ETIDIOH - NEW

  Abstract The ongoing epizootic of highly pathogenic avian influenza (HPAI) continues to cause massive deaths in wildlife . Fundamental understanding of its disease ecology in natural populations is urgently needed. This knowledge has been hindered by the difficulty of acquiring data on epidemic dynamics . Here, using data collected from a threatened population of Dalmatian pelicans (Pelecanus crispus), we recover the epidemiological and evolutionary history of one of the largest HPAI wildlife mortality events . The results show that this devastating outbreak was likely seeded by a single introduction associated with movement of the species . By estimating epidemiological features of two consecutive outbreaks in the same population, we show that panzootic H5N1 since 2022 likely exhibits higher transmissibility and longer shedding time in non-reservoir birds , compared to previous H5NX subtypes. We also evaluate effectiveness of past and future control measures : carcass removal du...

  Abstract AGILE (NCT04746183) is a Phase Ib/IIa platform, evaluating candidates to treat COVID-19 . Candidate Specific Trial 6 evaluated the safety and optimal dose of a novel intravenous formulation of favipiravir in a dose-escalating, open-label, randomized, controlled, Bayesian adaptive Phase Ib trial . Hospitalized adults with PCR-confirmed SARS-CoV-2 infection , within 14 days of symptomatic COVID-19 were randomized 2:1 in groups of 6 (n = 4 favipiravir, n = 2 standard of care) to ascending doses of intravenous favipiravir twice daily (b.i.d.) for 7 days or standard of care. Clinical data, safety evaluations, virology and pharmacokinetic samples were collected. The primary outcome was safety . Secondary outcomes included clinical, pharmacokinetic and virological endpoints . Twenty-four participants enrolled between September 10, 2022 and November 1, 2023 [10/24 female; median age 74 years (range 52–93)]. Favipiravir was well tolerated despite a high background rate of unrelat...

  ABSTRACT Respiratory viruses can infect hosts concurrently or sequentially, potentially influencing each other’s pathogenic trajectory . However, the underlying immune mechanisms governing these interactions remain poorly understood. In this study, we examined whether respiratory syncytial virus (RSV) infection modulates host susceptibility to subsequent SARS-CoV-2 infection using two murine models . We found that prior RSV infection conferred dose- and time-dependent heterologous protection against SARS-CoV-2 . Transcriptomic and immunological analyses revealed that RSV activated lung antigen-presenting cells (APCs) and SARS-CoV-2–reactive mucosal T cells by day 9 post-infection , with responses waning by 1 month . RSV also promoted expansion of pulmonary γδ T cells and upregulation of their metabolic pathways. Notably, RSV-infected TCRδ⁻/⁻ mice , which lack γδ T cells, exhibited diminished SARS-CoV-2–reactive mucosal T cell responses, elevated viral loads, and exacerbated lung ...

  Abstract In this study, the phenotypic consequences of naturally occurring single nucleotide polymorphisms (SNPs) in the Middle East respiratory syndrome coronavirus (MERS-CoV) Spike protein were investigated. The impact of Spike mutations on the syncytia formation and neutralisation of contemporary MERS-CoV strains is not currently well understood. Mutations were identified by aligning 584 MERS-CoV Spike sequences from either human clinical isolates collected between 2012 and 2024 or from a clinical isolate that had been passaged in human cells . Fifteen SNPs of interest occurring in the N-terminal domain (NTD), receptor binding domain (RBD) and adjacent to the S1/S2 cleavage site were selected for further characterisation based on their location in the Spike protein, frequency and identification in previous studies. A contemporary clade B, lineage 5 wildtype Spike sequence , obtained from a human MERS-CoV clinical isolate , was used as the backbone in this study . The mutations...

  Abstract We assessed impact and durability of an infection prevention and control (IPC) bundle intervention during the Kivu/Ituri Ebolavirus outbreak (2018-2020). IPC scores increased initially, then declined 6 months post-intervention (median 19/36, 30/36, and 28/36, p<0.0001). Without sustained IPC practices , health facilities remain vulnerable to nosocomial transmission in future Ebolavirus outbreaks. Source:  Link:  https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciag192/8526630 ____

  Abstract Azithromycin is a widely used antibiotic and was frequently used to treat hospitalized patients during the COVID-19 pandemic . The impact of empiric azithromycin use on the respiratory microbiome in patients with viral respiratory infections is unclear. Here we used longitudinal metatranscriptomics on nasal swabs from a prospective multicentre cohort of 1,164 patients hospitalized for COVID-19 . We compared the upper respiratory microbiome, resistome and systemic immune response in patients treated with azithromycin (n = 366) with those who received no antibiotics (n = 474) or other antibiotics (n = 324). We found that azithromycin altered microbiome composition and increased the expression and relative proportion of macrolide/lincosamide/streptogramin (MLS) resistance genes . These changes occurred after 1 day of exposure and persisted for over a week. MLS resistance gene expression was associated with commensals and potential pathogens , while there were no differences...

