Outcomes of laboratory‐confirmed SARS‐CoV ‐2 infection in the Omicron‐driven fourth wave compared with previous waves in the Western Cape Province, South Africa
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Abstract
OBJECTIVES
The objective was to compare COVID‐19 outcomes in the Omicron‐driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.
METHODS
In this cohort study, we included public sector patients aged ≥20 years with a laboratory‐confirmed COVID‐19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.
RESULTS
We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta‐driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).
CONCLUSIONS
In the Omicron‐driven wave, severe COVID‐19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta‐driven wave.
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SciScore for 10.1101/2022.01.12.22269148: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the University of Cape Town and Stellenbosch University Health Research Ethics Committees and Western Cape Government: Health.
Consent: Individual informed consent requirement was waived for this secondary analysis of de-identified data.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not 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:Our …
SciScore for 10.1101/2022.01.12.22269148: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the University of Cape Town and Stellenbosch University Health Research Ethics Committees and Western Cape Government: Health.
Consent: Individual informed consent requirement was waived for this secondary analysis of de-identified data.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not 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:Our analysis also has several limitations. First, we compared outcomes across waves as a proxy for the variant that dominated in each wave, and not in patients with genomically confirmed variants. Second, while health service pressures which impact disease outcomes are likely to be more similar at “equivalent wave periods”, identifying such “equivalent periods” across waves can be challenging. However, results were similar when using slightly different wave periods. Third, adjustment for comorbidities was limited to those algorithmically identified in the WCPHDC and does not include undiagnosed comorbidities and other important risk factors for poor COVID-19 outcomes such as obesity. Fourth, prior diagnosed infections substantially under-ascertain all prior infections, and while we addressed this by determining the likely impact of undiagnosed infections in wave four, this is based on assumptions. Fifth, we could not distinguish between admissions and deaths where the diagnosis of COVID-19 may have been incidental or contributory rather than causal. However, our main analysis focused on mortality and we found stronger protection of both wave four and vaccination against the more severe outcomes (severe hospitalization and/or death), suggesting that results are robust despite misclassification of admissions with incidental COVID-19. Nonetheless, a different clinical profile of hospitalized and deceased patients with COVID-19 has been reported, with less COVID-19 pneumonia and ...
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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