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We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.

Background: General population data on hepatitis C virus (HCV) prevalence in Italy come mostly from studies conducted in small towns. The highest rates have consistently been found in southern regions, especially in Calabria. Herein, we aimed to determine HCV prevalence, awareness, and risk factors in the general population of Catanzaro, the capital city of Calabria, Italy., Methods: A stratified probability-based random sample of adult population was drawn from the Census. Anti-HCV and HCV-RNA were assayed. Data on sociodemographycs, risk factors and awareness of infection status were also collected. Crude and age and sex directly standardized rates (DSR), using Catanzaro's general population as standard, were calculated. Log binomial regressions with sampling weights was used to identify independent predictors of infection., Results: The final study population consisted of 1003 people. Of them 27 (2.69%; 95% confidence interval, [CI] 1.78-3.89) (DSR: 2.34%; 95% CI: 1.37-3.30) and 9 (0.9%; 95% CI: 0.41-1.70) (DSR: 0.79%; 95% CI: 0.21-1.37) were anti-HCV and HCV RNA positive, respectively. Most HCV-positive participants were older people. Age ≥65 and past use of illicit drugs were both positive independent predictors of anti-HCV positivity, while female sex was an independent protective predictor of infection. Only 9 (33.3%) of anti-HCV positive participants had awareness of their status., Conclusions: We detected a much lower anti-HCV prevalence than those previously found in Calabria, along with a substantial change in HCV transmission modes. Infected people were almost only elderly and mostly unaware of their infection. Improving diagnosis and linkage to care for these infected persons would be needed.

Background: Most SARS-CoV-2 rapid antigen detection tests (RADTs) validation studies have been performed on specimens from COVID-19 patients and negative controls or from mostly symptomatic individuals. Herein we evaluated the diagnostic accuracy of AFIAS COVID-19 Ag, hereinafter denominated as AFIAS, during a COVID-19 screening program surveillance testing conducted among personnel of an Italian military airport., Methods: Nasopharyngeal swabs (NPSs) were collected from study participants and were analysed by both AFIAS and RT-PCR assay. A questionnaire collecting demographic and exposure data were administered to all participants. AFIAS accuracy parameters including Cohen's kappa (K) were determined., Results: Overall, from November 2020 to April 2021, 1294 (NPSs) were collected from 1183 participants (88.6% males, 11.4% females; mean age were 41.3, median age 42). Forty-nine NPSs (3.78%) were positive by RT-PCR, while 54 NPSs were positive by AFIAS. Overall baseline sensitivity, specificity, positive and negative predictive values were 0.633, 0.981, 0.574, 0.985, respectively and K was 0.585 (moderate). AFIAS sensitivity tended to be higher for NPSs with higher viral load. A higher sensitivity (0.944) compared to the overall baseline sensitivity (0.633) was also found for NPSs from participants with COVID-19 compatible symptoms, for which K was 0.891 (almost perfect). Instead, AFIAS sensitivity was quite poor for NPSs from asymptomatic participants. Most false negative NPSs in this group had moderate viral load., Conclusion: Overall, AFIAS showed high specificity but only moderate sensitivity, mainly because of the high proportion of asymptomatic participants. However, AFIAS showed good sensitivity for NPSs with high viral load and nearly optimal accuracy parameters for NPSs from participants with COVID-19 compatible symptoms. Thus, taking into consideration its performance features, this test can be useful for COVID-19 case identification and management as well as for infection control., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Verde et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

