ArticlePLOS global public health2022
The impact of sampling bias on viral phylogeographic reconstruction.
Article in PLOS global public health, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- A systematic review of epidemiological modelling in response to lumpy skin disease outbreaks.Frontiers in veterinary science · 2024Pooled it
- Phylogeographic epidemiology of Dabie bandavirus in East Asia: divergent transmission networks and genotype‑linked clinical severity.Infectious diseases of poverty · 2026Article
- Lineage Diversification and Evolutionary Dynamics of theMicroorganisms · 2026Article
- SAASI: Sampling Aware Ancestral State Inference.Nature communications · 2026Article
- Genomic epidemiology ofMicrobial genomics · 2026Article
- Molecular evolution and spatial transmission of severe fever with thrombocytopenia syndrome virus.Nature communications · 2026Article
- Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024.Communications medicine · 2026Article
- The role of wild birds in the global highly pathogenic avian influenza H5 panzootic, 2020-2023.npj biodiversity · 2026Review
- Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024-2025.PloS one · 2026Article
- varVAMP: degenerate primer design for tiled full genome sequencing and qPCR.Nature communications · 2025Article
- Mitochondrial DNA patterns describe the evolutionary history of the bonnethead shark Sphyrna tiburo (Linneus 1758) complex in the western Atlantic Ocean.Journal of fish biology · 2025Article
- Phylogeographic Characterizations of Recent (2015-2023) Senecavirus A Isolates from Canada.Viruses · 2025Article
- Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.Virus evolution · 2025Article
- Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden.Virus evolution · 2025Article
- Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region.Nature medicine · 2024Article
- Spatiotemporal evolution and transmission dynamics of Alpha and Delta SARS-CoV-2 variants contributing to sequential outbreaks in Cambodia during 2021.Communications medicine · 2024Article
- Genomic diversity and transmission patterns of Yersinia pestis in Inner Mongolia Autonomous Region, China.Communications biology · 2024Article
- COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses.Science (New York, N.Y.) · 2024Article
- Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile.PNAS nexus · 2024Article
- The evolutionary drivers and correlates of viral host jumps.Nature ecology & evolution · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform policy decisions related to viral movement among jurisdictions. However, phylogeographic reconstruction is impacted by the fact that the sampling and virus sequencing policies differ among jurisdictions, and these differences can cause bias in phylogeographic reconstructions. Here we assess the potential impacts of geographic-based sampling bias on estimated viral locations in the past, and on whether key viral movements can be detected. We quantify the effect of bias using simulated phylogenies with known geographic histories, and determine the impact of the biased sampling and of the underlying migration rate on the accuracy of estimated past viral locations. We find that overall, the accuracy of phylogeographic reconstruction is high, particularly when the migration rate is low. However, results depend on sampling, and sampling bias can have a large impact on the numbers and nature of estimated migration events. We apply these insights to the geographic spread of Ebolavirus in the 2014-2016 West Africa epidemic. This work highlights how sampling policy can both impact geographic inference and be optimized to best ensure the accuracy of specific features of geographic spread.
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Registered trials
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.