Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

Audrey Lacroix, Veasna Duong, Vibol Hul, Sorn San, Hull Davun, Keo Omaliss, Sokha Chea, Alexandre Hassanin, Watthana Theppangna, Soubanh Silithammavong, Kongsy Khammavong, Sinpakone Singhalath, Zoe Greatorex, Amanda E Fine, Tracey Goldstein, Sarah Olson, Damien O Joly, Lucy Keatts, Philippe Dussart, Aneta Afelt, Roger Frutos, Philippe Buchy, Audrey Lacroix, Veasna Duong, Vibol Hul, Sorn San, Hull Davun, Keo Omaliss, Sokha Chea, Alexandre Hassanin, Watthana Theppangna, Soubanh Silithammavong, Kongsy Khammavong, Sinpakone Singhalath, Zoe Greatorex, Amanda E Fine, Tracey Goldstein, Sarah Olson, Damien O Joly, Lucy Keatts, Philippe Dussart, Aneta Afelt, Roger Frutos, Philippe Buchy

Abstract

South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n=55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii.

Keywords: Bats; Cambodia; Coronaviruses; Genetic diversity; Lao PDR.

Copyright © 2016 Elsevier B.V. All rights reserved.

Figures

Graphical abstract
Graphical abstract
Fig. 1
Fig. 1
Phylogenetic analysis of coronavirus sequences based on a 320 nucleotides fragment on the RdRp gene. The tree was constructed using a Maximum Likelihood method with the GTR + G + I model. Bootstrap values (BP) were calculated after 1000 replicates. Tree is rooted to an avian coronavirus (FJ376622). The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1. The tree was constructed using a Maximum Likelihood method with the GTR + G + I model. Bootstrap values (BP) were calculated after 1000 replicates. Tree is rooted to an avian coronavirus (FJ376622). The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1.
Fig. 2
Fig. 2
Sequence analysis of 1370 nucleic acid fragments of the RdRp gene of coronavirus sequences. The tree was constructed using a Maximum Likelihood method with the GTR + G + I model. Boostrap values (BP) were calculated after 1000 replicates. Tree is rooted to an avian coronavirus (FJ376622). The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1. The tree was constructed using a Maximum Likelihood method with the GTR + G + I model. Boostrap values (BP) were calculated after 1000 replicates. Tree is rooted to an avian coronavirus (FJ376622). The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1.
Supplementary Fig. 2
Supplementary Fig. 2
Distribution of coronavirus sequences based on a 115 amino acid fragment encoded by the RdRp gene. The tree was constructed by neighbor joining and bootstrap values were determined by 1000 replicates. The tree is rooted to an avian coronavirus (FJ376622). The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1.
Supplementary Fig. 3
Supplementary Fig. 3
Distribution of coronavirus sequences based on a 115 amino acid fragment encoded by the RdRp gene. The tree was constructed by neighbor joining and bootstrap values were determined by 1000 replicates. The tree is rooted to an avian coronavirus (FJ376622). Bootstrap values (BP) were calculated after 1000 replicates. The sequences detected in this study are shown with a bullet. Accession numbers related to the sequences are presented in Supplementary Table 1.

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Source: PubMed

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