Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy.

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.

Hepatitis B and C virus infection in patients with Systemic and Cutaneous Lupus Erythematosus.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by a multifactorial etiology. The primary aim of this study was to estimate HCV and HBV infection prevalence in a cohort of SLE and Cutaneous Lupus Erythematosus (CLE). We assessed the frequency of these infections in our cohort and the possible associations with disease clinical/laboratory features and disease activity status. The prevalence of chronic HBV infection was 2.2% in the CLE group, while no HBsAg positive patients were identified in the SLE group. Conversely, the prevalence of anti-HCV positive was 2.2% in the SLE group while no anti-HCV positive patients were identified in the CLE group. We found no significant association between anti-HBc positive status and clinical manifestations or disease activity status in either group of patients. Hemodialysis resulted significantly associated with anti-HBc positivity in SLE. In the present study, we found HBsAg positivity in CLE patients but not in the Systemic form (SLE); conversely, a similar prevalence of anti-HBc antibodies in both groups was observed. A possible protective role exerted by SLE in HBV infection may be hypothesized. A higher frequency of HCV infection in SLE compared to CLE suggests a possible involvement of HCV in some SLE-related clinical and immunological features.

Diagnostic accuracy of a SARS-CoV-2 rapid antigen test among military and civilian personnel of an Air Force airport in central Italy.

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.

Molecular Characterization of Hepatitis B Virus Infection in a Patient with Cutaneous Lupus Erythematosus.

Hepatitis B virus (HBV) infection is a serious global health problem. Patients with autoimmune diseases, such as Lupus Erythematosus, are exposed to a higher risk of acquiring infections. In this study, a molecular characterization, genomic investigation of the Hepatitis B virus, polymerase (P) and surface (S) genes, from a patient affected by Cutaneous Lupus Erythematosus (CLE), was presented. Viral DNA was extracted from 200 µL of serum, and the HBV-DNA was amplified by real-time polymerase chain reaction (PCR) with the Platinum Taq DNA Polymerase. The PCR products were purified and sequencing reactions were performed. A phylogenetic analysis was performed through maximum likelihood and Bayesian approaches. The HBV CLE isolate was classified as sub-genotype D3 and related to other Italian HBV D3 genomes, and some from foreign countries. No drug resistant mutations were identified. One mutation (a.a. 168 M) was located in the last part of the major hydrophilic region (MHR) of the surface antigen (HBsAg). Moreover, three sites (351G, 526Y, 578C) in the polymerase were exclusively present in the CLE patient. The mutations identified exclusively in the HBsAg of our CLE patient may have been selected because of the Lupus autoantibodies, which are characteristic in the Lupus autoimmune disease, using a possible molecular mimicry mechanism.

Prevalence and risk factors for hepatitis E virus infection in blood donors: a nationwide survey in Italy, 2017 to 2019.

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.

Detection of antibodies against SARS-CoV-2 both in plasma pools for fractionation and in commercial intravenous immunoglobulins produced from plasma collected in Italy during the pandemic.

BACKGROUND: We investigated the presence of anti-SARS-CoV-2 antibodies in Italian plasma pools and intravenous immunoglobulins sent to our Institute (Italian National Institute of Health - Istituto Superiore di Sanità) in the context of the Official Control Authority Batch Release. The plasma pools were made up from donations collected in several different Italian regions from May 2017 to October 2020, i.e. in the pre-pandemic and pandemic periods. MATERIALS AND METHODS: All plasma pools were initially tested for the qualitative detection of anti-SARS-CoV-2 antibodies against the nucleocapsid protein using the Roche Elecsys® Anti-SARS-CoV-2 test kit. Plasma pools positive for these antibodies were further tested using the Roche Elecsys® Anti-SARS-CoV-2 S test kit for the quantitative detection of antibodies against SARS-CoV-2 spike receptor binding domain. All plasma pools showing reactivity to these antibodies were tested undiluted for the presence of SARS-CoV-2 RNA using the Grifols Procleix SARS-CoV-2 transcription-mediated amplification assay. Intravenous immunoglobulins were tested using both test kits to determine the presence of anti-SARS-CoV-2 antibodies. RESULTS: All plasma pools made up from donations collected in the pre-pandemic period were negative for anti-SARS-CoV-2 antibodies against the nucleocapsid protein. Of the plasma pools made up from donations collected from December 2018 to March 2020, only 1 pool out of 68 (1.4%), that was made up from donations from the Lombardy region, was reactive for these antibodies. Interestingly, 105 out of 174 (60.3%) of the plasma pools made up from donations collected from November 2018 to October 2020 showed the presence of these antibodies. All plasma pools positive for these antibodies were tested for antibodies against SARS-CoV-2 spike receptor binding domain and were confirmed positive. DISCUSSION: None of these plasma pools tested were reactive for SARS-CoV-2 RNA. In the case of intravenous immunoglobulins, 20 out of 25 (80%) batches showed the presence of both anti-SARS-CoV-2 antibodies, reflecting the concentration in the plasma pools used for their production.

