Influenza and Other Respiratory Viruses

Background The COVID-19 pandemic substantially altered respiratory pathogen circulation worldwide. However, longitudinal analyses of changes in respiratory pathogen ecology across the pandemic and post-pandemic periods remain limited. Methods We analyzed 19,968 respiratory samples tested with the BioFire(R) FilmArray(R) Respiratory Panel at a hospital in Tokyo, Japan, between January 2020 and March 2026. We evaluated temporal changes in pathogen circulation, age-specific epidemiology, co-detection patterns, pairwise pathogen associations, and clinical parameters. Results At least one respiratory pathogen was detected in 27.8% of tests. Respiratory pathogens resurged asynchronously following the relaxation of COVID-19-related public health measures. Influenza virus circulation remained markedly suppressed until late 2022 before re-emerging in successive large seasonal epidemics, whereas other pathogens, including RSV, human metapneumovirus, and Mycoplasma pneumoniae, exhibited distinct resurgence patterns. Pathogen distributions also varied by age. Human rhinovirus/enterovirus remained predominant among young children, whereas SARS-CoV-2 predominated among older adults. Co-detection occurred in 14.0% of positive specimens and was significantly more frequent in younger patients. Pairwise analysis identified both positive and negative pathogen associations; however, the patterns varied across age groups and study periods. Conclusions Respiratory pathogen circulation changed substantially during the transition from the COVID-19 pandemic to the post-pandemic period, with pathogen-specific, age- and period-dependent patterns. Continued surveillance is warranted to determine how respiratory pathogen circulation will evolve and to inform infection control strategies in the post-pandemic era.

The increasing incidence of H5N1 influenza virus transmission from animal species to humans has heightened concerns about an imminent H5N1 pandemic. Prior studies using recombinant hemagglutinin and neuraminidase proteins have reported age-dependent cross-reactivity to H5N1, attributed to immune imprinting from an individual's first influenza virus exposure. However, whether this pattern holds when using whole inactivated virus (WIV), capturing antibodies against diverse viral proteins, and is stable over time remains unknown. We therefore aimed to determine whether H5N1 cross-reactivity of pre-existing antibodies to whole virus follows an age-dependent or imprinting-specific pattern, and whether this pattern is stable over a five-year period. To this end, we measured serum antibody levels in adolescents, adults and seniors by ELISA using whole inactivated H5N1 virus as antigen rather than purified proteins. Detectable, albeit generally low, levels of H5N1-reactive antibodies were present in most individuals, irrespective of age. Comparison of antibody levels against H5N1 with those to five historical influenza virus strains revealed a consistent positive correlation between H5N1-reactive antibodies and responses to the H1N1pdm09 strain A/California/7/2009 (CA), across all age groups. Using unbiased clustering of antibody titers against H5N1, CA, and the H3N2 strain A/Perth/16/2009 (PE), we identified seven distinct age-transcending antibody profiles. These profiles covered individuals with varying titers to all three included viruses but also identified individuals with high anti-CA levels, yet low anti-H5N1 levels and vice versa. Moreover, despite stable antibody levels over a five-year interval in the study population, individual antibody levels and profiles fluctuated considerably over this period. Taken together, our results confirm the presence of H5N1-reactive antibodies in human sera and their association with previously circulating strains. However, they also caution against inferring antibody levels against a new strain based solely on responses to antigenically related strains and highlight the limitations of extrapolating immune status from single timepoint measurements.

