Back

Influenza and Other Respiratory Viruses

○ Wiley

Preprints posted in the last 30 days, ranked by how well they match Influenza and Other Respiratory Viruses's content profile, based on 46 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.

1
Age as a Leading Indicator: A Multi-Outcome Analysis of Influenza Lead-Lag Relationships

Serman, E. A.; Bleichrodt, A.; Jayawardena, I.; Liskey, C.; Rennert, L.

2026-10-05 epidemiology 10.64898/2026.09.29.26364022 medRxiv
Top 0.1%
30.5%
Show abstract

Prior work has shown that school-age children's influenza activity precedes that of adults by one to two weeks. Whether this is robust across outcomes or constant across a season's course is unexamined. Using electronic health record data from two health systems in South Carolina (2016-2026) on individuals with an influenza diagnosis or positive test, we tested age-group lead-lag relationships across six measures using differenced cross-correlation and Granger causality, with significance confirmed via heteroskedasticity-robust block permutation. We tested whether relationships differed between a season's growth and decline phases. Children 5-17 years led every other age group by approximately one week in four out of six outcomes and were the only group showing any nonzero-lag relationship across 60 pairwise combinations. A screen of 150 source-target combinations identified 26 permutation-confirmed instances of children's lower-acuity activity preceding elevated emergency department or inpatient burden in other age groups. The same-outcome lead was concentrated during a season's growth phase, while the cross-severity lead was robust throughout both a season's growth and decline. School-age children's influenza activity is a robust, multi-outcome leading indicator with distinct transmission-timing and severity-progression signals in different phases of seasonal epidemics, supporting incorporation of age-stratified, phase-aware indicators into influenza forecasting.

2
Interactions between respiratory viruses in US adults and children: a prospective cohort study

Hoffman, K. L.; Weil, A. A.; Wetzler, E. A.; Akinola, B. O.; Beauge, A.; Andy, C.; Adams, A.; Frivold, C.; Cox, S. N.; Ehmen, B.; Hatchie, T.; Clark, E. L.; Drummond, M.; Englund, J.; Han, P. D.; Kuntz, J. L.; Lo, N. C.; Lockwood, C.; Starita, L.; Mularski, R. A.; Naleway, A. L.; Carone, M.; Chu, H. Y.

2026-10-19 infectious diseases 10.64898/2026.10.15.26365672 medRxiv
Top 0.1%
12.9%
Show abstract

Background: The relationship between recent viral infection and subsequent susceptibility to, or protection against, other viruses remains unclear, particularly across ages and symptom status. Methods: A prospective cohort study enrolled participants aged 6 months to 49 years in Washington and Oregon, USA, 2022-2024. Weekly nasal swabs were tested for SARS-CoV-2, respiratory syncytial virus (RSV), and influenza A/B; additional swabs were collected during symptomatic illness and were also tested for parainfluenza (PIV) 1-4, endemic human coronaviruses (hCOV), adenovirus, human metapneumovirus, human rhinovirus (hRV), and enteroviruses. Proportional hazards regression models were used to characterize associations between incident symptomatic infection (illness) and history of recent illness due to other viruses (within 1-7, 8-14, 15-30, 31-60, 61-90, 91-180 days), adjusted for geographic region, age, sex, daycare/school/work attendance, household size, and number of children in the household. For SARS-CoV-2, influenza, and RSV, these analyses were repeated to study incidence of infection (including asymptomatic cases). Findings: Of 3,560 participants, 2,969 (83%) had [≥]1 illness over 4,299 person-years. Adjusted hazard ratios (aHRs) in the short term ([≤]2 weeks) after an illness were predominantly below 1, indicating that recent viral illness was often associated with lower risk of subsequent illness with other viruses. Across age groups, recent hRV illness was associated with lower risk of hCOV, PIV, and RSV illness (aHRs 0.07-0.27). SARS-CoV-2 illness was associated with a higher short-term risk of adenovirus and PIV illness (aHRs 3.20-3.33). In children aged 6 months-4 years, recent influenza illness was associated with higher short-term risk of SARS-CoV-2 illness. Including asymptomatic infections generally attenuated these associations. Interpretation: Some viral illnesses may alter short-term susceptibility to subsequent viral illnesses. Interactions may differ by age and symptom status. Funding: US Centers for Disease Control and Prevention; Washington State Department of Health.

