Science

In the three years since Omicron emergence, SARS-CoV-2 dynamics have exhibited persistent twice-yearly waves in the United States, peaking in late summer and winter, with heterogeneity in timing and intensity across states. This semiannual pattern sharply contrasts with typical annual respiratory pathogen dynamics in the US, yet their underlying mechanisms and whether this pattern will persist remain poorly understood. Here, we tested several hypothesized mechanisms and found that a combination ...

The risk of highly pathogenic avian influenza infection to humans is challenging to estimate because many human avian influenza virus (AIV) infections are undetected as they may be asymptomatic, symptomatic but not tested, and as contact tracing is difficult because human-to-human spread is rare. We derive equations that consider the evolutionary mechanisms that give rise to pandemics and are parameterized to be consistent with records of past pandemics. We estimate that thousands of human AIV i...

The emergence of variants has shaped the COVID-19 pandemic. The lack of directly observed precursors to these variants has led to proposals that variants emerge from either persistent infections, transmission in non-human animal populations after reverse-zoonosis, or cryptic transmission in the human population. We investigated the origin of variants by analyzing the molecular clock and rate of nonsynonymous and synonymous substitutions in SARS-CoV-2 circulating in human population, persistently...

Lassa fever is classically defined as a rural zoonosis constrained by the agricultural niche of its reservoir, Mastomys natalensis. However, current risk models rely on historical sampling heavily biased toward rural settings (>67%). Here, I reconstruct the realised niche of M. natalensis using an Integrated Multi-Species Occupancy Model (IMSOM) accounting for biotic interactions with invasive rodents. Contrary to climatic predictions of urban exclusion, I identify a cryptic reservoir niche in W...

Pathogenic organisms are typically thought to be constrained by a tradeoff between the rate and duration of transmission, an assumption that underpins a considerable body of evolutionary theory. Here we test for a transmission-duration tradeoff using detailed historical malaria infection data from an era prior to widespread use of antibiotics when humans were deliberately infected with malaria parasites as treatment for neurosyphilis (malariatherapy). These time series follow individual human in...

Human African Trypanosomiasis (HAT) remains a persistent public health threat in sub-Saharan Africa, with transmission dynamics tightly coupled to the ecology and physiology of its tsetse fly vector. Despite growing evidence that temperature strongly modulates vector survival, development, and biting behavior, most existing transmission models assume static environmental conditions. We develop a model for HAT that incorporates temperature-dependent vector recruitment, mortality, and biting rates...

Reunion island just experienced a massive chikungunya virus outbreak in 2024-2025, with more than 54,000 confirmed cases. This is the second major chikungunya outbreak on the island, following the first one that peaked 20 years ago. It has been assessed that this new outbreak finds its origin in a single introduction event into the island, offering a unique opportunity to exploit viral genomic data to understand the epidemiological and dispersal dynamics of the introduced transmission chain. We ...

Programmatic decisions regarding surveillance and intervention for trachoma are made at the district level, reflecting an implicit assumption that transmission within districts is sufficiently homogeneous. However, as trachoma transmission declines, residual pockets of transmission may become spatially heterogeneous at sub-district scales. Using cluster-level data from 12 districts in Amhara, Ethiopia (2019-2023), we assess the spatial structure of Pgp3 antibody responses, a sensitive measure of...

The recent SARS-CoV-2 pandemic has highlighted the growing importance of infectious disease analysis. An accurate and robust model can empower public health leaders to make timely decisions on social distancing and vaccination policies, thereby reducing the number of cases, hospitalizations and deaths. However, the emergence of new variants and subvariants can significantly alter the transmissibility, immune escape capacity and virulence of the pathogen in a short time, making the number of case...

BACKGROUNDUnderstanding SARS-CoV-2 antibody dynamics is critical for pandemic preparedness, particularly where population immunity has developed through high infection rates with minimal vaccination. Whether predominantly asymptomatic infections confer protective immunity and which biomarkers best predict protection in resource-limited settings remain unclear. METHODSWe conducted a household cohort study in The Gambia over 15 months (March 2021-June 2022) during Delta and Omicron waves, with we...

