Human Papillomavirus Infections in Cervical Samples From HIV-Positive Women: Evaluation of the Presence of the Nonavalent HPV Genotypes and Genetic Diversity.

Non-nonavalent vaccine (9v) Human papillomavirus (HPV) types have been shown to have high prevalence among HIV-positive women. Here, 1444 cervical samples were tested for HPV DNA positivity. Co-infections of the 9v HPV types with other HPV types were evaluated. The HPV81 L1 and L2 genes were used to investigate the genetic variability of antigenic epitopes. HPV-positive samples were genotyped using the HPVCLART2 assay. The L1 and L2 protein sequences were analyzed using a self-optimized prediction method to predict their secondary structure. Co-occurrence probabilities of the 9v HPV types were calculated. Non9v types represented 49% of the HPV infections; 31.2% of the non9v HPV types were among the low-grade squamous intraepithelial lesion samples, and 27.3% among the high-grade squamous intraepithelial lesion samples, and several genotypes were low risk. The co-occurrence of 9v HPV types with the other genotypes was not correlated with the filogenetic distance. HPV81 showed an amino-acid substitution within the BC loop (N75Q) and the FGb loop (T315N). In the L2 protein, all of the mutations were located outside antigenic sites. The weak cross-protection of the 9v types suggests the relevance of a sustainable and effective screening program, which should be implemented by HPV DNA testing that does not include only high-risk types.

The Use of Both Therapeutic and Prophylactic Vaccines in the Therapy of Papillomavirus Disease.

Human papillomavirus (HPV) is the most common sexually transmitted virus. The high-risk HPV types (i.e., HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59) are considered to be the main etiological agents of genital tract cancers, such as cervical, vulvar, vaginal, penile, and anal cancers, and of a subset of head and neck cancers. Three prophylactic HPV vaccines are available that are bivalent (vs. HPV16, 18), tetravalent (vs. HPV6, 11, 16, 18), and non-avalent (vs. HPV6, 11, 16, 18, 31, 33,45, 52, 58). All of these vaccines are based on recombinant DNA technology, and they are prepared from the purified L1 protein that self-assembles to form the HPV type-specific empty shells (i.e., virus-like particles). These vaccines are highly immunogenic and induce specific antibodies. Therapeutic vaccines differ from prophylactic vaccines, as they are designed to generate cell-mediated immunity against transformed cells, rather than neutralizing antibodies. Among the HPV proteins, the E6 and E7 oncoproteins are considered almost ideal as targets for immunotherapy of cervical cancer, as they are essential for the onset and evolution of malignancy and are constitutively expressed in both premalignant and invasive lesions. Several strategies have been investigated for HPV therapeutic vaccines designed to enhance CD4+ and CD8+ T-cell responses, including genetic vaccines (i.e., DNA/ RNA/virus/ bacterial), and protein-based, peptide-based or dendritic-cell-based vaccines. However, no vaccine has yet been licensed for therapeutic use. Several studies have suggested that administration of prophylactic vaccines immediately after surgical treatment of CIN2 cervical lesions can be considered as an adjuvant to prevent reactivation or reinfection, and other studies have described the relevance of prophylactic vaccines in the management of genital warts. This review summarizes the leading features of therapeutic vaccines, which mainly target the early oncoproteins E6 and E7, and prophylactic vaccines, which are based on the L1 capsid protein. Through an analysis of the specific immunogenic properties of these two types of vaccines, we discuss why and how prophylactic vaccines can be effective in the treatment of HPV-related lesions and relapse.

Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples.

BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel ß and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, ß, γ HPV types. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. RESULTS: HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, ß, γ) prevalence between men and women. Overall, ß species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, ß genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for ß1 species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, ß and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. CONCLUSION: This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection.

Oral human Papillomavirus DNA detection in HIV-positive men: prevalence, predictors, and co-occurrence at anal site.

