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. 2024 Nov 25;14(1):29234.
doi: 10.1038/s41598-024-79670-y.

Two decades of occurrence of non-pathogenic rabbit lagoviruses in Italy and their genomic characterization

Patrizia Cavadini  1   2 , Alice Vismarra  3   4 , Francesca Merzoni  3   5 , Vittoria Di Giovanni  3   5 , Maria Beatrice Boniotti  3 , Lorenzo Capucci #  3   5 , Antonio Lavazza #  3   5
Affiliations

Two decades of occurrence of non-pathogenic rabbit lagoviruses in Italy and their genomic characterization

Patrizia Cavadini et al. Sci Rep. .

Erratum in

Abstract

Lagoviruses are viruses of the Caliciviridae family affecting lagomorphs. Both pathogenic and non-pathogenic lagoviruses affect the European rabbit (Oryctolagus cuniculus), and they are phylogenetically distinguished. Rabbit Hemorrhagic Disease Virus (RHDV/GI.1) and Rabbit Hemorrhagic Disease Virus-2 (RHDV-2/GI.2) belong to the first group, while in the second group, several genotypes of Rabbit Calicivirus (RCV/GI.3-GI.4) are present. The first RCV strain was described in Italy in 1996, and since then, several RCV strains have been characterised in Europe and Australia. RCVs, different from the pathogenic hepatotropic RHDVs, have an enteric tropism and could be identified from the duodenum/intestine and faeces. This study aimed firstly to indirectly show through a seroepidemiological survey from 1998 to 2008 the circulation of RCVs strains in rabbit farms and then to genetically characterise RCV strains diagnosed in Italy in faecal and intestinal samples of wild and farmed rabbits collected in various regions in the following years (2000-2022). Of 262 analysed samples, 69 resulted in RT-PCR positive for lagovirus but negative for RHDV. Eleven RCV strains were characterised by complete vp60 sequencing. Phylogenetic analysis showed that the Italian RCV strains are grouped in European (RCV_E1/GI.3) and Australian (RCV_E2/GI.4) RCV clusters, with an estimated country prevalence of 26%. Based on the proposed genotype classification, considering the nucleotide differences of vp60 higher than 15%, we can hypothesise that two other genotypes, GI.5 and GI.6, might exist within the cluster of non-pathogenic viruses.

Keywords: Italy; Lagovirus; Phylogenesis; Rabbit calicivirus; Serology.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests. Ethics declarations: Ethical review and approval were waived for this study that did not involve killing animals. The samples did not originate from experimental trials. Still, they took advantage of diagnostic activity conducted on found dead animals to ascertain the cause of death or as a control of the health status of regularly slaughtered rabbits for human meat consumption. Therefore, since the sampling was not specifically programmed as an experimental study but originating from diagnostic activity, we believed that it does not fall under the provisions of the National Law (e.g. DLSG 4/3 2014, n. 26. Application at the national level of the EU Directive 2010/63/UE) and no ethical approval or permit for animal experimentation was required.

Figures

Fig. 1
Fig. 1
Sequenced strains, their identification and origin (municipality and province). Superscript symbols (*, ^, °) indicate strains found in the same farm at different times.
Fig. 2
Fig. 2
Maximum Likelihood (ML) phylogenetic tree performed for the structural genes VP60 (nucleotides 5240–6869; nucleotide substitutions model GTR + G + I). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Support for each cluster was obtained from 1.000 bootstrap replicates. Bootstrap values > 70% are shown. Genotype clusters, which do not include viruses sequenced in this study, were collapsed and annotated accordingly.
Fig. 3
Fig. 3
ORF1 NS genome analysis using a dataset of 139 lagoviruses present in GenBank (48nt-5239nt). (A) Nucleotide and amino acid identity values relative to the NS genes/proteins of RCV/Italy/BS2000, with representative strains of rabbit pathogenic and non-pathogenic lagoviruses (RCV-E1, RCV-E2 and RHDV). (B) Maximum-likelihood phylogenetic tree performed with the nucleotide substitution model (GTR + G + I); The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Support for each cluster was obtained from 1.000 bootstrap replicates. Bootstrap values > 70% are shown. Genotype clusters, which do not include virus variants sequenced in this study, were collapsed and annotated accordingly. The Italian sequence reported in this work is indicated (RCV/Italy/BS2000).
Fig. 4
Fig. 4
Geographical distributions of the farms sampled during the five serological surveys conducted on slaughtered rabbits.
See this image and copyright information in PMC

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