ArticleCell reports. Medicine2023
Sample size calculations for pathogen variant surveillance in the presence of biological and systematic biases.
Article in Cell reports. Medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Structural Constraints Acting on the SARS-CoV-2 Spike Protein Reveal Limited Space for Viral Adaptation.Genome biology and evolution · 2026Article
- Inequities and global declines in SARS-CoV-2 genomic data availability hinder response to emerging variants.Npj viruses · 2026Review
- Global solidarity in genomic surveillance improves early detection of acute respiratory virus threats.Nature communications · 2026Article
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- Large language models for biological sequence analysis in infectious disease research.Biosafety and health · 2025Review
- Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes.medRxiv : the preprint server for health sciences · 2025Article
- Surveillance strategies for the detection of new pathogen variants across epidemiological contexts.PLoS computational biology · 2024Article
- Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing.Briefings in bioinformatics · 2024Article
- Sampling for malaria molecular surveillance.Trends in parasitology · 2023Review
- Surveillance for variants of SARS-CoV-2 to inform risk assessments.Bulletin of the World Health Organization · 2023Article
- Towards a post-pandemic future for global pathogen genome sequencing.PLoS biology · 2023Article
- Toward a global virus genomic surveillance network.Cell host & microbe · 2023Review
- Identification of Multiple Variant Extensively Drug-Resistant Typhoid Infections across Pakistan.The American journal of tropical medicine and hygiene · 2023Article
- Comparative hospitalization risk for SARS-CoV-2 Omicron and Delta variant infections, by variant predominance periods and patient-level sequencing results, New York City, August 2021-January 2022.Influenza and other respiratory viruses · 2023Article
- SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs.Nature genetics · 2023Article
- SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs.medRxiv : the preprint server for health sciences · 2022Article
- Travel measures in the SARS-CoV-2 variant era need clear objectives.Lancet (London, England) · 2022Article
- Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection.Frontiers in public health · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tracking the emergence and spread of pathogen variants is an important component of monitoring infectious disease outbreaks. To that end, accurately estimating the number and prevalence of pathogen variants in a population requires carefully designed surveillance programs. However, current approaches to calculating the number of pathogen samples needed for effective surveillance often do not account for the various processes that can bias which infections are detected and which samples are ultimately characterized as a specific variant. In this article, we introduce a framework that accounts for the logistical and epidemiological processes that may bias variant characterization, and we demonstrate how to use this framework (implemented in a publicly available tool) to calculate the number of sequences needed for surveillance. Our framework is designed to be easy to use while also flexible enough to be adapted to various pathogens and surveillance scenarios.
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