Abstract:
BACKGROUND : Since there are currently no specific SARS-CoV-2 prognostic viral
biomarkers for predicting disease severity, there has been interest in using SARSCoV-
2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict
disease progression.
OBJECTIVE : This study assessed the association between in-hospital mortality
of hospitalized COVID-19 cases and Ct-values of gene targets specific to
SARS-CoV-2.
METHODS : Clinical data of hospitalized COVID-19 cases from Gauteng Province
from April 2020-July 2022 were obtained from a national surveillance system
and linked to laboratory data. The study period was divided into pandemic
waves: Asp614Gly/wave1 (7 June–22 Aug 2020); beta/wave2 (15 Nov 2020–6
Feb 2021); delta/wave3 (9 May–18 Sept 2021) and omicron/wave4 (21 Nov
2021–22 Jan 2022). Ct-value data of genes specific to SARS-CoV-2 according
to testing platforms (Roche-ORF gene; GeneXpert-N2 gene; Abbott-RdRp
gene) were categorized as low (Ct < 20), mid (Ct20–30) or high (Ct > 30).
RESULTS : There were 1205 recorded cases: 836(69.4%; wave1), 122(10.1%;wave2)
21(1.7%; wave3) and 11(0.9%;in wave4). The cases’ mean age(±SD) was 49 years
(±18), and 662(54.9%) were female. There were 296(24.6%) deaths recorded: 241
(81.4%;wave1), 27 (9.1%;wave2), 6 (2%;wave3), and 2 (0.7%;wave4) (p < 0.001).
Sample distribution by testing platforms was: Roche 1,033 (85.7%), GeneXpert
169 (14%) and Abbott 3 (0.3%). The median (IQR) Ct-values according to
testing platform were: Roche 26 (22–30), GeneXpert 38 (36–40) and Abbott
21 (16–24). After adjusting for sex, age and presence of a comorbidity, the
odds of COVID-19 associated death were high amongst patients with Ct
values 20–30[adjusted Odds Ratio (aOR) 2.25; 95% CI: 1.60–3.18] and highest amongst cases with Ct-values <20 (aOR 3.18; 95% CI: 1.92–5.27), compared
to cases with Ct-values >30.
CONCLUSION : Although odds of COVID19-related death were high amongst cases
with Ct-values <30, Ct values were not comparable across different testing
platforms, thus precluding the comparison of SARS-CoV-2 Ct-value results.
Description:
DATA AVAILABILITY STATEMENT : The data analyzed in this study is subject to the following
licenses/restrictions: Only anonymized data were provided to the
investigators for analysis. Requests to access these datasets should
be directed to National Institute of Communicable Diseases;
lucilleb@nicd.ac.za.