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Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History.
J Virol. 2017 03 01; 91(5)JV

Abstract

Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.

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Authors+Show Affiliations

Tao Y
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Shi M
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
Chommanard C
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Queen K
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Zhang J
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Markotter W
Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
Kuzmin IV
Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Holmes EC
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
Tong S
Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA sot1@cdc.gov.

MeSH

Amino Acid SequenceAnimalsChiropteraConserved SequenceCoronavirus InfectionsCoronavirus NL63, HumanEpidemiological MonitoringEvolution, MolecularGenetic VariationGenome, ViralKenyaPhylogenyPhylogeographyPrevalenceRecombination, GeneticRespiratory Tract InfectionsSequence Analysis, DNAViral Proteins

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28077633

Citation

Tao, Ying, et al. "Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History." Journal of Virology, vol. 91, no. 5, 2017.
Tao Y, Shi M, Chommanard C, et al. Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. J Virol. 2017;91(5).
Tao, Y., Shi, M., Chommanard, C., Queen, K., Zhang, J., Markotter, W., Kuzmin, I. V., Holmes, E. C., & Tong, S. (2017). Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. Journal of Virology, 91(5). https://doi.org/10.1128/JVI.01953-16
Tao Y, et al. Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. J Virol. 2017 03 1;91(5) PubMed PMID: 28077633.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History. AU - Tao,Ying, AU - Shi,Mang, AU - Chommanard,Christina, AU - Queen,Krista, AU - Zhang,Jing, AU - Markotter,Wanda, AU - Kuzmin,Ivan V, AU - Holmes,Edward C, AU - Tong,Suxiang, Y1 - 2017/02/14/ PY - 2016/09/29/received PY - 2016/12/04/accepted PY - 2017/1/13/pubmed PY - 2017/5/30/medline PY - 2017/1/13/entrez KW - Africa KW - HCoV-229E KW - HCoV-NL63 KW - bats KW - coronavirus KW - recombination KW - zoonoses JF - Journal of virology JO - J Virol VL - 91 IS - 5 N2 - Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5' and 3' ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential. SN - 1098-5514 UR - https://www.unboundmedicine.com/medline/citation/28077633/Surveillance_of_Bat_Coronaviruses_in_Kenya_Identifies_Relatives_of_Human_Coronaviruses_NL63_and_229E_and_Their_Recombination_History_ DB - PRIME DP - Unbound Medicine ER -