3
Comparative immunogenicity and relative vaccine efficacy of recombinant and cell culture-based influenza vaccines: Results from a randomized trial of adults in the United States, 2024-2025

Sumner, K. M.; Noble, E. K.; Grant, L. B.; Meeker, J. R.; Murugan, V.; Nordstrom, L.; House, S. L.; Presti, R.; Walter, E. B.; Williams, O. L.; Saade, E. A.; Canaday, D. H.; Williams, K. V.; Zimmerman, R.; Gross, F. L.; Valencia, S.; Gurbaxani, B. M.; Lewis, N. M.; Li, Z.-N.; Mishin, V.; Gubareva, L.; Zhou, B.; Levine, M. Z.; Flannery, B. M.; Ellington, S.; US Flu VE Network Collaborators,

2026-10-02 epidemiology 10.64898/2026.10.01.26364413 medRxiv
Top 0.1%
12.8%
Show abstract

Background: Recombinant (RIV) and cell culture-based inactivated (ccIIV) influenza vaccines could improve seasonal influenza prevention; however, evidence is limited in how protection may differ among non-egg-based vaccines. Methods: We conducted a randomized trial of RIV versus ccIIV to compare vaccine immunogenicity in adults aged 18 to 64 years during the 2024-25 influenza season (ClinicalTrials.gov, NCT06518577). Active surveillance for influenza-like illness was conducted for six months post-vaccination and cumulative incidence of influenza by vaccine type was compared to estimate relative vaccine efficacy. Participants were tested for influenza by reverse-transcription polymerase chain reaction or rapid antigen tests. Immunogenicity was evaluated by hemagglutination inhibition (HAI), virus microneutralization (MN), and neuraminidase inhibition (NAI) assays in a subset of blood specimens collected pre-vaccination and one-month post-vaccination. Results: Among the 591 participants, 25 cases of influenza A were detected; 2.4% cumulative incidence among RIV recipients versus 6.1% among ccIIV recipients. The probability of influenza was 61% lower with RIV than ccIIV (95% confidence interval: 7 to 84). Among 151 participants, post-vaccination HAI and MN titers vaccine components were higher among RIV recipients while NAI titers were higher among ccIIV recipients. Conclusions: RIV provided better protection than ccIIV against influenza A illness in adults during the U.S. 2024-2025 season.

4
Distinct Longitudinal Antibody Responses Following Primary Influenza Infection or Vaccination in Infants: A Prospective Birth Cohort Study

Joshi, D.; Kumar, S.; Zarnitsyna, V. I.; Burrell, A. R.; Rolhfs, C.; Danzy, S.; Charles, T. P.; Mbadugha, F. A.; Xu, L.; Payne, D. C.; Kohlmeier, J.; Lowen, A. C.; Allen Staat, M.; Wrammert, J.

2026-09-30 immunology 10.64898/2026.09.28.755012 medRxiv
Top 0.1%
12.7%
Show abstract

The longitudinal effects of initial influenza exposure on the magnitude, persistence, and antigen specificity of antibody responses during infancy remain incompletely understood. We investigated humoral antibody responses following primary influenza infection or seasonal vaccination in a prospective US birth cohort with weekly respiratory surveillance for influenza infection. Influenza-specific serum IgG binding to H1 and H3 haemagglutinin (HA) antigens, HA inhibition (HAI), and live-virus neutralizing antibody responses were assessed longitudinally. To minimize influence of maternally derived antibodies, analyses of primary exposure responses were restricted to infants for whom influenza-specific maternal antibodies had declined below the assay detection limit before exposure. Antibody responses were compared following primary infection and vaccination and examined after subsequent annual vaccination. We found that maternal influenza-specific IgG declined rapidly during early infancy. Among infants without detectable pre-exposure influenza-specific antibodies, primary influenza infection was associated with greater post-exposure antibody responses and less measurable decline over follow-up than primary vaccination. These groups differed in age, calendar season, and exposure characteristics, limiting direct attribution of these differences to route of exposure. In infants with previous influenza infection followed by vaccination, responses after subsequent vaccination initially showed greater binding to the previously infecting subtype among the tested HA antigens. With repeated vaccination, responses became more distributed across the tested antigens. Our findings reveal differences in the magnitude, persistence, and antigen specificity of antibody responses according to the nature and sequence of influenza exposure. By prospectively capturing early-life exposures, this study provides longitudinal evidence linking exposure history to subsequent humoral antibody responses.

5
Direct and indirect effects of COVID-19 on infant bronchiolitis: a population-wide registry study from Northern Italy

Nazzari, V.; Navarro Gallinad, A.; Ghirardi, L.; Gianbartolomei, C.; Paganoni, A. M.; Bardaji, A.; Zuccolo, L.

