Phylogeny and population dynamics of respiratory syncytial virus (Rsv) A and B.

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in infants and young children. RSV is characterised by high variability, especially in the G glycoprotein, which may play a significant role in RSV pathogenicity by allowing immune evasion. To reconstruct the origin and phylodynamic history of RSV, we evaluated the genetic diversity and evolutionary dynamics of RSV A and RSV B isolated from children under 3 years old infected in Italy from 2006 to 2012. Phylogenetic analysis revealed that most of the RSV A sequences clustered with the NA1 genotype, and RSV B sequences were included in the Buenos Aires genotype. The mean evolutionary rates for RSV A and RSV B were estimated to be 2.1 × 10(-3) substitutions (subs)/site/year and 3.03 × 10(-3) subs/site/year, respectively. The time of most recent common ancestor for the tree root went back to the 1940s (95% highest posterior density-HPD: 1927-1951) for RSV A and the 1950s (95%HPD: 1951-1960) for RSV B. The RSV A Bayesian skyline plot (BSP) showed a decrease in transmission events ending in about 2005, when a sharp growth restored the original viral population size. RSV B BSP showed a similar trend. Site-specific selection analysis identified 10 codons under positive selection in RSV A sequences and only one site in RSV B sequences. Although RSV remains difficult to control due to its antigenic diversity, it is important to monitor changes in its coding sequences, to permit the identification of future epidemic strains and to implement vaccine and therapy strategies.

High performance of a new PCR-based urine assay for HPV-DNA detection and genotyping.

Human papillomavirus (HPV) testing has been proposed as a means of replacing or supporting conventional cervical screening (Pap test). However, both methods require the collection of cervical samples. Urine sample is easier and more acceptable to collect and could be helpful in facilitating cervical cancer screening. The aim of this study was to evaluate the sensitivity and specificity of urine testing compared to conventional cervical smear testing using a PCR-based method with a new, designed specifically primer set. Paired cervical and first voided urine samples collected from 107 women infected with HIV were subjected to HPV-DNA detection and genotyping using a PCR-based assay and a restriction fragment length polymorphism method. Sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) were calculated using the McNemar's test for differences. Concordance between tests was assessed using the Cohen's unweighted Kappa (k). HPV DNA was detected in 64.5% (95% CI: 55.1-73.1%) of both cytobrush and urine samples. High concordance rates of HPV-DNA detection (k = 0.96; 95% CI: 0.90-1.0) and of high risk-clade and low-risk genotyping in paired samples (k = 0.80; 95% CI: 0.67-0.92 and k = 0.74; 95% CI: 0.60-0.88, respectively) were observed. HPV-DNA detection in urine versus cervix testing revealed a sensitivity of 98.6% (95% CI: 93.1-99.9%) and a specificity of 97.4% (95% CI: 87.7-99.9%), with a very high NPV (97.4%; 95% CI: 87.7-99.9%). The PCR-based assay utilized in this study proved highly sensitive and specific for HPV-DNA detection and genotyping in urine samples. These data suggest that a urine-based assay would be a suitable and effective tool for epidemiological surveillance and, most of all, screening programs.

Epidemiological and clinical features of respiratory viral infections in hospitalized children during the circulation of influenza virus A(H1N1) 2009.

BACKGROUND: Seasonal influenza viruses and respiratory syncytial virus (RSV) are primary causes of acute respiratory tract infections (ARTIs) in children. New respiratory viruses including human metapneumovirus (hMPV), human bocavirus (hBoV), and influenza 2009 A(H1N1) virus have a strong impact on the pediatric population. OBJECTIVES: To evaluate epidemiological and clinical features of ARTIs in hospitalized children. METHODS: From December 1, 2008, to December 31, 2009, all children under age fifteen (n = 575) hospitalized for ARTIs were investigated for influenza A (subtype H1N1, H3N2, and 2009 H1N1) and B, RSV A and B, hMPV, and hBoV by PCR. RESULTS: Fifty-one percent of samples were positive for these respiratory viruses. The frequencies of virus detection were RSV 34·1%, hBoV 6·8%, hMPV 5%, seasonal influenza A 5%, and seasonal influenza B 0%. From April 2009, 11·6% of collected samples were influenza 2009 A(H1N1) positive. Respiratory syncytial virus activity peaked in January, hBoV in February, and hMPV in April. Seasonal influenza A was detected only between January and April 2009, while influenza 2009 A(H1N1) peaked in November. Respiratory syncytial virus and hMPV were mainly associated with lower respiratory tract infections (LRTIs) and with necessity of O(2) administration. The 2009 pandemic influenza was more frequently detected in elder children (P < 0·001) and was associated with higher, longer-lasting fevers compared with other viral infections (P < 0·05). CONCLUSIONS: All considered viruses were involved in LRTIs. The primary clinical relevance of RSV and a similar involvement of both seasonal influenza and emerging viruses investigated were observed on the pediatric population.

