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We performed next-generation sequencing (NGS), phylogenetic analysis, gene flows, and N- and O-glycosylation prediction on SARS-CoV-2 genomes collected from lab-confirmed cases from different Italian regions. To this end, a total of 111 SARS-CoV-2 genomes collected in Italy between 29 January and 27 March 2020 were investigated. The majority of the genomes belonged to lineage B.1, with some descendant lineages. The gene flow analysis showed that the spread occurred mainly from the north to the center and to the south of Italy, as confirmed by epidemiological data. The mean evolutionary rate estimated here was 8.731 × 10−4 (95% highest posterior density, HPD intervals 5.809 × 10−4 to 1.19 × 10−3), in line with values reported by other authors. The dated phylogeny suggested that SARS-CoV-2 lineage B.1 probably entered Italy between the end of January and early February 2020. Continuous molecular surveillance is needed to trace virus circulation and evolution.

Influenza viruses remain a major cause of respiratory disease in both developed and developing countries. Nevertheless, there is little information on the prevalence of this respiratory infection in many developing countries, such as Papua New Guinea, since most of the available data originate from studies carried out in industrialized countries. In the present study, a serosurvey among residents of 47 remote villages of Papua New Guinea was conducted to evaluate the intensity of exposure to human influenza A and B viruses. The data obtained confirm the co-circulation of these antigenic variants, reported having circulated in the Southern Hemisphere. Variations in seroprevalence of influenza A and B virus infection were found within the study area. J. Med. Virol. 78:820–824, 2006. © 2006 Wiley-Liss, Inc.

BACKGROUND: Pigs play a key epidemiologic role in the ecology of influenza A viruses (IAVs) emerging from animal hosts and transmitted to humans. Between 2008 and 2010, we investigated the health risk of occupational exposure to swine influenza viruses (SIVs) in Italy, during the emergence and spread of the 2009 H1N1 pandemic (H1N1pdm) virus. METHODOLOGY/PRINCIPAL FINDINGS: Serum samples from 123 swine workers (SWs) and 379 control subjects (Cs), not exposed to pig herds, were tested by haemagglutination inhibition (HI) assay against selected SIVs belonging to H1N1 (swH1N1), H1N2 (swH1N2) and H3N2 (swH3N2) subtypes circulating in the study area. Potential cross-reactivity between swine and human IAVs was evaluated by testing sera against recent, pandemic and seasonal, human influenza viruses (H1N1 and H3N2 antigenic subtypes). Samples tested against swH1N1 and H1N1pdm viruses were categorized into sera collected before (n. 84 SWs; n. 234 Cs) and after (n. 39 SWs; n. 145 Cs) the pandemic peak. HI-antibody titers ≥10 were considered positive. In both pre-pandemic and post-pandemic peak subperiods, SWs showed significantly higher swH1N1 seroprevalences when compared with Cs (52.4% vs. 4.7% and 59% vs. 9.7%, respectively). Comparable HI results were obtained against H1N1pdm antigen (58.3% vs. 7.7% and 59% vs. 31.7%, respectively). No differences were found between HI seroreactivity detected in SWs and Cs against swH1N2 (33.3% vs. 40.4%) and swH3N2 (51.2 vs. 55.4%) viruses. These findings indicate the occurrence of swH1N1 transmission from pigs to Italian SWs. CONCLUSION/SIGNIFICANCE: A significant increase of H1N1pdm seroprevalences occurred in the post-pandemic peak subperiod in the Cs (p

The human respiratory syncytial virus (HRSV) is the most important cause of admission to hospital for acute lower respiratory tract infections in infants and young children worldwide. Only few studies have investigated the molecular evolution of HRSV, and none has been conduct ed in Italy. The genetic diversity of the G glycoprotein of 59 subgroup A strains obtained from two clinical centers located in Northern and Central Italy was studied, during seven nonconsecutive epidemic seasons (1997-2006). The nucleotide sequences encompassing 624 bp, at the carboxy terminus of the G glycoprotein gene, were compared to sequences representative of previously defined HRSV genotypes. Phylogenetic analysis indicated that most Italian group A isolates clustered into two different lineages (GA2 and GA5), whereas only few isolates grouped into the other known lineages. Eight positively selected sites were found and it was predicted that serine and threonine of positively selected sites 117 and 262 (respectively) are O-glycosilated. The presence of multiple identical sequences in three lineages (GA1, GA5, and BE/A1) suggests that certain strains are predominant in a given epidemic season. Although most of the sites of the G glycoprotein gene of HRSV-A strains seem invariable because of strong purifying selection, some evolutionary "hot spots" may be present. Since the G glycoprotein is a major target (together with the F glycoprotein) of the HRSV humoral immune response, it is important to provide information about its genetic heterogeneity in order to address better both therapeutic and vaccine strategy.

This study examined the antibody response against the three vaccine antigens and the epidemic A/H3N2 drift variant (A/California) and the prevention of laboratory diagnosed influenza infections in a group of elderly institutionalized people vaccinated with the 2004/2005 influenza vaccine. Antibody titres were measured by hemagglutination inhibition (HI) in sera collected before and 1 month after vaccination. Laboratory diagnosis was done examining throat swabs (RT-PCR or MDCK cell culture) or by serology (seroconversion comparing HI titres in sera collected 1 and 5 months after vaccination). Results obtained showed that influenza vaccination induced an adequate immune response against the three vaccine antigens and the epidemic A/H3N2 variant, however it was not capable of preventing an influenza outbreak due to the new A/H3N2 (A/California) variant.

Laboratory investigations of virus isolation and serum antibodies in a Mediterranean country (Italy) demonstrated that influenza A and B viruses, and often both, circulated every winter in Italy. The winter 1987/88 was characterized by a low level of influenza activity, as shown by the limited number (47) of influenza virus isolates, the majority of which (61%) belonged to the influenza B type. In contrast, the 1988/89 influenza season was exclusively associated with the circulation of influenza type A viruses. The A(H1H1) subtype was largely predominant (97%), as compared to the low incidence of the A(H3N2) subtype (3%). During the 1989/90 winter a co-circulation of A and B influenza viruses was observed, A(H3N2) strains being responsible for 96% of the virologically confirmed cases. Antigenic analysis of the virus isolates showed some antigenic variation in influenza A viruses of both H1N1 and H3N2 subtypes, whilst antigenic stability was found among the influenza B virus isolates. Overall, the above virological findings correlate with the data concerning the pattern of influenza virus circulation in Northern Europe and the UK during the three years surveyed. The results of serum antibody surveys conducted in each post-epidemic period are also reported.

Limited information is available on the viral aetiology of influenza-like illness (ILI) in Southern European countries. Hereby we report the main findings of a survey conducted in the area of Rome during the 2004-2005 winter season. ILI cases were defined as individuals with fever >37.5°C and at least one constitutional symptom and one respiratory symptom, recruited during the survey period. Influenza and other respiratory viruses were identified using polymerase chain reaction (PCR) on throat swabs. Basic individual information was collected through a standard form. Of 173 ILI cases enrolled, 74 tested positive for one virus, and two tested positive for two viruses. Overall, 33.5% of the cases were positive for influenza viruses, 5.2% for adenoviruses, 3.5% for parainfluenza viruses, 1.7% for coronaviruses, and 1.2% for the respiratory syncitial virus. The proportion of influenza virus detection was higher in the ‘high influenza activity’ period. The distribution of viral agents varied across age groups, influenza viruses being more likely to be detected in younger patients. Viral pathogens were identified in less than 50% of ILI cases occurred during a high activity influenza season. The detection of other than influenza viruses was sporadic, without evidence of large outbreaks due to specific agents.