A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer

Abstract

Background: Although astroviruses (AstV) have been detected in a variety of host species, there are only limited records of their occurrence in deer. One of the most important game species in Europe, due to its meat and antlers, is roe deer. Infected game animals can pose a threat to the health of other animals and of humans, so more attention needs to be focused on understanding the diversity of viruses in wildlife. The complete genome and organization of the roe deer AstV genome have not so far been described. Results: In our study, 111 game animals were screened for the presence of AstV. While no AstVs were detected in red deer, wild boar, chamois and mouflon, AstV RNA was present in three samples of roe deer. They were further subjected to whole genome sequencing with next generation sequencing. In this study, two AstV genomes were assembled; one in sample D5-14 and one in sample D12-14, while, in sample D45-14, no AstV sequences were identified. The complete coding sequences of the AstV SLO/D5-14 strain genome and of the almost complete genome of the AstV SLO/D12-14 strain were determined. They showed a typical Mamastrovirus organization. Phylogenetic analyses and amino acid pairwise distance analysis revealed that Slovenian roe deer AstV strains are closely related to each other and, also, related to other deer, bovine, water buffalo, yak, Sichuan takin, dromedary, porcine and porcupine AstV strains -thus forming a highly supported group of currently unassigned sequences. Conclusions: Our findings suggest the existence of a new Mamastrovirus genogroup might be constituted while this aforementioned group is distantly related to Mamastrovirus genogroups I and II. In this study, additional data supporting a novel taxonomic classification are presented.

Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea

“…Recombination has been reported to require co-infection with different viruses in the same host cells [ 57 ]. It was worth noting that the roe deer AstV (CcAstV) strain (AstV SLO/D12–14) from Slovenia [ 58 ] and the Sichuan takin AstV strain from China [ 59 ] were the major and minor parents of the recombinant BoAstV HLJ-2, respectively. Since Sichuan takin and roe deer belonged to completely different species, and they were geographically separately, recombination of these two viruses hinted the occurrence of cross-species cross-geographical regions transmission event, which could be explained as follows.…”

Epidemiological investigation and pathogenicity analysis of waterfowl astroviruses in some areas of China

“…Their genomes are about 6.1 to 7.9 kb long and are organized in the following order: 5′ untranslated region (UTR), open reading frames (ORF1a, ORF1b, ORF2), 3′UTR and a poly (A) tail ( An et al, 2020 ). ORF1a and ORF1b encode non-structural polyproteins (nsp1a and nsp1ab), ORF2 encoding capsid protein, which is a highly variable region of the genome and the main protein inducing host immune response in the immune response process ( Méndez et al, 2007 ; Jamnikar-Ciglenecki et al, 2020 ).…”

“…Their genomes are about 6.1 to 7.9 kb long and are organized in the following order: 5′ untranslated region (UTR), open reading frames (ORF1a, ORF1b, ORF2), 3′UTR and a poly (A) tail (An et al, 2020). ORF1a and ORF1b encode non-structural polyproteins (nsp1a and nsp1ab), ORF2 encoding capsid protein, which is a highly variable region of the genome and the main protein inducing host immune response Li et al 10.3389/fmicb.2024.1375826 Frontiers in Microbiology 02 frontiersin.org in the immune response process (Méndez et al, 2007;Jamnikar-Ciglenecki et al, 2020). The International Committee on Taxonomy of Viruses (ICTV) depending on the host infected by astroviruses classified them as two viral genera, including Mamastrovirus (mammal astrovirus, MAstV) and Astroviruses (avian astrovirus, AAstV) (An et al, 2020) Among them, MAstV mainly causes gastroenteritis and encephalitis in mammals, while AAstV mainly causes nephritis and enteritis in chickens, hepatitis in ducks, gout and nephritis in goslings (Chu et al, 2012;Zhang et al, 2018).…”