Genomic Surveillance for SARS-CoV-2 at Southeast Michigan

A local investigation of viral temporal and spatial dispersion and efficacy of response in Southeast Michigan is imperative to improve preparedness tailored to this area. Genomic surveillance allows for the close monitoring of viral propagation and identification of vulnerable communities. A collaborated effort between Wayne State University and the Detroit Health Department established a genetic surveillance pipeline in support of national surveillance efforts directed by the CDC. Samples were collected from Henry Ford, Detroit Health Department, and Ion Diagnostics. The samples were bio banked before being subject to automated nucleic acid extraction, PCR for virus genome testing, and whole genome sequencing. A barcode monitoring system tracked SARS-CoV-2 samples archived in the biobank and undergoing RNA extraction through a semi-automated preparation system and then used for qPCR and high-throughput sequencing. With this established system, 7,508 samples were archived, among which 80% were sequenced.