SARS-CoV-2 Genomic Variants and Their Relationship with the Expressional and Genomic Profile of Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Serine Protease 2 (TMPRSS2)

Abstract

Over the past four years, angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) have been extensively studied, given their important role in SARS-CoV-2 replication; however, most studies have failed to compare their behavior in the face of different SARS-CoV-2 genomic variants. Therefore, this study evaluated the influence of different variants in ACE2/TMPRSS2 expressional and genomic profiles. To achieve this, 160 nasopharyngeal samples, previously detected with SARS-CoV-2 via RT-qPCR (June 2020-July 2022), were quantified for ACE2/TMPRSS2 expression levels, also using RT-qPCR; SARS-CoV-2 genomic variants, along with polymorphisms in the ACE2/TMPRSS2 coding genes, were identified using nanopore sequencing. In order of appearance, the B.1.1.28, Zeta, Gamma, and Omicron variants were identified in this study. The ACE2 levels were higher when B.1.1.28 was present, possibly due to the ACE2/spike binding affinity; the TMPRSS2 levels were also higher in the presence of B.1.1.28, probably attributable to inefficient usage of the TMPRSS2 pathway by the other variants, as well as to the decrease in protease transcription factors when in the presence of Omicron. The rs2285666 (ACE2) polymorphism was less frequent when B.1.1.28 was present, which is befitting, since rs2285666 increases ACE2/spike binding affinity. In conclusion, SARS-CoV-2 genomic variants appear to exhibit varying impacts in regards to ACE2/TMPRSS2 genomic and expressional behavior.

Keywords: genomic variants; host–parasite; viral infection.

Figure 1

Description of sampling periods, along with the most prevalent SARS-CoV-2 variant, the number of selected samples, and the total number of samples available for each period. Each sampling period (Period I–Period IV) was 4 months long. Below the table are listed the most prevalent SARS-CoV-2 variants within each sampling period, and above the table, the total number of available samples that followed the selection criteria is included. * Indicates a greater difference between the number of selected samples and the total number of available samples.

Figure 2

Number of cases of each SARS-CoV-2 genomic variant within the sampling period. Demonstration of the number of identified cases for different SARS-CoV-2 genomic variants during the sampling periods.

Figure 3

ACE2 expression in nasopharyngeal samples infected with different SARS-CoV-2 genomic variants. Comparison of ACE2 expression levels in nasopharyngeal samples detected for SARS-CoV-2 variants B.1.1.28, Zeta, Gamma, and Omicron. After the employment of an independent samples Kruskal–Wallis test, significant differences were established, represented by * p < 0.05. The Y-axis plots the absolute quantity (AQ) of RNA per microliter of sample, while the X-axis plots the different genomic variants. Box plots display the median (line), interquartile range (box), and minimum and maximum values (bars).

Figure 4

TMPRSS2 expression in nasopharyngeal samples infected with different SARS-CoV-2 genomic variants. Comparison of TMPRSS2 expression levels in nasopharyngeal samples detected with SARS-CoV-2 variants B.1.1.28, Zeta, Gamma, and Omicron. After the employment of an independent samples Kruskal–Wallis test, significant differences were established, represented by * p < 0.05. The Y-axis plots the absolute quantity (AQ) of RNA per microliter of sample, while the X-axis plots the different genomic variants. Box plots display the median (line), interquartile range (box), and minimum and maximum values (bars).

Figure 5

Agarose gel with PCR products for the four SNPs research regions. Picture of the 1.5% agarose gel with PCR products of the multiplex PCR for the four SNPs research regions, alongside a 100 bp ladder; bp: base pairs.

Figure 6

Frequency of rs2285666 in nasopharyngeal samples with the presence of different genomic SARS-CoV-2 variants. Comparison of the frequency of rs2285666 in nasopharyngeal samples detected for SARS-CoV-2 variants B.1.1.28, Zeta, Gamma, and Omicron. After the employment of a Pearson’s chi-squared test, significant differences were established, represented by * p < 0.05. The Y-axis plots the frequency of rs2285666 SNP, while the X-axis plots the different genomic variants.

Figure 7

ACE2 and TMPRSS2 expression in health professionals’ and non-health professionals’ nasopharyngeal samples. Comparison of ACE2 and TMPRSS2 expression in SARS-CoV-2-detected nasopharyngeal samples of health professionals (HP) and non-health professionals (NHP). After the employment of an independent samples Kruskal–Wallis test, significant differences were established, represented by * p < 0.05. The Y-axis plots the absolute quantity (AQ) of RNA per microliter of sample, while the X-axis plots the results for the health professionals (HP) and non-health professionals (NHP). Box plots display the median (line), interquartile range (box), and minimum and maximum values (bars).