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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p

Pre-analytic phase in molecular biology: criticism and non-compliance management

Introduction: During workflow in Laboratories the most delicate and important step is pre-analytic sample treatment because it involves more than one operator of the same structure and often different health services. In fact, the biological materials used for the diagnosis should be collected, sent and properly treated before the analytic phase. Correct methods for collecting and handling biological materials, including guidelines to users of laboratory services, improve performance of Laboratory testing activity. In the pre-analytic phase the operators check sample integrity, and prepare the sample for the subsequent analytic phase: in all these steps monitoring and control of “non- compliance” is crucial. Methods: During 2007-2008 we created a “non- compliance” check-list, to monitor errors which occurred in different sectors of the preanalytic phase, particularly in the nucleic acid extraction step. These “non-compliances” are analysed to identify and to remove errors, adopting preventive and corrective proceedings. Since 2008 we have been using DNA/RNA internal controls synthesized in our Laboratory. They can be amplified by the same primers and recognized by different probes. Results: Examination of the “non compliance” check-list for molecular biology investigations shows that the percentage of urine repeat samples decreased from 17% to 2% and the percentage of stool repeat samples from 27% to 2%. Regarding use of internal controls, they allow the assessment of inhibitory factors that can prevent gene amplification. Conclusions: Monitoring “non-compliance” cases and dividing them by typology allow us identifying the most frequent causes of incorrect sample handling, as a non optimal procedure of pre-treatment, thus improving the pre-analytic phase. Therefore by monitoring the preanalytic phase we can prevent the introduction of confounding factors that may negatively influence the accuracy of results and their interpretation. Before proceeding to gene amplification, biological samples must be properly purified to eliminate lipids, proteins, polysaccharides and other potential inhibitors of DNA polymerase

Prevalence study of HPV mixed infections in Italian HIV positive women

Introduction: HIV positive women, show a higher frequency of multiple HPV infections than HIV negative.The immune response seems to be genotype-specific, but evidence on different genotypes distribution and involvement of coinfections in the development of invasive cervix cancer (ICC) remains limited. The aim of our study was to assess the prevalence of multiple infections in a group of Italian HIV positive women, the distribution of High risk (HR) strains and Low Risk (LR) strains in multiple and single infections, and their correlation with immune status and cervical lesions. Methods: 553 women were considered in the study. HPV search was performed with MY09-MY11 primers. HPV positive samples were typed with the Clinical Genomic array (HPV) test (Genomica, Spain). Results: 244 samples were HPV positive (44.1%).129/244 (52.9%) had a single infection and 103/244 (42.2%) multiple infections.Among the 412 performed typing, 223 (54.1%) were HR strains, while 189 (45.9%) were LR strains.The HPV61 (40 times) was more frequent among the LR strains.Among HR strains, the most frequently observed was the HPV16 (30 times). In 92% of multiple infections, at least one HR strain was found. 36% of LR strains was presented in single infections compared to 27% of HR strains (p = 0.06). The clades A3 (n = 124, 65.3% multiple infections) and A10 (n = 37, 56.8% multiple infections) were the most represented in LR;A9 (n = 95, 67.4% multiple infections) and A6 (n = 57, 70.2%) clades were the most representative among HR strains. Differences in age between women with single infection and those with multiple infection were not observed (p = 0.33) .Women with the best immune status (CD4 cell count of &gt;500 cell/ mm3) showed a higher prevalence of single infection. HPV was positive in 75% of ASCUS/LSIL lesion and 77.3% of H-SIL. Conclusions: HPV-16 is the most frequent in both single and multiple infections as reported in a recent study about HIV negative women. Follow-up studies are necessary to assess the impact of multiple infections on the progression of different cervical lesion degrees

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

Abstract 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 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

Comparative evaluation of subtyping tools for surveillance of newly emerging HIV-1 strains

HIV-1 non-B subtypes/circulating recombinant forms (CRFs) are increasing worldwide. Since subtype identification can be clinically relevant, we assessed the added value in HIV-1 subtyping using updated molecular phylogeny (Mphy) and the performance of routinely used automated tools. Updated Mphy (2015 updated reference sequences), used as a gold standard, was performed to subtype 13,116 HIV-1 protease/reverse transcriptase sequences and then compared with previous Mphy (reference sequences until 2014) and with COMET, REGA, SCUEAL, and Stanford subtyping tools. Updated Mphy classified subtype B as the most prevalent (73.4%), followed by CRF02-AG (7.9%), C (4.6%), F1 (3.4%), A1 (2.2%), G (1.6%), CRF12-BF (1.2%), and other subtypes (5.7%). A 2.3% proportion of sequences were reassigned as different subtypes or CRFs because of misclassification by previous Mphy. Overall, the tool most concordant with updated Mphy was Stanford-v8.1 (95.4%), followed by COMET (93.8%), REGA-v3 (92.5%), Stanford-old (91.1%), and SCUEAL (85.9%). All the tools had a high sensitivity (\ue2\u89\ua598.0%) and specificity (\ue2\u89\ua595.7%) for subtype B. Regarding non-B subtypes, Stanford-v8.1 was the best tool for C, D, and F subtypes and for CRFs 01, 02, 06, 11, and 36 (sensitivity, \ue2\u89\ua592.6%; specificity, \ue2\u89\ua599.1%). A1 and G subtypes were better classified by COMET (92.3%) and REGA-v3 (98.6%), respectively. Our findings confirm Mphy as the gold standard for accurate HIV-1 subtyping, although Stanford-v8.1, occasionally combined with COMET or REGA-v3, represents an effective subtyping approach in clinical settings. Periodic updating of HIV-1 reference sequences is fundamental to improving subtype characterization in the context of an effective epidemiological surveillance of non-B strains