Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam

Berto A, Anh PH, Carrique-Mas JJ, Simmonds P, Van Cuong N, Tue NT, Van Dung N, Woolhouse ME, Smith I, Marsh GA, Bryant JE, Thwaites GE, Baker S, Rabaa MA, the VIZIONS consortium, Kiet BT, Boni MF, Phu BD, Campbell JI, Hung DM, Huong DT, Oanh DT, Day JN, Van Tan D, van Doorn HR, Han DA, Farrar JJ, Trang HTT, Nghia HDT, Long HB, Van Duong H, Thu HTK, Cuong LC, Hung M, Phuong T, Phuc T, Phuong T, Luat X, Ha LTT, Van Chuong L, Loan MTP, Nadjm B, Bao NT, Tu NC, Thuan ND, Dong N, Chuyen NK, An NN, Vinh NN, Hung NQ, Dung NT, Minh NT, Binh NT, Tham NTH, Tien NTH, Chuc NTK, Le Ngoc NT, Ha NTL, Lien NTN, Diep NTN, Nhung NT, Chau NTS, Chi NTY, Trinh NT, Van NT, Van Hung N, Van Kinh N, Van Minh Hoang N, Van My N, Van Thang N, Van Thanh N, Van Vinh Chau N, Van Xang N, My PH, Khoa PTM, Tam PTT, Van Lao P, Van Minh P, Van Be Bay P, Rahman M, Thompson C, Ngan TTD, Nhu TDH, Chau THM, Toan TK, Phuc TM, Hong TTK, Dung TTN, Thanh TTT, Minh TTT, Nguyen TT, Hien TT, Tri TQ, Hien VB, Tai VN, Cuong VQ, Phat VV, Huong VTL, Hang VTT, Wertheim H, Bogaardt C, Brierley L, Chase-Topping M, Ivens A, Lu L, Rambaut A, Woolhouse M, Cotten M, Oude Munnink BB, Kellam P, Phan MVT, van der Hoek L, Deijs M, Jebbink MF, Farsani SMJ, Saylors K & Wolfe N

(2018) Zoonoses and Public Health 65, 30-42.

Bats and rodents are being increasingly recognized as reservoirs of emerging zoonotic viruses. Various studies have investigated bat viruses in tropical regions, but to date there are no data regarding viruses with zoonotic potential that circulate in bat and rat populations in Viet Nam. To address this paucity of data, we sampled three bat farms and three wet markets trading in rat meat in the Mekong Delta region of southern Viet Nam. Faecal and urine samples were screened for the presence of RNA from paramyxoviruses, coronaviruses and filoviruses. Paramyxovirus RNA was detected in 4 of 248 (1%) and 11 of 222 (4.9%) bat faecal and urine samples, respectively. Coronavirus RNA was detected in 55 of 248 (22%) of bat faecal samples; filovirus RNA was not detected in any of the bat samples. Further, coronavirus RNA was detected in 12 of 270 (4.4%) of rat faecal samples; all samples tested negative for paramyxovirus. Phylogenetic analysis revealed that the bat paramyxoviruses and bat and rat coronaviruses were related to viruses circulating in bat and rodent populations globally, but showed no cross-species mixing of viruses between bat and rat populations within Viet Nam. Our study shows that potentially novel variants of paramyxoviruses and coronaviruses commonly circulate in bat and rat populations in Viet Nam. Further characterization of the viruses and additional human and animal surveillance is required to evaluate the likelihood of viral spillover and to assess whether these viruses pose a risk to human health. ? 2017 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH

Andrew Rambaut, 2007