SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco

Chamie, Gabriel; Marquez, Carina; Crawford, Emily; Peng, James; Petersen, Maya; Schwab, Daniel; Schwab, Joshua; Martinez, Jackie; Jones, Diane; Black, Douglas; Gandhi, Monica; Kerkhoff, Andrew D; Jain, Vivek; Sergi, Francesco; Jacobo, Jon; Rojas, Susana; Tulier-Laiwa, Valerie; Gallardo-Brown, Tracy; Appa, Ayesha; Chiu, Charles; Rodgers, Mary; Hackett, John; Kistler, Amy; Hao, Samantha; Kamm, Jack; Dynerman, David; Batson, Joshua; Greenhouse, Bryan; DeRisi, Joe; Havlir, Diane V

BACKGROUND: There is urgent need to understand the dynamics and risk factors driving ongoing SARS-CoV-2 transmission during shelter-in-place mandates. METHODS: We offered SARS-CoV-2 reverse transcription-PCR and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (≥4 years) and workers in a San Francisco census tract (population: 5,174) at outdoor, community-mobilized events over four days. We estimated SARS-CoV-2 point prevalence (PCR-positive) and cumulative incidence (antibody or PCR-positive) in the census tract and evaluated risk factors for recent (PCR-positive/antibody-negative) versus prior infection (antibody-positive/PCR-negative). SARS-CoV-2 genome recovery and phylogenetics were used to measure viral strain diversity, establish viral lineages present, and estimate number of introductions. RESULTS: We tested 3,953 persons: 40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black. Overall, 2.1% (83/3,871) tested PCR-positive: 95% were Latinx and 52% asymptomatic when tested. 1.7% of census tract residents and 6.0% of workers (non-census tract residents) were PCR-positive. Among 2,598 tract residents, estimated point prevalence of PCR-positives was 2.3% (95%CI: 1.2-3.8%): 3.9% (95%CI: 2.0-6.4%) among Latinx vs. 0.2% (95%CI: 0.0-0.4%) among non-Latinx persons. Estimated cumulative incidence among residents was 6.1% (95%CI: 4.0-8.6%). Prior infections were 67% Latinx, 16% White, and 17% other ethnicities. Among recent infections, 96% were Latinx. Risk factors for recent infection were Latinx ethnicity, inability to shelter-in-place and maintain income, frontline service work, unemployment, and household income &$50,000/year. Five SARS-CoV-2 phylogenetic lineages were detected. CONCLUSION: SARS-CoV-2 infections from diverse lineages continued circulating among low-income, Latinx persons unable to work from home and maintain income during San Francisco’s shelter-in-place ordinance.