Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low-pathogenic (LPAI) progenitor viruses currently is poorly understood. To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages. Notably, an ultradeep-sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several individual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI. The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high-and low-pathogenicity viruses undertaken to date and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties. IMPORTANCEThe Italian H7 AI epidemic of 1999 to 2001 was one of the most important AI outbreaks described in Europe. H7 viruses have the ability to evolve into HP forms from LP precursors, although the mechanisms underlying this evolutionary transition are only poorly understood. We combined epidemiological information, whole-genome sequence data, and ultradeep sequencing approaches to provide the most complete characterization of the evolution of HPAI from LPAI viruses undertaken to date. Our analysis revealed that the LPAI viruses were the direct ancestors of the HPAI strains and identified low-frequency minority variants with HPAI mutations that were present in the LPAI samples. Spatial analysis provided key information for the design of effective control strategies for AI at both local and global scales. Overall, this work highlights the importance of implementing rapid eradication measures to prevent the emergence of novel influenza viruses with severe pathogenic properties.

A two year study (2008-2009) was carried out to monitor the Usutu virus (USUV) circulation in Italy. Sentinel horses and chickens, wild birds and mosquitoes were sampled and tested for the presence of USUV and USUV antibodies within the WND National Surveillance plan. Seroconversion evidenced in sentinel animals proved that in these two years the virus has circulated in Tuscany, Emilia Romagna, Veneto and Friuli Venezia Giulia regions. In Veneto USUV caused a severe blackbird die-off disease involving at least a thousand birds. Eleven viral strains were detected in organs of 9 blackbirds (52.9%) and two magpies (0.5%) originating from Veneto and Emilia Romagna regions. USUV was also detected in a pool of Culex pipiens caught in Tuscany. According to the alignment of the NS5 partial sequences, no differences between the Italian USUV strains isolated from Veneto, Friuli and Emilia Romagna regions were observed. The Italian North Eastern strain sequences were identical to those of the strain detected in the brain of a human patient and shared a high similarity with the isolates from Vienna and Budapest. Conversely, there were few differences between the Italian strains which circulated in the North Eastern regions and the USUV strain detected in a pool of C. pipiens caught in Tuscany. A high degree of similarity at both nucleotide and amino acid level was also found when the full genome sequence of the Italian North Eastern isolate was compared with that of the strains circulating in Europe. The North Eastern Italian strain sequence exhibited 97% identity to the South African reference strain SAAR-1776. The deduced amino acid sequences of the Italian strain differed by 10 and 11 amino-acids from the Budapest and Vienna strains, respectively, and by 28 from the SAAR-1776 strain. According to this study two strains of USUVs are likely to have circulated in Italy between 2008 and 2009. They have developed strategies of adaptation and evolution to spread into new areas and to become established.

In winter 2016–17, highly pathogenic avian influenza A(H5N8) and A(H5N5) viruses of clade 2.3.4.4 were identified in wild and domestic birds in Italy. We report the occurrence of multiple introductions and describe the identification in Europe of 2 novel genotypes, generated through multiple reassortment events.

Following the avian influenza epidemics that occurred in Italy between 1997 and 2003, the Italian Ministry of Health in collaboration with veterinary authorities promoted, funded and implemented a national surveillance programme. The main objectives of the surveillance effort were to identify avian influenza viruses circulating in wild birds and to investigate the role of backyard poultry flocks in the dynamics of infection in a densely populated poultry area. Over 2 years (2004 to 2006), 164 backyard flocks and 4083 wild birds (mainly migratory Anseriformes and Charadriiformes) were sampled in three regions in the North of Italy. Samples collected were screened by means of real-time reverse transcriptase-polymerase chain reaction and the positive samples were processed for attempted virus isolation in embryonated fowl's specific pathogen free eggs. At the end of the study period, 27 low-pathogenic avian influenza viruses had been isolated from backyard flocks and 49 strains obtained from wild birds. Of these, 26 belonged to the H5 or H7 subtype and were closely related to contemporary low-pathogenic strains of Eurasian lineage. The findings confirm that backyard free-range farming is at high risk for avian influenza virus introduction, and confirm the role of wild waterfowl in the introduction and perpetuation of low-pathogenic avian influenza viruses during the winter season in Southern Europe.

After 10 years, West Nile virus (WNV) re-emerged in Italy in August 2008. As on 31 December 2008, the infection affected eight Provinces in three Regions (Emilia Romagna, Veneto, Lombardy), where a total of 794 cases of WNV infection in 251 equine stables were detected on the basis of the clinical signs and as a result of a serological screening in horses living in the area. Only 4.0% (32/794) of the serologically positive animals showed clinical signs, and the 32 clinical cases were reported in 18 different farms. The observed case-fatality rate was 15.6% (5/32). The confirmed clinical cases were detected from end August to mid October. Significant levels of positivity by RT-PCR were also observed in magpies (Pica pica) (9.1%, 95% confidence levels: 6.1-13.4%), carrion crows (Corvus corone) (7.4%, 95% confidence levels: 3.6-14.4%) and rock pigeons (Columba livia) (12.9%, 95% confidence levels: 7.6-21.2%).

