Lower respiratory tract (LRT) infections represent a major cause of mortality, particularly among critically ill patients. Molecular diagnostic tests have improved the detection of respiratory pathogens; however, most commercial assays are validated exclusively in upper RT (URT) specimens, limiting their applicability in LRT samples, which better reflect disease severity. This study evaluated the diagnostic performance of two commercially available assays, the BioFire Respiratory Panel 2.1 Plus and the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay, on bronchoalveolar lavage (BAL) specimens, using the Allplex Respiratory Panel 1/2/3 and the Allplex SARS-CoV-2 assay as reference methods validated for both matrices. Overall, 132 BAL samples were analyzed. BioFire identified more positives than Allplex, particularly for human rhinovirus/enterovirus (HRV/EV), human parainfluenza virus (HPIV), and non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The overall agreement was fair (κ = 0.237), and pathogen-specific concordance was almost perfect for SARS-CoV-2 (κ = 0.841), influenza A/B (κ = 0.808), and HPIV (κ = 0.884). The Panther assay showed substantial agreement with Allplex (κ = 0.719) and near-perfect concordance for SARS-CoV-2 and influenza viruses, while BioFire and Panther exhibited almost perfect interassay agreement (κ = 0.903). These findings demonstrate that assays validated for URT specimens can perform reliably on BAL samples, underlining the diagnostic potential of LRT matrices and the need for expanded validation of molecular respiratory panels across specimen types.

Background: Limited information is available on the extent of HDV genetic diversification in ribozyme (critical for HDV replication) and HDAg domains (crucial for viral morphogenesis and containing cytotoxic T lymphocytes epitopes [CTLE]) and their correlation with virological and biochemical parameters.Methods: 103 individuals with chronic HDV infection were included. Full-length HDV genome sequences were obtained by Illumina (median [IQR] reads/seq: 62045[30460-91899]). Sub-genotypes 1 were defined by phylogenetic analysis. Amino acid (aa) residues were defined conserved if not mutated in 99% of sequences. HDAg domains and CTLE (N=18) were defined according to Pascarella 2010 and Kohsar 2021.Results:Individuals were mostly males with a median age of 54 (44-60) years, mainly from Eastern Europe (EE, 51%) and Italy (IT, 44.8%). Serum HDV-RNA and ALT were 5.6 (4.9-6.2)logIU/ml and 94 (65-152)U/L. Sub-genotypes 1c and 1e were the most prevalent (47.1% and 45.2%): 1c predominated in individuals from EE(77.6% vs 22.4%, P<0.001) while 1e in IT(77.5% vs 22.5%, P<0.001).HDV ribozyme was characterised by a high degree of genetic conservation. An opposite scenario was observed for HDAg in which the number of conserved aa in HDAg dropped to 36.7% (79/214), with 18.2% in coiled coil sequence (CCS), 27.3% RNA binding domain (RDB)2, 30.8% in RBD1, 33.3% in nuclear localization sequence (NLS), 40% in virus assembly signal (VAS) and 63.3% in RBD3. The degree of genetic conservation of CTLEs ranges from 11.1% in CTLEs 46-54 and 43-51 to 60.0% in 140-149.Notably, CTLE 170-179 from individuals with HDV-RNA >5logIU/ml (70% of conserved aa with vs 20% without HDV-RNA <5 logIU/ml, P=0.025) showed lower genetic conservation, suggesting that an enrichment of mutations in this CTLE can enhance viral replication.Finally, despite a comparable degree of genetic conservation between sub-genotypes 1e and 1c, they were characterized by divergent genetic pathways. In particular, sub-genotype 1c was significantly associated with the selection of 7 specific mutations (I16T/V, N22S, D47E, R112K, T180A, A202S, prevalence ranging from 26.5% to 44.9% vs 0% in 1e, P<0.001). Conversely, sub-genotype 1e was significantly associated with the selection of 6 specific mutations (D29E, D46E, K113R, R131K, M171L, I188V prevalence ranging from 23.9% to 43.5% vs 0% in 1c, P<0.009). Notably, in sub-genotype 1c, the co-presence of I16V/T+D47E+A202S correlated with ALT>3ULN (100% vs 27.5%, P=0.001)Conclusion: Sub-genotypes 1 are characterized by a conspicuous degree of genetic diversification in HDAg that has contributed to the selection of divergent genetic signatures. The enrichment of mutations in specific CTL epitopes could potentially hamper HDV recognition by immune response and in turn enhancing viral replication.Overall, the role of the high degree of genetic variability in affecting the proper HDV detection by the currently available diagnostic assays deserves further investigation.