Background Severe acute respiratory infections (SARI) strain healthcare systems. Sentinel surveillance remains central to SARI monitoring, but routinely collected hospital discharge data offer a scalable, population-wide complement. In Finland, national registers now enable register-based surveillance, yet SARI case definitions remain unevaluated. Aim To evaluate whether routinely collected electronic health records can support register-based SARI surveillance and establish a national case definition. Methods We conducted a retrospective register-based study linking inpatient discharge data from the Finnish Care Register for Health Care (Hilmo) and laboratory-confirmed pathogen notifications from the National Infectious Diseases Register (NIDR). Admissions were aggregated into hospitalisation episodes using generic and pathogen-specific respiratory ICD-10 codes and linked to laboratory-confirmed respiratory pathogens within an admission-centred window. We assessed the impact of diagnostic coding position, laboratory linkage windows and alternative case definitions on age distribution, seasonality and epidemic trend detection. Results We included 145,435 respiratory hospitalisation episodes. Laboratory confirmations clustered around admission, and a -7-to-+3-day window was selected; 51,498 (35.4%) had a linked laboratory confirmation. Specific primary-position diagnoses preserved clear seasonality and age distributions consistent with SARI epidemiology, whereas secondary-position diagnoses showed attenuated seasonality. A combined case definition incorporating specific primary diagnoses and laboratory-supported syndromic episodes produced stable epidemic curves while improving sensitivity over laboratory confirmation alone. Conclusion National discharge and laboratory registers can support robust SARI surveillance in Finland when case definitions are carefully designed. A combined register-based definition balances specificity, sensitivity and feasibility, complementing sentinel surveillance and integrated respiratory monitoring. Keywords Severe acute respiratory infection (SARI); surveillance; electronic health records; ICD-10; case definition; Finland

Seasonal influenza remains a major cause of morbidity and mortality worldwide. Although neuraminidase inhibitors improve outcomes, influenza-related deaths persist. We evaluated the impact of early aspirin (ASA) and non-aspirin nonsteroidal anti-inflammatory drug (NSAID) use on outcomes in adults hospitalized with influenza. This retrospective study included adults admitted to the University of Minnesota Medical Center from 2016 to 2018. Continuous variables were summarized as medians with interquartile ranges (IQRs) and categorical variables as counts and percentages. Group comparisons used Wilcoxon rank-sum, Chi-square, or Fishers exact tests. Analyses included case-control comparisons, assessments by vaccination status, and subgroup analyses by early ASA or NSAID use. Among 2,816 patients, 320 had laboratory-confirmed influenza, with vaccination less common among cases. Unvaccinated patients had higher rates of intensive care unit (ICU) admission (23.6% vs. 11.1%; P = 0.003) and ventilatory support (15.0% vs. 6.1%; P = 0.009). In vaccinated patients, early ASA use was associated with older age and higher in-hospital mortality, whereas early NSAID use was associated with no in-hospital deaths, better one- and three-year survival (P < 0.001), and fewer, though not statistically significant, cardiovascular complications. In unvaccinated patients, ASA use was associated with lower three-year survival (59.1% vs. 79.2%; P = 0.013), while NSAID use was associated with fewer ICU admissions and no cardiovascular or renal complications. In both vaccinated and unvaccinated adults hospitalized with influenza, early NSAID use was associated with improved survival and fewer complications, whereas ASA use was associated with worse outcomes.

Seasonal Influenza and COVID-19 vaccination programmes are critical for reducing morbidity and mortality in older adults, yet uptake remains uneven across populations. We aimed to profile vaccination attitudes and examine predictors of COVID-19/influenza vaccination uptake among a UK participatory surveillance system - FluSurvey. We analysed FluSurvey data from participants aged [&ge;]65 years who were eligible for both vaccines in the 2023-2024 and 2024-2025 Autumn - Winter seasonal campaigns. Descriptive analyses examined self-reported attitudes to influenza vaccination. Logistic regression examined factors (age, sex, socioeconomic status, education, employment, transport, smoking and chronic conditions) associated with influenza and COVID-19 vaccination uptake in each season, adjusting for confounders. Belonging to a risk group and reducing risk of influenza were frequently reported motivations for influenza vaccination, while building natural immunity and concerns around safety and adverse effects were frequently reported barriers. Individuals vaccinated against COVID-19 were more likely to receive an influenza vaccination (aOR2023-2024=13.90 [9.28-21.17]; aOR2024-2025=8.54 [5.82-12.60]), and vice-versa (aOR2023-2024=13.91 [9.30-21.19]; aOR2024-2025=8.52 [5.81-12.58]). Lower educational attainment was associated with lower odds of COVID-19 vaccination (aOR2023-2024=0.59 [0.45-0.78], aOR2024-2025: 0.56 [0.39-0.79]). Other results were weaker or demonstrated variation by season. Our findings highlight recent attitudes and barriers to influenza and COVID-19 vaccination among the FluSurvey cohort, which may inform approaches to improve vaccination coverage in the population.

