, Université d'Antananarivo, Antananarivo, Madagascar.
¹⁵ Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
¹⁶ Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Bogor, Indonesia.
¹⁷ Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.
¹⁸ Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan.
¹⁹ Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States.

Abstract

Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.

Keywords: Suncus murinus; Thottapalayam thottimvirus; genetic diversity; phylogeography; shrew-borne hantavirus.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Africa
Animals
China
Genetic Variation*
India
Nepal
Pakistan
Phylogeny
Phylogeography
Shrews*

Grants and funding

P30 GM114737/GM/NIGMS NIH HHS/United States