Evaluation of HIV-1 transmitted drug-resistance among subtypes circulating from 2022 to 2024 in Italy: A refined analysis through next-generation sequencing Daniele Armenia, Claudia Alteri, Valeria Micheli, Tiziano Allice, Celestino Bonura, et al. Journal of Antimicrobial Chemotherapy, 2026 Background Monitoring HIV-1 subtype circulation and transmitted drug resistance (TDR) remains a key priority, particularly since the rollout of high-sensitivity next-generation sequencing (NGS). Methods Routine plasma HIV-1 RNA NGS genotyping data were collected from newly diagnosed individuals in Italy over 2022–24. HIV-1 TDR and genotypic susceptibility were evaluated through HIVdb with NGS set at 10% and 20%. Subtype and transmission clusters (TC) were determined through the maximum likelihood phylogeny based on the GTR + F + R9 model. Results Seven hundred and forty-two individuals were included, 51.9% harbouring non-B strains [CRF02_AG (18.1%); CRF BF (6.1%); A1/A3/A6 (7.1%); others (20.5%)]. TDR prevalence to any class was 11.7% at Sanger-like NGS-setting (>20%), slightly increased (15.0%) at 10% NGS-setting, and significantly varied across subtypes, with the highest prevalence observed in B subtype. Most antiretrovirals showed full genotypic activity in nearly 99% of individuals, except for efavirenz and rilpivirine (proportion of individuals with full activity <92%). A total of 57 TC were detected: 40 pairs, 17 clusters (>2 sequences). Thirteen TC (22.8%, 8 pairs, 5 clusters) involved individuals harbouring TDR. TDR was detected as minority mutations in five TC. Conclusions A high proportion of HIV-1 non-B subtypes circulate in Italy. TDR prevalence is around 12% using NGS at Sanger-like threshold and moderately increases to 15% when NGS is set at 10%. However, the impact of the detected TDR on the susceptibility to currently used antiretrovirals in clinical practice is negligible.
Diagnostic Concordance of Two- and Three-Gene SARS-CoV-2 Molecular Assays in Cameroon: Implications for Efficient Pandemic Response in Low- and Middle-Income Countries Aurelie Minelle Kengni Ngueko, Sandrine Claire Djupsa Ndjeyep, Ezechiel Ngoufack Jagni Semengue, Alex Durand Nka, Collins Ambe Chenwi, et al. Journal of Clinical Laboratory Analysis, 2026 Background The scale‐up of molecular assays for diagnosing emerging pathogens has increased in low‐and‐middle‐income countries (LMICs) since the advent of COVID‐19. We herein evaluated the diagnostic concordance of three different assays for SARS‐CoV‐2 in Cameroon. Methods A laboratory‐based comparative study was performed on nasopharyngeal samples collected between March‐2020 to March‐2023 from the biobank of Chantal Biya International Reference Centre (CIRCB), Yaoundé‐Cameroon. Samples were analyzed using DaAn Gene (N/ORF1ab‐genes), ThermoFisher (N/ORF1ab/S‐genes), and GeneXpert (N2/E‐genes). Validated cycle thresholds (CT) for positivity were CT < 37 for DaAn Gene/ThermoFisher and CT < 40 for GeneXpert. Cohen's Kappa coefficient evaluated diagnostic concordance with DaAn Gene as reference. Results We analysed 249 samples (55.8% males, median‐age [IQR], 36 [27–50] years including 21.3% symptomatic participants). Overall positivity rates (median [IQR]) were 55.0% (CT: 30.6 [23.1–35.5]); 53.4% (CT: 26.6 [21.2–30.9]); 22.1% (CT: 32.7 [26.9–36.1]) for GeneXpert, DaAn Gene and ThermoFisher respectively. GeneXpert showed stronger concordance with DaAn Gene (83.1%; k = 0.66, 95% CI: 0.57–0.75) than ThermoFisher (67.9%; k = 0.38, 95% CI: 0.29–0.47). At validated thresholds, GeneXpert showed higher positive agreement with DaAn Gene (85.0%, 113/133) as compared to ThermoFisher (41.3%, 55/133), while maintaining comparable negative agreement (81.0% [GeneXpert] and 98.3% [ThermoFisher]). At low CTs (< 20) however, positive agreement with DaAn Gene was high for GeneXpert (100%, 15/15) and ThermoFisher (93.3%, 14/15). Conclusion GeneXpert exhibits superiority over ThermoFisher in detecting cases of COVID‐19. As expected, agreement between two‐ and three‐genes assays at CT < 20 was excellent, suggesting interoperability of these platforms during outbreaks for high viral loads cases. However, two‐genes assays may be decisive to guide decision‐making for effective public health response while facing intermediate to low‐level viral loads in LMICs.