Long COVID (LC) impacts quality of life, daily functioning, and healthcare utilization. Understanding the onset and duration of symptoms, characteristics of those at higher risk, and the barriers and facilitators for healthcare access and therapeutics are key to addressing this growing disease burden. In 2024 the Arizona CoVHORT, an ongoing 6-year longitudinal study, distributed a cross-sectional LC survey to gain additional in-depth information. Of 1,543 participants, 700 reported LC symptoms lasting 2-49 months. Following their first infection, LC+ participants had a 21% higher risk for a second infection and were 3.2 times more likely to report LC symptoms after that second infection compared to LC- participants. Significant factors associated with LC included female sex (OR=2.3), Hispanic ethnicity (OR=1.5), BMI>34.5 (OR= 1.7) and >2 infections (OR=3.2), while vaccination prior to first infection decreased the odds of reporting LC by 51% (R=0.49). Qualitative analyses detailed significant barriers to care and encounters with providers who lacked knowledge to test for or treat LC symptoms. With an estimated 400 million people impacted globally by LC, it is critical to gain in-depth information from patients to improve both access and quality of care, improve messaging, and target mitigation strategies to decrease the burden over time.

Importance: Maternal vaccination and long-acting monoclonal antibodies are now available in the U.S. to prevent RSV. Long-acting monoclonal antibody administration in the U.S. commonly occurs after hospital discharge in outpatient settings, leaving some infants unprotected early in life when severe RSV risk is highest. Comparative effectiveness between the two interventions and whether delays affect effectiveness estimates have not been quantified. Objective: To evaluate the effectiveness of infant long-acting monoclonal antibody strategies and a maternal vaccination strategy, each compared to no intervention, and the comparative effectiveness of intervention strategies when accounting for real-world delays in monoclonal antibody receipt. Design: Cohort study using target trial emulation to compare four strategies for prevention of RSV-related outcomes. Setting: The U.S. between 2023 and 2025 using a nationwide database of employer-sponsored commercial insurance claims. Participants: 120,586 commercially insured mother-infants, whose infants were born in the U.S. during the 2023-2024 or 2024-2025 RSV season. Infants who could not be paired with their mother's record, did not enroll in commercial insurance within 75 days from birth, received palivizumab, and had an implausible birth date were excluded. Interventions: Comparison of four RSV prevention strategies: (i) maternal RSVpreF; (ii) long-acting monoclonal antibody given within the first week of life (mAb as intended); (iii) long-acting monoclonal antibody given within a six-month grace period from birth (mAb within grace period); and (iv) a control. Main outcomes and measures: Effectiveness against first RSV-associated hospitalization and medically-attended RSV illness was summarized using adjusted hazard ratios (aHR) and estimated using an inverse propensity weighting approach, with weights accounting for maternal age, maternal comorbidities affecting pregnancy, obstetric and newborn complications, season, region, and birth timing relative to October 1. A weighted Kaplan Meier estimator was used to estimate strategy-specific cumulative incidence of RSV outcomes over time. Results: In the first five weeks of life, the mAb within grace period strategy doubled the hazard of RSV hospitalization (aHR: 2.0 [95% CI: 1.0-4.9]) and increased the hazard of medically-attended RSV (aHR: 1.6 [95% CI: 1.0-2.7]) compared to the maternal RSVpreF strategy. The hazard for RSV hospitalization was similar for the mAb as intended strategy compared to the maternal RSVpreF strategy (aHR = 0.9 [95% CI: 0.3-1.9]). Conclusions and relevance: RSVpreF and monoclonal antibodies were similarly effective when monoclonal antibodies were administered close to birth, but when accounting for real-world delays in monoclonal antibody receipt, the maternal RSVpreF strategy was more effective than the mAb within grace period strategy.

