Abstract
ObjectiveCoronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed.ResultsCoV-RNA was detected in ten specimens (47.6%, n = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.
Highlights
Coronaviridae consists of a large family of viruses that cause infections and diseases in a large range of vertebrates
The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV
CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus
Summary
Bat CoVs identified in this study formed four novel monophyletic clades referred to as Borneo Beta-1 (GenBank: MZ574070, MZ574071), and Borneo Beta-2 (MZ574073, MZ574074), and Borneo Alpha-1 (MZ574065-MZ574067) and Borneo Alpha-2 (MZ574068, MZ574069, MZ573072) (Fig. 2). Blast analysis revealed that Borneo Alpha-1 and Borneo Alpha-2 are most related to Alpha/Yunnan/ HlYN23/2020 (MZ081388) (81.96–83.76% nt identity) and Alpha/H.dia/SbhMY/52/2013 (KX284940) (84.43–85.01% nt identity) from China and Sabah (North Borneo) respectively. Borneo Beta-1 and Borneo Beta-2 are most closely related to Beta/H.gal/ SbhMY/51/2012 (KX284939) (86.5–87.5% nt identity) and Beta/H.pom/LAP/7521 (MN312609) (89.7–90.4% nt identity) from Sabah state and and Laos respectively [2, 9]. Phylogenetic analysis revealed the close relationship of Borneo Alpha-1 and Borneo Alpha-2 with Decacovirus, Decacovirus-1 and Decacovirus-2 respectively with strong MLb/PPv support. Borneo Beta-1 is monophyly to Sarbecovirus, while Borneo Beta-2 is related to a currently uncategorised betacoronavirus
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