2026-09-23 epidemiology 10.64898/2026.09.22.26363663 medRxiv
Top 0.1%
12.2%
Show abstract

BackgroundCOVID-19 pandemic modified trends of infant bronchiolitis, leading cause of emergency room (ER) attendance in infants in high income countries, primarily due to Respiratory Syncytial Virus. Understanding recent pandemic-related epidemiological shifts could inform affordable prevention efforts to improve sustainability and coverage of prophylactic treatments beyond maternal vaccines and infant monoclonal antibodies. MethodsWe estimated incidence rates (IR) of bronchiolitis ER presentations in 0-6month olds in 2012-2023 in a region-wide cohort of almost 1 million births using administrative health data from Lombardy, Italy. To assess potential contributors, we investigated direct and indirect COVID-19-related factors, including disease severity, shape of the epidemic peak, parental health seeking behaviour and vaccine coverage. We estimated COVID-19 maternal vaccination associations using mothers-infants data linkages and multivariable-adjusted logistic regression. FindingsCompared to pre-pandemic levels, IRs doubled in 2021-2023 (from 2 to [≥] 4/100 person-time). The surge could not be explained by changes in infant age at ER visit, clinical severity or in the shape of the epidemic peak. Adjusted models showed little support for a role of infant routine or maternal COVID-19 vaccination on bronchiolitis episodes (respectively hazard ratio 1.09, 95%CI: 0.98-1.22 and odds ratio 0.91, 95%CI: 0.76-1.09). InterpretationThe post-pandemic increase in infant bronchiolitis is likely driven by multiple epidemiological changes rather than a single factor. As maternal RSV vaccination and infant RSV monoclonal antibodies are introduced and scale up, identifying these mechanisms will be critical to maximise their public health impact, inform complementary prevention strategies, and improve preparedness for future RSV epidemics.

6
Development and Evaluation of a Regional Health Information Exchange (HIE)-Based Platform for Population-Level Infectious Disease Surveillance

Sandoval, M.; Mikhail, J.; He, H.; Denton, C.; al Rustem, H.; Troisi, C.; Cao, T.; Deegan, J.; Hanson, B.; Bauer, C.; Boerwinkle, E.

2026-10-06 epidemiology 10.64898/2026.10.04.26364717 medRxiv
Top 0.1%
9.7%
Show abstract

Background: Health Information Exchanges (HIEs) offer a potential resource for timely, population-level infectious disease surveillance by integrating electronic health record data across healthcare systems. Methods: We developed an end-to-end informatics pipeline for near-real-time community-level health surveillance based in a regional HIE serving Southeast Texas. We identified deidentified individual-level COVID-19, influenza, and RSV cases using diagnosis codes and laboratory results and assessed demographic and temporal trends from January 2022 through August 2026. Results: We identified 492,242 COVID-19 cases, 343,977 influenza cases, and 33,159 RSV cases during the study period. Surveillance data captured expected seasonal patterns, including recurring winter COVID-19 and influenza peaks and shifting RSV epidemiology, while enabling monitoring of laboratory test positivity metrics and hospitalization trends across age groups. Conclusions: HIE-based surveillance provides scalable, near-real-time monitoring of disease targets across large populations. HIE infrastructure can enhance public health situational awareness and complement traditional surveillance systems by harmonizing vital health data across systems and providers and delivering timely, standardized, and representative population health indicators.

7
Human Infection with Avian Influenza A(H7N7) Virus, Taiwan, 2026

Li, Y.-T.; Lin, Y.-T.; Chen, B.-S.; Kuo, C.-Y.; Huang, H.-Y.; Ko, H.-Y.; Huang, P.-Y.; Smith, G. J.; Lin, Y.-L.; Liu, M.-T.

2026-10-11 infectious diseases 10.64898/2026.10.09.26365013 medRxiv
Top 0.1%
8.0%
Show abstract

Low pathogenic avian influenza A(H7N7) virus detected in a poultry worker in Taiwan, 2026 was related to viruses circulating in Asian wild birds and possessed PB2 E627K, a mammalian adaptation marker. Enhanced surveillance for H7 viruses in poultry and rapid characterization of human cases are essential to assess pandemic potential.

8
Patterns of Influenza Vaccine Uptake by Age Group and Product Type in Michigan, 2017-2021

Zhou, Z.; Malosh, R.; Sudan, S.; Wagner, A.; Eisenberg, M. C.; Monto, A.; Martin, E. T.

2026-10-21 epidemiology 10.64898/2026.10.19.26365920 medRxiv
Top 0.1%
7.2%
Show abstract