A new epidemic wave of Bordetella pertussis in paediatric population: impact and role of co-infections in pertussis disease Rossana Scutari, Giulia Linardos, Stefania Ranno, Mara Pisani, Anna Chiara Vittucci, et al. Italian Journal of Pediatrics, 2025 Background In recent months, Bordetella pertussis has reappeared after maintaining a low rate for many years. Although pertussis is usually characterized by a favorable course, several factors can contribute to the severity of the disease, such as mixed respiratory infections. In this study, we evaluate B.pertussis cases observed in the pediatric population followed at the Bambino Gesù Children's Hospital and analyzed the potential impact of co-infections in relation to disease severity. Methods From January to May 2024, a total of 1,151 children and adolescents (both inpatients and outpatients) were screened for the presence of respiratory pathogens, including B.pertussis, with clinically relevant respiratory symptoms. Results Among the 1,151 patients screened, 66 tested positive for B.pertussis. Fourteen patients had respiratory failure, and six of them required intensive care unit (ICU) admission, while 52 had mild infection. 23.3% of patients had B.pertussis alone, while 76.7% had co-infections (including 5 patients admitted to the ICU). A higher co-infection rate was observed in patients with respiratory failure than in those without failure (92.9% vs. 69.0%, p-value:0.041). Rhinovirus, Metapneumovirus and Parainfluenza-virus were the most prevalent in our pediatric population. Co-infections of human bocavirus with B.pertussis were observed exclusively in patients with respiratory failure. Conclusions Our results highlighted an increase in B.pertussis cases from January to May 2024, reaching a peak of cases in the month of May. This study shows a high rate of B.pertussis co-infection, and a trend toward association between B.pertussis and specific viruses, that might play a role in increasing disease severity.
Whole-Genome Sequencing of Adenovirus Genotypes and Clinical Implications in Pediatric Patients Lorena Forqué, Valeria Fox, Rossana Scutari, Martina Mastropaolo, Pietro Merli, et al. Viruses, 2025 Human adenoviruses (HAdV) comprise more than 100 genotypes with species-specific differences in tropism and immune response and can cause severe infections in immunocompromised patients. This study aimed to characterise the HAdV species involved in pediatric infections to assess their clinical impact and guide future therapeutic strategies based on AdV-specific T-cell responses. Between January and October 2024, 595 pediatric HAdV diagnoses were made at the Bambino Gesù Children’s Hospital (Rome), and whole-genome sequencing was performed on 60 samples. Most patients (91.7%) were hospitalised, including both immunocompetent (75%) and immunocompromised (25%) children. Gastrointestinal and respiratory symptoms were more common in immunocompetent patients, whereas immunocompromised patients experienced longer hospitalisations and persistent viral infections. Species F (F41) was most prevalent (63.3%), especially among immunocompetent patients, while species C and A predominated in immunocompromised children, with species A associated with severe disease. Viral loads were significantly higher for species F than for species A and C, independent of immune status. Co-infections were frequent (63.3%), with species C particularly linked to them. In conclusion, HAdV distribution differed by immune status, with species F predominating in immunocompetent children and species C and A more common in immunocompromised patients. Whole-genome sequencing may enhance surveillance, enable earlier diagnosis, and support the development of genotype-specific immunotherapies.
