Molecular identification of Betacoronavirus in bats from Sardinia (Italy): first detection and phylogeny

Abstract

Bats may be natural reservoirs for a large variety of emerging viruses, including mammalian coronaviruses (CoV). The recent emergence of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) in humans, with evidence that these viruses may have their ancestry in bats, highlights the importance of virus surveillance in bat populations. Here, we report the identification and molecular characterization of a bat β-Coronavirus, detected during a viral survey carried out on different bat species in the island of Sardinia (Italy). Cutaneous, oral swabs, and faecal samples were collected from 46 bats, belonging to 15 different species, and tested for viral presence. Coronavirus RNA was detected in faecal samples from three different species: the greater horseshoe bat (Rhinolophus ferrumequinum), the brown long-eared bat (Plecotus auritus), and the European free-tailed bat (Tadarida teniotis). Phylogenetic analyses based on RNA-dependent RNA polymerase (RdRp) sequences assigned the detected CoV to clade 2b within betacoronaviruses, clustering with SARS-like bat CoVs previously reported. These findings point to the need for continued surveillance of bat CoV circulating in Sardinian bats, and extend the current knowledge on CoV ecology with novel sequences detected in bat species not previously described as β-Coronavirus hosts.

Keywords: Bats; Coronavirus; RNA-dependent RNA polymerase; Rhinolophus ferrumequinum; Sardinia.

Fig. 1

Phylogenetic analysis based on 1090 bp of the RdRp gene. RNA-dependent RNA polymerase-based phylogeny including the novel bat coronavirus detected in this study (SarBatCoV1) and other 16 RdRp sequences from bat coronaviruses. Coronavirus sequence identified in this study is shown in bold and assigned to the β-CoV genus. Bootstrap percentage values from 1000 resamplings are located at nodes of the tree

Fig. 2

Phylogenetic analysis based on 396 bp of the RdRp gene. Phylogenetic tree of the partial RNA-dependent RNA polymerase gene (396 bp) of coronavirus strains found in bats and humans, showing the assignment of the sequence detected in this study (SarBatCoV1) to clade 2b, within the β-CoV genus. Percentage values from 1000 replicates of bootstrapping are located at nodes of the tree