Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is an essential diagnostic tool used to accurately identify and confirm SARS-CoV-2 infection in patients who are showing symptoms or are suspected of being infected. The WHO recommends a combination of viral-specific genes, including the Envelope (E), the RdRP/Helicase (Hel), the spike protein-encoding gene (S), and the ORF1ab gene, as molecular targets for detection. Among the possible PCR targets, the E gene of SARS-CoV 2 is considered to be the least specific and it shows significant sequence homology to other common coronaviruses. The present study aimed at investigating the dynamics of ORF1ab and E gene from COVID–19 positive patients considering the Ct values of both genes. The study included population of 130 patients who showed symptoms of COVID-19 between November 2021 and February 2022 in Central Bosnia and Herzegovina. Out of these patients, 86 tested positive for the virus. For molecular confirmation of SARS-CoV-2, the RT-qPCR protocol was performed. Average Ct values were automatically generated with values ≤Ct30 reported as positive.