Cycle threshold values and SARS-CoV-2 variant associations with breakthrough infections: a retrospective study in Accra, Ghana

Breakthrough infections are defined as SARS-CoV-2 infections occurring ≥ 14 days after completing the primary COVID-19 vaccination series and remain a public health challenge, particularly in regions where immune-evasive variants are circulating. However, data on their virological and clinical profiles in low-resource settings are limited. This retrospective study was conducted from July to December 2022 in Accra, Ghana, among individuals testing positive for SARS-CoV-2. Real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) was performed using the Allplex™ 2019-nCoV Assay. Cycle threshold (Ct) values for the nucleocapsid (N), RNA-dependent RNA polymerase (RdRP), and envelope (E) genes, categorised as < 25, 25–30, or > 30. Variant identification targeted Alpha, Delta, and Omicron mutations using mutation-specific RT-PCR. Logistic regression was used to assess associations between vaccination status and demographic, clinical, and virological factors. Of the 268 samples analysed, 81 tested positive; 43.20% [n = 35] were vaccinated individuals. Median Ct-values for the N [27.13, IQR: 21.59–31.96] and E [24.57, IQR: 19.43–29.43] genes were significantly higher among vaccinated cases, indicating lower viral loads. Breakthrough infections were strongly associated with the Omicron variant [aOR = 4.38, p = 0.034]. Diarrhoea [aOR = 9.67, p = 0.022], sore throat [aOR = 8.99, p = 0.038], headache [aOR = 10.156, p = 0.039] and chills [aOR = 3.316, p = 0.046] were mostly associated with breakthrough infections. Ct-values of 25–30 [aOR = 11.33, p = 0.012] and > 30 [aOR = 4.01, p = 0.047] were significantly associated with breakthrough infection compared to Ct < 25 in breakthrough infections. Vaccinated individuals with SARS-CoV-2 infection had lower viral loads and were more likely to be infected with the Omicron variant. These findings reinforce the role of vaccination in reducing viral load and support the adoption of practical surveillance strategies, such as Ct value-based surveillance and variant screening in low middle-income countries facing similar constraints in genomic capacity and vaccine deployment.