Proteogenomic studies integrating genetic, molecular, and phenotypic data have transformed target discovery, yet remain heavily biased toward European populations. Here, we present a large-scale proteogenomic atlas in a non-European population, analysing 7,289 plasma proteins profiled by SomaScan v4.1 in 3,965 Chinese adults. Genome-wide association analyses identified 3,212 protein quantitative trait loci (pQTLs), including 1,092 proteins with a cis-pQTL. Integrating these data with East Asian ...

Collective interaction of individuals in various settings is crucial for exposure to infections, encompassing complex viral interplay and amplifying infectious risk through phenomena such as social reinforcement, clustering and superspreading events, during the COVID-19 pandemic. However, standard epidemic models often inadequately capture such heterogeneity, overlooking the higher-order social structural. Spatiotemporal variation in transmission, an essential feature of the pandemic, remains po...

The two largest US measles outbreaks in over two decades (2025 Gaines County, Texas: 414 cases, contained; 2025-2026 Spartanburg County, South Carolina: 923+ cases, ongoing) occurred in counties with similar sub-threshold K-12 MMR coverage (85.1% vs 88.8%), yet their trajectories diverged dramatically. Using kernel density estimation with a common bandwidth and bootstrap uncertainty quantification, we compared sub-county vaccination data at the district level for Texas (3 districts, 3,560 studen...

During an outbreak, infectious disease can spread among populations through host movement, potentially fueling local outbreaks with their own epidemiological dynamics. However, it is difficult to know how often infections between populations are transmitted by diseased travelers infecting healthy residents when abroad, rather than by diseased residents infecting healthy travelers, who later return home with the new pathogen. In this paper, we introduce a phylogeographic model where pathogens spr...

BackgroundCOVID-19 epidemic waves display pronounced temporal structure in mortality, with substantial variation in wave shape, duration, and asymmetry across regions. These dynamics are commonly interpreted within transmission-based compartmental models, in which epidemic growth is driven by interactions between infectious and susceptible individuals. However, several empirical features of observed mortality curves, including prolonged declines, asymmetric wave shapes, and coherent temporal pat...

BackgroundNorovirus causes substantial burden to healthcare systems. England experienced high activity in recent seasons alongside a shift in the dominant genotype from GII.4 to GII.17. It remains unclear whether this increased burden reflects changes in severity or other transmission mechanisms associated with the strain replacement. MethodsIndividual-level testing and mortality data in England from 2022/23-2024/25 seasons were linked from national surveillance systems. Piece-wise exponential ...

SARS-CoV-2 mutations play a key role in viral evolution, in immune escape, and potentially in disease severity. However, the clinical impact of most mutations remains poorly understood, particularly across different variants. A historical observational study was conducted using SARS-CoV-2 whole-genome sequencing data linked to clinical metadata from 175,503 COVID-19 cases in Israel. The dataset was stratified into four variant-specific periods: B.1.1.7, B.1.617.2, BA.1, and BA.2. Logistic regres...

A new H3N2 variant (named subclade K) possesses several key hemagglutinin substitutions and is circulating widely during the 2025-2026 influenza season. In this report, we completed experiments to determine if the 2025-2026 seasonal influenza vaccine elicits antibodies in humans that recognize this variant. We find that H3N2 subclade K viruses are antigenically advanced; however, the 2025-2026 seasonal influenza vaccine elicited antibodies in many individuals that efficiently recognized these vi...

BackgroundStrikingly low allocation of SARS-CoV-2 vaccine to the African Continent limits its capacity to control transmission. Characterizing the trajectory of vaccination efforts and their impact on the expected burden of SARS-CoV-2 will help planning vaccine delivery strategies, and public health interventions more broadly. As the burden is strongly age-dependent, this requires an understanding of the age-structured dynamics of susceptible individuals, accounting for the combined effects of v...

We examined whether the recent emergence of influenza A(H3N2) subclade K, associated with an unusually early influenza season in the Northern hemisphere, was accompanied by a reduction in human population immunity. Using virus neutralisation assays on pre-epidemic human sera collected in May 2025, we found evidence of moderate antigenic drift. Further, vaccines used in the 2024/2025 season induced cross-neutralising immunity. These findings provide timely insight for interpreting recent influenz...