Background: Mortality and hospital admissions due to Severe Acute Respiratory Infection (SARI) peaked between January and August 2025 in Brazil. Methods: The Brazilian Ministry of Health data on hospital admissions and deaths caused by SARI were compiled by age group (<5, 5-14, 15-49, 50-64, 65+ years) and quarter between January 2023 and June 2025. SARI causes were aggregated into SARS-Cov-2, Influenza, Respiratory Syncytial Virus (RSV), and other viruses (parainfluenza, adenovirus, rhinovirus, bocavirus, metapneumovirus). Multinomial regression was used to impute likely causes of death when these were not laboratory confirmed. Results: In the second quarter of 2025 (2025/2), RSV mortality rate among children <5 years reached 60 per 100,000, which is a 43% increase compared with 2024/2. Mortality rate for the joint impact of parainfluenza, adenovirus, rhinovirus, bocavirus, and metapneumovirus in the same age group doubled from 20 to 40 on the same scale in 2025/2 compared to 2024/2. Over the same period, influenza mortality tripled among the aged, whereas mortality due to other respiratory viruses increased less dramatically, except for SARS-CoV-2, which decreased among the aged from 150 to 25 per 100,000 between 2023/1 and 2025/2. Other age groups remained relatively stable over the period. The variation in hospital admissions largely followed that of mortality. Conclusions: While deaths and hospital admissions caused by SARS-CoV-2 declined rapidly since 2023, mortality rates of other respiratory viruses, mainly influenza and RSV, increased significantly among children <5 years and the aged in 2025/2. Public health policies that facilitate vaccine uptake against these infections should be given high priority.

The ongoing panzootic of clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 viruses has reached a critical point, marked by unprecedented mammalian spillover and sustained outbreaks in U.S. dairy cattle. While these viruses remain highly lethal in traditional ferret models, human infections-primarily linked to the B3.13 and D1.1 lineages-have been notably mild, typically presenting as conjunctivitis with minimal respiratory involvement. In this study, we address this disconnect by evaluating the infectivity of recent H5N1 isolates using a physiologically relevant air-liquid interface (ALI) culture system that incorporates an aerosol settling chamber. We demonstrate that while direct liquid inoculation leads to efficient replication, aerosolized H5N1 strains exhibit a significant defect in their ability to infect human respiratory epithelium. In contrast, a prototypic H5N1 virus remains highly pathogenic and lethal in ferrets regardless of the inoculation route, showing systemic dissemination to the brain and other organs. Our findings identify two primary viral determinants driving this respiratory restriction: reduced neuraminidase (NA) enzymatic activity and impaired polymerase activity. Collectively, these results suggest that commonly used mammalian models may overstate current human pandemic risk. This work highlights the critical need for alternative risk-assessment platforms to identify the specific genetic shifts required for these viruses to overcome existing barriers to human adaptation.

Forecasting influenza hospitalizations informs public health preparedness, yet questions remain about which types of forecasts best guide action. We evaluate categorical trend forecasts, which communicate probabilities of upcoming increases or decreases in epidemic trajectories, submitted to CDC's FluSight Forecasting Challenge between Fall-2024 and Spring-2026. Teams submitted probability distributions over five categories describing direction and magnitude of week-over-week changes in laboratory-confirmed influenza hospital admissions. We assessed performance using Ranked Probability Skill Score, Brier Skill Score, and measures of forecast-observation agreement. Most models outperformed an equal-probability baseline; the FluSight ensemble ranked among the top three in the 2024-25 and 2025-26 seasons. Forecasts were most accurate during stable periods and least during periods of rapid change, with most models underestimating observed trends. Conclusions were robust to choice of scoring metric and reference model. These results support categorical trend ensembles as an approach to communicating infectious disease forecasts that may inform public health decision-making.

