A national cohort study of COVID-19 in-hospital mortality in South Africa: the intersection of communicable and non-communicable chronic diseases in a high HIV prevalence setting

  1. WAASILA JASSAT
  2. Cheryl Cohen
  3. Stefano Tempia
  4. Maureen Masha
  5. Susan Goldstein
  6. Tendesayi Kufa-Chakezha
  7. Pelagia Murangandi
  8. Dana Savulescu
  9. Sibongile Walaza
  10. Jamy-Lee Bam
  11. Mary-Ann Davies
  12. Hans W Prozesky
  13. Jonathan Naude
  14. Trevor Mnguni
  15. Charlene A Lawrence
  16. Hlengani Mathema
  17. Jarrod Zamparini
  18. John Black
  19. Ruchika Mehta
  20. Arifa Parker
  21. Perpetual Chikobvu
  22. Halima Dawood
  23. Ntshengedzeni Muvhango
  24. Riaan Strydom
  25. Tsholofelo Adelekan
  26. Bhekizizwe Mdlovu
  27. Nirvasha Moodley
  28. Eunice L Nemavhandu
  29. Paul Rheeder
  30. Jacqueline Venturas
  31. Nombulelo Magula
  32. Lucille Blumberg

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Abstract

Background: The interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis (TB) are unclear, particularly in low- and middle-income countries in Africa. South Africa has a national adult HIV prevalence of 19% and TB prevalence of 0.7%. Using a nationally representative hospital surveillance system in South Africa, we investigated the factors associated with in-hospital mortality among individuals with COVID-19. Methods: Using data from national active hospital surveillance, we describe the demographic characteristics, clinical features, and in-hospital mortality among hospitalised individuals testing positive for SARS-CoV-2, during 5 March 2020 to 27 March 2021. Chained equation multiple imputation was used to account for missing data and random effect multivariable logistic regression models were used to assess the role of HIV-status and underlying comorbidities on in-hospital COVID-19 mortality. Findings: Among the 219,265 individuals admitted with laboratory confirmed SARS-Cov-2, 51,037 (23.3%) died. Most commonly observed comorbidities among individuals with available data were hypertension (61,098/163,350; 37.4%), diabetes (43,885/159,932; 27.4%), and HIV (13,793/151,779; 9.1%), while TB was reported in 3.6% (5,282/146,381) of individuals. While age was the most important predictor, other factors associated with in-hospital COVID-19 mortality were HIV infection [aOR 1.34, 95% CI: 1.27-1.43), past TB [aOR 1.26, 95% CI: 1.15-1.38), current TB [aOR 1.42, 95% CI: 1.22-1.64) and both past and current TB [aOR 1.48, 95% CI: 1.32-1.67) compared to never TB, as well as other described risk factors for COVID-19, such as male sex, non-white race, and chronic underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy. After adjusting for other factors, PLWH not on ART [aOR 1.45, 95% CI: 1.22-1.72] were more likely to die in-hospital compared to PLWH on ART. Among PLWH, the prevalence of other comorbidities was 29.2% compared to 30.8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with increased mortality risk in both PLWH and HIV-uninfected individuals. Interpretation: Identified high risk individuals (older individuals and those with chronic comorbidities and PLWH, particularly those not on ART) would benefit from COVID-19 prevention programmes such as vaccine prioritisation, as well as early referral and treatment. Funding: South African National Government

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  1. Version published to 10.1101/2020.12.21.20248409v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2020.12.21.20248409: (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

    No key resources detected.

    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:
    (57) Strengths and Limitations: The main strengths of the DATCOV hospital surveillance system are the large numbers of hospital admissions reported, that it is representative across all provinces and the public and private health sector in South Africa, and that it provides real-time data. The limitations of this surveillance are representation bias as DATCOV did not initially include all public hospitals with COVID-19 admissions and therefore may have a bias towards the private sector of South Africa. The Department of Health decided in mid-July to implement this surveillance system across all hospitals, and DATCOV will soon be a fully representative surveillance system. Furthermore, DATCOV only reports hospital-based admissions and deaths and therefore does not include deaths occurring outside hospitals. Non-COVID-19 deaths were reported following medical panel review, however it is possible that some deaths were misclassified. Data quality in a surveillance system is dependent on the information submitted by healthcare institutions. We used multiple imputation to address missing data; however, the validity of the imputed data relies on the assumption that data were missing at random. Fields with the highest proportion of incomplete data include race and comorbidities. HIV prevalence among hospitalised cases was less than community HIV prevalence because of higher reporting of data by the private sector; however, HIV prevalence among hospitalised individuals in the public 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.

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  3. Version published to 10.1101/2020.12.21.20248409v1 on medRxiv