The virus-host interface: Molecular interactions of Alphacoronavirus-1 variants from wild and domestic hosts with mammalian aminopeptidase N.

The Alphacoronavirus-1 species include viruses that infect numerous mammalian species. To better understand the wide host range of these viruses, better knowledge on the molecular determinants of virus-host cell entry mechanisms in wildlife hosts is essential. We investigated Alphacoronavirus-1 infection in carnivores using long-term data on Serengeti spotted hyenas (Crocuta crocuta) and molecular analyses guided by the tertiary structure of the viral spike (S) attachment protein's interface with the host receptor aminopeptidase N (APN). We sequenced the complete 3'-end region of the genome of nine variants from wild African carnivores, plus the APN gene of 15 wild carnivore species. Our results revealed two outbreaks of Alphacoronavirus-1 infection in spotted hyenas associated with genetically distinct canine coronavirus type II (CCoVII) variants. Within the receptor binding domain (RBD) of the S gene the residues that directly bind to the APN receptor were conserved in all variants studied, even those infecting phylogenetically diverse host taxa. We identified a variable region within RBD located next to a region that directly interacts with the APN receptor. Two residues within this variable region were under positive selection in hyena variants, indicating that both sites were associated with adaptation of CCoVII to spotted hyena APN. Analysis of APN sequences revealed that most residues that interact with the S protein are conserved in wild carnivores, whereas some adjacent residues are highly variable. Of the variable residues, four that are critical for virus-host binding were under positive selection and may modulate the efficiency of virus attachment to carnivore APN.

A retrospective study of porcine epidemic diarrhoea virus (PEDV) reveals the presence of swine enteric coronavirus (SeCoV) since 1993 and the recent introduction of a recombinant PEDV-SeCoV in Spain.

A retrospective evaluation of PEDV-positive samples recovered in Spain before and after the re-emergence of this coronavirus in several European countries was carried out. We described for the first time recombinant SeCoV circulating in Spain between 1993 and 2014 and its misidentification as PEDV when diagnostic assays based on the S-protein or S-gene of the PEDV were used. The complete S-gene sequence of 7 Spanish SeCoV and 30 PEDV Spanish isolates was phylogenetically analysed including the S-gene sequences of the three SeCoV and a representative selection of the PEDV strains with complete genome sequences available in the GenBank. The tree showed a common ancestor for the S-gene of the PEDV and SeCoV, but no evolution from any known PEDV clade was shown for the SeCoV strains. Moreover, complete genome sequences were obtained from 23 PEDV strains recovered in Spanish swine farms since 2014. The phylogenetic tree showed the INDEL type genogroup of these Spanish strains, supporting the lower pathogenicity of this genogroup since no significant economic losses were reported in the affected Spanish swine farms. Four subgroups were detected among PEDV strains in Spain, closely related to the recent European strains. Moreover, eight of the most recent Spanish PEDV isolates formed a subclade together with three European strains from 2015, showing a new evolution branch with a recombinant virus.