BackgroundIn high-income countries, hepatitis E virus (HEV) infection is mainly a zoonosis. However, it is also transfusion-transmissible and some countries, but not Italy, have introduced HEV screening for blood donations.AimWe assessed HEV infection prevalence and risk factors in a nationwide sample of Italian blood donors.MethodsWe selected 107 blood establishments (BE) distributed in the 20 Italian regions by a stratified two-stage design and invited them to participate in the study. Donors were tested for anti-HEV IgG and IgM and HEV RNA. Sociodemographic data and risk factors were collected through a questionnaire.ResultsOverall, 60 BE from 60 provinces in 19 Italian regions joined the study. We assessed HEV markers in 7,172 blood donors, of whom 6,235 completed the questionnaire. Overall crude and adjusted anti-HEV IgG prevalences were 8.3% and 5.5%, respectively. Overall anti-HEV IgM prevalence was 0.5%, while no blood donor was HEV RNA-positive. Anti-HEV IgG prevalence varied widely among regions (range: 1.3%-27.20%) and hyperendemic prevalences (> 40%) were detected in some provinces in two regions. Older age (AOR = 1.81; 95% CI: 1.36-2.41), foreign nationality (AOR = 2.77; 95% CI: 1.06-7.24), eating raw pork liver sausages (AOR = 2.23; 95% CI: 1.55-3.20) and raw homemade sausages (AOR = 3.63; 95% CI: 2.50-5.24) were independent infection predictors.ConclusionItalian blood donors showed a low to moderate HEV seroprevalence. High levels in some regions and/or provinces were mainly attributable to eating habits. Prevention should include avoiding consumption of raw or undercooked meat and safe production of commercial pork products.

Background: Evaluation of clinical performance of the anti-hepatitis C virus (HCV) rapid tests were carried out mostly in chronic hepatitis C patients and in individuals at high risk of HCV infection., Methods: The aim of this study was to evaluate the performance of OraQuick and Wantai rapid tests on archived serum samples from 1408 individuals (mean age 46, range 18-90; 65% female) recruited with a systematic sampling procedure during a general population survey., Results: The analysis of samples by Ortho HCV 3.0 ELISA and Cobas Taqman HCV RNA assays resulted in 69 anti-HCV antibody positive sera, including 42 HCV RNA positive (group 1) and 27 HCV RNA negative (group 2) samples. The performance of rapid tests was evaluated on the 69 anti-HCV positive (group 1+2) and 206 (OraQuick) and 198 (Wantai) anti-HCV negative sera, randomly selected from the 1339 anti-HCV negative samples. The OraQuick and Wantai rapid assays showed a sensitivity in group 1 of 92.9% and 90.5%, respectively. The sensitivity in group 2 was 40.7% and 51.9%, respectively. The anti-HCV antibodies signal/cutoff mean value was the only parameter that statistically differed between group 1 and group 2 individuals (P<0.0001). Further, 3 (OraQuick) and 4 samples (Wantai) from group 1, with very low HCV RNA level (<25 UI/mL), were misdiagnosed by rapid assays as false negative., Conclusions: The proportion of infections with low level of viremia and the risk associated with rapid assay failure remained to be carefully estimated in general population.

Hepatitis B virus (HBV) is the main cause of diseases liver related infecting more than 200 milion persons worldwide. HBV infection shows high level of prevalence in South-East Europe and in Mediterranean basin. In Tunisia, a country with an intermediate level endemicity, HbsAg prevalence ranges from 2 to 5%. Most of the HBV isolates from Tunisia were classified as subgenotype D7 whose circulation is restricted to a specific area of North Africa including Maghreb region. In this paper, the phylogeny of HBV-D7 isolated from 38 Tunisian patients was investigated by analyzing the S gene region of HBV. A Bayesian coalescent-based framework was used to estimate the origin of the HBV-D7 in the country. The Tunisian D7 isolates were found to share a common ancestor whose origin was traced back to 1958. Population dynamics indicated that HBV-D7 epidemic in Tunisia grew exponentially from 1960s to 1990s. After that, the curve reached a plateau around the years 2000 likely due to the implementation of the infant vaccination program in 1996. Epidemiological data suggested that the exponential growth phase was likely sustained by intra-familial transmission events occurring during infancy. Further characterization of HBV-D7 isolates should be performed to evaluate, in the post-vaccination era, the emergence of new transmission routes, and to monitor the efficacy of the vaccination program. J. Med. Virol. 89:469-475, 2017. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)