  ABSTRACT H9N2 avian influenza viruses (AIVs) remain a significant economic burden on poultry production and a persistent zoonotic threat . Hemagglutinin (HA), a surface glycoprotein mediating viral entry and pathogenesis , critically depends on thermostability for its function. Our previous study indicated that recent H9N2 AIVs have experienced a reduction in hemagglutination activity and exhibit low HA thermostability ; however, the underlying molecular determinants for this instability remain poorly defined. To address this gap, we employed an in vitro-directed evolution approach to identify HA mutations that enhance thermostability. By subjecting a diverse HA mutant library to iterative heat selection at 48°C , we isolated several HA-stabilizing mutations , including L29I, N133S, N210D, G266R, D387N, A423T, and E509G, and confirmed their effect by site-directed mutagenesis. Further characterization revealed a complex interplay between HA stability, receptor binding specificity...

  Abstract Background   Tropical low – and middle –income countries are highly vulnerable to zoonoses and vector-borne diseases , with risks amplified by climatic events , environmental change , and limited surveillance capacity. Cambodia is particularly exposed due to its ecological diversity, seasonal flooding , and rapidly changing land use . Globally, however, field based One Health approaches remain under –implemented, limiting practical evidence on how to address these complex threats.  Methods   This protocol describes a longitudinal One Health study conducted in three villages of Battambang province, Cambodia , designed to investigate the prevalence and transmission dynamics of zoonotic and potentially zoonotic pathogens at the human –animal –environment interface . The study examines how vector density, diversity, and pathogen circulation are influenced by hydrological variation and seasonality , and assesses the sociodemographic, behavioral, and environment...

  Abstract Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool . However, IAV is at low abundance in wastewater , making it difficult to sequence . We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods . Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes . However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome segments. Probe-capture methods were resilient to RNA degradation and mismatches, potentially enabling broader surveillance and detection of emerging strains. However, probes were ...

  Abstract Background Most studies of human metapneumovirus (HMPV) epidemiology have been among inpatients . This study examined the epidemiology of HMPV compared with other common viruses among outpatients seeking care for an acute respiratory illness (ARI) during 5 influenza seasons (2016–2017 to 2019–2020, before the coronavirus disease 2019 pandemic, and in 2021–2022, during the pandemic). Methods Outpatients ≥6 months old seeking care for ARI and presenting with cough of ≤7 days’ duration provided nasal and pharyngeal swab samples , demographic data, and access to electronic medical record data. Samples were tested with reverse-transcription polymerase chain reaction assays for HMPV , influenza, parainfluenza virus (PIV) 1–4, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Student′s t and χ2 tests were used to compare HMPV cases with other ARIs. Results After exclusion of 68 coinfections , 7143 patients remained; 2017 had in...

  Abstract Oropouche fever (OF), caused by Oropouche virus (OROV), has expanded beyond its Amazonian range into Minas Gerais (MG), Brazil, raising concern about transmission in extra-Amazonian Atlantic Forest landscapes . Critical gaps persist regarding Culicoides vector communities , anthropophily , and climate-sensitive transmission risk in these newly affected regions. We conducted targeted entomological surveys outbreak-driven by human OF cases , standardized across five MG communities using CDC light traps and Protected Human Attraction (PHA) to characterize Culicoides composition. Females of Culicoides underwent RT-qPCR for OROV (n = 819) and physiological assessment (n = 312). We developed an entomological alert framework that integrates blood-fed abundance, minimum infection rate (MIR) upper confidence bounds, and environmental drivers (i.e., mean temperature, relative humidity and precipitation) via generalized additive mixed models , which explained 68% of the variability...

  Abstract Background :  Continuous, non-invasive viral surveillance is essential to monitor emerging pathogens and guide public health responses. Most environmental surveillance studies use targeted qPCR approaches , and comparisons between wastewater and indoor air surveillance remain limited. We aimed to compare the utility of emergency department indoor air and urban wastewater for tracking circulating viruses and resolving genomic information.  Methods :  We conducted a matched-pair study comparing 19 weekly indoor air samples from the central ventilation exhaust shaft of an emergency department and 19 24-hour composite municipal wastewater samples in Leuven, Belgium , from December 2024 to April 2025. Both sample sets were processed using probe-based hybrid-capture viral metagenomics targeting over 3000 viral species , using influenza A as a clinically relevant test case.  Findings :  Wastewater captured higher overall viral diversity (233 versus 106 ...

  Highlights •  MERS-CoV remains an endemic camel-associated betacoronavirus with ongoing zoonotic spillover. •  Viral evolution shows three major clades with lineage B predominance and documented recombination. •  DPP4-mediated entry, immune suppression , and T-cell apoptosis drive severe disease and high fatality. •  Diagnosis relies primarily on rRT-PCR , while treatments and vaccines remain experimental. •  Strengthened One-Health surveillance , IPC, and genomic monitoring are essential for pandemic preparedness. Abstract Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic beta coronavirus identified in 2012 that circulates in dromedary camels and occasionally infects humans. Although community spread is limited , the disease shows a high case fatality rate near 36 percent and has caused hospital outbreaks such as the 2015 South Korea event . The viral spike binds the DPP4 (CD26) receptor, enabling entry into airway epithelial and sele...