We compared the immunogenicity of three licensed egg-based inactivated influenza vaccines, including TetrAnflu (Sinovac quadrivalent), Fluarix Tetra (GSK quadrivalent), and Vaxigrip (Sanofi trivalent), in adult healthcare workers in Hong Kong during the 2025/26 season. Paired pre- and post-vaccination sera from age- and sex-matched recipients (n=30 to 40 per group) were tested by hemagglutination-inhibition assays against vaccine strains. After adjustment for age, sex, and sampling interval, the vaccines induced broadly comparable rises in antibody titers, proportions achieving titers >=40, and seroconversion rates, with a superior response to A(H1N1) after TetrAnflu. These real-world findings support the interchangeability of these vaccines for influenza vaccination programs.

Influenza surveillance has typically been carried out using influenza-like illness (ILI) rates and proportions of laboratory tests positive for influenza as metrics to monitor, with sample sizes for the number of tests to carry out based on the precision of the resulting estimate of proportions positive. The transition out of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic period has encouraged the establishment of integrated surveillance of respiratory pathogens, in the context of multiple surveillance objectives, as set out by WHO in its revised integrated surveillance guidance and Mosaic Respiratory Surveillance Framework. These objectives include outbreak detection, situational awareness and intensity evaluation, among others. We illustrate how to design respiratory surveillance in primary care, by considering multiple surveillance objectives for different metrics of different types of respiratory pathogen circulation seasons in England, the USA and Hong Kong. We focus on a proxy of influenza activity as a metric to compare between these countries/regions. Taking advantage of England's integrated sentinel primary care surveillance system, we propose further metrics to monitor: a proxy of respiratory activity, novelly defined as the product of an acute respiratory infection (ARI) consultation rate and the proportion of tests positive for \emph{at least one pathogen}; pathogen-specific ARI-based activity proxies for more detailed monitoring of influenza and SARS-CoV-2; and integrated monitoring of proportions positive for all pathogens tested. We use a simulation approach to determine sample sizes by optimising either the probability of, or time to, detection of different events in monitored metrics, according to the different surveillance objectives. We find that sample sizes to maximise detection probabilities or minimise detection times vary by metric, objective, event and country/region. At a national level, the current sample sizes used are sufficient to detect most events in most weeks for both the USA and Hong Kong, but for England the numbers of swabs taken for ILI consultations may not be sufficient in all weeks, particularly at the start of the season when outbreak detection is important. However, broadening the criteria for swabbing to acute respiratory symptoms does allow for sufficient sample sizes.

Background: Respiratory syncytial virus (RSV) remains a leading cause of hospitalization in infancy, with severe outcomes influenced by both contact patterns and passive immunity. Non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic suppressed RSV circulation and reduced opportunities for maternal immune boosting, potentially altering protection among newborns. We evaluated whether incorporating time-varying maternal immunity improves the ability of an age-structured transmission model to predict post-pandemic RSV hospitalization patterns in infants. Methods: We analyzed population-based RSV hospitalizations among Ontario (Canada) infants (<1 year) from July 2, 2017 to June 25, 2024, using linked administrative databases. A deterministic compartmental model across seven age classes was calibrated against pre-pandemic data using Latin Hypercube Sampling. We compared a model incorporating time-varying contact rates alone against a specification that additionally included time-varying maternal immunity. Results: Both specifications accurately reproduced pre-pandemic seasonality and macro-level post-pandemic resurgence features. The constant maternal immunity model showed slightly better accuracy in capturing the 2021/22 peak compared to the time-varying maternal immunity specification. However, both qualitatively captured the continued near-absence of RSV and the observed peak was captured within the 95% credible intervals. While both models precisely captured the timing and overwhelming surge of admissions that occurred in 2022/23, they failed to capture the premature peak timing and magnitude in 2023/24. Conclusions: Incorporating time-varying maternal immunity did not improve model accuracy post-pandemic. While maternal protection is essential for evaluating infant immunizations, population-level contact shifts primarily shaped post-pandemic RSV seasonality, indicating that models must account for these mechanisms of RSV transmission dynamics.

