Viruses

18 pages, 5317 KB

Open AccessArticle

Molecular Characterization of H5N1 Clade 2.3.4.4B Virus in Vaccinated Layer Chickens

by Ahmed H. Salaheldin, Mustafa Ozan Atasoy, Juliane Lang, Ann Kathrin Ahrens, Anne Pohlmann, Mohammed A. Rohaim, Hatem S. Abd El-Hamid and Elsayed M. Abdelwhab

Viruses 2026, 18(6), 589; https://doi.org/10.3390/v18060589 - 22 May 2026

Abstract

The global emergence of the avian influenza virus (AIV) H5N1 clade 2.3.4.4B since 2016 has caused substantial losses in wild bird and poultry populations, along with heightened risks of transmission to humans and other mammals. Vaccination of poultry has been a key strategy to curb the virus’s spread and mitigate its socioeconomic impact. This report describes an outbreak of high pathogenicity avian influenza virus (HPAIV) H5N1 clade 2.3.4.4B in a flock of 15,000 brown layer chickens (170 days old), all of which had received a four-dose vaccination regimen with H5N1/H5N8 commercial vaccines at 17, 50, 100, and 125 days of age. Despite this vaccination history, H5N1 infection was confirmed approximately seven weeks post-vaccination. H5N1 infection was confirmed by RT-qPCR, virus isolation, and full genome sequencing covering all eight gene segments, followed by phylogenetic and molecular analyses. Clinical signs included reduced feed intake, decreased egg production, and a cumulative mortality rate of 35% over 52 days. Hemagglutination inhibition (HI) testing with various H5 antigens revealed inconsistent antibody titers (geometric mean: 4.0 to 9.1 log2). Genetic analysis of the full-length HA and NA gene sequences further revealed strong similarity to contemporaneous H5N1 clade 2.3.4.4B strains circulating in Egypt, with multiple mutations in the HA head domain, particularly near immunogenic epitopes and receptor binding sites. These findings highlight the limitations of current vaccination strategies under conditions of antigenic mismatch and complex immunization schedules, emphasizing the need for improved vaccine matching and continuous molecular surveillance. To improve outbreak management in poultry, enhanced vaccination protocols, stringent biosecurity measures, and rigorous monitoring practices are critical. Full article

(This article belongs to the Special Issue Molecular Epidemiology, Evolution, and Transmission of Avian Influenza Viruses: 2nd Edition)

23 pages, 3968 KB

Open AccessArticle

Optimizing HIV-1 Genotypic Resistance Testing for Low- and Middle-Income Countries: High-Impact HIV-1 Mutations Across WHO-Defined Scenarios

by Robert W. Shafer, Kaiming Tao, Tom Loosli, Ana Abecasis, Daniele Armenia, George Bwire, Ricardo Sobhie Diaz, Joseph Fokam, Amalia Giron, Seth Inzaule, Rami Kantor, Cissy Kityo, Roger D. Kouyos, Swarali Kurle, Anne-Genevieve Marcelin, Roger Paredes, Martine Peeters, Victor F. Pimentel, Jonathan M. Schapiro, Kim Steegen, Marco Vitoria, Annemarie M. Wensing, Neil Parkin and Michael R. Jordan Show full author list Hide full author list

