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

  1. Gabriel Chamie
  2. Carina Marquez
  3. Emily Crawford
  4. James Peng
  5. Maya Petersen
  6. Daniel Schwab
  7. Joshua Schwab
  8. Jackie Martinez
  9. Diane Jones
  10. Douglas Black
  11. Monica Gandhi
  12. Andrew D Kerkhoff
  13. Vivek Jain
  14. Francesco Sergi
  15. Jon Jacobo
  16. Susana Rojas
  17. Valerie Tulier-Laiwa
  18. Tracy Gallardo-Brown
  19. Ayesha Appa
  20. Charles Chiu
  21. Mary Rodgers
  22. John Hackett
  23. CLIAhub Consortium
  24. Amy Kistler
  25. Samantha Hao
  26. Jack Kamm
  27. David Dynerman
  28. Joshua Batson
  29. Bryan Greenhouse
  30. Joe DeRisi
  31. Diane V Havlir

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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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  1. Version published to 10.1093/cid/ciaa1234
  2. ScreenIT

    SciScore for 10.1101/2020.06.15.20132233: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementConsent: At the time of testing, we obtained verbal consent for participation and conducted COVID-19 symptom screening.
    IRB: 19 Ethics Statement & Funding: The UCSF Committee on Human Research determined that the study met criteria for public health surveillance.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Study Outcomes: Outcomes included the estimated point prevalence of all PCR-positive infections, recent infections (PCR-positive/antibody-negative) and prior infections (antibody-positive/PCR-negative).
    antibody-positive/PCR-negative
    suggested: None
    Cumulative incidence of infection was defined as any PCR or antibody-positive result.
    antibody-positive result.
    suggested: None
    Software and Algorithms
    SentencesResources
    Study Setting and Community Mobilization: U.S. census tract 022901 is a population-dense, 16-square-block (0.1 square-mile) area in San Francisco’s Mission District, with 5,174 residents of whom 58% are Latinx, 34% White/Caucasian, 5% Asian/Pacific Islander, and 1% Black/African American.
    Islander
    suggested: (Islander, RRID:SCR_007758)
    The study was supported by the Chan Zuckerberg Biohub, UCSF, and a Program for Breakthrough Biomedical Research award.
    Breakthrough Biomedical
    suggested: None
    ARCHITECT SARS-CoV-2 test kits were provided by Abbott Laboratories.
    Abbott Laboratories
    suggested: None
    To test for population structure, we used the Python package scikit-allel to compute Hudson’s F ST8 between the Mission District study census tract and sequences from GISAID9 representing the rest of San Francisco (Supplemental Table S3), including at most 1 sample per household (the first lexicographically), and including all variant sites in the multiple alignment with at most 5 missing alleles.
    Python
    suggested: (IPython, RRID:SCR_001658)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has several limitations. SARS-CoV-2 PCR tests do not detect all cases and antibody sensitivity may be lower in asymptomatic infection which could have resulted in underestimation of cumulative incidence. False positive antibody results could result in overestimation of cumulative incidence and misclassification of prior infections. Fingerstick sampling could also impact antibody test performance. However, the EUA antibody test we used has been shown to have a high sensitivity (96.9-100%) at ≥17-22 days post symptom onset, and high specificity (≥99.6%) with venous drawn plasma,24,25 and our estimates of cumulative incidence accounted for sensitivity and specificity of the PCR and antibody assays used. Second, selection bias in who chose to test may have affected our estimates. Although we adjusted for demographic differences between participants and community composition based on 2018 American Community Survey data, these data may not fully reflect tract demographics in 2020. However, population-based testing in a census tract allowed for greater clarity in understanding who did not participate. Lastly, we relied on self-reported symptoms and survey responses, which may have resulted in misclassification. With follow-up of PCR-positive participants over two weeks, we were able to further explore symptom status, allowing for monitoring and reclassification. In conclusion, improving access to SARS-CoV-2 testing, regardless of symptoms, through community-led, low-barrie...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a protocol registration statement.

    About SciScore

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  3. Version published to 10.1101/2020.06.15.20132233v1 on medRxiv