Background We examined whether two key housing quality indicators, energy efficiency and household overcrowding, were associated with lower respiratory tract infection (LRTI) hospital admissions in infants. Methods We used a cohort of all singleton births in Scotland 2010-2012, created through linked vital statistics and health data. LRTI admissions were characterised in hospital records. Overcrowding (defined using the national room standard) and median postcode-level energy efficiency were defined using maternal Census and postcode-level Energy Performance Certificate data linked to the cohort, respectively. We used logistic regression to model the odds of at least one infant LRTI admission. Results The cohort included 136,123 infants of whom 4.0% had at least one LRTI admission. Overcrowding was more common among infants of younger mothers and those in rented housing. Energy efficiency was lower among infants of older mothers, living in owner occupied homes, in less deprived areas. Compared with infants living in homes with excess rooms (under-occupied housing), those whose homes were below, or met, the minimum room standard had higher odds of LRTI admission (adjusted odds ratio 1.07, 95% CI 0.98-1.17; 1.10, 95% CI 1.03-1.17, respectively). Postcode-level energy efficiency was not associated with LRTI admission odds. Conclusion Overcrowding was more common in socioeconomically disadvantaged households and associated with increased risk of LRTI admission in infancy. Lower energy efficiency was associated with factors commonly linked to socioeconomic advantage and was not associated with LRTI admissions. Improving access to housing with adequate living space may reduce the burden of LRTIs in early life.

Since its emergence in 2020, multiple genotypes of the H5N1 clade 2.3.4.4b have been identified, with B3.13 and D1.1 emerging in the USA as two major and concerning genotypes. However, their relative pathogenicity and transmissibility in mammals have not been fully elucidated. We compared the pathogenicity and transmissibility of the first two human H5N1 clade 2.3.4.4b cases caused by B3.13 in Texas (A/Texas/37/2024; HPhTX B3.13) and D1.1 in Louisiana (A/Louisiana/12/2024; HPhLA D1.1) in a ferret model of infection and transmission. HPhTX B3.13 infection resulted in more severe clinical disease and enhanced viral shedding, with evidence of increased transmission relative to HPhLA D1.1. Histopathological analysis revealed more extensive lung pathology in animals infected with HPhTX B3.13, consistent with increased viral loads and inflammatory responses. Importantly, both genotypes showed no significant differences in reactivity to ferret sera raised against candidate vaccine virus (CVV) strains, receptor binding properties, or neuraminidase (NA) activity and thermostability. Whole-genome sequencing revealed no adaptive mutations in HPhTX B3.13 following infection or transmission. In contrast, HPhLA D1.1 showed rapid acquisition of the mammalian-adaptive mutation E627K in infected ferrets and both E627K and Q194K in the only fatal contact animal. Both mutations were associated with enhanced polymerase activity and computational analyses suggested that they enhance interactions with the mammalian host factors ANP32A and B. Our findings indicate that B3.13 is already well adapted for mammalian infection and transmission whereas D1.1 retains evolutionary potential through the rapid acquisition of adaptive mutations, highlighting important genotype-specific differences relevant to zoonotic risk assessment and pandemic preparedness. SignificanceInfluenza H5N1 viruses continue to diversify genetically while expanding into mammalian hosts, increasing opportunities for viral adaptation and zoonotic transmission, including humans. However, whether the predominant clade 2.3.4.4b genotype differs in its capacity to infect, transmit, and evolve in mammals remains poorly understood. Using the ferret model of influenza infection and transmission, we demonstrated that the currently circulating B3.13 and D1.1 genotypes exhibit distinct pathogenic and transmission characteristics despite retaining similar receptor-binding characteristics, NA functions, and antigenic profiles. While B3.13 readily infects and transmits in ferrets and does not develop further adaptive mutations associated with increased replication and transmission, D1.1 rapidly acquires mammalian-adaptive mutations after a single infection and/or transmission event, highlighting its evolutionary potential. These findings show that genotype-specific biological properties can influence zoonotic risk independently of antigenic similarity and emphasize the importance of integrating phenotypic characterization with genomic surveillance to improve pandemic preparedness and guide public health risk assessment.