Background: Hepatitis E virus diagnosis still presents difficulties due to discordant results among diagnostic tests., Objectives: The aim of this study was to evaluate the performance of two rapid tests for detection of anti-HEV IgM antibodies., Study Design: The rapid tests were compared with three commercial anti-HEV ELISA assays and one Real-Time PCR assay on 59 sera from patients with acute viral non-AC hepatitis., Results: The presence of anti-HEV IgM antibodies was evaluated by two rapid tests (Wantai and Assure) on 25 HEV RNA positive samples. Anti-HEV IgM antibodies were detected in 24/25 and 23/25 samples respectively. The sensitivity and specificity of Wantai and Assure Rapid tests were evaluated using the 25 HEV RNA positive samples and 50 HEV RNA negative samples (including sera from acute-phase HAV and HBV infections and blood donors). Overall, the sensitivity of Wantai Rapid and Assure Rapid tests was 96.1% and 92.6% respectively; the specificity of the 2 tests was 100%., Conclusion: Our data suggest the potential use of anti-HEV IgM rapid assays as a first line test in primary health care settings, particularly useful for patients with chronic liver disease or pregnant women who urgently need an antiviral treatment., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Background: The detection of baseline resistance mutations to new direct-acting antivirals (DAAs) in HCV chronically infected treatment-naïve patients could be important for their management and outcome prevision. In this study, we investigated the presence of mutations, which have been previously reported to be associated with resistance to DAAs in HCV polymerase (NS5B) and HCV protease (NS3) regions, in sera of treatment-naïve patients., Findings: HCV RNA from 152 naïve patients (84 % Italian and 16 % immigrants from various countries) infected with different HCV genotypes (21,1a; 21, 1b; 2, 2a; 60, 2c; 22, 3a; 25, 4d and 1, 4k) was evaluated for sequence analysis. Amplification and sequencing of fragments in the NS5B (nt 8256-8640) and NS3 (nt 3420-3960) regions of HCV genome were carried out for 152 and 28 patients, respectively. The polymorphism C316N/H in NS5B region, associated with resistance to sofosbuvir, was detected in 9 of the 21 (43 %) analysed sequences from genotype 1b-infected patients. Naturally occurring mutations V36L, and M175L in the NS3 protease region were observed in 100 % of patients infected with subtype 2c and 4., Conclusion: A relevant proportion of treatment naïve genotype 1b infected patients evaluated in this study harboured N316 polymorphism and might poorly respond to sofosbuvir treatment. As sofosbuvir has been approved for treatment of HCV chronic infection in USA and Europe including Italy, pre-treatment testing for N316 polymorphism on genotype 1b naïve patients should be considered for this drug.

Background: Hepatitis B virus infection (HBV) is widespread and it is considered a major health problem worldwide. The global distribution of HBV varies significantly between countries and between regions of the world. Among the many factors contributing to the changing epidemiology of viral hepatitis, the movement of people within and between countries is a potentially important one. In Italy, the number of migrant individuals has been increasing during the past 25 years. HBV genotype D has been found throughout the world, although its highest prevalence is in the Mediterranean area, the Middle East and southern Asia. We describe the molecular epidemiology of HBV in a chronically infected population of migrants (living in Italy), by using the phylogenetic analysis., Methods: HBV-DNA was amplified and sequenced from 43 HBV chronically infected patients. Phylogenetic and evolutionary analysis were performed using both maximum Likelihood and Bayesian methods., Results and Conclusion: Of the 43 HBV S gene isolates from migrants, 25 (58.1 %) were classified as D genotype. Maximum Likelihood analysis showed an intermixing between Moldavian and foreigners sequences mostly respect to Italian ones. Italian sequences clustered mostly together in a main clade separately from all others. The estimation of the time of the tree's root gave a mean value of 17 years ago, suggesting the origin of the tree back to 1992 year. The skyline plot showed that the number of infections softly increased until the early 2005s, after which reached a plateau. Comparing phylogenetic data to the migrants date of arrival in Italy, it should be possible that migrants arrived in Italy yet infected from their country of origin. In conclusion, this is the first paper where phylogenetic analysis and genetic evolution has been used to characterize HBV sub genotypes D1 circulation in a selected and homogenous group of migrants coming from a restricted area of Balkans and to approximately define the period of infection besides the migration date.