Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality

• Published in: Frontiers in Epidemiology (Online) 2024, Vol.4, p.1375975-1375975
• Main Authors: Sikhosana, Mpho L, Welch, Richard, Musekiwa, Alfred, Makatini, Zinhle, Ebonwu, Joy, Blumberg, Lucille, Jassat, Waasila
• Format: Article
• Language: English
• Subjects: Ct values; mortality; PCR; SARS-CoV-2; South Africa
• ISSN: 2674-1199; 2674-1199
• DOI: 10.3389/fepid.2024.1375975

Since there are currently no specific SARS-CoV-2 prognostic viral biomarkers for predicting disease severity, there has been interest in using SARS-CoV-2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict disease progression. 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. 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  30). 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) (