Background. Direct livestock exposure is a risk factor for zoonotic influenza, including H5N1 highly pathogenic avian influenza (HPAI) A virus. But whether living in regions of high poultry and swine production intensity (PPI, SPI) increases risk of exposure to zoonotic influenza viruses independent of occupational livestock contact remains unclear. Objectives. To determine whether livestock workers and community members with no occupational livestock exposure in North Carolina, where poultry and swine production are increasingly co-located, are at higher risk of exposure to zoonotic influenza. Methods. Saliva samples from industrial livestock operation worker (ILO-W), ILO neighbor (ILO-N) and metropolitan area (Metro) households were analyzed for mucosal influenza A (H5N1, H1N1, and H3N2) hemagglutinin (HA) IgA and IgG antibodies to determine associations of PPI, SPI, exposure group, and detection of a swine-specific fecal contamination marker (Pig-2-Bac DNA) with influenza A antibody levels. Results. Residing in the highest PPI and SPI tertile was associated with significantly higher mucosal H5 and H1 HA IgA levels, including among residents without occupational livestock exposure. Households with occupational poultry or swine contact had significantly higher H5 IgA and IgG and H1 IgA levels compared to Metro households. In regression models accounting for clustering at the participant level, log10 anti-H5 HA mucosal IgA increased 0.16 (95% CI: 0.06, 0.27, p<0.005) and 0.10 (95% CI: 0.03, 0.17, p<0.005), per log10 increase in PPI and SPI, respectively, and 0.16 (95% CI: 0.03, 0.19, p<0.02) when Pig-2-Bac DNA was detected on household surfaces. Conclusions. Mucosal H5 HA IgA and IgG and H1 HA IgA were consistently elevated across different metrics of livestock exposure intensity, including residential exposure, occupational contact within a household, and a molecular marker of household swine fecal contamination in a state with intensive poultry and swine production.

Abstract Introduction: Diarrheal diseases and acute respiratory infections (ARI) disproportionately affect young children and families facing disadvantages at the individual, household, and neighborhood level. This unequal burden especially impacts children in low-and middle-income countries, such as Nepal. Data limitations impede the ability to understand children's illness episodes and treatment trajectories across the course of early childhood and their relationship to household- and neighborhood-level social determinants of health. The Chitwan Valley Family Study (CVFS) is a 30-year panel study providing a wealth of information about household- and neighborhood-level social determinants in Southern Nepal. Drawing on a cohort of young children in CVFS households, this study will measure incidents of acute illness among children under five and leverage existing data from the panel study to understand how intergenerational disadvantages, place, and other social determinants affect the frequency and duration of childhood illness and subsequent healthcare utilization. Methods and Analysis: This study will use daily symptom diaries to track children's illness symptoms (diarrhea, fever, cough, runny nose, difficulty breathing or wheezing, fatigue, loss of appetite) over the course of a year. Mother respondents will complete a baseline interview, daily symptom diaries, and a weekly phone interview with a trained interviewer to describe the prior week's symptoms and, in the case of any symptoms, healthcare utilization, treatment, expenditures, and related information. All eligible children aged 3-59 months may participate in two waves of 52 weeks of data collection. We will measure the frequency and duration of diarrhea and ARI, healthcare utilization outcomes, socio-economic status, and distance to healthcare facilities, then merge these measures with prior CVFS data related to parents' childhood circumstances, health facility characteristics, and neighborhood characteristics. Ethics and Dissemination: We received IRB approval from the Nepal Health Research Council and the University of Michigan. Informed consent will be obtained from respondents for all aspects of data collection. Identifying information will be restricted to the data collection team in Nepal and stored separately from survey data. Interviewers will check that all children with danger signs identified according to WHO/UNICEF Integrated Management of Childhood Illness clinical guidelines have received adequate treatment; a study nurse will follow up and refer those who have not. We will disseminate study findings to respondents, local partners, and nationally in Nepal, as well as in academic journals and at conferences. Datasets will be available for public and restricted-use through the Data Sharing for Demographic Research program at the Inter-university Consortium for Political and Social Research at the University of Michigan.

