Dataset Information

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe.

ABSTRACT: The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.

SUBMITTER: Crook JM

PROVIDER: S-EPMC8289822 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe.

Crook Jack M JM Murphy Ivana I Carter Daniel P DP Pullan Steven T ST Carroll Miles M Vipond Richard R Cunningham Andrew A AA Bell Diana D

Scientific reports 20210719 1

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding ...[more]

PMID: 34282196

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Project description:Bats are highly diverse and ecologically important mammals. They harbor various bacteria, viruses, and fungal communities that are either beneficial or potentially pathogenic. Extensive metagenomic studies in bats are limited, particularly for the gut, and to date, there are no reports on the bacterial diversity of Rhinolophus monoceros from Meghalaya, India. There are limited studies on the isolation of potential harmful or beneficial bacteria and their interactions with the environment through culture-dependent approaches. Therefore, high-throughput screening was used to understand the population structure, genetic diversity, and ecological role of the microorganisms. High-throughput sequencing of the 16S rRNA marker for gene mapping showed that the gut samples constitute a diverse group of bacteria that is dominated by Proteobacteria, followed by Firmicutes. The bacterial genera Corynebacterium and Mycobacterium were also observed in the Illumina dataset. Illumina sequencing revealed eight bacterial phyla composed of 112 genera. The metagenomic analysis of the OTUs from the gut revealed diverse bacterial communities as well as zoonotic and human pathogens. There were differences in the bacterial communities between the two methods used in this study, which could be related to host specificity, diet, and habitat. The culture-dependent technique resulted in the isolation of 35 bacterial isolates, of which Bacillus cereus and B. anthracis are well-known bacterial pathogens that show virulent traits including hemolytic and proteolytic activities. Pseudomonas stutzeri is an opportunistic human pathogen that was also isolated and showed similar traits. Antibiotic sensitivity tests were performed on all 35 isolates, and different antibiotics were used for Gram-positive and -negative bacteria. The result showed that some isolates are resistant to antibiotics such as penicillin G and Cefoxitin. This report on gut bacterial communities could attract interest in the possibility of isolating and characterizing bacteria for the production of antibiotics, enzymes, plant growth promoters, and probiotics. However, the presence of potential pathogenic bacteria that may impose health hazards cannot be ignored and needs to be studied further.

Project description:While the spike proteins from severe acute respiratory syndrome coronaviruses-1 and 2 (SARS-CoV and SARS-CoV-2) bind to host angiotensin-converting enzyme 2 (ACE2) to infect cells, the majority of bat sarbecoviruses cannot use ACE2 from any species. Despite their discovery almost 20 years ago, ACE2-independent sarbecoviruses have never been isolated from field samples, leading to the assumption these viruses pose little risk to humans. We have previously shown how spike proteins from a small group of ACE2-independent bat sarbecoviruses may possess the ability to infect human cells in the presence of exogenous trypsin. Here, we adapted our earlier findings into a virus isolation protocol and recovered two new ACE2-dependent viruses, RsYN2012 and RsYN2016A, as well as an ACE2-independent virus, RsHuB2019A. Although our stocks of RsHuB2019A rapidly acquired a tissue-culture adaption that rendered the spike protein resistant to trypsin, trypsin was still required for viral entry, suggesting limitations on the exogenous entry factors that support bat sarbecoviruses. Electron microscopy revealed that ACE2-independent sarbecoviruses have a prominent spike corona and share similar morphology to other coronaviruses. Our findings demonstrate a broader zoonotic threat posed by sarbecoviruses and shed light on the intricacies of coronavirus isolation and propagation in vitro. IMPORTANCE Several coronaviruses have been transmitted from animals to people, and 20 years of virus discovery studies have uncovered thousands of new coronavirus sequences in nature. Most of the animal-derived sarbecoviruses have never been isolated in culture due to cell incompatibilities and a poor understanding of the in vitro requirements for their propagation. Here, we built on our growing body of work characterizing viral entry mechanisms of bat sarbecoviruses in human cells and have developed a virus isolation protocol that allows for the exploration of these understudied viruses. Our protocol is robust and practical, leading to successful isolation of more sarbecoviruses than previous approaches and from field samples that had been collected over a 10-year longitudinal study.

Dataset Information

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe.

Publications

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe.

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