  Abstract The global spread of viruses highlights the need for timely and effective genomic surveillance to detect new variants and inform rapid public health responses . However, high costs and uneven sequencing capacity hinder equitable global implementation. Surveillance focused on international travelers at major travel hubs has been proposed as a way to complement robust local surveillance, but its potential benefits have not been fully quantified . Here, we develop and calibrate a multiple-strain metapopulation model of global SARS-CoV-2 transmission using extensive epidemiological, phylogenetic, and high-resolution air travel data . Retrospective analyses of the Omicron BA.1/BA.2 emergence and forward simulations for hypothetical novel variants show that targeted enhancement of traveler surveillance at key hubs can shorten variant detection delays, with reduced total surveillance efforts. Practical “non-disruptive” strategies, such as prioritizing a small number of highly c...

  Highlights •  A Nipah virus real-time RT-PCR was developed for this study and display dynamic amplification, with sensitive (limit of detection 3.7-4.2 copies/µL) and specific detection. •  The assay was adapted for use on a portable, battery-powered real-time thermocycler . •  When paired with instrument-free RNA extraction , Nipah virus RNA was rapidly detected from contrived whole blood and nasopharyngeal swabs without electricity. •  The combined of Extract & Store and the Palm PCR S1e device offers a viable solution for field-based molecular detection of Nipah virus. Abstract Background Nipah virus (NiV) is a highly pathogenic, zoonotic paramyxovirus with significant public health implications due to high associated mortality and potential for human-to-human transmission. Current diagnostic testing options for NiV are limited and require extensive laboratory infrastructure. Objective Develop a field-deployable testing workflow for timely NiV detection...

  Abstract Currently, there is limited knowledge on the impact of immunity to hemagglutinin (HA) and/or neuraminidase (NA) on the transmission of influenza viruses . Therefore, using intramuscular vaccination , intranasal vaccination , or infection with reassortant viruses , we induced immunity to each antigen alone or both antigens combined in ferrets . We then assessed transmission of the 2009 pandemic H1N1 virus from these ferrets to naïve respiratory contacts . For all strategies used to induce immunity, combined immunity to HA and NA resulted in the largest reductions in transmission . Moreover, immunity to HA and NA conferred additive rather than synergistic reductions in transmission. No escape variants emerged in our transmission studies, and logistical regression showed that the probability of transmission was less than 50% when viral titers in donors were reduced to 101.5 and 102 median tissue culture infectious dose per ml on days 1 and 3 postinfection, respectively. The...

  Antiviral Res ZHANG J, Deng S, Zhang M, Wu X, et al Porcine epidemic diarrhea virus infection activates SREBP2 and induces RORgamma expression to enhance cholesterol biosynthesis and virus replication. Antiviral Res. 2026 Mar 6:106391. doi: 10.1016/j.antiviral.2026.106391. PubMed           Abstract available Clin Infect Dis KHADER K, Haroldsen C, Stevens V, Visnovsky L, et al Estimating changes in facility MRSA infection rates due to changes in MRSA precaution policy. Clin Infect Dis. 2026 Mar 13:ciag176. doi: 10.1093. PubMed           Abstract available Int J Infect Dis LUGTU EJ, Iv DYP, Cabunoc MH, Bautista JL, et al Prevalence of Post-COVID Symptoms Across Variants of Concern and Follow-up Periods: A Systematic Review and Meta-Analysis. Int J Infect Dis. 2026 Mar 10:108522. doi: 10.1016/j.ijid.2026.108522. PubMed           Abstract available TANG X, Memedi M,...

  Ann Intern Med LALANI HS, DiResta R, Baron RJ, Scales D, et al Addressing Viral Medical Rumors and False or Misleading Information. Ann Intern Med. 2023 Jul 18. doi: 10.7326/M23-1218. PubMed           Abstract available Antimicrob Agents Chemother ZHENG X, You X, Liu Y, Wu B, et al Spatiotemporal dynamics and multiple driving factors of antimicrobial resistance in China during the COVID-19 pandemic (2019-2023): a provincial panel data analysis. Antimicrob Agents Chemother. 2026 Feb 9:e0160025. doi: 10.1128/aac.01600. PubMed           Abstract available Antiviral Res ZHANG T, Wang ZL, Li XY, Luo RH, et al Onvansertib and vilazodone inhibit SARS-CoV-2 replication via suppression of METTL3 RNA-m(6)A enzymatic activity. Antiviral Res. 2026 Feb 19:106376. doi: 10.1016/j.antiviral.2026.106376. PubMed           Abstract available YURGELONIS I, Rai DK, Li Z, Washington ...