Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

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.

Distribution of bat-borne viruses and environment patterns

“…Bats were collected from 43 sites in Cambodia and Lao PDR between 2010 and 2013 as previously described (Lacroix et al, 2017a(Lacroix et al, , 2017b ( Supplementary Table 1; Fig. 1).…”

“…1). Sampling was conducted in two phases (Lacroix et al, 2017a(Lacroix et al, , 2017b. Phase 1 was performed in 2010 by the Institut Pasteur in Cambodia (IPC).…”

“…Viral RNA was extracted from rectal swabs, oral swabs and lung samples as previously described (Lacroix et al, 2017a(Lacroix et al, , 2017b ( Table 1). The detection was based on broadly reactive reverse transcription-polymerase chain reaction (RT-PCR) assays, following previously described procedures (Chu et al, 2008;Watanabe et al, 2010).…”

“…Bats were discovered as a reservoir for the progenitor virus of the SARS-coronavirus (SARS-CoV) species, responsible for the SARS pandemic between 2002 and 2004 (Wang et al, 2006). Coronaviruses belonging to alpha-CoV and beta-CoV, including MERS-like viruses have been recently detected in Cambodia and Lao bat populations (Lacroix et al, 2017a). Several other viral families have also been detected, including astroviruses, flaviviruses, lyssaviruses, bunyaviruses or henipaviruses (Salaün et al, 1974;Olson et al, 2002;Osborne et al, 2003;Reynes et al, 2004Reynes et al, , 2005Lacroix et al, 2017b).…”

Analysis and Applications of GlobeLand30: A Review

“…These include quantifying land use for each watershed in Panamanian drainage basins [55]; identifying types of sampling sites based on the hydrology and land-use characteristics to monitor contaminants in river sediments [46][47][48][49][50][51][52][53][54][55][56][57], discriminating fire types from MODIS active fire products, such as forest fire, grassland fire, agricultural burning and so on [58]; assessing flooded arable land of a major flood in Myanmar [46]; selecting eddy-covariance flux towers with relatively homogenous land cover in the light use efficiency models to simulate GPP [59]; analyzing habitat of bats in Lao PDR and Cambodia [60][61][62]; and providing validation sources to evaluate the classification performance of the water body extraction from MODIS eight-day products [62]. In particular, GlobeLand30 data has been used to derive useful information about the status and change of land cover, to examine their causes and consequence analysis, and to explore future development scenarios.…”