Background Influenza vaccines have seen many changes over recent years in terms of both policy recommendations and product types. Immune responses and vaccine effectiveness vary by vaccine strain composition and product type. This study aimed to explore this variation on a regional level through examining spatial and temporal autocorrelations of vaccine uptake of different product types within Michigan from 2017 to 2021. Methods Influenza vaccine administration data from the 2017/18 to 2021/22 seasons were obtained from the Michigan Care Improvement Registry. Population size estimates for 2017 and 2019 were obtained from the Michigan Department of Health and Human Services. Age-standardized and age-stratified vaccination rates were computed. Disparate county-level vaccine uptake clusters were constructed using spatial autocorrelation indicators and spatiotemporal clusters were identified using scan statistics. Linear mixed effect models were used to study the impact of social vulnerability and urbanicity level on seasonal influenza vaccination rate. Results Vaccination incidence rates for adjuvanted, recombinant, and nasal sprays vaccines and for any vaccines increased significantly through the study period. County-level spatiotemporal clusters of type-specific uptake rates were identified. Most notably, we identified an emerging cluster with high uptake of adjuvanted vaccine radiating from Ottawa County, located in suburban Grand Rapids, and the disappearance of high uptake cluster for high-dose vaccine uptake in the area. Vaccination rates by any product type were found to vary seasonally and showed weak negative association with more rural regions. The overall vaccination rates appear to be lower among counties with higher social vulnerability in certain urbanicity levels, but social vulnerability and urbanicity were not significantly associated with overall vaccination rate during the study period. Conclusions Vaccine type-specific uptake was spatially and temporally diverse in Michigan between 2017 and 2022. Mid and Northern Michigan had consistently relatively lower vaccination rate compared to other regions in Michigan.

9
Potential impact of changes in influenza vaccination coverage and effectiveness on pediatric influenza burden in the United States, 2022/23-2024/25

Morris, S. E.; Mathis, S. M.; Chung, J. R.; DeCuir, J.; Olson, S. M.; Ellington, S.; O'Halloran, A.; Ujamaa, D.; Bozio, C. H.; Jain, A.; Srivastav, A.; Lu, P.-j.; Grohskopf, L. A.; Reed, C.; Iuliano, A. D.; Biggerstaff, M.

2026-10-01 epidemiology 10.64898/2026.09.25.26363797 medRxiv
Top 0.1%
6.7%
Show abstract

Background and Objectives: Influenza vaccination has a strong safety record and is effective in reducing pediatric influenza-associated morbidity and mortality. However, pediatric vaccination coverage (VC) has declined since the 2019/20 influenza season in the United States. We estimated the impact of increased vaccine protection (through increased VC and/or vaccine effectiveness [VE]) on pediatric influenza-associated burden during the 2022/23-2024/25 seasons. Methods: We used a compartmental model and laboratory-confirmed influenza-associated hospitalization, VC, and VE data among children 6 months-17 years to estimate influenza burden from 2022/23-2024/25 (the 'baseline' scenario) and the impact of vaccination. We simulated scenarios that (1) increased VC by five percentage points; (2) increased VE by five percentage points; (3) increased VC and VE by five percentage points; and (4) increased VC to levels achieved in 2019/20 (the season with the highest pediatric VC to date). We estimated the difference in hospitalizations and deaths between each scenario and the baseline scenario. Results: Among children 6 months-17 years, an estimated 120,000 influenza-associated hospitalizations and 1,650 deaths occurred across all seasons at baseline. Increasing VC to 2019/20 levels had the greatest estimated impact, reducing hospitalizations by 8,670 (7.2%) and deaths by 130 (7.9%). Increasing both VC and VE by five percentage points reduced hospitalizations by 6.6% and deaths by 6.7%, whereas increasing VC or VE by five percentage points reduced hospitalizations by 3.1% and deaths by 3.2%. Conclusions: Increasing pediatric influenza vaccination coverage back to 2019/20 levels was estimated to significantly reduce pediatric influenza-associated morbidity and mortality.

10
InfluProto: Predicting Cross-Species Transmission of Influenza A Virus via Prototype Learning

Geng, Z.; Li, L.; Ye, R.; Wang, Y.; Song, S.

2026-10-08 microbiology 10.64898/2026.10.07.757480 medRxiv
Top 0.1%
4.8%
Show abstract

Zoonotic influenza A viruses pose constitute a significant persistent threat to global public health, yet quantitative approaches for assessing their cross-species transmission potential remain limited. Here, we present InfluProto, a deep learning model that introduces prototype learning into host prediction for influenza A virus, framing conceptualizing host adaptation as a continuous process rather than a discrete outcome. InfluProto embeds viral sequences into a continuous representation space anchored by human, swine, and avian prototypes, using cosine distances as a quantitative measure of host adaptation. InfluProto accurately discriminated among the three host classes, achieving recall and precision exceeding 0.97, and substantially outperformed conventional classification models models--particularly on challenging zoonotic strains, including the 2009 pandemic H1N1 (pdm09) lineage. Beyond host classification, the learned representations captured biologically meaningful host-adaptive signatures,; notably, with pdm09 viruses occupying occupied an intermediate position between human and swine clusters, consistent with their evolutionary origin. Analysis of simulated reassortment further revealed that the introduction of human-origin segments into swine influenza viruses reduced their distance to the human prototype, indicating that InfluProto can detect reassortment-associated shifts in host adaptation. To facilitate broad public useaccess, we have developed an interactive web service for InfluProto. Collectively, our work establishes a continuous framework for characterizing host adaptation and evaluating zoonotic risk in influenza A viruses, with potential implications for pandemic surveillance and preparedness.

