viruses Article Rodent-Borne Orthohantaviruses in Vietnam, Madagascar and Japan Fuka Kikuchi 1,2 , Kae Senoo 2,3 , Satoru Arai 2, * , Kimiyuki Tsuchiya 4,† , Nguyễn Trường Sơn 5,6 , Masaharu Motokawa 7 , Marie Claudine Ranorosoa 8 , Saw Bawm 9 , Kyaw San Lin 10 , Hitoshi Suzuki 11 , Akira Unno 12 , Keisuke Nakata 12 , Masashi Harada 13 , Keiko Tanaka-Taya 2 , Shigeru Morikawa 14 , Motoi Suzuki 2 , Tetsuya Mizutani 1 and Richard Yanagihara 15   Citation: Kikuchi, F.; Senoo, K.; Arai, S.; Tsuchiya, K.; Sơn, N.T.; Motokawa, M.; Ranorosoa, M.C.; Bawm, S.; Lin, K.S.; Suzuki, H.; et al. Rodent-Borne Orthohantaviruses in Vietnam, Madagascar and Japan. Viruses 2021, 13, 1343. https://doi.org/10.3390/ v13071343 Academic Editors: Kumiko Yoshimatsu and Hiroaki Kariwa Received: 16 June 2021 Accepted: 9 July 2021 Published: 12 July 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan; S203828z@st.go.tuat.ac.jp (F.K.); tmizutan@cc.tuat.ac.jp (T.M.) 2 Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; ksenoo@niid.go.jp (K.S.); ktaya@nih.go.jp (K.T.-T.); mosuzuki@niid.go.jp (M.S.) 3 Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan 4 Laboratory of Bioresources, Applied Biology Co., Ltd., Tokyo 107-0062, Japan 5 Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam; ntson@iebr.vast.vn 6 Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam 7 The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan; motokawa.masaharu.6m@kyoto-u.ac.jp 8 Mention Foresterie et Environnement, Ecole Supérieur des Sciences Agronomiques, Université d’Antananarivo, Antananarivo 101, Madagascar; maricollaris@gmail.com 9 Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar; bestshadow@gmail.com 10 Department of Aquaculture and Aquatic Disease, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar; kyawsanlinuvs@gmail.com 11 Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan; htsuzuki@ees.hokudai.ac.jp 12 Local Independent Administrative Agency Hokkaido Research Organization, Bibai 079-0198, Japan; unno-akira@hro.or.jp (A.U.); nakata-keisuke@hro.or.jp (K.N.) 13 Laboratory Animal Center, Osaka City University, Sumiyoshi, Osaka 545-8585, Japan; haradam2651@gmail.com 14 Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari 794-8555, Japan; s-morikawa@vet.ous.ac.jp 15 Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA; ryanagih@hawaii.edu * Correspondence: arais@nih.go.jp † Deceased. Abstract: Hantaviruses are harbored by multiple small mammal species in Asia, Europe, Africa, and the Americas. To ascertain the geographic distribution and virus-host relationships of rodent- borne hantaviruses in Japan, Vietnam, Myanmar, and Madagascar, RNAlater™-preserved lung tissues of 981 rodents representing 40 species, collected in 2011–2017, were analyzed for hantavirus RNA by RT-PCR. Our data showed Hantaan orthohantavirus Da Bie Shan strain in the Chinese white- bellied rat (Niviventer confucianus) in Vietnam, Thailand; orthohantavirus Anjo strain in the black rat (Rattus rattus) in Madagascar; and Puumala orthohantavirus Hokkaido strain in the grey-sided vole (Myodes rufocanus) in Japan. The Hokkaido strain of Puumala virus was also detected in the large Japanese field mouse (Apodemus speciosus) and small Japanese field mouse (Apodemus argenteus), with evidence of host-switching as determined by co-phylogeny mapping. Keywords: Hantaan orthohantavirus; Thailand orthohantavirus; Puumala orthohantavirus; spill- over infection; rodents Viruses 2021, 13, 1343. https://doi.org/10.3390/v13071343 https://www.mdpi.com/journal/viruses