Bayesian Comparison of Covid Origins Hypotheses

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   Mismatched and underrepresented: bat–virus diversity and phylogeographic bias in experimental infection studies

   Luis R. Víquez-R, Thomas P. Y. Mazzarulli, Melissa T. R. Hawkins et al. · 2026 · Frontiers in Immunology · Not summarized yet

   Abstract

   Despite growing interest in bat–virus interactions, experimental infection studies (EIS) remain taxonomically and geographically restricted, limiting inference about bat immunology and zoonotic risk. We performed a systematic literature search (Jan 1900–Jan 2025) and manually curated peer-reviewed primary studies of viral experimental infections in live bats and bat-derived cell lines (BdCL). From 545 candidate records we retained 127 papers (83 live-bat, 44 BdCL), comprising 315 unique bat–virus trials. We categorized host taxonomy, viral family (ICTV), and biogeographical congruence, to quantify temporal trends, taxonomic coverage, and host–virus pairing patterns. Results show stark underr…

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   A joint Bayesian hierarchical model for estimating SARS-CoV-2 diagnostic and subgenomic RNA viral dynamics and seroconversion

   Tracy Q. Dong, Elizabeth R. Brown · 2023 · Applications · AI summary available

   Abstract

   Understanding the viral dynamics and immunizing antibodies of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for devising better therapeutic and prevention strategies for COVID-19. Here, we present a Bayesian hierarchical model that jointly estimates the diagnostic RNA viral load reflecting genomic materials of SARS-CoV-2, the subgenomic RNAs (sgRNA) viral load reflecting active viral replication, and the rate and timing of seroconversion reflecting presence of antibodies. Our proposed method accounts for the dynamical relationship and correlation structure between the two types of viral load, allows for borrowing of information between viral load and antibody da…

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   Phylodynamic analysis of the spread of COVID-19 in the National Capital Region, Philippines during the early stages of the pandemic

   I. G. Panogalinog, Imari Joy Borda, Z. P. Lachica et al. · 2026 · SciEnggJ · Not summarized yet

   Abstract

   In epidemiological studies, key parameters could be incorrectly estimated when case data are underreported, as demonstrated during the early spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylodynamic models, which integrate viral genomic data, offer an alternative approach to understand SARS-CoV-2 transmission dynamics. Here we aimed to understand the early spread of SARS-CoV-2 in the National Capital Region of the Philippines (NCR) through phylogenetic and phylodynamic analysis of viral sequences. We investigated how government-imposed community quarantines influenced viral spread and compared these estimates with those from conventional compartmental models. W…

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   Will there be a warning for the next pandemic?

   J. Lessler, C. Metcalf · 2026 · Science Advances · Not summarized yet

   Abstract

   How to best allocate resources to combat the threat of pathogen emergence remains an important open question. Using archetypes that characterize the link from genotype to fitness in both zoonotic reservoirs and humans, we show that, across a range of plausible conditions, emergences of pathogens with pandemic potential in humans are unlikely to be preceded by detectable, failed, attempts. Yet, the number of “failed” emergence events contains information about the emergence potential of zoonotic pathogens, and should modify our beliefs about the underlying fitness landscape. Our work suggests that the most important, modifiable, risk factors for emergence may be phenomena that alter fitness l…

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   Statistical inference of virus evolution using ancestral recombination graphs

   Christopher H. C. Leung, C. Houldcroft, A. Scally · 2026 · bioRxiv · Not summarized yet

   Abstract

   Ancestral recombination graphs (ARGs) represent the coalescent history at every locus in the genome, subject to mutation and recombination. Modelling viruses using the coalescent with recombination remains less explored, due to the potential for complex, multi-scale dynamics. Using perturbative methods, we establish mathematical bounds that describe the balance between inter-host and within-host coalescence, and demonstrate that the highly-recombinant Epstein-Barr Virus (EBV) coalesces predominantly at the inter-host level. We then modify SINGER, a tool from diploid genetics, for haploid ARG inference with fine-grained variable recombination rates. We provide insight into the paradox of high…

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   Bayesian calibration of adaptive-behavior SIR models for multi-wave COVID-19 incidence in New York City

   Luis A. Barboza, Carlos Pasquier, Baltazar Espinoza et al. · 2026 · Not summarized yet

   Abstract

   Epidemic incidence reflects both transmission dynamics and adaptive human behavior, yet these mechanisms may be difficult to distinguish from aggregate case data alone. We calibrated four susceptible--infected--recovered (SIR) specifications to weekly confirmed COVID-19 incidence in New York City from June to December 2020, comparing a single continuous SIR trajectory, a wave-initialized SIR model, and two adaptive-behavior models with either shared or wave-specific transmission. Inference was performed using rejection Approximate Bayesian Computation (ABC), and in-sample reconstruction was assessed using root mean squared error (RMSE) and the weighted interval score (WIS). Reinitializing th…

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   Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy

   P. Varilly, Mark Schifferli, Katherine Yang et al. · 2026 · Nature · Not summarized yet

   Abstract

   Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12–13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14, 15, 16–17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy. Delphy’s central data structure, an explicit mutation-annotated tree, takes advantage of the high sequence similarity of large-scale epidemic datasets18, 19–20 for efficient tree exploration and convergence. By reproducing key analyses from recent major epidemics, inc…

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   Parameter non-identifiability limits ecological inference from historical plague mortality records

   Nich W. Martin, Nicolas Gauthier · 2026 · bioRxiv · Not summarized yet

   Abstract

   Historical plague mortality records provide unusually detailed temporal records of epidemic dynamics. However, the ecological processes underlying those dynamics are rarely observed. This creates a fundamental challenge for inference into ecological mechanisms, as multiple combinations of unobserved ecological parameters and initial conditions may produce similar mortality trajectories. We investigated this problem by examining the geometry of parameter compensation for models of the Barcelona plague outbreak of 1490. We fit a mechanistic rat-flea-human transmission model to daily human mortality data under three values of flea search efficiency, then characterized the resulting joint poster…