Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions

Shannan N. Rich, Veronica Richards, Carla Mavian, Brittany Rife Magalis, Nathan Grubaugh, Sonja A. Rasmussen, Simon Dellicour, Bram Vrancken, Christine Carrington, Rebecca Fisk-Hoffman, Demi Danso-Odei, Daniel Chacreton, Jerne Shapiro, Marie Nancy Seraphin, Crystal Hepp, Allison Black, Ann Dennis, Nídia Sequeira Trovão, Anne Mieke Vandamme, Angela RasmussenMichael Lauzardo, Natalie Dean, Marco Salemi, Mattia Prosperi

Research output: Contribution to journalArticlepeer-review


Background: In the wake of the SARS-CoV-2 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real time. Open source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained popularity for their ability to illuminate spatial-temporal transmission patterns worldwide. However, the utility of such tools to inform public health decision-making for COVID-19 in real time remains to be explored. Objective: The aim of this study is to convene experts in public health, infectious diseases, virology, and bioinformatics—many of whom were actively engaged in the COVID-19 response—to discuss and report on the application of phylodynamic tools to inform pandemic responses. Methods: In total, 4 focus groups (FGs) occurred between June 2020 and June 2021, covering both the pre- and postvariant strain emergence and vaccination eras of the ongoing COVID-19 crisis. Participants included national and international academic and government researchers, clinicians, public health practitioners, and other stakeholders recruited through purposive and convenience sampling by the study team. Open-ended questions were developed to prompt discussion. FGs I and II concentrated on phylodynamics for the public health practitioner, while FGs III and IV discussed the methodological nuances of phylodynamic inference. Two FGs per topic area to increase data saturation. An iterative, thematic qualitative framework was used for data analysis. Results: We invited 41 experts to the FGs, and 23 (56%) agreed to participate. Across all the FG sessions, 15 (65%) of the participants were female, 17 (74%) were White, and 5 (22%) were Black. Participants were described as molecular epidemiologists (MEs; n=9, 39%), clinician-researchers (n=3, 13%), infectious disease experts (IDs; n=4, 17%), and public health professionals at the local (PHs; n=4, 17%), state (n=2, 9%), and federal (n=1, 4%) levels. They represented multiple countries in Europe, the United States, and the Caribbean. Nine major themes arose from the discussions: (1) translational/implementation science, (2) precision public health, (3) fundamental unknowns, (4) proper scientific communication, (5) methods of epidemiological investigation, (6) sampling bias, (7) interoperability standards, (8) academic/public health partnerships, and (9) resources. Collectively, participants felt that successful uptake of phylodynamic tools to inform the public health response relies on the strength of academic and public health partnerships. They called for interoperability standards in sequence data sharing, urged careful reporting to prevent misinterpretations, imagined that public health responses could be tailored to specific variants, and cited resource issues that would need to be addressed by policy makers in future outbreaks. Conclusions: This study is the first to detail the viewpoints of public health practitioners and molecular epidemiology experts on the use of viral genomic data to inform the response to the COVID-19 pandemic. The data gathered during this study provide important information from experts to help streamline the functionality and use of phylodynamic tools for pandemic responses.

Original languageEnglish (US)
Article numbere39409
JournalJMIR Formative Research
StatePublished - 2023


  • COVID-19
  • SARS-CoV-2
  • bioinformatics
  • data
  • epidemiology
  • genomic
  • genomic surveillance
  • molecular epidemiology
  • monitoring
  • pandemic
  • phylodynamic
  • phylogenetic
  • response
  • surveillance
  • transmission
  • variants
  • virology

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Health Informatics


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