Genomic characterization and cross-species transmission potential of hedgehog coronavirus

Abstract

In the 21st century, three betacoronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have emerged in humans worldwide as a result of animal spillover, causing severe respiratory infections and resulting in more than seven million deaths. In 2013, a novel Betacoronavirus closely related to MERS-CoV (Betacoronavirus cameli) was discovered in European hedgehogs (Erinaceus europaeus), raising questions on the possibility of hedgehog-to-human transmission. Hence, the present study aimed to investigate and characterize the presence and genetic diversity of coronaviruses in hedgehogs from Portugal, as well as their potential for cross-species transmission. To achieve this, fecal samples from 110 hedgehogs at two recovery centers and one environmental non-governmental organization were tested for coronaviruses using a broad-spectrum nested RT-PCR assay targeting the RdRp gene. Of these samples, 24.5 % tested positive, most belonging to the Betacoronavirus genus. However, the present study also reports, for the first time, Alphacoronaviruses in hedgehogs, showing 100 % identity with a Bat coronavirus (a variant of Alphacoronavirus miniopteri). The genome sequencing of one betacoronavirus-positive sample yielded 65 % of a full-length genome, with the closest homology (93.5 %) to Betacoronavirus erinacei from the United Kingdom. Computational protein-protein docking studies predicted the binding affinity between the spike protein of hedgehog coronavirus and cell receptors of mammal species that interact with hedgehogs. The results obtained raise the question of whether hedgehog CoV uses the same receptor as MERS-CoV or a different receptor to enter host cells. Thus, this study enhances our understanding of the epidemiology of coronaviruses, emphasizing the need for further investigation into cross-species transmission risks.

Keywords: Coronavirus; Erinaceus coronavirus; Hedgehogs; Portugal; Public health.

Fig. 1

Geographical location, by municipalities, of the hedgehog capture sites in Portugal.

Fig. 2

Phylogenetic analysis of the RdRp coronavirus nucleotidic sequences (403 bp) identified in this study (in bold) and reference sequences retrieved from GenBank. Genetic distances were calculated using the General Time Reversible model. Sequences are named with GenBank accession number and name of virus. Orange branches correspond to Alphacoronavirus, green to Betacoronavirus, pink to Gammacoronavirus and blue to Deltacoronavirus. Bootstrap values equal to or greater than 50 % are represented at the nodes. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Genome organization of the partial genome derived from this study.

Fig. 4

Phylogenetic tree generated for the RBD amino acid sequence obtained in the present study (in bold) and reference sequences retrieved from Genbank, using the Whelan and Goldman + Freq. model.

Fig. 5

The model of the hedgehog CoV RBD model (light green) was superimposed onto the crystal structure of MERS-CoV RBD (pink) complexed with human DPP4 (beige) (PDB ID 4L72). The residues of MERS-CoV RBD known to contact with DPP4 are colored yellow (d < 3.6 Å). The β5-β6 linking loop of the MERS-CoV RBD is indicated with a red arrow and the β6-β7 linking loop is indicated with a black arrow. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 6

Models of structural interaction between the hedgehog CoV RBD (light green) and (A) human (beige), (B) dog (blue), (C) cat (purple), (D) fox (orange), (E) badger (grey) and (F) hedgehog (yellow) DPP4. The hedgehog CoV RBD residues that are within 5 Å of the contact surface with DPP4 are shown in red. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 7

Models of structural interaction between the hedgehog CoV RBD (light green) and (A) human (beige), (B) dog (blue), (C) cat (purple), (D) fox (orange), (E) badger (grey) and (F) hedgehog (yellow) ACE2. The hedgehog CoV RBD residues that are within 5 Å of the contact surface with ACE2 are shown in red. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)