BACKGROUND: HIV-positive patients carry an increased risk of HPV infection and associated cancers. Therefore, prevalence and patterns of HPV infection at different anatomical sites, as well as theoretical protection of nonavalent vaccine should be investigated. Aim was to describe prevalence and predictors of oral HPV detection in HIV-positive men, with attention to nonavalent vaccine-targeted HPV types. Further, co-occurrence of HPV DNA at oral cavity and at anal site was assessed. METHODS: This cross-sectional, clinic-based study included 305 HIV-positive males (85.9% MSM; median age 44.7 years; IQR: 37.4-51.0), consecutively observed within an anal cancer screening program, after written informed consent. Indication for anal screening was given by the HIV physician during routine clinic visit. Paired oral rinse and anal samples were processed for the all HPV genotypes with QIASYMPHONY and a PCR with MY09/MY11 primers for the L1 region. RESULTS: At the oral cavity, HPV DNA was detected in 64 patients (20.9%), and in 28.1% of these cases multiple HPV infections were found. Prevalence of oral HPV was significantly lower than that observed at the anal site (p < 0.001), where HPV DNA was found in 199 cases (85.2%). Oral HPV tended to be more frequent in patients with detectable anal HPV than in those without (p = 0.08). Out of 265 HPV DNA-positive men regardless anatomic site, 59 cases (19.3%) had detectable HPV at both sites, and 51 of these showed completely different HPV types. At least one nonavalent vaccine-targeted HPV type was found in 17/64 (26.6%) of patients with oral and 199/260 (76.5%) with anal infection. At multivariable analysis, factors associated with positive oral HPV were: CD4 cells <200/µL (versus CD4 cells >200/µL, p = 0.005) and >5 sexual partners in the previous 12 months (versus 0-1 partner, p = 0.008). CONCLUSIONS: In this study on Italian HIV-positive men (predominantly MSM), oral HPV DNA was detected in approximately one fifth of tested subjects, but prevalence was significantly lower than that observed at anal site. Low CD4 cell count and increasing number of recent sexual partners significantly increased the odds of positive oral HPV. The absence of co-occurrence at the two anatomical sites may suggest different routes or timing of infection.

Dynamics of HCV genotype 4 resistance-associated variants during virologic escape with pIFN/RBV+daclatasvir: a case study using ultra deep pyrosequencing.

BACKGROUND: Daclatasvir (DCV) is an approved NS5A inhibitor with potent anti-HCV activity and broad genotype coverage. DCV resistance-associated variants (RAVs) have been described for patients infected with genotype (GT) 1, but increased GT4 prevalence in European countries as a result of immigration has boosted interest in this genotype. OBJECTIVES: Establishment of NS5A variability in treatment-naive patients with HCV genotype 4 infection and a case study of the dynamics of resistance-associated variants in a virologic failure receiving pIFN/RBV+DCV, as assessed by ultra-deep sequencing. STUDY DESIGN: Five treatment-naïve GT4 patients (GT4a [n = 1], GT4d [n = 3], GT4o [n = 1]) were evaluated for inclusion in the COMMAND-4 study and treatment with pIFN/RBV±DCV. RESULTS: Patient (Pt) 1 received pIFN/RBV; Pts2-4 received pIFN/RBV + DCV; Pt5 was a screening failure. Pt1 relapsed; Pt2 experienced breakthrough at Wk4; Pts3 and 4 achieved a sustained virologic response. No substitutions associated with DCV-resistance were detected at baseline. In terms of viremic time points for Pts1 and 2, the extent of NS5A diversity pre-treatment was not significantly related to viral load (r = -0568; p = 0.035). In Pt2, multiple substitutions associated with DCV-resistance were observed after breakthrough at NS5A amino acid positions 28, 31 and 93. These substitutions were frequently observed on the same haplotype (L28S + M31I = 55.52, 82.50, and 99.36% at Wk4, 8 and 9; L28S + M31I + Y93H = 11.77, 5.01 and <0.6% at Wk4, 8 and 9). CONCLUSIONS: This is the first report to describe DCV-resistance in patients infected with GT4d, supporting a possible role for a recently described RAV (L28S), and presenting the dynamics of HCV quasispecies during therapy failure, with indications of changes of diversity and association of mutations.

Temporal trend and characteristics of recent HIV-1 infections: application of an algorithm for the identification of recently acquired HIV-1 infections among newly diagnosed individuals over a 10-year period.

Identification of recent infections (RI) may contribute to improve the quality of human immunodeficiency virus (HIV) surveillance, monitoring ongoing transmission and planning and evaluating prevention programs. Our study applied an algorithm combining clinical and serological information to identify RI in individuals newly diagnosed with HIV in Rome, during the years 1999-2008, in order to describe the trend and characteristics of recently infected individuals. RI were documented seroconverters, or people with an HIV avidity index (AI)<0.80. Individuals with advanced infection (CD4 count <200 cells/?L or AIDS-defining illness) or with AI ?0.80 were considered long-standing infections. Overall, we observed 2,563 new HIV diagnoses. The algorithm was applied in 2124/2563 (82.9%). Of these, 355 were RI (16.7%). RI was found independently associated with calendar year (adjusted odds ratio [aOR]= 1.06, 95% confidence intervals [CI]=[CI 1.02-1.11], for every year of increase), HIV-risk category (men having sex with men: aOR=1.44, [CI 1.04-1.98]; injecting drug users: aOR=1.58, [CI 1.03-2.42] vs. heterosexuals), country of origin (foreign-born: vs Italians: aOR=0.46, [CI 0.33-0.62]), and recruitment site (inpatient vs outpatient clinic: aOR=0.49, [CI 0.37-0.66]). By the application of our algorithm we could characterize the pattern of ongoing HIV transmission, identifying groups needing more urgent prevention programs.