Co-circulation of genetically distinct human metapneumovirus and human bocavirus strains in young children with respiratory tract infections in Italy.

The discovery of human Metapneumovirus (hMPV) and human Bocavirus (hBoV) identified the etiological causes of several cases of acute respiratory tract infections in children. This report describes the molecular epidemiology of hMPV and hBoV infections observed following viral surveillance of children hospitalized for acute respiratory tract infections in Milan, Italy. Pharyngeal swabs were collected from 240 children ≤3 years of age (130 males, 110 females; median age, 5.0 months; IQR, 2.0-12.5 months) and tested for respiratory viruses, including hMPV and hBoV, by molecular methods. hMPV-RNA and hBoV-DNA positive samples were characterized molecularly and a phylogenetical analysis was performed. PCR analysis identified 131/240 (54.6%) samples positive for at least one virus. The frequency of hMPV and hBoV infections was similar (8.3% and 12.1%, respectively). Both infections were associated with lower respiratory tract infections: hMPV was present as a single infectious agent in 7.2% of children with bronchiolitis, hBoV was associated with 18.5% of pediatric pneumonias and identified frequently as a single etiological agent. Genetically distinct hMPV and hBoV strains were identified in children examined with respiratory tract infections. Phylogenetic analysis showed an increased prevalence of hMPV genotype A (A2b sublineage) compared to genotype B (80% vs. 20%, respectively) and of the hBoV genotype St2 compared to genotype St1 (71.4% vs. 28.6%, respectively). Interestingly, a shift in hMPV infections resulting from A2 strains has been observed in recent years. In addition, the occurrence of recombination events between two hBoV strains with a breakpoint located in the VP1/VP2 region was identified.

Influenza surveillance in a cohort of HIV-infected children and adolescents immunized against seasonal influenza.

During the 2006-2007 season, 19 HIV-uninfected and 33 HIV-infected children and adolescents with full immunovirologic response to HAART were immunized against influenza and subsequently followed up. One month post-immunization all subjects had protective antibodies titres which persisted for the whole influenza season. Seven vaccinees (four HIV-infected and three HIV-uninfected) were found to be infected by influenza viruses during the epidemic, but disease was lab-confirmed only in two HIV-infected subjects. Both presented a benign clinical course and were infected by an A/Brisbane/10/07-H3N2-like virus. These data indicate that HIV-infected subjects benefit from routine seasonal influenza vaccination.

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Human papillomavirus genotypes and phylogenetic analysis of HPV-16 variants in HIV-1 infected subjects in Italy.

A cross-sectional study was carried out to improve the state of evidence regarding the spectrum of HPV types and HPV-16 LCR variants circulating among men and women infected with HIV-1 in Italy. This study, conducted in 518 HIV-positive subjects (346 males and 172 females), showed a high prevalence of HPV anal infections (88.7%) in men and of cervical infections (65.1%) in women. A wide spectrum of HPV genotypes has been observed, as both single and multiple infections. Low-risk HPV types 6, 11 and 61 were frequently detected. HPV-16 was the prevalent high-risk type. Fourteen different HPV-16 LCR variants were found. Ten belonged to the European lineage (78.7% were detected in Italian subjects and 21.3% in foreign-born, all homo/bisexual men), two to the Asiatic lineage and two to the African-2 lineage. This study underlines the great genotypic heterogeneity characterizing anal and cervical HPV infections and the marked polymorphism of the predominant HPV-16 in this high-risk population in Italy.

Influenza vaccination in patients with cirrhosis and in liver transplant recipients.

To assess the safety and immunogenicity of influenza vaccination, patients with cirrhosis undergoing treatment or not and liver transplant recipients under standard immunosuppression were vaccinated and followed up for 6 months. One month after vaccination, seroprotection rates and antibody GMTs against the three vaccine antigens were higher than baseline levels in all three patients groups. No differences in seroconversion and seroprotection rates were found within groups, but antibody GMTs against A/H1N1 and A/H3N2 strains were lower in liver transplant recipients than in patients with cirrhosis without treatment. No serious adverse events and no alteration of the liver function tests were observed. Patients with cirrhosis, including those under treatment, and liver transplant recipients benefit from influenza vaccination and can be safely immunized.

The changing face of the epidemiology of type A, B, and D viral hepatitis in Italy, following the implementation of vaccination.

