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

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID- 19) pan-demic, 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 epi-demiology, 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 chal-lenges 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,

Automated summary

During the COVID-19 pandemic, the capacity for pathogen genomics in public health expanded rapidly. However, many public health laboratories lacked the infrastructure to handle the large amount of SARS-CoV-2 sequence data. The California Department of Public Health, in partnership with Theiagen Genomics, created a SARS-CoV-2 genomic surveillance system called California COVIDNet. This initiative combined the efforts of over 40 sequencing laboratories across government, academia, and industry to establish a successful bioinformatics infrastructure.