11
Mortality and vaccine-preventable deaths from severe acute respiratory infections in Brazil in 2026

Kupek, E.

2026-10-05 epidemiology 10.64898/2026.10.03.26364639 medRxiv
Top 0.1%
4.2%
Show abstract

Background: A large increase in mortality from severe acute respiratory infections (SARI) in Brazil in 2025 was mainly driven by influenza A and respiratory syncytial virus (RSV) among children and the aged, but 2026 data remain largely unpublished. Methods: Secondary data on SARI by age group (<2, 2-4, 5-14, 15-49, 50-64, 65+ years) and virus (Influenza A/B, RSV, SARS-CoV-2, adenovirus, rhinovirus, bocavirus, and metapneumovirus) were retrieved for 35 weeks of 2026. Weekly variations in infection rate (IR) and mortality rate (MR) were described by virus and age group. Case fatality ratio (CFR) and vaccine-preventable deaths from influenza, RSV, and SARS-CoV-2 were analysed by age group. Missing virus classification was estimated by multinomial regression. Poisson-based 95% confidence intervals (CI) were calculated for MR. Results: Influenza A infections quintupled during February and March, with a mortality peak in April, mainly due to H2N3. RSV and rhinovirus caused more deaths than influenza viruses, especially among young children (<2) and the aged (65+). The former were most frequently infected by RSV and the latter by rhinovirus. For those 50 years or older, influenza B reached a CFR of about 20%, compared with 5-15% for influenza A, metapneumovirus, rhinovirus, and other non-subtyped viruses. The highest vaccine-preventable MRs per 100,000 were 17.23 for the oldest and 8.62 for the youngest. Under ideal conditions, 6418 lives could have been saved, about half among children and adolescents <15 years old. Conclusions: Vaccine-preventable SARI in Brazil exerted a high toll in fall and winter 2026, mainly due to influenza A, RSV, and rhinovirus. Better vaccine coverage may significantly reduce this toll.

12
Highly Pathogenic Avian Influenza Viruses H5N1 and H5N5 in Red Foxes (Vulpes vulpes) in Norway during 2022-2024

Reiten, M. R.; Boe, C. A.; Olsen, L.; Saghafian, M.; Rohringer, A.; Akerstedt, J.; Ytrehus, B.; Gjerset, B.; Granstad, S.; Hungnes, O.; Tonnessen, R.

2026-09-25 microbiology 10.64898/2026.09.25.754393 medRxiv
Top 0.2%
4.0%
Show abstract

Since 2020, highly pathogenic avian influenza (HPAI) A(H5Nx) clade 2.3.4.4b viruses have spread globally, causing extensive outbreaks in domestic and wild birds. Increased circulation has resulted in frequent spillover to mammals, and occasional mammal-to-mammal transmission. Although human infections remain rare, the zoonotic potential of these viruses continues to be a public health concern. We investigated six cases of HPAI in red foxes (Vulpes vulpes) in Norway during 2022-2024 and identified infections with H5N1 and H5N5 viruses. Pathological and virological investigations demonstrated systemic infection, with prominent lesions in the brain and/or lungs. Phylogenetic analyses showed high similarity between viruses detected in foxes and those concurrently circulating in wild birds. The mammalian adaptation marker PB2:E627K was identified in one H5N1 virus and as a minority variant in a second H5N1 virus.

13
Worsening pre-existing health conditions in U.S. adults with Long COVID

Edwards, D. L.; Rollins, A. F.; Ford, N. D.; Pratt, C.; Bloodworth, R.; Pogreba-Brown, K.; Jones, R.; Sharma, V.; Reina Ortiz, M.; Saydah, S.; Track PCC Study Group,

2026-09-23 infectious diseases 10.64898/2026.09.22.26363331 medRxiv
Top 0.2%
3.5%
Show abstract

PurposeLong COVID literature often describes new-onset symptoms or conditions following SARS-CoV-2 infection; however, Long COVID also encompasses the exacerbation of pre-existing conditions. We describe health conditions reportedly worsened by COVID-19 illness and associated concerns in U.S. adults. MethodsWe collected longitudinal data from adults 18 years and older participating in the Track Post COVID-19 Conditions, an active Long COVID cohort surveillance project. Respondents completed surveys 3-, 6-, and 12- months after COVID-19 illness, beginning in July 2023. In each survey, respondents were asked whether they had any health conditions or concerns that were made worse by COVID-19. Those with an affirmative response were asked to specify the worsening condition(s) via free text. Some respondents used this free text to describe challenges or experiences related to their worsening conditions. This report categorizes and quantifies reported conditions and concerns by body system categories and qualitatively describes associated challenges and experiences using direct quotes from respondents free text responses. ResultsAmong 2,227 adults, 263 (11.8%) respondents reported at least one worsening condition or concern following COVID-19 illness. Of these, nearly 32% reported a worsening respiratory condition or concern. Adults with worsening pre-existing conditions reported challenges accessing adequate care, completing daily activities, and managing their symptoms following COVID-19. DiscussionWhile Long COVID literature often focuses on the development of new-onset long-term symptoms, more than 1 in 10 adults reported worsening of a pre-existing condition following COVID-19. Reported challenges with accessing care and daily activities highlight potential need for accommodations or support for adults with Long COVID.

