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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Optimal capacity sharing for global genomic surveillance.

Zsombor Z Méder¹, Robert Somogyi²

¹Institute of Psychology, Leiden University, P.O. Box 9555, 2300 RB Leiden, Netherlands.

|June 7, 2023

Summary

Genomic surveillance optimizes pathogen detection during pandemics. Optimal sequencing capacity distribution depends on whether the goal is variant prevalence estimation or new variant identification.

Keywords:

Capacity constraint Genomic surveillance International cooperation Optimal allocation

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Area of Science:

Epidemiology
Genomics
Public Health

Background:

Technological advances and cost reductions enable pathogen genomic surveillance during pandemics.
Full genome sequencing is crucial for tracking pathogen evolution and spread.
Capacity constraints necessitate strategic allocation of sequencing resources.

Purpose of the Study:

To determine the optimal distribution of genomic sequencing capacities among countries.
To compare two primary goals of genomic surveillance: variant prevalence estimation and new variant identification.
To provide quantifiable guidance for enhancing pandemic genomic surveillance efficiency.

Main Methods:

Developed a model to solve for optimal distribution of sequencing capacities under constraints.
Analyzed the impact of different surveillance goals (prevalence estimation vs. variant detection) on capacity allocation.
Applied the model to SARS-CoV-2 sequencing data from 2021, comparing observed and optimal distributions globally and within the EU.

Main Results:

Optimal capacity distribution for prevalence estimation is less than proportional to country size.
Optimal capacity distribution for new variant detection favors regions with higher infection rates.
Significant differences were observed between actual and suggested optimal sequencing capacity distributions for SARS-CoV-2 in 2021.

Conclusions:

Strategic allocation of genomic sequencing resources is critical for effective pandemic response.
The optimal distribution of sequencing capacity is goal-dependent, prioritizing either broad prevalence monitoring or targeted variant detection.
Implementing data-driven capacity allocation can significantly improve the efficiency and impact of global genomic surveillance efforts.