Virological surveillance of influenza virus type A, B, C, D in Italy

Background: Influenza A, B, C and D viruses (IAV, IBV, ICV, IDV) are genus of Orthomixoviridae family and can cause influenza in humans and animals. IAVs infect humans, mammals and avian species. IBV is considered a common seasonal human pathogen but can occasionally infect pigs and seals, while ICV causes mild infection in humans. ICV has been isolated once from swine in China. IDV was first identified in 2011 in pigs with influenza-like illness but it was shown to be widespread and fairly common in cattle. IDV zoonotic role is currently under investigation. AIM: To investigate the circulation of IAV, IBV, ICV, and IDV in cattle, swine and humans in Italy. Methods: From 2015 onwards we performed a virological screening by real-time RT-PCR for IVs on respiratory samples collected in Northern Italy from cattle (IBV, ICV, IDV) and swine (IAV, IBV, ICV, IDV). Full genomes of IAVs and IDVs were sequenced. Human samples collected from influenza-like illness cases in the framework of InfluNet (annual active surveillance of IAV and IBV in humans) were examined for ICV and IDV by real-time RT-PCR. Results: Swine: we examined 856 herds and found 34% positive for IAV and 1.7% for IDV. IBV and ICV were not detected. Cattle: we examined 888 herds and found 7.6% positive for IDV. IBV and ICV were not detected. Humans: IAV or IBV were detected in 46.9% of analysed samples. 1491 respiratory samples that resulted IAV/IBV-negative were examined, and ICV was detected in 0.7% of cases. IDV was not detected. Genetic analysis of IDV from swine and cattle confirmed the circulation of viruses clustering with D/swine/Oklahoma/1334/2011 while the genetic analysis of IAVs from swine showed a more complex situation with the circulation of multiple reassortant genotypes (H1N1, H1N2, and H3N2). Conclusion: The study results showed that cattle are the most susceptible species to IDV infection whilst it was confirmed that IAV circulates with high prevalence among pigs. The high genotypic variability of Italian swine IAVs has undergone further progression. Circulation of ICV or IBV in cattle or swine was not demonstrated. The study did not prove IDV circulates among humans while ICV was detected only in 0.7% of respiratory illness. Despite the high circulation of IAV and IBV in humans, introduction of genes from human IVs to animal species was limited to H1N1pdm09 derived viruses detected in swine population.