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Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling.

Catalina M Medina1, Julia A Palacios2, Volodymyr M Minin1

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This study introduces a new phylodynamic method to accurately estimate pathogen genetic diversity closer to real-time. This approach mitigates reporting delays, improving infectious disease surveillance and policy decisions.

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Area of Science:

  • Epidemiology
  • Computational Biology
  • Genetics

Background:

  • Accurate infectious disease surveillance is vital for public health policy.
  • Phylodynamic analysis uses pathogen genetic data to track epidemics but is hampered by reporting delays.
  • Traditional surveillance data can have biases, such as preferential testing of symptomatic individuals.

Purpose of the Study:

  • To develop a phylodynamic method that provides reliable estimation of effective population size closer to data collection.
  • To mitigate the impact of reporting delays on real-time phylodynamic analyses.
  • To enable more timely public health policy decisions based on recent epidemiological data.

Main Methods:

  • Developed a novel phylodynamic method incorporating historical sampling-to-reporting times into the sampling model.
  • Utilized coalescent-based phylodynamics to estimate effective population size (a proxy for genetic diversity).
  • Applied the methodology to simulated data and SARS-CoV-2 sequences from Washington State in 2021.

Main Results:

  • The new method provides reliable estimation of effective population size trajectories closer to the time of data collection.
  • The approach successfully mitigates the negative effects of reporting delays on real-time phylodynamic analyses.
  • Demonstrated the methodology's effectiveness on both simulated and real-world SARS-CoV-2 surveillance data.

Conclusions:

  • This phylodynamic method enhances real-time infectious disease surveillance by overcoming reporting delays.
  • The improved accuracy allows for more informed and timely public health policy and situational awareness.
  • Phylodynamics offers a robust tool for epidemic tracking, especially when integrated with methods addressing data limitations.