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

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.

[1]  M. Heinemann,et al.  Epidemiological Profile of Wild Rabies in Brazil (2002–2012) , 2017, Transboundary and emerging diseases.

[2]  Edward C. Holmes,et al.  Seqotron: a user-friendly sequence editor for Mac OS X , 2016, BMC Research Notes.

[3]  Ben Hu,et al.  Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft , 2016, Virologica Sinica.

[4]  H. Field,et al.  Spatiotemporal Aspects of Hendra Virus Infection in Pteropid Bats (Flying-Foxes) in Eastern Australia , 2015, PloS one.

[5]  C. D. de Jong,et al.  Routes of Hendra Virus Excretion in Naturally-Infected Flying-Foxes: Implications for Viral Transmission and Spillover Risk , 2015, PloS one.

[6]  J. Farrar,et al.  The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases , 2015, EcoHealth.

[7]  A. Peterson,et al.  Ecological approaches in veterinary epidemiology: mapping the risk of bat-borne rabies using vegetation indices and night-time light satellite imagery , 2015, Veterinary Research.

[8]  F. Leendertz,et al.  Assessing the Evidence Supporting Fruit Bats as the Primary Reservoirs for Ebola Viruses , 2015, EcoHealth.

[9]  J. Epstein,et al.  Molecular evidence of Ebola Reston virus infection in Philippine bats , 2015, Virology Journal.

[10]  H. Field,et al.  Natural Hendra Virus Infection in Flying-Foxes - Tissue Tropism and Risk Factors , 2015, PloS one.

[11]  T. Sironen,et al.  Erratum to: Evolutionary trends of European bat lyssavirus type 2 including genetic characterization of Finnish strains of human and bat origin 24 years apart , 2015, Archives of Virology.

[12]  Sironen Tarja,et al.  Evolutionary trends of European bat lyssavirus type 2 including genetic characterization of Finnish strains of human and bat origin 24 years apart , 2015, Archives of Virology.

[13]  C. Calisher,et al.  Bats and zoonotic viruses: can we confidently link bats with emerging deadly viruses? , 2015, Memorias do Instituto Oswaldo Cruz.

[14]  S. Morand,et al.  Rodents and risk in the Mekong Delta of Vietnam: seroprevalence of selected zoonotic viruses in rodents and humans. , 2015, Vector borne and zoonotic diseases.

[15]  Dale L. Anderson,et al.  Ecological dynamics of emerging bat virus spillover , 2015, Proceedings of the Royal Society B: Biological Sciences.

[16]  M. Shi,et al.  Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China , 2014, Virology.

[17]  C. Tan.  Nipah Encephalitis - An Update , 2014 .

[18]  K. Yew.  Arteria Lusoria and Persistent Left Superior Vena Cava: Vessel Aberrancy is A Bane for Cardiologist Too. , 2014, The Medical journal of Malaysia.

[19]  D. Durrheim,et al.  Cross sectional survey of human-bat interaction in Australia: public health implications , 2014, BMC Public Health.

[20]  Christian Drosten,et al.  Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS , 2013, Antiviral Research.

[21]  B. A. Sherrini,et al.  Nipah encephalitis - an update. , 2014, The Medical journal of Malaysia.

[22]  D. D. Kulkarni,et al.  Nipah virus infection: current scenario , 2013, Indian Journal of Virology.

[23]  L. Nel,et al.  Diversity and Epidemiology of Mokola Virus , 2013, PLoS neglected tropical diseases.

[24]  C. Schwegmann-Wessels,et al.  Differential Sensitivity of Bat Cells to Infection by Enveloped RNA Viruses: Coronaviruses, Paramyxoviruses, Filoviruses, and Influenza Viruses , 2013, PloS one.

[25]  V. Borisevich,et al.  Pathogenesis of Hendra and Nipah virus infection in humans. , 2013, Journal of infection in developing countries.

[26]  J. Wood,et al.  Novel, Potentially Zoonotic Paramyxoviruses from the African Straw-Colored Fruit Bat Eidolon helvum , 2012, Journal of Virology.

[27]  H. Sawa,et al.  Molecular detection of a novel paramyxovirus in fruit bats from Indonesia , 2012, Virology Journal.

[28]  P. Woo,et al.  Novel Variant of Beilong Paramyxovirus in Rats, China , 2012, Emerging infectious diseases.

[29]  M. Knörnschild,et al.  Bats host major mammalian paramyxoviruses , 2012, Nature Communications.

[30]  Kimihito Ito,et al.  Detection of all known filovirus species by reverse transcription-polymerase chain reaction using a primer set specific for the viral nucleoprotein gene. , 2011, Journal of virological methods.

[31]  J. Ragle,et al.  IUCN Red List of Threatened Species , 2010 .

[32]  Yasuhiro Yoshikawa,et al.  Bat Coronaviruses and Experimental Infection of Bats, the Philippines , 2010, Emerging infectious diseases.

[33]  P. Woo,et al.  Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China , 2010, Virology.

[34]  胡伯齊.  高頭蝠(Scotophilus kuhlii)棲所利用與忠誠度 , 2010 .

[35]  E. Kalko,et al.  Henipavirus RNA in African Bats , 2009, PloS one.

[36]  David Posada,et al.  Selection of models of DNA evolution with jModelTest. , 2009, Methods in molecular biology.

[37]  M. Pallansch,et al.  Sensitive and Broadly Reactive Reverse Transcription-PCR Assays To Detect Novel Paramyxoviruses , 2008, Journal of Clinical Microbiology.

[38]  J. Peiris,et al.  Detection of Group 1 Coronaviruses in Bats Using Universal Coronavirus Reverse Transcription Polymerase Chain Reactions , 2007, Methods in molecular biology.

[39]  Samson S. Y. Wong,et al.  Bats as a continuing source of emerging infections in humans , 2006, Reviews in medical virology.

[40]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[41]  Y. Guan,et al.  Prevalence and Genetic Diversity of Coronaviruses in Bats from China , 2006, Journal of Virology.

[42]  H. Field,et al.  Bats: Important Reservoir Hosts of Emerging Viruses , 2006, Clinical Microbiology Reviews.

[43]  L. McElhinney,et al.  Heminested PCR assay for detection of six genotypes of rabies and rabies-related viruses , 1997, Journal of clinical microbiology.