14
Lung FDG-PET is an early pharmacodynamic biomarker of antiviral efficacy in preclinical influenza

Victorio, C. B. L.; Ganasarajah, A.; Gupta, S.; Ong, J.; Chacko, A.-M.

2026-10-08 microbiology 10.64898/2026.10.06.756978 medRxiv
Top 0.2%
3.3%
Show abstract

Background. Influenza remains a major cause of global morbidity and mortality. Pharmacodynamic biomarkers that quantify treatment response within the lung could accelerate influenza therapeutic development. We evaluated [18F]-fluorodeoxyglucose positron emission tomography ([18F]-FDG-PET) as a non-invasive biomarker of antiviral efficacy. Methods. Serial [18F]-FDG-PET was evaluated in two murine H1N1 influenza models using mouse-adapted PR8 strain and CA-09 clinical isolate following treatment with favipiravir, baloxavir marboxil, or ribavirin. PET measures were compared with pulmonary viral burden, inflammatory cytokine expression, computed tomography (CT) imaging, and respiratory function measured by whole-body plethysmography (WBP). Results. Antiviral treatment in PR8 infection model reduced lung [18F]-FDG uptake by 27-49% and metabolic lung volume (MLV) by 40.5-74.6% (both p < 0.001). Antiviral response was detectable as early as 3 days post-infection, when uptake decreased by 28.7-53.2% and MLV by 33.8-75.0%. Lung uptake also strongly correlated with MLV (r = 0.93, p < 0.001) and with pulmonary viral burden and inflammatory mediators. These findings were reproduced in a model of pandemic H1N1/CA-09, where baloxavir reduced uptake by 37.4% (p = 0.02) and MLV by 67.5% (p < 0.001) at day 3. In both models, changes in [18F]-FDG-PET parameters preceded improvements in lung CT and respiratory function. Conclusions. Lung [18F]-FDG-PET provides an early, quantitative measure of antiviral response in experimental influenza, supporting its further evaluation as a translational pharmacodynamic endpoint.

15
Quantifying advances in infectious disease forecast skill across seasons and pathogens

Bay, C.; Moghaddas, N. R.; Davis, J. T.; Borchering, R.; Biggerstaff, M.; Vespignani, A.; Johansson, M. A.

2026-10-01 public and global health 10.64898/2026.09.29.26364307 medRxiv
Top 0.2%
3.2%
Show abstract

Infectious disease forecasting supports public health preparedness and response by informing resource allocation, intervention planning, and situational awareness. Infectious disease forecasting capabilities in the United States have grown over the past decade yet whether forecast quality has improved over this time remains unclear. Current evaluation metrics describe relative performance for a common set of forecast targets but cannot evaluate performance across different outcomes, seasons, and pathogens. We addressed this challenge by developing a novel skill score metric to assess forecasts based on performance relative to two benchmark models: a hindcast as an idealized upper bound of performance and a baseline model as a minimal performance standard. To study the impact of the baseline choice, we considered three types of baseline models with varying levels of complexity. Using this skill score framework, we retrospectively evaluated short-term influenza (influenza-like illness and hospitalization) and COVID-19 (case, death, and hospitalization) forecasts, focusing on how the performance of team and multi-model ensemble forecasts changed over time. The ensemble outperformed 99% of forecasts from a simplistic, naive baseline, and 84-91% of forecasts from more complex baseline models that incorporate recent data. We found consistent improvements in ensemble and team forecast skill over time for both influenza forecast targets, with 4-week horizon forecasts in the most recent year having higher skill scores than 1-week horizon forecasts in the first year of each challenge. Results were mixed for COVID-19 forecasts. This framework provides a comprehensive picture of progress in infectious disease forecasting over the past decade enabled by improved standardization, data, models, and collaboration.

16
The mammalian-adaptive PB2-E627K substitution preserves viral fitness of clade 2.3.4.4b H5N1 HPAIV in birds.

Billington, E.; Riccio, S.; Brown, M. D.; Mollett, B.; Quantrill, J. L.; Johnson, S.; Di Genova, C.; Yang, J.; Sadeyen, J.-R.; Schlachter, A.-L.; Roper, K. J.; Hassan, J.; Clifton, B.; Ralh, K.; Warren, C. J.; Ward, G.; De Silva, D.; Nunez, A.; Coombes, H. A.; Slomka, M. J.; Iqbal, M.; Barclay, W. S.; Peacock, T.; Banyard, A. C.; James, J.

