Investigation of mRNA expressions in nasopharyngeal and oropharyngeal swab samples in active SARS-CoV-2 infection and after SARS-CoV-2 infection

SARS-CoV-2 enters host cells primarily through angiotensin-converting enzyme 2 (ACE2) and requires proteolytic activation by transmembrane serine protease 2 (TMPRSS2) or cysteine proteases cathepsin B and L (CTSB/L). The expression levels of these host factors may influence viral entry, tissue tropism, and disease severity. This study aimed to investigate differences in ACE2, TMPRSS2, CTSB, and CTSL gene expression in nasopharyngeal and oropharyngeal swab samples obtained from individuals during active SARS-CoV-2 infection and in the post-infection period. Nasopharyngeal and oropharyngeal swab samples (active infection: n = 24; post-infection: n = 24) were collected and placed in viral transport medium. After RNA isolation was performed, complementary DNA synthesis was carried out with FIREScript RT cDNA Synthesis Mix with Oligo (dT), and gene expression was quantified using 5× HOT FIREPol EvaGreen qPCR Mix Plus (no ROX) (Solis BioDyne®). Relative expression levels were determined using the 2−ΔΔCT method. ACE2 expression was 4.2-fold higher in the active infection group than in the post-infection group (p < 0.05), whereas TMPRSS2, CTSB, and CTSL expression did not differ significantly between groups (p > 0.05). Within the active infection group, CTSB expression was 10.4-fold higher in nasopharyngeal swabs compared to oropharyngeal swabs (p = 0.035). TMPRSS2 expression showed a non-significant trend toward a 3-fold reduction in nasopharyngeal samples (p = 0.051). In the post-infection group, CTSB expression was approximately 2-fold higher and CTSL expression 3-fold lower in nasopharyngeal versus oropharyngeal samples (p > 0.05). Notably, TMPRSS2 expression was significantly reduced (~ 7-fold) in nasopharyngeal compared to oropharyngeal swabs (p = 0.041). Our findings demonstrate that ACE2, TMPRSS2, CTSB, and CTSL exhibit dynamic and site-specific expression patterns during and after SARS-CoV-2 infection. The elevated ACE2 expression in active infection and differential regulation of proteases between nasopharyngeal and oropharyngeal sites suggest distinct host–virus interactions depending on anatomical localization.