The morbidity and mortality rates of viral hepatitis A, B and Delta have dramatically dropped in Italy during the last decades. Thanks to the general improvements in hygiene and sanitation, hepatitis A has shifted from a high to an intermediate/low endemicity status. Vaccination against hepatitis A is recommended to people at increased risk, including travellers to endemic areas, military personnel and individuals at occupational risk. The implementation of universal anti-hepatitis B vaccination of infants and adolescents has resulted in a dramatic decline in disease burden and in the carrier rate. An additional benefit of hepatitis B vaccination is that hepatitis Delta has also substantially declined.

Molecular characterization of influenza viruses circulating in Northern Italy during two seasons (2005/2006 and 2006/2007) of low influenza activity.

The influenza activity and circulation of influenza viruses in Lombardy (the most populous Italian region) were observed during two consecutive seasons (2005/2006 and 2006/2007) characterized by low influenza activity by the Italian Influenza Surveillance Network. The molecular characteristics of circulating viruses were analyzed to evaluate the introduction of new variants and emergence of vaccine-escape viruses. In both seasons, the epidemic in Lombardy was sustained almost exclusively by influenza A viruses, accounting for 80.5% and 93.6% of total detections, respectively, and the co-circulation of A/H3 viruses belonging to distinct phylogenetic groups was observed. The A/H1N1 viruses isolated during the 2005/2006 season were closely related to A/New Caledonia/20/99, while the hemagglutinin (HA) sequences of the A/H1N1 viruses from the 2006/2007 season exhibited a greater diversity. These viruses were A/Solomon Islands/3/2006-like and showed several variants. All B isolates were similar to B/Malaysia/2506/2004 belonging to the B/Victoria/2/87-lineage. Influenza B virus was the dominant virus in Europe in the 2005/2006 season and accounted for the 20% of total detections in Lombardy. Overall, the viruses studied presented heterogeneity in their HA sequences suggesting the circulation of a miscellaneous set of variants during the two seasons notwithstanding the medium-low activity of influenza. The importance of virological surveillance of influenza viruses is recognized widely and the molecular characterization of the viruses, especially in vaccinated subjects, is of particular importance to evaluate the introduction and circulation of new variants.

Long-term immunogenicity of a virosomal subunit inactivated influenza vaccine in children with asthma.

To evaluate long-term immunogenicity of a virosomal subunit inactivated influenza vaccine in children with asthma, a prospective study was conducted during 2005-2006 influenza season in six public pediatric clinics in Milan and surroundings, Northern Italy. A single dose (0.5 ml) of a virosomal subunit inactivated influenza vaccine (Inflexal V) was injected in 106 asthmatic children aged 3-9 years. Serum hemagglutinin inhibition antibody titers were determined against the recommended influenza strains A/New Caledonia (H1N1), A/California (H3N2), and B/Shanghai (B), at pre-vaccination and 1 and 6 months after vaccination. Seroconversion rate (95% CI) against the strains A/H1N1, A/H3N2 and B was, respectively, 78% (68.6-85.7), 57% (46.7-66.9) and 66% (55.8-71.2) at 1 month. Seroprotection (titer> or =40) rate for A/H1N1, A/H3N2 and B was, respectively, 87% (77.8-92.2), 82% (72.6-89.7) and 90% (82.6-94.8) at 1 month and 74% (64.3-82.3), 77% (67.5-84.8), and 77% (67.5-84.8) at 6 months. Seroprotection rate was high and persistent (>95%) in children with pre-existing antibodies (titer> or =10) at pre-vaccination for any specific strain. In children without pre-existing antibodies, seroprotection rate for A/H1N1, A/H3N2 and B was, respectively, 67.6%, 66.7% and 74.4% at 1 month, and 35.1%, 56.2% and 41.0% at 6 months after vaccination. Vaccine was well tolerated. These results indicate that in unvaccinated children with asthma vaccination with a single dose of virosomal-adjuvanted influenza vaccine is well tolerated and effective as a whole. However, while immunity response and persistence are excellently high in children with pre-existing antibodies, in children naive for the antigens the immune parameters are lower at 6 months after vaccination.

Lack of effect of a booster dose of influenza vaccine in hemodialysis patients.

