Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California

Hilt, Evann E; Boocock, James; Trejo, Marisol; Le, Catherine Q; Guo, Longhua; Zhang, Yi; Sathe, Laila; Arboleda, Valerie A; Yin, Yi; Bloom, Joshua S; Wang, Pin-Chieh; Elmore, Joann G; Kruglyak, Leonid; Shrestha, Lasata; Bakhash, Shah A Mohamed; Lin, Michelle; Xie, Hong; Huang, Meei-Li; Roychoudhury, Pavitra; Greninger, Alexander; Chandrasekaran, Sukantha; Yang, Shangxin; Garner, Omai B

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. METHODS: We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. RESULTS: We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. CONCLUSIONS: We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.