Comparison of the Abbott RealTime High Risk HPV with Genomica HPV Clinical Array for the detection of human papillomavirus DNA.

Human papillomavirus (HPV) has been identified as the major cause of cervical cancer worldwide and HPV DNA testing is recommended in primary cervical cancer screening. Several molecular tests for detection/typing of HPV DNA with different sensitivity and specificity are commercially available. The present study compared the performance of the Abbott RealTime High Risk HPV assay and the Genomica HPV Clinical Array CLART2 in 78 specimens (63 cervical smears and 15 rectal/urethral swabs).The typing results of the Genomica assay were in absolute agreement with each of the four possible result categories of the Abbott assay (HPV16, HPV18, Other HR HPV, not detected) in 87.2% (68/78) of the samples, with a Cohen' kappa agreement coefficient for every HR type of 0.62 (95% CI: 0.39-0.85), higher in cervical swabs (k = 0.74, 95% CI: 0.50-0.99) than in rectal/urethral swabs (k = 0.36, 95% CI: 0.00-0.82). There was an excellent agreement of the Genomica results with those of Abbott in cervical samples harbored HPV single infection (100% agreement). Nonetheless, both methods may lose sensitivity for detecting HPV types in multiple infections, giving discordant results (10/78). This underlines the importance of establishing the analytical sensitivity in HPV type detection in single and multiple HPV infections. In rectal/urethral swabs, 5 of 15 (33%) discordant cases were observed, most of which became compatible when the Genomica assay was performed starting from nucleic acid extracted with the Abbott m2000sp system. These results suggest that nucleic extraction based on the magnetic beads technique is suitable for HPV DNA detection in urethral/rectal swabs.

HIV incidence estimate combining HIV/AIDS surveillance, testing history information and HIV test to identify recent infections in Lazio, Italy.

BACKGROUND: The application of serological methods in HIV/AIDS routine surveillance systems to identify persons with recently acquired HIV infection has been proposed as a tool which may provide an accurate description of the current transmission patterns of HIV. Using the information about recent infection it is possible to estimate HIV incidence, according to the model proposed by Karon et al. in 2008, that accounts for the effect of testing practices on the number of persons detected as recently infected. METHODS: We used data from HIV/AIDS surveillance in the period 2004-2008 to identify newly diagnosed persons. These were classified with recent/non-recent infection on the basis of an avidity index result, or laboratory evidence of recently acquired infection (i.e., previous documented negative HIV test within 6 months; or presence of HIV RNA or p24 antigen with simultaneous negative/indeterminate HIV antibody test). Multiple imputation was used to impute missing information. The incidence estimate was obtained as the number of persons detected as recently infected divided by the estimated probability of detection. Estimates were stratified by calendar year, transmission category, gender and nationality. RESULTS: During the period considered 3,633 new HIV diagnoses were reported to the regional surveillance system. Applying the model, we estimated that in 2004-2008 there were 5,465 new infections (95%CI: 4,538-6,461); stratifying by transmission category, the estimated number of infections was 2,599 among heterosexual contacts, 2,208 among men-who-have-sex-with-men, and 763 among injecting-drug-users. In 2008 there were 952 (625-1,229) new HIV infections (incidence of 19.9 per 100,000 person-years). In 2008, for men-who-have-sex-with-men (691 per 100,000 person-years) and injecting drug users (577 per 100,000 person-years) the incidence remained comparatively high with respect to the general population, although a decreasing pattern during 2004-2008 was observed for injecting-drug-users. CONCLUSIONS: These estimates suggest that the transmission of HIV infection in Lazio remains frequent and men-who-have-sex-with men and injecting-drug-users are still greatly affected although the majority of new infections occurs among heterosexual individuals.

Frequency and multiplicity of human papillomavirus infection in HIV-1 positive women in Italy.