Background & Aim: The entry of Hepatitis D Virus (HDV) depends on HBV surface proteins (HBsAg) composed of three isoforms: large-, middle, and small HBsAg. Here, we investigate the levels of total HBsAg and HBsAg isoforms and their correlations with HDV-RNA, HBcrAg, and transaminases in the setting of untreated chronic hepatitis D (CHD). Methods: This study includes 316 HBeAg-negative patients: 192 CHD and 124 with chronic hepatitis B (CHB) as a control group. HBsAg isoforms were quantified by ad hoc-designed ELISAs. Results: The composition of HBsAg isoforms varied between the two groups of patients, with remarkably higher small HBsAg, middle-HBsAg, and large HBsAg in CHD than in CHB. This data was confirmed by multivariable analysis (p < 0.0001). Among CHD, HBsAg isoforms positively correlated with HDV-RNA (p < 0.0001) and HBcrAg (p < 0.0001) but not with HBV-DNA. The results were confirmed by stratifying patients according to HDV-RNA (< or >1000 IU/mL) and HBcrAg (< or >3 logU/mL). Furthermore, CHD patients with ALT > upper limit of normal presented significantly higher S-HBsAg and M-HBsAg levels. Conclusions: CHD is characterized by a more elevated HBsAg isoform production, paralleling HDV-RNA and HBcrAg release. This may suggest a preferential recruitment of HBsAg isoforms in HDV virions at the expense of HBV virions. The association of HBsAg isoforms with higher ALT also suggests their potential contribution in supporting HDV-induced pro-inflammatory stimuli.

INTRODUCTION:A reliable quantification of hepatitis D virus (HDV) RNA is of paramount importance for monitoring patients under antiviral therapy. This quality control study compares the diagnostic performances of quantitative HDV-RNA assays used in clinical practice. METHODS:Two HDV-RNA sample panels were quantified in 30 centers by RoboGene (N = 9 laboratories), EurobioPlex (N = 7), RealStar (N = 4), AltoStar (N = 1), Bosphore (N = 3), Bosphore-on-InGenius (N = 1), Dia.Pro (N = 2), Nuclear-Laser-Medicine (N = 1) and 3 in-house assays. Panel A and B comprised 8 serial dilutions of WHO/HDV standard (range: 0.5-5.0 log10 IU/ml) and 20 clinical samples (range: 0.5-6.0 log10 IU/ml), respectively. The following parameters were determined: sensitivity by 95 % LOD (limit of detection), precision by intra- and inter-run CV (coefficient of variation), accuracy by the differences between expected-observed HDV-RNA, linearity by linear regression analysis. RESULTS:95 % LOD varied across assays and centers underlining heterogeneous sensitivities: AltoStar had the lowest 95 % LOD (3 IU/ml) followed by RealStar (10 [min-max: 3-316] IU/ml), Bosphore-on-InGenius (10 IU/ml), RoboGene (31 [3-316] IU/ml), Nuclear-Laser-Medicine (31 IU/ml) and EuroBioplex (100 [100-316] IU/ml). Moreover, 6 assays (RoboGene, EurobioPlex, RealStar, AltoStar, Nuclear-Laser-Medicine and In-house) showed <0.5 log10 IU/ml differences between expected and observed HDV-RNA for all dilutions while other assays had >1 log10 IU/ml underestimations. RealStar, Bosphore-on-InGenius and EurobioPlex had the highest precision (mean intra-run CV < 20 %). Inter-run CV was higher for all assays, with CVs < 25 % for RealStar, AltoStar, Nuclear-Laser-Medicine and EurobioPlex. Seven assays (RoboGene/AltoStar/RealStar/EurobioPlex/Nuclear-Laser-Medicine/In-house) showed a good linearity (R2 > 0.90), but for HDV-RNA < 1000 IU/ml only Bosphore-on-InGenius, AltoStar, RealStar and Robogene showed a R2 > 0.85. CONCLUSIONS:This study underlines heterogeneous sensitivities (inter- and intraassays), that could hamper proper HDV-RNA quantification, particularly at low viral loads. This raises the need to improve the diagnostic performance of most assays for properly identifying virological response to anti-HDV drugs.