Nucleic acid extraction remains the principal infrastructure barrier to molecular influenza testing outside centralised laboratories, since bead-based purification is normally tied to mains-powered extractors and trained operators. We evaluated SmartLid, a centrifugation-free format in which a removable magnetic key shuttles paramagnetic beads through pre-aliquoted lysis/binding, wash, and elution buffers without pipetting or powered instrumentation, against an automated magnetic-bead extractor (Nextractor NX-48S) on 311 nasopharyngeal specimens from the 2024-2025 influenza season at a National Influenza Centre. Paired eluates were amplified under identical monoplex RT-qPCR conditions for influenza A(H1N1)pdm09, A(H3), and B/Victoria. Both methods gave 100% specificity (47/47 negatives; no false positives). Subtyping succeeded in 263/264 reference-positive specimens after SmartLid extraction versus 241/264 after automated extraction (99.62% versus 91.29%; difference 8.33 percentage points; discordant pairs 23 versus 1; McNemar P < 0.001). Across 240 complete pairs, cycle threshold (Ct) values were lower after SmartLid extraction (median paired difference -2.78 cycles; estimated location shift -2.60 cycles, 95% CI -2.82 to -2.37; P < 0.001) with rank-ordering of specimens conserved between methods (Spearman rho = 0.84). The advantage was preserved across all three subtypes and in both fresh and frozen specimens (adjusted P < 0.001). Specimens recovered only after SmartLid extraction had higher Ct values than dual-detected specimens (median 34.37 versus 28.54; P < 0.001), locating the gain near the assay detection limit. An instrument-free manual format can therefore exceed the extraction efficiency of an automated reference workflow, extending quality-assured influenza subtyping beyond centralised laboratories.

Influenza vaccine effectiveness (VE) is estimated from a limited number of clinics using a test-negative design. These standard estimates face geographic, temporal, and operational constraints. Using Twitter/X data, we applied few-shot chain-of-thought prompting to identify self-reported vaccination status and influenza test results, then implemented a test-negative-like design to estimate VE. Our estimates fell within the range of interim reports and could complement current systems, improving feasibility, timeliness, and scalability.

The continuous accumulation of genetic mutations in influenza A viruses (IAVs) drives antigenic drift, necessitating precise antigenic prediction for optimal vaccine strain selection. While sequence-based methods have advanced antigenic surveillance, they neglect the three-dimensional structural context that fundamentally dictates viral antigenicity. Here, we introduce Vir3D, which leverages ESMFold-derived structural information from amino acid sequences to precisely predict viral antigenicity and guide vaccine strain selection. Across both human H3 and highly pathogenic avian H5 subtypes, Vir3D not only accurately discriminates antigenic variants and infers pairwise antigenic distances, but also mechanistically delineates key structural residues driving viral immune evasion. In a decade-long retrospective analysis, Vir3D-prioritized vaccines consistently achieve broader antigenic coverage of circulating strains than World Health Organization (WHO) recommendations. Crucially, Vir3D successfully predicts that the emerging U.S. dairy cattle H5N1 virus (TX/24) remains antigenically stable relative to clade 2.3.4.4b vaccine strains, and subsequent wet-laboratory validation of hemagglutination inhibition (HI) assays definitively corroborates this finding. Overall, Vir3D establishes a powerful, structure-driven framework for proactive influenza surveillance and pandemic preparedness.