2026-10-06 microbiology 10.64898/2026.10.06.757006 medRxiv
Top 0.2%
3.2%
Show abstract

Since emerging in 2020, clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has disseminated globally, causing substantial infection and mortality in wild birds and poultry. Additionally, numerous spill-over events into mammals have occurred, including mass mortalities and sporadic human infections. Such events can drive the acquisition of mammalian-adaptive mutations, which further increase the risk to humans; the most well characterised mutation is the glutamate to lysine change at amino acid position 627 in the polymerase basic 2 protein (PB2-627K). Across avian influenza viruses, PB2-627K enhances polymerase activity and replication in mammalian cells, increasing zoonotic and pandemic potential. However, bioinformatic analyses indicate that PB2-627K remains rare among clade 2.3.4.4b H5N1 viruses circulating in avian populations. Here, we investigated the impact of PB2-627K on viral fitness in avian hosts to assess the potential for mammalian-adapted viruses to re-establish in birds, mimicking infection of avian species following scavenging on mammalian species where PB2-627K has already emerged. Using a representative H5N1 virus (European genotype AB), PB2-627K increased polymerase activity and replication in human cells without compromising replication in avian cells. A mammalian-derived PB2-627K H5N1 isolate from a fox exhibited comparable replication kinetics and transmission efficiency in chickens and ducks to a closely related PB2-627E virus. Notably, PB2-627K remained genetically stable at consensus level following infection and transmission in both avian hosts. These findings demonstrate that mammalian-adaptive mutations acquired during spill-over can be maintained in avian populations, potentially elevating zoonotic risk and underscoring the importance of surveillance for such mutations in birds.

17
Absolute and Relative Effectiveness of High-Dose vs Standard-Dose Influenza Vaccines Against Severe Outcomes in Older Adults

Le Vu, S.; Gutierrez-Melo, N.; Cartailler, T.; Jabagi, M.-J.; Botton, J.; Olie, V.; Weill, A.; Dray-Spira, R.; Zureik, M.

2026-10-06 infectious diseases 10.64898/2026.10.05.26364731 medRxiv
Top 0.2%
2.8%
Show abstract

Importance Several influenza vaccine products are available for older adults, but evidence combining both their absolute effectiveness and head-to-head comparisons within the same large population remains scarce, limiting product-specific vaccination guidance for this high-risk group. Objective To estimate the relative and absolute effectiveness of influenza vaccines against influenza-related hospitalization and in-hospital mortality among older adults. Design, Setting, and Participants Nationwide cohort study using the French National Health Data System (SNDS), including all adults born in 1958 or earlier, living in metropolitan France, at the start of the 2023-2024 campaign. Relative effectiveness (rVE) was assessed using a landmark design with exposure fixed before epidemic onset. Absolute effectiveness (VE) was assessed using a sequential trial emulation with weekly matching of newly vaccinated individuals to yet unvaccinated controls. Follow-up ran from December 5, 2023 to April 19, 2024. Exposures Vaccination with a high-dose (Efluelda) or one of three standard-dose quadrivalent vaccines (Influvac, Fluarix, Vaxigrip), compared individually or by dosage category, and against no vaccination. Main Outcomes and Measures Hospitalization with a diagnosis of influenza and death during such hospitalization. Effectiveness was estimated as 1 minus the hazard ratio from weighted Cox models, with corresponding numbers needed to vaccinate to prevent one case. Results Among 13.8 million eligible individuals, 5.7 million (41%) were vaccinated at the beginning of follow-up. The high-dose vaccine showed greater rVE than standard-dose vaccines against hospitalization (27% [95%CI, 23 to 31%]) and in-hospital death (27% [95%CI,14 to 38%]). Absolute VE was 39% (95%CI, 38 to 41%) against hospitalization and 45% (95%CI, 40 to 49%) against in-hospital death, and was higher for the high-dose vaccine (50%) than standard-dose vaccines (36%) against hospitalization. This difference was most evident among adults 70 years and older, while overall effectiveness declined with age. Conclusions and Relevance In this study, influenza vaccination conferred moderate protection against severe outcomes in older adults, and high-dose vaccination was associated with significantly greater effectiveness than standard-dose vaccines, particularly among adults 70 years and older. These findings support product-level differentiation in vaccination strategy for this population.

18
Detecting measles virus in hospital air during a local outbreak

Barbian, H. J.; Funk, M.; Black, S. R.; Hayden, M. K.; Zelencik, S.; Borah, B. F.; Zhang, D.; Bartlett, A. H.; Kociolek, L. K.; Rosenthal, A.; Farhat, N.; McSorley, V. E.; Kittner, A.

