| Contributors: |
Matuozzo, D.; Talouarn, E.; Marchal, A.; Zhang, P.; Manry, J.; Seeleuthner, Y.; Zhang, Y.; Bolze, A.; Chaldebas, M.; Milisavljevic, B.; Gervais, A.; Bastard, P.; Asano, T.; Bizien, L.; Barzaghi, F.; Abolhassani, H.; Abou Tayoun, A.; Aiuti, A.; Alavi Darazam, I.; Allende, L. M.; Alonso-Arias, R.; Arias, A. A.; Aytekin, G.; Bergman, P.; Bondesan, S.; Bryceson, Y. T.; Bustos, I. G.; Cabrera-Marante, O.; Carcel, S.; Carrera, P.; Casari, G.; Chaibi, K.; Colobran, R.; Condino-Neto, A.; Covill, L. E.; Delmonte, O. M.; El Zein, L.; Flores, C.; Gregersen, P. K.; Gut, M.; Haerynck, F.; Halwani, R.; Hancerli, S.; Hammarstrom, L.; Hatipoglu, N.; Karbuz, A.; Keles, S.; Kyheng, C.; Leon-Lopez, R.; Franco, J. L.; Mansouri, D.; Martinez-Picado, J.; Metin Akcan, O.; Migeotte, I.; Morange, P. -E.; Morelle, G.; Martin-Nalda, A.; Novelli, G.; Novelli, A.; Ozcelik, T.; Palabiyik, F.; Pan-Hammarstrom, Q.; De Diego, R. P.; Planas-Serra, L.; Pleguezuelo, D. E.; Prando, C.; Pujol, A.; Reyes, L. F.; Riviere, J. G.; Rodriguez-Gallego, C.; Rojas, J.; Rovere-Querini, P.; Schluter, A.; Shahrooei, M.; Sobh, A.; Soler-Palacin, P.; Tandjaoui-Lambiotte, Y.; Tipu, I.; Tresoldi, C.; Troya, J.; Van De Beek, D.; Zatz, M.; Zawadzki, P.; Al-Muhsen, S. Z.; Alosaimi, M. F.; Alsohime, F. M.; Baris-Feldman, H.; Butte, M. J.; Constantinescu, S. N.; Cooper, M. A.; Dalgard, C. L.; Fellay, J.; Heath, J. R.; Lau, Y. -L.; Lifton, R. P.; Maniatis, T.; Mogensen, T. H.; Von Bernuth, H.; Lermine, A.; Vidaud, M. |
| Description: |
Background: 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. Methods: 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. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 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], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 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], P = 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; P = 1.68 × 10−5). Conclusions: 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 60years old. |