Viruses 2026, 18(6), 588; https://doi.org/10.3390/v18060588 - 22 May 2026

Abstract

Introduction: Drug resistance testing may improve the management of people living with HIV (PLWH) in several scenarios in low- and middle-income countries (LMICs). To guide assay development, the WHO published a target product profile (TPP) outlining two priority use cases (scenarios) for genotypic resistance testing: (1) PLWH with confirmed virological failure (VF) on an integrase strand transfer inhibitor (INSTI)-based regimen, such as tenofovir (TFV) disoproxil fumarate, lamivudine (3TC), and dolutegravir (DTG) and (2) heavily treated PLWH, including infants and young children, with confirmed VF after receiving multiple regimens including a boosted protease inhibitor (PI). An additional potential scenario includes PLWH testing positive for HIV-1 while on pre-exposure prophylaxis (PrEP). Methods: To identify drug-resistance mutations (DRMs) most likely to influence clinical management of PLWH in each WHO TPP scenarios and to inform development of assays that detect individual DRMs and the interpretation of sequence-based assays, we reviewed prevalence and in vitro susceptibility data on HIV-1 DRMs in the Stanford HIV Drug Resistance Database associated with the nucleoside RT inhibitor (NRTI), nonnucleoside RT inhibitor (NNRTI), PI, and INSTI classes and the capsid inhibitor lenacapavir. Results: In the first scenario, the most informative NRTI DRMs were K65R and M184V/I; and the most informative INSTI DRMs were G118R, N155H, Q148H/K/R, and R263K. In the second scenario, a broader spectrum of DRMs is likely to be clinically relevant, including additional NRTI DRMs, the PI DRMs associated with reduced susceptibility to darunavir, and the NNRTI DRMs associated with reduced susceptibility to etravirine and doravirine. In PLWH testing positive for HIV-1 despite PrEP, the most informative NRTI and INSTI DRMs overlap with those in the first scenario, together with the capsid DRMs reported in persons experiencing VF while receiving lenacapavir. Conclusions: As global ART programs increasingly rely on INSTI-based regimens, and as the number of heavily treated individuals and difficult-to-treat pediatric cases grows, many LMICs have begun introducing HIV drug resistance testing for patient management. Although sequence-based assays provide the most comprehensive information for managing individual PLWH, assays that detect individual DRMs are also likely to be highly useful in the three WHO TPP scenarios. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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18 pages, 2192 KB

Open AccessArticle

Interactomics of SARS-CoV-2 Macrodomain 1 Reveals Putative Clients of ADP-Ribosyl Hydrolase Activity

by Crissey D. Cameron, Grace Heilmann, Brynn K. Roman and Lars Plate

Viruses 2026, 18(6), 587; https://doi.org/10.3390/v18060587 - 22 May 2026

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has greatly impacted public health due to high rates of transmissibility and mutation during the COVID-19 pandemic. Macrodomain 1 (Mac1) of non-structural protein 3 remained well conserved across variants and is critical to suppression of host immune response to infection, making Mac1 a promising target for therapeutic development. Mac1 binds and cleaves the post-translational modification ADP-ribose and is hypothesized to have a downstream effect on the host interferon response, but the exact cellular targets of Mac1 are still unknown. Characterizing the substrates of Mac1 ADP-ribosyl hydrolase activity using a catalytically inactive mutant N40D can reveal critical virus–host interactions to identify protein targets of Mac1 and reveal mechanisms of host interferon suppression. Here, we performed affinity enrichment with WT Mac1 and Mac1 N40D in HEK293T and A549 cells and quantified changes in protein interactions by TMT-multiplexed tandem mass spectrometry. We identified interactions between Mac1 and ADP-ribosylated substrates involved in DNA damage response, cytoskeletal components, and cell cycle regulation. Additionally, several members of the TRiC complex involved in protein folding were selectively enriched with mutant Mac1 from A549 cells. These findings suggest a novel role of Mac1 in regulating host protein folding. Full article

(This article belongs to the Special Issue Coronavirus Pathogenesis and Virus-Host Interaction)

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14 pages, 1049 KB

Open AccessArticle

Temporal Trends in the Use of Healthcare Services for Respiratory Infections in the Paediatric Population of Anoia (2017–2024): Primary and Hospital Care

by María José Macías Reyes, Josep Vidal-Alaball, Laia Sola Reguant and Anna Ruiz-Comellas

Viruses 2026, 18(6), 586; https://doi.org/10.3390/v18060586 - 22 May 2026

Abstract

Respiratory infections are among the leading causes of healthcare consultations in paediatric populations. The SARS-CoV-2 pandemic significantly altered both the circulation of respiratory pathogens and the utilisation of healthcare services. This retrospective longitudinal observational study analysed temporal trends in consultations for respiratory infections among children under 15 years of age in the Anoia region between 2017 and 2024. Descriptive analyses and time-series modelling using negative binomial regression were performed. A total of 71,918 consultations were recorded, of which 71.7% occurred in primary care and 28.9% in hospital settings. The mean age of patients was lower in the hospital setting (3.4 years) than in primary care (8.7 years). During the pandemic, consultations decreased by 38% compared with the pre-pandemic period, followed by a rebound in 2022, particularly in hospital care. In the post-pandemic period, hospital consultations remained above pre-pandemic levels, whereas primary care activity tended to stabilise. No increase in bronchiolitis consultations was observed compared with the pre-pandemic period. Full article

(This article belongs to the Special Issue Advances in Respiratory Viruses Research: From Basic Studies to Public Health)

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Viruses, Volume 18, Issue 6 (June 2026) – 4 articles

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