To assess whether the administration of a booster dose of influenza vaccine may enhance immune response in hemodialysis patients, 58 subjects were given two doses of the 2003/2004 season influenza vaccine, 1 month apart. "European Agency for the Evaluation of Medicinal Products" (EMEA) criteria were fully met in terms of percentage of response and of mean-fold increase of hemagglutination inhibiting (HI) antibody titer, but not in terms of seroprotection rates (HI antibody titers > or =1:40). The second vaccine administration did not result in additional increase in seroprotection rate or in geometric mean titers. Protective immune response against the epidemic A/H3N2 Fujian-like strain, antigenically distant from that included in the vaccine (A/Panama/2007/99) was observed in 94.7% of vaccinees protected against the A/H3N2 vaccine strain 1 month after immunization. No adverse reactions were reported during follow-up. The study findings suggest that immune response to influenza vaccination may be suboptimal in hemodialysis patients and that the administration of an additional second dose of vaccine does not improve the humoral response.

Impact of hepatitis B vaccination in a highly endemic area of south Italy and long-term duration of anti-HBs antibody in two cohorts of vaccinated individuals.

The aims of this study were to evaluate the impact of hepatitis B vaccination on the changing pattern of HBV infection in a former hyperendemic area (Afragola, South Italy), and to assess the long-term persistence of anti-HBs in two cohorts of individuals vaccinated as infants 18 and 23 years ago. Our data shows a significant decline in the prevalence of hepatitis B virus (HBV) markers in the general population from 1978 to 2006 (HBsAg: 13.4% versus 0.91%; anti-HBc: 66.9% versus 7.6%; p<0.001). Data from two cohorts of vaccinees provides further evidence regarding the long-term persistence of vaccine-induced anti-HBs. Data here reported indicates that the implementation of vaccination had a great impact in the control and prevention of hepatitis B in Italy.

Viable Newcastle disease vaccine strains in a pharmaceutical dump.

To assess the viability of discarded and buried vaccine strains, we examined vaccines that had been buried for >20 years in an industrial waste dump in the city of Milan, Italy. Viability results showed potential biological risk associated with uncontrolled burial of pharmaceutical industry waste, including some live vaccines.

Changing patterns of hepatitis B infection in Italy and NAT testing for improving the safety of blood supply.

In Italy, as in most industrialized countries, the burden of hepatitis B has progressively declined in recent decades as a consequence of general improvements in hygiene and standard of living, the introduction of several public health measures, refinement in blood screening and the implementation of specific vaccination programmes. Universal hepatitis B vaccination for all infants and adolescents as well as individuals at increased risk has resulted in considerable progress towards prevention and control of HBV infection. The residual risk of transmitting blood-borne viruses through transfusion is currently very low. Nucleic acid testing can shorten the window period and, consequently, further reduce the risk of viral transmission. Blood donor screening for HCV by NAT was initiated in Italy in 2001 and became mandatory in June 2002. NAT for HIV is currently mandatory in four regions, not mandatory but almost universally performed in another thirteen regions, and not yet introduced in the remaining four regions. NAT for HBV is currently mandatory in four regions and under evaluation in the remaining. NAT for HBV may be a useful tool in detecting acute viral infections in the window phase as well as the occult infections. Its efficacy in improving the safety of blood supply is expected to be higher in countries with intermediate/high endemicity, where anti-HBc antibody screening cannot be routinely performed. There is agreement that, at present, the implementation of HBV DNA testing will not allow for discontinuation of screening for HBsAg.

Human herpesvirus type 8 infection in an area of Northern Italy with high incidence of classical Kaposi's sarcoma.

Previous studies have reported a large variation in the incidence of classical Kaposi's sarcoma across different Districts of the province of Mantua (Northern Italy). To assess whether such differences might be explained by different anti-HHV8 antibody prevalence, a serological study was conducted in 343 healthy elderly individuals resident in two adjacent Districts, at the highest and the lowest classical Kaposi's sarcoma incidence rate, respectively. Qualitative and quantitative determinations of IgG antibodies against both latent and lytic HHV-8 antigens were performed by indirect immunofluorescence assay. The assay's sensitivity was studied in 26 patients with classical Kaposi's sarcoma. Overall, anti-HHV8 antibodies were detected in 25 out of 26 patients (96%), confirming the high sensitivity of this assay. The prevalence of anti-HHV-8 antibodies was higher among individuals living in the District had a high incidence of classical Kaposi's sarcoma compared to those living in the District with low incidence (19.4% vs 9.8%, and 15.9% vs 8%; P<0.05, for latent and lytic antibodies, respectively). Anti-lytic antibody GMT was higher in people living in the District at high incidence rate compared to those of the other area (328.9 vs. 180.4; P<0.01). A higher prevalence of HHV-8 infection was found among persons living in municipalities surrounded by watercourses (OR 2.2, 95% CI: 1.10-4.32). In conclusion, variation in HHV-8 prevalence appears to explain differences in the incidence rates of classical Kaposi's sarcoma observed in different areas of the province.