BACKGROUND: Natural history of HPV infection is altered in HIV positive women, with increased risk of cervical dysplasia. Limited data are available about the influence of HPV genotypes and HPV multiple infections on cervical disease in HIV positive women. OBJECTIVES: We determined HPV genotype prevalence in cervical samples from 553 HIV-infected women attending the gynaecological service at "L. Spallanzani" Hospital. Association of HPV multiple infections with cervical abnormalities was investigated. STUDY DESIGN: MY09/MY11 consensus primers were used to detect HPV-DNA; HPV typing was performed by RFLP. A commercial array based kit was used to define unresolved RFLP patterns. RESULTS: HPV was detected in 244/553 (44.1%) patients, correlating with low CD4 counts (p<0.001) and age (p=0.001). Multiple HPV types were observed in 44.4% of cases, more frequently involving HR than LR HPV (OR=12.8, p<0.00001). Multiple HPV infections were associated with low CD4 counts (OR=3.8 in CD4<200 vs CD4≥500 cells/mm(3)). Dyskaryosis was associated with decreased CD4 counts (≥500 vs 200-499 vs <200 cells/mm(3), χ(2) for trend, p=0.001) and with HPV types multiplicity (1 vs 2-3 vs ≥4, χ(2) for trend, p<0.00001). Notably, in 3 H-SIL cases only LR types were detected (HPV62, n=2; HPV81, n=1). CONCLUSIONS: Multiple HPV infections, often involving HR types, are frequent in HIV-infected women. Association between multiple HPV infection, low CD4 count and cytological abnormalities supports the interplay of virological and immunological factors in cervical cancer pathogenesis. Assessment of multiple HPV infections might gain importance in cervical cancer screening, particularly in patients with predisposing factors like immuno-suppression.

Genetic variability in E6, E7 and L1 protein of HPV81 from HIV-1 positive women in Italy.

The genetic variability of E6, E7 and L1 of HPV81 from HIV-1 positive women carrying multiple HPV infections was investigated by clonal analysis for E6 and E7. The range of maximal divergence from the prototype was 0.6%-2.6% for E6 and 1.0%-3.1% for E7. Compared to prototype HPV81, 13 and 10 mutations were identified in E6 and E7, respectively. In the pRB binding domain of E7, all HPV81 clones showed D21, as reported for prototype HPV81 and for HPV16 and 18, while G22 is reported in HPV6 and 11. In the CR3 region, CxxC motif was conserved in all but one clone. The L1 sequence of a single clone from 5 study patients was also established. The range of similarity with prototype HPV81 was 97.8%-99.2%, with 25 polymorphic sites. Two substitutions (R492K and T493S) were observed in 5/5, one (T287N) in 4/5 patients. Among L1 immune-related regions, BC loop presented T56N in 1/5, while FGb loop presented T287N in 4/5 patients. Our data indicate the presence of polymorphisms in all 3 HPV81 genes analyzed, with a certain degree of intra-patient diversity. The importance of polymorphisms on HPV81 persistence and pathogenicity needs to be addressed in longitudinal studies involving larger patient numbers.

[Rapid differential diagnosis of Orthopoxviruses and Herpesviruses based upon multiplex real-time PCR]. / Un nuovo metodo rapido, basato su real-time PCR multiplex, per la diagnosi differenziale di infezioni da Orthopoxvirus e Herpesvirus.

OBJECTIVE: Variola virus, belonging to Orthopoxviridae family, is one of the most dangerous human pathogens that could be used as biological weapon. We have developed a new rapid assay, based upon Real-time PCR and melting temperatures analysis of amplicons, for the contemporary detection of Orthopoxvirus, VZV and HSV1-2, that are the most important infectious agents to be considered for differential diagnosis. METHODS: The target for detection of orthopoxvirus DNA has been a region of the crmB gene which is common to Variola virus and to other old world orthopoxviruses pathogenic for humans. The targets for VZV and HSV1-2 have been ORF 29 and DNA polymerase, respectively. Suitability of the amplified fragments to RFLP or sequencing analysis, to recognize the involved viral species, has been also tested. RESULT: The selected primers have showed high sensitivity, specificity and compatibility with common amplification conditions. A mean melting temperature difference of 8.7 degree C was observed between the amplicons from the two virus types. Further identification of individual pathogens was made using RFLP analysis. CONCLUSION: The PCR-based protocol set up in this study for presumptive differential diagnosis of variola and herpesviral infections is rapid and specific and it can be used also to detect other orthopoxviral infections, like monkeypox.