Association of inhibitory NKG2A and activating NKG2D natural killer cell receptor genes with resistance to SARS-CoV-2 infection in a western Indian population

We have evaluated the association of polymorphisms in the intronic variable-number tandem repeat (VNTR) regions of the human NKG2D , NKG2A , and IL-1RN genes with resistance and/or susceptibility to SARS-CoV-2 infection in a total of 209 patients with SARS-CoV-2 infection (125 asymptomatic patients and 84 symptomatic patients with mild symptoms) and 355 healthy controls, using the PCR-RFLP method. The genotypic and allelic frequency distributions for an IL-1RN (VNTR) single-nucleotide polymorphism (SNP) were found to be comparable among the patient groups. Overall, in SARS-CoV-2 patients, NKG2A (rs2734440) showed a protective association in the codominant [(A/A vs. A/G): (OR = 0.53, 95% CI = 0.34–0.83, p = 0.006)], recessive [(A/A vs. A/G+G/G): (OR = 0.6, 95% CI = 0.39–0.92, p = 0.02)] and over-dominant [(A/A+G/G vs. A/G): (OR = 0.57, 95% CI = 0.38–0.84, p = 0.005)] models. Similarly, NKG2D (rs7980470) showed a protective association in the codominant [(A/A vs. A/G): (OR = 0.46, 95% CI = 0.3–0.7, p = 0.0003), codominant (A/A vs. G/G): (OR = 0.54, 95% CI = 0.31–0.71, p = 0.027)], recessive [(A/A vs. A/G+G/G): (OR = 0.47, 95% CI = 0.32–0.7, p = 0.0001) and over-dominant [(A/A+G/G vs. A/G): (OR = 0.56, 95% CI = 0.38–0.82, p = 0.003)] models. At the allelic level, there was a higher frequency of the “G” allele of NKG2D (rs7980470) in healthy controls than in patients with SARS-CoV-2 infection, suggesting that individuals with the “G” allele in the intronic region of NKG2D are likely to be protected against SARS-CoV-2 infection. Overall, our data suggest that polymorphisms in the host NKG2D and NKG2A genes have a protective role in SARS-CoV-2 infection, although the functional impact of these polymorphisms on control of SARS-CoV-2 infection remains unknown.