2026-09-27 infectious diseases 10.64898/2026.09.25.26363929 medRxiv
Top 0.2%
2.8%
Show abstract

In 2024, Chicago experienced a measles virus outbreak. Air samples collected as part of routine respiratory virus surveillance from three hospitals that received measles patients were retrospectively analyzed. Measles virus was detected in air samples from one emergency department across five weeks when measles patients were present and another when no known cases were present. Two of three viral sequences derived from air samples were identical to measles patients. The source of one diverging sequence could not be identified and may represent a case not identified by traditional surveillance methods. Air sampling may supplement measles investigation, surveillance and response.

19
SickMix: Temporal Changes in Social Contact Patterns among People with Acute Infection and Their Close Contacts

Ibiebele, J. C.; Tuli, A.; Lopes, G.; Lombard, G.; Shapiro, A.; Donald, J.; Schmidt, M. A.; Litvinova, M.; Chen, D.; Jenness, S.; Lopman, B.; Shioda, K.

2026-09-22 public and global health 10.64898/2026.09.21.26362162 medRxiv
Top 0.2%
2.7%
Show abstract

Infected individuals drive infectious disease transmission, yet empirical data on social interactions during acute infection remain limited. We conducted a prospective longitudinal study of 1,000 medically attended acute gastroenteritis and acute respiratory infection cases and 709 household members in the northwestern United States from 2024 to 2025 to quantify illness-associated changes in social contacts and their implications for transmission modeling. Cases substantially reduced social contacts during peak illness; weighted mean number of contacts increased 2.0-fold (95% confidence interval, 1.8-2.2) over the two-week follow-up. In transmission modeling, the simulated outbreak trajectory and estimated effectiveness of interventions differed substantially between models that did and did not account for temporal reductions in social contacts during acute infection. These findings show that behavioral responses during acute infection could substantially influence transmission dynamics and intervention evaluation, and provide an empirical framework for incorporating illness-associated behavioral change into infectious disease models.

20
Respiratory Syncytial Virus infections in immunosuppressed adults <65 years old: a comparative analysis with Influenza and SARS-CoV2

Danysz, M.; Barnes, E.; Lim, S. H.; Richter, A. H.; Stuart, B.; Willicombe, M.

2026-09-23 infectious diseases 10.64898/2026.09.22.26363680 medRxiv
Top 0.3%
2.4%
Show abstract

ObjectivesRespiratory Syncytial Virus (RSV) vaccine policies have varied globally since their approval in 2023. In the UK, policy has adapted in line with National evidence generation such that from Autumn 2026 at-risk persons [&ge;]65 years old will become eligible for vaccination. Immunosuppressed persons <65 years will still not be offered protection. The objective of this study is to investigate the relative burden of RSV infection by age and immunosuppressed status (IC). DesignRetrospective observational cohort study using routine healthcare data from North West London Integrated Care System. ParticipantsPatients with a confirmed diagnosis of a respiratory viral infection (RSV, Influenza A and B, SARS-CoV2) between October 2021 and July 2025. Main outcomes measuresPrevalence and severity of RSV infection in immunosuppressed persons <65 years old, and to provide a comparative analysis with Influenza and SARS-CoV2 in a sub-cohort tested using a 4-in-1 combined rapid PCR test. ResultsDuring the study period, 1226 patients were diagnosed with RSV of whom 596 (48.6%) were <65 years old. In 1091 patients with clinical data, 341 (31.3%) were IC. Fifty (9.9%) patients <65 years old had severe infection (ICU admission or death within 28 days of diagnosis), of whom 14 (28.0%) were IC. Proportionally, 16.7% of all RSV-associated deaths and 55.1% of all ICU RSV-admissions occurred in adult patients <65 years old. RSV accounted for 665 (10.1%) infections confirmed by 4-in-1 viral PCR testing. Eight-nine (13.4%), 172 (9.3%) and 448 (12.0%) patients with RSV, Influenza A and SARS-COV2 experienced severe infection, of whom 32 (36.0%), 82 (47.7%) and 156 (34.8%) were <65 years old respectively. Eight (25.0%), 20 (24.4%) and 52 (33.3%) of patients <65 years old with severe infection were IC. On adjusted analysis, having an immunosuppressive condition increased the odds of a severe SARS-CoV2 infection, OR (95% CI) 1.36 (1.08-1.71) but not a severe RSV or Influenza infection. ConclusionsSevere RSV infections occur in persons <65 years old, with a significant proportion of patients having an immunosuppressive condition. Urgent research is needed to investigate the potential benefit of extending the current UK RSV vaccine policy to protect younger immunosuppressed adults.