Hepatitis E virus infection prevalence among men who have sex with men involved in a hepatitis A virus outbreak in Italy.

BACKGROUND: The routes of hepatitis E virus (HEV) transmission have still not been fully clarified. Here, we evaluated the possibility of sexual transmission of HEV, which remains a highly disputed issue. MATERIALS AND METHODS: Hepatitis E virus sexual transmission risk was assessed by comparing the prevalence of HEV infection in a sample of 196 Italian men who have sex with men (MSM) involved in a multi-country hepatitis A virus (HAV) outbreak, and in 3,912 Italian male blood donors selected from the same regions and provinces as the MSM. Selection of study of participants was motivated by the fact that HEV prevalence among Italian blood donors has been found to vary enormously between different geographical areas. RESULTS: Anti-HEV IgG prevalence was 14.8% and 5.6% in blood donors and MSM, respectively. Adjusted anti-HEV IgG prevalence was significantly lower in MSM than in blood donors (odds ratio [OR], 0.40; 95% confidence interval [CI]: 0.22-0.75; p<0.01), among residents in northern (OR, 0.45; 95% CI: 0.37-0.55; p<0.01) and southern (OR, 0.45; 95% CI: 0.35-0.58; p <0.01) Italy than among residents in Central Italy, while the prevalence was significantly higher in participants over 50 years of age than in those under 50 years of age (OR, 1.83; 95% CI: 1.48-2.27; p<0.01). DISCUSSION: Our findings suggest that sexual intercourse does not have a relevant role in HEV transmission. In particular, sexual transmission of HEV is unlikely to influence the prevalence of HEV infection at population level.

A nationwide retrospective study on prevalence of hepatitis E virus infection in Italian blood donors.

BACKGROUND: In Europe, hepatitis E virus (HEV) infection is mainly a food-borne zoonosis, but it can also be transmitted by blood transfusion. It is usually a mild and self-limited infection. However, immunocompromised persons, who are also those more likely to undergo blood transfusions, may develop chronic hepatitis and often cirrhosis. Since this is a potential threat to blood safety, we aimed to investigate HEV prevalence in Italian blood donors. MATERIALS AND METHODS: We used plasma donations collected during 2015-2016 by blood services (BS) scattered throughout the Italian regions and intended for the production of plasma-derived medicines. Plasma samples were tested for IgG and IgM anti-HEV and for HEV RNA using validated assays. Data concerning donor's age and sex, and the location of the BS were collected. RESULTS: A total of 10,011 plasma samples were tested. Overall IgG and IgM prevalence rates were 8.7 and 0.4%, respectively. No sample was HEV RNA-positive. IgG prevalence was significantly higher in males and in donors aged 44 years and over. IgG prevalence differed greatly according to region. Overall regional rates over 15% were found in Abruzzo and in Sardinia, and rates of 10-15% were found in Lazio, Umbria and the Marche. Considering IgG prevalence according to the province where the BS was located, rates over 30% were found in Sardinia and Abruzzo. Age, sex and donor's region of residence were independently associated with IgG positivity. BS location produced significant heterogeneity on prevalence rates within the regions. DISCUSSION: The detected IgG rate of 8.7% in this study represents one of the lowest seroprevalence rates reported among blood donors in Europe. Particularly high prevalence rates in some regions and provinces may be explained by local eating habits and/or intensive environmental HEV contamination. Before considering the introduction of HEV RNA screening for blood donations in Italy, further important issues should be addressed and prospective incidence and reliable cost-benefit studies are needed.

Detection of West Nile virus RNA (lineages 1 and 2) in an external quality assessment programme for laboratories screening blood and blood components for West Nile virus by nucleic acid amplification testing.

BACKGROUND: A second Italian external quality assessment programme was run in 2011 to assess the performance of blood transfusion centres in detecting West Nile virus RNA in plasma. MATERIALS AND METHODS: Each participant received two panels containing negative samples and samples positive for West Nile virus lineages 1 and 2, some of which with a viral concentration close to or below the 95% limit of detection of the respective commercial nucleic acid amplification test assay: the PROCLEIX WNV assay or the Cobas TaqScreen West Nile virus test. RESULTS: Eleven laboratories took part in the external quality assessment programme. All of them correctly identified the positive samples with a viral concentration above the 95% limit of detection. No false positive results or pre-/post-analytical errors were observed. DISCUSSION: The External quality assessment programme run in 2011 allowed participants to assess the performance of the nucleic acid amplification test methods applied in their seasonal routine screening of blood donations. The results confirm the 95% limit of detection reported by the test kits' manufacturers for both West Nile virus lineages.