Prevalence evolution of SARS-CoV-2 infection in the city of São Paulo, 2020–2021

  1. José Olimpio Moura de Albuquerque
  2. Gabriela Akemi Kamioka
  3. Geraldine Madalosso
  4. Selma Anequini Costa
  5. Paula Bisordi Ferreira
  6. Francisco Alberto Pino
  7. Ana Paula Sayuri Sato
  8. Ana Carolina Aguiar de Carvalho
  9. Ana Beatriz Pagliaro Amorim
  10. Caroline Cotrim Aires
  11. Ana Paula Arruda Geraldes Kataoka
  12. Elisa San Martin Mouriz Savani
  13. Thirsa Alvares Franco Bessa
  14. Breno Souza de Aguiar
  15. Marcelo Antunes Failla
  16. Edson Aparecido dos Santos
  17. Edjane Maria Torreão Brito
  18. Maria Cristina Honório dos Santos
  19. Solange Maria Saboia e Silva
  20. Luiz Artur Vieira Caldeira
  21. Luiz Carlos Zamarco
  22. Sandra Maria Sabino Fonseca
  23. Marcia Maria de Cerqueira Lima
  24. Ivanilda Argenau Marques
  25. Fabiana Érica Vilanova da Silva
  26. Paula Regina Glasser
  27. Patrícia Carla Piragibe Ramos Burihan
  28. Cinthya Luzia Cavazzana
  29. Debora Silva de Mello
  30. Alessandra Cristina Guedes Pellini
  31. Fernando Yoshiki Nishio
  32. Fernanda Miyashiro Kian
  33. Elza de Santana Braga
  34. Nilza Maria Piassi Bertelli
  35. Wagner Fracini
  36. Marcelo Dell Áquila Gonçalves
  37. Paulete Secco Zular
  38. Regiane de Santana Piva
  39. Eduardo Masi

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Abstract

OBJECTIVE To estimate the evolution of the prevalence of SARS-CoV-2 virus infection among residents aged 18 years or over in the municipality of São Paulo. METHODS This is a population-based household survey conducted every 15 days, between June and September 2020, and January and February 2021. In total, the study comprised 11 phases. The presence of antibodies against SARS-CoV-2 was identified in venous blood using a lateral flow test, Wondfo Biotech. In the last phase, the researchers combined it with an immunoenzymatic test, Euroimmun. The participants also answered a semi-structured questionnaire on sociodemographic and economic factors, and on social distancing measures. Prevalence estimates and the 95% confidence interval were estimated according to regions, Human Development Index, sex, age group, ethnicity, education, income, and variables associated with risk or prevention of infection. To compare the frequencies among the categories of each variable, the chi-square test with Rao-Scott correction was used, considering a significance level of 5%. RESULTS In total, 23,397 individuals were interviewed and had their samples collected. The estimated prevalence of antibodies against SARS-CoV-2 ranged from 9.7% (95%CI: 7.9–11.8%) to 25.0% (95%CI: 21.7–28.7). The prevalence of individuals with antibodies against the virus was higher among black and brown people, people with lower schooling and income, and among residents of regions with lower Human Development Index. The lowest prevalences were associated with recommended measures of disease protection. The proportion of asymptomatic infection was 45.1%. CONCLUSION The estimated prevalence of the infection was lower than the cumulative incidence variation, except for the last phase of the study. The differences in prevalence estimates observed among subpopulations showed social inequality as a risk of infection. The lower prevalence observed among those who could follow prevention measures reinforce the need to maintain social distancing measures as a way to prevent SARS-CoV-2 infection.

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  1. Version published to 10.11606/s1518-8787.2021055003970
  2. ScreenIT

    SciScore for 10.1101/2021.06.16.21256530: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethical aspects: The study was approved by the Brazilian’s National Ethics Committee (CAAE 32947920.3.0000.0008).
    Consent: Blood sample were collected and the individual were interviewed only after written informed consent from all participants.
    Sex as a biological variablenot detected.
    RandomizationFor statistical data analyses, four phases were randomly chosen from the 11 phases performed in this study.
    Blindingnot detected.
    Power AnalysisThe sample size was increased to 12 dwellings to maintain the accuracy of the estimates affected by the non-response (closed households or refusals to participate in the study).

    Table 2: Resources

    Antibodies
    SentencesResources
    Testing and questionnaire: Testing was performed using the SARS-CoV-2 Antibody test® (Wondfo Biotech, Guangzhou, China) that detects IgM/IgG antibodies against SARS-CoV-2, without discriminating the type of immunoglobulin.
    SARS-CoV-2
    suggested: None
    In the last phase, to increase the sensitivity and the specificity of virus detection, the samples were also processed using an immunoenzymatic test (anti-SARS-CoV-2 ELISA) from EUROIMMUN, which uses the S1 spike protein as an antigen for the detection of IgG antibodies against SARS-CoV-2 in serum12,13.
    anti-SARS-CoV-2 ELISA
    suggested: None
    Software and Algorithms
    SentencesResources
    Data processing and analysis were performed using the statistical packages R and STATA version 13.
    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:
    This study has some limitations. It included the high rate of non-response, the address or the dwelling selected in the database were not identified (29.0%) or the selected individual refused to receive the work team or participate in the study (26.7%), since venous blood samples were collected instead of finger prick in order to increase the sensitivity of the test, as shown by Hallal et al.20 and Tess et al.21 The large number of teams (471) composed of employees of the primary healthcare units and responsible for data collection may have contributed to divergences in the approach of individuals to undergo the interview and the sample collection. The design effect (deff) observed for the prevalence estimates for the municipality and for the regions was higher than expected for stratified samples, possibly due to the large number of strata in the study8. The high deff contributed to the low accuracy of the estimates; therefore, future studies should review the sample design. Individuals under 18 years of age were not included in the sample. The use of a second test in phase 11 enhanced the sensitivity of the test. ELISA test detected 53.8% more positive cases than the rapid test. Possibly, the prevalence estimates may have been underestimated in phases 1 to 10. Serological tests may present false-negative results in the first days of the infection, therefore, it has little diagnostic value for acute cases. The proportion of negative cases among symptomatic individuals with s...

    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.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.06.16.21256530v1 on medRxiv