Viral Burden of Respiratory Syncytial Virus and Viral Coinfections as Factors Regulating Paediatric Disease Severity Velia Chiara Di Maio, Rossana Scutari, Martina Mastropaolo, Luna Colagrossi, Giulia Linardos, et al. Viruses, 2025 Background: Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections (ARIs) in children. However, the clinical impact of RSV co-infection with other respiratory viruses remains unclear. This study investigates the frequency and clinical outcomes of RSV infections in a large paediatric cohort. Methods: Paediatric patients with RSV-positive respiratory samples admitted to Bambino Gesù Children’s Hospital between January 2022 and April 2024 were analysed. Results: Within 17,259 respiratory samples from 9877 paediatric patients, 952 (9.6%) were RSV-positive. Among these, 637 patients with ARI were included. RSV affected the lower respiratory tract in 549 cases (86.2%) and the upper tract in 88 (13.8%) cases. RSV mono-infection was found in 286 (44.9%) patients, while 351 (55.1%) patients had co-infections. Mono-infections showed lower cycle-threshold (CT) than co-infections in both upper and lower tract (p-value:0.002 and 0.037, respectively). Pneumonia was associated with RSV co-infection (N = 48, 15.4%), whereas bronchiolitis was mostly seen in mono-infection (N = 196, 78.1%, p-value:0.002). Regression analysis showed an association between pneumonia and co-infection (AOR: 1.97 [1.06–3.64], p-value = 0.031), higher CT (AOR [95% CI]: 1.07 [1.02–1.11], p-value = 0.006) and older age (AOR [95% CI]: 1.48 [1.31–1.68], p-value < 0.001), whereas bronchiolitis was associated with mono-infection, younger age and lower CT. Conclusions: This study highlights the role of RSV in paediatric disease and emphasises the importance of early diagnosis, personalised treatment and preventive strategies to improve outcomes and reduce the burden of disease.
Parvovirus B19 Rebound Stefania Ranno, Cristina Russo, Luna Colagrossi, Valeria Fox, Velia Chiara Di Maio, et al. Journal of Medical Virology, 2025 Human parvovirus B19 (B19V) is responsible for a wide clinical spectrum ranging from asymptomatic infection, through mild disease, up to life‐threatening one. Outbreaks are registered every 3–4 years, and a recent international alert for a new outbreak has been released. The experience of B19 virus circulation in a 600‐bed tertiary care pediatric hospital in Rome from 2018 to 2024 is reported here. This retrospective study involved a total of 9695 blood samples (about 8500 patients), 11 amniotic fluids (11 pregnant women), and 10 827 sera (about 9500 patients), processed in the Virology Unit of Bambino Gesù Children's Hospital in Rome for B19V direct and indirect detection. In our population, the annual positivity rate for B19V DNA ranged from 0.8% in 2023 to 9.8% in 2018 and 32.8% in 2024; the same trend resulted from the analysis of the immunoglobulins M and G anti‐B19V. Focusing on the last year, 314 patients resulted positive for B19V DNA detection: 204/314 (65%) had a primary infection, 150/204 (73.5%) were hospitalized, and 17/150 (11.3%) needed Intensive Care Unit (ICU) for cardiovascular, central nervous, and gastrointestinal pathologies. Two patients died from myocarditis. Among patients with the most severe clinical picture, over half had no concurring disease, and one patient died. Four amniotic fluids were positive for pregnant women who came to our observation. B19V typing of a subset of samples revealed the presence of only subtype 1A and a low intragenotypic diversity between strains from severe and mild disease. In conclusion, in 2024, a significant increase in B19V circulation was observed with profound effects on clinical outcome and consequent hospitalisation, either in patients with comorbidities or those without. This widespread circulation of the virus also had an impact on infections in pregnancy, with the known severe consequences for unborn children.
