ArticlePLoS computational biology2026
Utilizing virus genomic surveillance to predict vaccine effectiveness.
Article in PLoS computational biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Integrating Genomic Data into Test-negative Designs for Estimating Lineage-specific COVID-19 Vaccine Effectiveness.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSince the development of the first vaccines targeting the original SARS-CoV-2 virus sequence in 2020, mRNA-based vaccines have been updated three times: targeting Omicron BA.4/BA.5 in 2022, the XBB lineage in 2023, and the KP.2 variant in 2024. While genomic surveillance has advanced our understanding of pathogen diversity, gaps remain in incorporating genomic information to evaluate vaccine effectiveness (VE) against emerging variants. This study aims to characterize the relationship between VE and sequence-based genetic distance, to establish a framework for predicting near real-time changes in the level of vaccine protection from virus surveillance data.
methodsWe analyzed 10,156 whole genome sequences of SARS-CoV-2 cases from Connecticut, USA, between April 2021 to July 2024. We first assessed how genetic distance, specifically the number of amino acid substitutions in the spike gene between COVID-19 case sequences and the mRNA vaccine formulation sequence(s), correlates with vaccine protection levels. Incorporating data from over 1 million test-negative controls, we developed a Bayesian time-varying model with autoregressive terms to assess VE at a weekly level. The analysis was adjusted for ZIP-code-level income, age, sex, and prior vaccine doses received. We then employed a random effects meta-regression to explore the relationship between VE and amino acid distance over time. Finally, we used the meta-regression model to estimate potential vaccine protection against emerging variants.
findingsWe found that spike gene amino acid distance showed a negative correlation with VE over time. Stepwise increases in amino acid distance aligned with sharp VE declines during variant emergence, while accumulation of within-variant changes was also associated with gradual VE decline. Each 10 amino acid increase in distance in the spike gene corresponds to a predicted 15.4% (95% credible intervals (CrI): -2.0%, 34.6%) reduction in VE. For the 2023/24 updated vaccine, spike distance rose from 12.25 to 30.23, predicting a 43.4% (95% CrI: -5.7%, 90.1%) drop in VE using sequence information alone.
conclusionOur framework quantifies how the emergence of new variants is expected to affect VE for SARS-CoV-2. By quantifying the relationship between amino acid substitutions and time-varying VE, we leverage intrinsic pathogen features, such as spike amino acid distance, to inform future vaccine updates using genomic sequences. As genomic surveillance data becomes more widely available across pathogens, this framework can serve as a near-real time surveillance tool to infer population-level protection and offers valuable insights for vaccine update decisions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.