Using RT-PCR Testing to Assess the Effectiveness of Outbreak Control Efforts in São Paulo State, the Pandemic’s Epicenter in Brazil, according to Socioeconomic Vulnerabilities

  1. Tatiane C M Sousa
  2. Natália P Moreira
  3. Jose E. Krieger
  4. Isabel S C Rosa
  5. Marcela M. Zamudio
  6. Maria Amélia S M Veras
  7. Brigina Kemp
  8. Lorena G. Barberia

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Abstract

Background

The testing of infected persons with SARS-CoV-2 is one of the cornerstones of an effective strategy deployed for pandemic control. The public health diagnostic effort is particularly important in regions with a critical transmission scenario and in vulnerable populations in these districts, such as São Paulo state, the Brazilian epicenter of the COVID-19 pandemic.

Methods

We developed an RT-PCR testing intensity effort index (RT-PCR TIEI) composed of seven indicators to assess the survelliance efforts in the São Paulo State. We used dynamic time-series cross-sectional models to analyze the association between the RT-PCR TIEI, the population living under high socioeconomic vulnerability levels, dependent on public health service (SUS), per capita income, and population density.

Results

On average, the RT-PCR TIEI score was 21.07. In the long-run, the RT-PCR TIEI is negatively associated with socioeconomic vulnerability (p-value=0.000, 95% CI −0.887, - 0.811), with a higher proportion of the population dependent on SUS (p-value= 0.000, 95% CI −0.871, −0.805), per capita income (p-value= 0.000, 95% CI −0.849,-0.792) and with population density (p-value=0.000, 95% CI −0.853; −0.801).

Conclusion

Testing efforts declined as the pandemic advanced, and the the lowest RT-PCR TIEI values were found in the most socioeconomic vulnerable RHDs. Local public laboratory presence was a predictor of a higher score. Thus, the low testing RT-PCR efforts and local laboratory inequalities affected surveillance capability, especially for socioeconomic vulnerable populations.

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  1. ScreenIT

    SciScore for 10.1101/2020.10.29.20221960: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All analyses were performed using STATA version 16.
    STATA
    suggested: (Stata, RRID:SCR_012763)

    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:
    There are limitations to this study. The Health Secretariat’s Intelligent Monitoring System does not report anonymized individual RT-PCR testing data conducted in private labs (12). Given these limitations, we were not able to estimate the diagnostic RT-PCR test turnaround time. Given our goal of assessing RT-PCR testing efforts in public laboratories, our study also highlights that the Brazilian Health System (SUS) can play an instrumental role in reducing inequalities. Its decentralized structure allows for targeted policies, considering the distinct epidemiological profiles and vulnerabilities (33). During pandemics, control measures must be guided by the characteristics of the pandemic settings and the health system’s capacity in different locations. In this regard, the SUS allows municipalities and RHDs to adopt distinct strategies to test, identify, and isolate infected people, contact tracking, and quarantine infected people. Finally, our data suggest that in addition to the improvement in testing capacity, the autonomy of RHDs to modify their surveillance and control measures requires that federal and state authorities adopt policies that are aligned with these efforts, which was not the case through the course of the pandemic.

    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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  2. Version published to 10.1101/2020.10.29.20221960v3 on medRxiv
  3. Version published to 10.1101/2020.10.29.20221960v2 on medRxiv
  4. Version published to 10.1101/2020.10.29.20221960v1 on medRxiv