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Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco.

  • Author(s): 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;
  • CLIAhub Consortium;
  • Kistler, Amy;
  • Hao, Samantha;
  • Kamm, Jack;
  • Dynerman, David;
  • Batson, Joshua;
  • Greenhouse, Bryan;
  • DeRisi, Joe;
  • Havlir, Diane V
  • et al.
Abstract

Background

There is an urgent need to understand the dynamics and risk factors driving ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during shelter-in-place mandates.

Methods

We offered SARS-CoV-2 reverse-transcription polymerase chain reaction (PCR) and antibody (Abbott ARCHITECT IgG) testing, regardless of symptoms, to all residents (aged ≥4 years) and workers in a San Francisco census tract (population: 5174) at outdoor, community-mobilized events over 4 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) vs 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 3953 persons (40% Latinx; 41% White; 9% Asian/Pacific Islander; and 2% Black). Overall, 2.1% (83/3871) tested PCR positive: 95% were Latinx and 52% were asymptomatic when tested; 1.7% of census tract residents and 6.0% of workers (non-census tract residents) were PCR positive. Among 2598 tract residents, estimated point prevalence of PCR positives was 2.3% (95% confidence interval [CI], 1.2%-3.8%): 3.9% (95% CI, 2.0%-6.4%) among Latinx persons vs 0.2% (95% CI, .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.

Conclusions

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.

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