West Nile virus (WNV) is a recently re-emerged health problem in Europe. In Italy, an increasing number of outbreaks of West Nile disease, with occurrences of human cases, have been reported since 2008. This is particularly true in northern Italy, where entomological surveillance systems have been implemented at a regional level. The aim of this study was to use, for the first time, all the entomological data collected in the five regions undergoing surveillance for WNV in northern Italy to characterize the viral circulation (at a spatial and temporal scale), identify potential mosquito vectors, and specify relationships between virus circulation and meteorological conditions. In 2013, 286 sites covering the entire Pianura Padana area were monitored. A total of 757,461 mosquitoes were sampled. Of these, 562,079 were tested by real-time PCR in 9,268 pools, of which 180 (1.9%) were positive for WNV. The largest part of the detected WNV sequences belonged to lineage II, demonstrating that, unlike those in the past, the 2013 outbreak was mainly sustained by this WNV lineage. This surveillance also detected the Usutu virus, a WNV-related flavivirus, in 241 (2.6%) pools. The WNV surveillance systems precisely identified the area affected by the virus and detected the viral circulation approximately two weeks before the occurrence of onset of human cases. Ninety percent of the sampled mosquitoes were Culex pipiens, and 178/180 WNV-positive pools were composed of only this species, suggesting this mosquito is the main WNV vector in northern Italy. A significantly higher abundance of the vector was recorded in the WNV circulation area, which was characterized by warmer and less rainy conditions and greater evapotranspiration compared to the rest of the Pianura Padana, suggesting that areas exposed to these conditions are more suitable for WNV circulation. This observation highlights warmer and less rainy conditions as factors able to enhance WNV circulation and cause virus spillover outside the sylvatic cycle.

Calves are highly susceptible to disease and mortality occurrence within the first month of life. Even if failed transfer of passive immunity (FTPI) is commonly recognized as a main factor affecting calf health and survival, conflicting results are reported in literature about the association between passive immunity (PI) and calf health, especially regarding enteric diseases. Therefore, a prospective cohort study was conducted on 78 calves of three Italian dairy farms during winters of years 2014-2016, with the specific aim of evaluating the association between PI and health status of calves within 30 days of age under field conditions. Blood samples were collected between 1 and 5 days of age from each calf included in the study, and disease and mortality occurrence was monitored throughout the first month of life. Additionally, fecal samples were collected from calves with scours before treatment. Blood serum samples were tested by an electrophoretic method for the assessment of immunoglobulin (Ig) concentration, whereas fecal samples were submitted to ELISA test for positivity to Escherichia coli K99, rotavirus, coronavirus, and Cryptosporidium spp. Only enteric diseases occurred in calves of this study. Calves that suffered from diarrhea or died within the first month of life had lower serum Ig concentrations than those that remained healthy or survived (P < .05). Even if not significantly (P = .127), lower serum Ig concentrations were observed in sick calves that had been treated with antibiotics compared to those that had not been treated. The odds of disease and mortality occurrence were 24 (95% CI = 3-231) and 11 (95% CI = 1-111) times higher, respectively, for calves with FTPI (serum Ig concentration <10.0 g/L) than for those with an adequate PI transfer (P < .05). Calves with adequate PI transfer had also a 6-day delay in the age at first disease onset compared to those with FTPI (P < .01). Even if estimated on a small number of calves, those with FTPI had higher risks of enteric infections by rotavirus (odds ratio = 12; 95% CI = 1-137) and Cryptosporidium spp. (odds ratio = 9; 95% CI = 1-72) (P < .05). In this study, the PI level influenced the occurrence of enteric diseases and mortality in calves under one month of age, confirming the importance of a proper colostrum provision to calf health and, consequently, to the reduction of antimicrobial use in dairy farming. However, further investigations are needed, particularly focusing on the relationship between PI and specific enteropathogen infections in calves.

Zoonotic strains of hepatitis E virus (HEV) in Europe have been reported to belong to genotypes 3 and 4. In 2012 and 2013, 57 pig farms in Northern Italy that had previously resulted seropositive for HEV were surveyed for the presence of the virus, with positive samples subsequently genotyped. Hepatitis E RNA was identified in 17/57 (29·8%) seropositive farms. Phylogenetic analysis demonstrated that distinct subtypes of genotype 3 were circulating in the north-east of Italy; as well, for the first time in the Italian swine population, genotype 4 was identified and attributed to subtype d.