Data from: Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

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.