National SARS-CoV-2 Genomic Sequencing and Public Health
In response to an acknowledged paucity of pathogen genome sequencing ‘horsepower,’ expertise, and know-how in public health laboratories across the country, the Centers for Disease Control and Prevention turned to academic sequencing centers with expertise in pathogen genomics to fill the gap. cMEDA investigators from Microbiology & Immunology, Pediatrics, Infectious Diseases, Pathology, and Computer Science teamed up to provide that expertise.
They developed and implemented an ‘in house’ SARS-CoV-2 detection assay prior to the availability of a reliable test from the CDC and applied this to thousands of samples in the early days of the Covid-19 pandemic. In parallel, pathogen genomics investigators from cMEDA established and validated the Pathogenic Virus Amplification and Sequencing Protocol (PVASP) to rapidly and accurately sequence the SARS-CoV-2 genomes in discarded pathology samples.
These successful efforts led to the generation of genomic sequences of thousands of SARS-CoV-2 full genomic sequences in 2021-2023. This coalition and the results obtained were instrumental in the competitive application for the Pathogen Genomics Center of Excellence.