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We report here the whole-genome sequence of the African swine fever virus (ASFV) genotype II, strain 20355/RM/2022_Italy, identified in a wild boar in the city of Rome (Lazio region, Italy) in April 2022.

We sequenced the complete genome of bovine viral diarrhea virus (BVDV) strain UM/126/07. It belongs to subgenotype 1h. The complete genome is composed of 12,196 nucleotides organized as one open reading frame encoding 3,898 amino acids. This is the first report of a full-length sequence of BVDV-1h.

Recent studies have suggested that certain classes of endogenous retroviruses (ERVs) may be present in cattle. The aim of this study was increase the scope of knowledge regarding bovine ERVs. The ovine ERV β1 pro/pol sequence was used to design a primer set for polymerase chain reaction (PCR) amplification of a similar sequence in the bovine genome. Through phylogenetic and bioinformatic analysis of the PCR product sequence together with its flanking region, a sequence 8107 bp in length was characterized. This sequence had a typical 5'-LTR-gag-pro-pol-env-LTR-3' organization, and phylogenetic investigation defined it as a bovine ERV β1. Thus, we were able to identify a novel bovine endogenous retrovirus element.

Border disease virus (BDV) belongs to the Pestivirus genus in the family Flaviviridae. Genetic analyses of pestiviruses that have been isolated from sheep and goat have led to the proposal that BDV isolates can be phylogenetically segregated into at least seven clusters, subtypes BDV-1 to BDV-7. In order to investigate the genetic heterogeneity of small ruminant pestivirus isolates in Italy, a selection of 5′-UTR sequences from isolates that were collected from clinical specimens between 2002 and 2014 was analysed. Phylogenetic reconstructions indicated that the BDV-positive samples clustered within the BDV-1, BDV-3, BDV-5, and BDV-7 groups. These results suggested high genetic diversity within the Italian BDV field isolates. The phylogenetic analysis indicated the first evidence of BDV-1 and BDV-5 circulation in Italy. The marked diversity of the pestivirus isolates might reflect the sheep trade with foreign countries.

Sequence-based genotyping was recently used to distinguish between the BVDV-1 and BVDV-2 species of the bovine viral diarrhoea virus (BVDV). Quite recently, a new putative species, BVDV-3, was also detected. The phylogenetic analysis of the 5'-untranslated region (UTR) and Npro region has revealed at least 17 distinct subtypes for BVDV-1 to date. The aim of this study was to further investigate the genetic heterogeneity of BVDV-1 in Italy, by analysing 173 virus sequences from isolates collected over an 18-year period (1997-2014). Viral RNA was extracted from the original biological samples identified as BVDV-1-positive. Reverse transcription (RT) and polymerase chain reaction (PCR) assays targeting a 288-base pair (bp) region of the 5'-UTR and a 428-bp region encoding the autoprotease Npro were performed, and the RT-PCR products were sequenced. The phylogenetic analysis of the 5'-UTR and Npro sequences re-confirmed the circulation of ten out of eleven subtypes previously discovered in Italy. Interestingly, four isolates differed significantly from all of the bovine pestiviruses identified so far, thereby providing evidence for the circulation of three novel subtypes that have not been documented so far. The growing number of reports on BVDV-1 heterogeneity, including the recent findings reported herein, raises concern related to the emergence and spread of new BVDV variants, with possible implications for animal health and disease control. This global issue needs to be addressed with the highest priority.

Border disease virus belongs to the Pestivirus genus, within the family Flaviviridae. Genetic analysis of pestiviruses isolated from sheep in continental Europe have led to the proposal that BDV isolates are segregated into at least seven clusters. In 2005 the molecular analysis of an Italian caprine BDV strain provided evidence for the presence of an atypical pestivirus, which may represent the first member of a putative novel pestivirus sub-group. To further build on this study, ovine pestivirus strains were isolated from small ruminant flocks and characterized both genetically and antigenically. A defined section of the 5'UTR and the complete N(pro) coding region were amplified and used for phylogenetic analysis. This revealed that these pestiviruses belong to the BDV species but differed significantly from all previously described ovine pestiviruses providing evidence for the presence of a novel genetic group. Four of the five isolates were also typed antigenically with a panel of pestivirus specific mAbs directed against NS2/3, E(rns) and E2 proteins. The four isolates reacted with a distinct set of mAbs, in particular against the BDV-E2 and the BDV-E(rns) epitopes. The isolates were greatly reactive for E(rns) and NS2/3 mAbs, which are otherwise typical for BVDV-2, and one E2 mAb that typically stains BVDV-1. The Italian pestiviruses analysed in this study, according to their antigenic and genetic properties, clustered into a novel phylogenetic group, that we propose to term BDV-7.