Introduction Human Immunodeficiency virus (HIV) is effectively suppressed in the blood by the Antiretroviral Therapy in people living with HIV, but in rare cases can be present in some tissues and body fluids. In recent years, integrated systems were validated for detecting HIV-1 in plasma or serum. but not in cerebrospinal fluid (CSF). We evaluated the performance of ELITE InGenius® in comparison with the cobas® in this area. Methods To test the diagnostic accuracy of the HIV-1 ELITe MGB® kit on CSF samples, we tested CSF samples previously characterised with the cobras® HIV1 test. Archived CSF samples were also spiked with serial dilutions of the 4th WHO International Standard for HIV-1 NAT and assays and tested to assess the repeatability and reproducibility of the ELITechGroup assay. Results The HIV-1 ELITe MGB® Kit confirmed all the HIV-1 negative CSF samples from patients HIV positive in plasma and from non-HIV1 patients. All the CSF samples that were HIV-1 positive by the cobas®, were confirmed positive by the ELITe InGenius®. Concordance across the methods was also observed when processing the CSF dilutions spiked at medium-low titre, mimicking HIV-1 low-load infections. Conclusions The two systems were equivalent in the detection and quantification of HIV-1 RNA in CSF samples.

Objectives: Here we investigate Hepatitis D virus (HDV)-prevalence in Italy and its fluctuations over time and we provide an extensive characterization of HDV-infected patients. Methods: The rate of HDV seroprevalence and HDV chronicity was assessed in 1579 hepatitis B surface antigen (HBsAg)+ patients collected from 2005 to 2022 in Central Italy. Results: In total, 45.3% of HBsAg+ patients received HDV screening with an increasing temporal trend: 15.6% (2005-2010), 45.0% (2011-2014), 49.4% (2015-2018), 71.8% (2019-2022). By multivariable model, factors correlated with the lack of HDV screening were alanine-aminotransferase (ALT) less than two times of upper limit of normality (<2ULN) and previous time windows (P <0.002). Furthermore, 13.4% of HDV-screened patients resulted anti-HDV+ with a stable temporal trend. Among them, 80.8% had detectable HDV-ribonucleic acid (RNA) (median [IQR]:4.6 [3.6-5.6] log copies/ml) with altered ALT in 89.3% (median [IQR]:92 [62-177] U/L).Anti-HDV+ patients from Eastern/South-eastern Europe were younger than Italians (44 [37-54] vs 53 [47-62] years, P <0.0001), less frequently nucleos(t)ide analogs (NUC)-treated (58.5% vs 80%, P = 0.026) with higher HDV-RNA (4.8 [3.6-5.8] vs 3.9 [1.4-4.9] log copies/ml, P = 0.016) and HBsAg (9461 [4159-24,532] vs 4447 [737-13,336] IU/ml, P = 0.032). Phylogenetic analysis revealed the circulation of HDV subgenotype 1e (47.4%) and -1c (52.6%). Notably, subgenotype 1e correlated with higher ALT than 1c (168 [89-190] vs 58 [54-88] U/l, P = 0.015) despite comparable HDV-RNA. Conclusions: HDV-screening awareness is increasing over time even if some gaps persist to achieve HDV screening in all HBsAg+ patients. HDV prevalence in tertiary care centers tend to scarcely decline in native/non-native patients. Detection of subgenotypes, triggering variable inflammatory stimuli, supports the need to expand HDV molecular characterization.

