Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History

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...

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Vydané v:	Journal of virology Ročník 91; číslo 5
Hlavní autori:	Tao, Ying, Shi, Mang, Chommanard, Christina, Queen, Krista, Zhang, Jing, Markotter, Wanda, Kuzmin, Ivan V, Holmes, Edward C, Tong, Suxiang
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States 01.03.2017
Predmet:	Amino Acid Sequence Animals Chiroptera - virology Conserved Sequence Coronavirus Infections - epidemiology Coronavirus Infections - veterinary Coronavirus NL63, Human Epidemiological Monitoring Evolution, Molecular Genetic Variation Genome, Viral Kenya - epidemiology Phylogeny Phylogeography Prevalence Recombination, Genetic Respiratory Tract Infections - epidemiology Respiratory Tract Infections - veterinary Sequence Analysis, DNA Viral Proteins - chemistry Viral Proteins - genetics bats HCoV-229E recombination Africa HCoV-NL63 coronavirus zoonoses
ISSN:	1098-5514, 1098-5514
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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 bats and 229E-like viruses circulating in 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. 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 and 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.
AbstractList	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.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. 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 bats and 229E-like viruses circulating in 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. 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 and 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.
Author	Shi, Mang Zhang, Jing Tao, Ying Kuzmin, Ivan V Chommanard, Christina Tong, Suxiang Holmes, Edward C Markotter, Wanda Queen, Krista
Author_xml	– sequence: 1 givenname: Ying surname: Tao fullname: Tao, Ying organization: Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA – sequence: 2 givenname: Mang surname: Shi fullname: Shi, Mang organization: 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 – sequence: 3 givenname: Christina surname: Chommanard fullname: Chommanard, Christina organization: Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA – sequence: 4 givenname: Krista surname: Queen fullname: Queen, Krista organization: Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA – sequence: 5 givenname: Jing surname: Zhang fullname: Zhang, Jing organization: Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA – sequence: 6 givenname: Wanda surname: Markotter fullname: Markotter, Wanda organization: Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa – sequence: 7 givenname: Ivan V surname: Kuzmin fullname: Kuzmin, Ivan V organization: Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA – sequence: 8 givenname: Edward C surname: Holmes fullname: Holmes, Edward C organization: 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 – sequence: 9 givenname: Suxiang surname: Tong fullname: Tong, Suxiang email: sot1@cdc.gov organization: Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA sot1@cdc.gov
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SubjectTerms	Amino Acid Sequence Animals Chiroptera - virology Conserved Sequence Coronavirus Infections - epidemiology Coronavirus Infections - veterinary Coronavirus NL63, Human Epidemiological Monitoring Evolution, Molecular Genetic Variation Genome, Viral Kenya - epidemiology Phylogeny Phylogeography Prevalence Recombination, Genetic Respiratory Tract Infections - epidemiology Respiratory Tract Infections - veterinary Sequence Analysis, DNA Viral Proteins - chemistry Viral Proteins - genetics
Title	Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History
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