Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Abstract

<h3>Background</h3><p>We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases.</p><h3>Methods</h3><p>We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.</p><h3>Results</h3><p>No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was <em>TLR7</em>, with an OR of 27.68 (95%CI 1.5–528.7, <em>P</em> = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], <em>P</em> = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported <em>TYK2</em> and <em>TLR7</em> COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], <em>P</em> = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], <em>P</em> = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; <em>P</em> = 1.68 × 10−5).</p><h3>Conclusions</h3><p>Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.</p>