Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet

Abstract

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data generated. The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet. While challenges remain for public health genomic surveillance worldwide, California COVIDNet serves as a framework for a scaled and successful bioinformatics infrastructure that has expanded beyond SARS-CoV-2 to other pathogens of public health importance.

Keywords: California COVIDNet; SARS-CoV-2; bioinformatics; pathogen genomics; public health; whole-genome sequencing.

Fig. 1.

Visualizations from the SARS-CoV-2 Dashboard in Google Looker Studio. (a) Differences in the proportion of SARS-CoV-2 Nextclade clades by collection date in California for 2022. (b) Pango lineage by county from October–December 2022.