Universal Polymerase Chain Reaction and Antibody Testing Demonstrate Little to No Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community

  1. Ayesha Appa
  2. Saki Takahashi
  3. Isabel Rodriguez-Barraquer
  4. Gabriel Chamie
  5. Aenor Sawyer
  6. Elias Duarte
  7. Jill Hakim
  8. Keirstinne Turcios
  9. Joanna Vinden
  10. Owen Janson
  11. Aashish Manglik
  12. Michael J Peluso
  13. Steven G Deeks
  14. Timothy J Henrich
  15. Leonel Torres
  16. Mary Rodgers
  17. John Hackett
  18. Charles Chiu
  19. Diane Havlir
  20. Bryan Greenhouse

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Abstract

Background

Limited systematic surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the early months of the US epidemic curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using polymerase chain reaction (PCR) and antibody testing.

Methods

We conducted a cross-sectional survey of SARS-CoV-2 infection in the rural town of Bolinas, California (population 1620), 4 weeks after shelter-in-place orders. Participants were tested between April 20 and 24, 2020. Prevalence by PCR and seroprevalence from 2 forms of antibody testing were performed in parallel (Abbott ARCHITECT immunoglobulin [Ig]G and in-house IgG enzyme-linked immunosorbent assay).

Results

Of 1891 participants, 1312 were confirmed Bolinas residents (>80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (P < .05) if there were >3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% credible interval [CrI], 0.02%–0.46%). The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI, 95.75%–99.94%), compared with PPV 44.19%–63.32% (95% CrI, 3.25%–98.64%) if 1 test was utilized.

Conclusions

Four weeks after shelter-in-place, SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low-prevalence setting, use of 2 antibody tests increased seroprevalence estimate precision. This was one of the first community-wide studies to successfully implement synchronous PCR and antibody testing, particularly in a rural setting. Widespread testing remains an underpinning of effective disease control in conjunction with consistent uptake of public health measures.

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  1. Version published to 10.1093/ofid/ofaa531
  2. ScreenIT

    SciScore for 10.1101/2020.08.15.20175786: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: To pre-register, participants completed an online consent and survey (available in both English and Spanish), which included questions related to demographics, movement information, and past and current symptoms.
    IRB: Ethics Statement: The study protocol was submitted to UCSF’s Institutional Review Board, and the study was deemed public health surveillance not requiring IRB oversight [IRB number 20–30636].
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Samples were tested using two independent assays: 1) the ARCHITECT SARSCoV-2 IgG immunoassay, for antibodies to the SARS-CoV-2 nucleoprotein (Abbott Laboratories, Abbott Park, IL, USA)[17], and 2) an in-house ELISA assay detecting IgG to the receptor binding domain of spike protein, based on published protocols.[18,19] For the ELISA, all samples which had an optical density (OD) above the cutoff (plate-specific OD for the CR3022 monoclonal antibody at 8 ng/uL), were repeated with titering to obtain an estimate of antibody concentration.
    CR3022
    suggested: None
    Software and Algorithms
    SentencesResources
    The 2010 census estimated population was 1,620 persons with population density of 278 persons per square mile[15], while the American community survey (ACS) in 2018 estimated the population size to have declined to 1,077 persons, 46% percent of whom were aged 65 years and older.[16] The majority of the community is White/Caucasian (88%), including 2% Latinx, with 3% Asian/Pacific Islander and 9% reporting multiple races.
    Islander
    suggested: (Islander, RRID:SCR_007758)
    Samples were tested using two independent assays: 1) the ARCHITECT SARSCoV-2 IgG immunoassay, for antibodies to the SARS-CoV-2 nucleoprotein (Abbott Laboratories, Abbott Park, IL, USA)[17], and 2) an in-house ELISA assay detecting IgG to the receptor binding domain of spike protein, based on published protocols.[18,19] For the ELISA, all samples which had an optical density (OD) above the cutoff (plate-specific OD for the CR3022 monoclonal antibody at 8 ng/uL), were repeated with titering to obtain an estimate of antibody concentration.
    Abbott Laboratories
    suggested: None
    To further interpret the PCR results, we calculated the probability of observing x PCR positive cases, conditional on there being K true cases in the population of size N (of which we tested n).[20,21] Models also accounted for the sensitivity and specificity of the PCR test; we used values of 80% and 100%, respectively.[22,23] We used a Bayesian modeling approach to estimate population seroprevalence based on the results of the two antibody testing platforms, accounting for test performance characteristics.[24] For validation data, we used the package insert data for the Abbott test[17] (1066 of 1070 negative controls tested negative; 88 of 88 PCR+ positive controls tested positive), and in-house validation of the ELISA test (95 of 95 negative controls tested negative; 42 of 44 positive controls tested positive).
    Abbott
    suggested: (Abbott, RRID:SCR_010477)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study was subject to important limitations. For nearly all SARS-CoV-2 antibody tests, the true sensitivity when applied to a community-based sample where the majority of infected individuals will have experienced mild or asymptomatic SARS-CoV-2 infections is unknown, as test performance characteristics have generally been calculated based on severe infections only.[37–39] We note that here, at least, sensitivity for the ELISA was evaluated largely on mild (though not asymptomatic) infections. In this particular population with low prevalence of active or prior infection, false negative results were less of a concern and would have minimally changed seroprevalence estimates. Next, it is possible that we sampled a biased subset of the community, e.g. with certain demographic groups or those experiencing illness less likely to leave their homes for testing. However, we estimated relatively high community ascertainment (>80%) and also tested home-bound participants, mitigating this factor. Finally, not all participants completed the epidemiologic survey, which may have introduced selection bias in that those who elected to share information about mask-wearing and movement during shelter-in-place were more likely to report socially desirable values. However, community members reported anecdotal observations consistent with our overall study findings. In conclusion, active and prior SARS-CoV-2 infections were rare in this rural town with a high uptake of mask-wearing and compli...

    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.
    • No protocol registration statement was detected.

    About SciScore

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  3. Version published to 10.1101/2020.08.15.20175786v1 on medRxiv