Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s. We report the phylogenetic relationship of swine enteric coronaviruses collected in Italy during 2007–2014 and identify a drastic shift in PEDV strain variability and a new swine enteric coronavirus generated by recombination of transmissible gastroenteritis virus and PEDV.
Porcine circovirus type 3 (PCV3) was recently proposed as a new porcine circovirus. It has been described by researchers in the USA and China and associated with porcine dermatitis and nephropathy syndrome, reproductive failure and systemic inflammation disease. The study reports the occurrence of the new virus in Italy. PCV3 was detected in the tissues of foetuses and stillborn piglets coming from two farms located in the Po Valley. The genome sequences of the two Italian strains share 99.7% to 97.8% of nucleotide identity with those available in GenBank. Results strengthen the hypothesis of PCV3 as a new emerging porcine circovirus, widespread all over the world. It follows the urgency of investigating in depth epidemiology and pathogenicity associated with this new virus.
24The lung homogenate proved to be positive for both influenza type A (gene M) and H1N1pdm real time RT-
25PCRs. Virus isolation (A/Sw/It/116114/2010) was obtained from both SPF CEE and Caco-2 cells.
26Phylogenetic analysis showed that all of the genes of A/Sw/It/116114/2010, with the exception of 27 neuraminidase (NA), belonged to the H1N1pdm cluster. The NA was closely related to two H1N2 double
73multiplex PCR and PCR assays respectively, as previously described (Calsamiglia et al., 1999; Ouardani et 74 al., 1999; Suarez et al., 1994).
92were made using ClustalW and maximum parsimony phylogenetic trees were created using MEGA4 93 (Tamura et al., 2007). Each tree is a consensus of 500 bootstrap replicates.
94The identification as a novel reassortant strain was confirmed by full length sequencing of HA and NA genes 95 performed directly on lung homogenates.
106The presence of influenza A and the H1N1pdm was detected on AF and Caco-2 CS by real time RT-PCRs.
107A multiplex RT-PCR specific for subtype determination was further used to subtype both AF and CS that
Influenza D virus (IDV), a new member of the Orthomyxoviridae family, was first reported in 2011 in swine in Oklahoma, and consequently found in cattle across North America and Eurasia. To investigate the circulation of IDV among pigs in Italy, in the period between June 2015 and May 2016, biomolecular and virological tests were performed on 845 clinical samples collected from 448 pig farms affected by respiratory distress located in the Po Valley. Serological tests were conducted on 3698 swine sera, including archive sera collected in 2009, as well as samples collected in 2015 from the same region. Viral genome was detected in 21 (2.3%) samples from 9 herds (2%), while virus was successfully isolated from 3 samples. Genetic analysis highlighted that Italian swine IDVs are closely related to the D/swine/Oklahoma/1334/2011 cluster. Sera collected in 2015 showed a high prevalence of IDV antibody titers (11.7%), while archive sera from 2009 showed statistically significant lower positivity rates (0.6%). Our results indicate an increasing epidemiological relevance of the pathogen and the need for in-depth investigations towards understanding its pathogenesis, epidemiology and possible zoonotic potential of this emerging virus.
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