BACKGROUND:Acute coronary syndromes (ACS) are a major cause of morbidity and mortality. As cytomegalovirus (CMV) may contribute to cardio-vascular (CV) manifestations, we sought to provide a proof-of-concept for the involvement of coronary and/or systemic CMV-reactivation as a possible ACS trigger.METHODS:We prospectively enrolled consecutive patients undergoing a coronary angiography for ACS (acute-cases, N.=136), or non-ACS reasons (chronic-cases, N.=57). Matched coronary and peripheral blood-samples were processed for quantification of CMV-DNAemia (RT-PCR), CMV-IgG/IgM, and CMV-IgG avidity (ELISA). Peripheral-blood samples from 17 healthy subjects were included as controls.RESULTS:Out of the 193 cases included, 18.1% were aged ≤55 years, 92.5% were Central-European, and 100% immunocompetent. CMV-IgG seroprevalence was 91.7% (95%CI: 87.8-95.6), significantly higher than in healthy-controls (52.9% [95%CI: 29.2-76.5]; P<0.001), yet consistent across age-groups (P=0.602), male/females (P=0.765), and acute/chronic-cases (P=0.157). Median (IQR) IgG titers were 110 (84-163) AU/mL, with 0.62 (0.52-0.72) avidity, supporting a long history of infection. No acute CMV infections were found. In 22.6% (n/N.=40/177) of the IgG-positive cases low-level coronary and/or systemic CMV-DNAemia (always <40 copies/mL) was detected. While no differences in peripheral CMV-DNAemia prevalence were observed nor among cases nor controls, coronary CMV-DNAemia was more frequent in acute-cases without modifiable CV risk-factors (n/N.=4/10; 40.0%), than in chronic-cases (n/N.=6/55, 10.9%; P=0.029), or acute-cases with risk-factors (n/N.=16/112, 14.3%; P=0.058).CONCLUSIONS:CMV-IgG seroprevalence was high in patients with heart diseases. CMV-DNAemia can be found, although uncommonly, in coronary circulation during an ACS, with increased prevalence in older subjects and in absence of CV risk-factors, identifying possible areas for novel interventions.

Background: In the last two years, the SARS-CoV-2 pandemic has determined radical changes in human behaviors and lifestyles, with a drastic reduction in socialization due to physical distancing and self-isolation. These changes have also been reflected in the epidemiological patterns of common respiratory viruses. For this reason, early discrimination of respiratory viruses is important as new variants emerge. Methods: Nasopharyngeal swabs of 2554 patients, with clinically suspected Acute Respiratory Infections (ARIs) from October 2019 to November 2021, were collected to detect 1 or more of the 23 common respiratory pathogens, especially viruses, via BioFilmArray RP2.1plus, including SARS-CoV-2. Demographical characteristics and epidemiological analyses were performed as well as a laboratory features profile of positive patients. Results: An observational study on 2300 patients (254 patients were excluded because of missing data) including 1560 men and 760 women, median age of 64.5 years, was carried out. Considering the respiratory virus research request, most of the patients were admitted to the Emergency Medicine Department (41.2%, of patients), whereas 29.5% were admitted to the Infectious Diseases Department. The most frequently detected pathogens included SARS-CoV-2 (31.06%, 707/2300, from March 2020 to November 2021), InfA-B (1.86%, 43/2300), HCoV (2.17% 50/2300), and HSRV (1.65%, 38/2300). Interestingly, coinfection rates decreased dramatically in the SARS-CoV-2 pandemic period. The significative decrease in positive rate of SARS-CoV-2 was associated with the massive vaccination. Conclusion: This study represents a dynamic picture of the epidemiological curve of common respiratory viruses during the two years of pandemic, with a disregarded trend for additional viruses. Our results showed that SARS-CoV-2 had a preferential tropism for the respiratory tract without co-existing with other viruses. The possible causes were attributable either to the use of masks, social isolation, or to specific respiratory receptors mostly available for this virus, external and internal lifestyle factors, vaccination campaigns, and emergence of new SARS-CoV-2 variants.

The present multicentric (n = 11 laboratories) study aimed to identify conversion factors from copies/mL to international units (IU)/mL for the normalization of HCMV DNA load using the first WHO International Standard for HCMV nucleic acid amplification techniques and to enhance interlaboratory agreement of HCMV DNA quantification methods. Study protocols for whole blood and plasma (extraction and amplification) were performed to calculate conversion factors from HCMV DNA copy number to IU. The greatest variability was observed in samples with lower HCMV concentrations (3.0 Log10) in both biological matrices. Overall, 73.1% (206/282) of whole blood and 82.2% (324/394) of plasma samples analyzed fell within an acceptable variation range (±0.5 Log10 difference). An average of 0.64 (range 0.21-1.17) was the conversion factor calculated for the HCMV whole blood panel and 0.82 (range 0.39-2.2) for the HCMV plasma panel.