Proceedings of the National Academy of Sciences

The transmission of respiratory pathogens is fundamentally shaped by human behaviors such as interpersonal contacts, use of face masks, and vaccination. Political party affiliation has been shown to be associated with health-related behaviors. Yet, partisan heterogeneity in health-related behaviors is typically not included in infectious disease transmission models. Here, we leveraged uniquely detailed data from the Berkeley Interpersonal Contacts Study (BICS) on partisan differences in contact ...

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...

Nipah virus (NiV) is a sporadic yet extremely deadly zoonotic pathogen, with reported case fatality rates of 40%-75% in impacted areas. Prolonged incubation, documented relapse, and delayed-onset encephalitis following apparent recovery indicate that NiV dynamics are influenced by intricate temporal processes. However, mechanistic contributions of these processes to epidemic persistence remain poorly understood. In this study, we develop and analyze a delay differential equation model for NiV tr...

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...

Epigenetic clocks estimate biological age from DNA methylation patterns at CpG sites, providing robust predictions of mortality and morbidity risk. "Blue zones"--regions of exceptional longevity--offer a unique opportunity to investigate how biological aging diverges from chronological age. However, standard clocks are typically trained on large, heterogeneous datasets, reflecting average population trends rather than region-specific dynamics. Using data from the Costa Rican Longevity and Health...

BackgroundViral interference, in which infection with one pathogen reduces susceptibility to another, may influence respiratory virus dynamics. Inference from surveillance data is complicated by time-varying testing behavior that can induce correlated detection patterns independent of biological interaction. MethodsWe developed a multi-pathogen renewal model augmented with a ratio penalty that constrains interference estimates to be consistent with observed log-odds ratios of pathogen positivit...

Measles resurgence in high-income countries that previously achieved elimination reveals a critical surveillance failure: current systems rely on county-level aggregates that obscure fine-scale clustering where outbreaks originate. We assembled the nationwide multiscale vaccination database spanning 45 US states (2013-2025), encompassing over 50,000 schools, 13,000 districts, and 3,000 counties. We developed a gravity-based transmission framework and demonstrate that school-level effective repro...

Defining and quantifying exceptional familial human survival is a persistent challenge in longevity research. Traditional approaches rely on binary thresholds, arbitrary cutoffs, or simple descriptive measures, which discard information on variation among the oldest individuals, ignore differences in background mortality, and yield unstable family-level summaries. We propose a principled, model-based framework that transforms survival times into percentiles relative to population life tables, st...

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...

Metastatic dissemination in lung cancer (LC) and other solid tumors is influenced not only by tumor-intrinsic biology and immune-inflammatory responses, but also by the physical properties of the vascular system through which circulating tumor cells (CTCs) migrate. Peripheral arterial disease (PAD), particularly when manifesting as aneurysmal dilation, is frequent among long-term smokers and is associated with chronic vascular inflammation and altered hemodynamics. We hypothesized that PAD-relat...

In a recent article in Science, Shenhar et al. report that human life span heritability reaches [~]55% after removing "extrinsic" mortality, roughly seven-fold higher than recent large pedigree estimates. This conclusion rests on classifying deaths from infections and accidents as environmental noise independent of genetics. This premise is biologically untenable: susceptibility to severe infection is substantially heritable, with adoptee studies showing relative risks exceeding 5 for infection ...

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...

Dengue, a vector-borne disease, puts at risk of infection nearly four billion people worldwide. Spread primarily by Aedes mosquitos, suitable mosquito habitat favoring survival, population maintenance, and an optimal extrinsic incubation period is required for successful transmission. Many areas, however, fall within the geographic range of the mosquito vector and favorable climatological conditions but experience only sporadic and short-lived outbreaks. Here, we characterized local dengue viru...

The consumption of sugar-sweetened beverages (SSBs) has risen significantly in both developing and developed economies, despite well-documented evidence of their adverse health consequences. Although price-based regulations, primarily through SSB taxation, are widely recognized as a policy instrument to reduce consumption and improve public health outcomes, interventions targeting SSBs have received relatively limited attention in Bangladesh. Using the 2022 Household Income and Expenditure Surve...

Human contact network structure fundamentally shapes infectious disease transmission and control. Most COVID-19 epidemic models assumed approximately homogeneous contact patterns, yet real-world networks are highly heterogeneous. We analysed 59,585 daily non-household contact reports from Germanys COVIMOD study (2020-2021) using a novel heavy-tail regression framework. Throughout the pandemic, contact distributions remained strongly heavy-tailed despite substantial non-pharmaceutical interventio...

Biological and behavioral differences between genders influence infectious disease dynamics. Yet, most epidemiological models overlook these aspects in favor of age stratification alone. Here, we systematically evaluate the impact of incorporating gender-specific features into an age-structured epidemic compartmental model, calibrated to COVID-19 mortality data from the second wave in Italy (Autumn 2020-Winter 2021). We develop eight model versions representing different combinations of three da...

Assessing epidemic risk following pathogen introduction is crucial in infectious disease epidemiology. Risk is commonly encoded through reproduction ratios, which underpin operational decision-making. In spatially structured populations, both local and cross-community transmission shape epidemic trends, a feature that standard reproduction ratios fail to capture simultaneously. Here, we use multitype branching processes to define the outbreak reproduction ratio Rob, a reformulation applicable ac...

As malignant transformation arises from dysregulated cellular programming with characteristic morphological changes, we hypothesized that cancer cells exhibit a unique morphological signature detectable in microscopy images of cells in vitro and in situ across modalities. To test this, we developed CellSign, an AI-based framework to generate Cell Dynamics Fingerprints, which (a) reconstruct morphological progression, (b) remove physiological variation, and (c) support automated malignancy assess...

Mathematical models of infectious disease dynamics are routinely fitted to surveillance data to estimate epidemiological parameters and inform public health decisions. Such data are typically discrete and noisy, but before attempting estimation, it is essential to ask whether the model structure itself permits unique parameter identification at least under perfect (continuous, noise-free) observations. This mathematical property of a model with respect to observation(s), known as structural iden...