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

Autor: Daniela, Matuozzo, Estelle, Talouarn, Astrid, Marchal, Jeremy, Manry, Yoann, Seeleuthner, Yu, Zhang, Alexandre, Bolze, Matthieu, Chaldebas, Baptiste, Milisavljevic, Peng, Zhang, Adrian, Gervais, Paul, Bastard, Takaki, Asano, Lucy, Bizien, Federica, Barzaghi, Hassan, Abolhassani, Ahmad Abou, Tayoun, Alessandro, Aiuti, Ilad Alavi, Darazam, Luis M, Allende, Rebeca, Alonso-Arias, Andrés Augusto, Arias, Gokhan, Aytekin, Peter, Bergman, Simone, Bondesan, Yenan T, Bryceson, Ingrid G, Bustos, Oscar, Cabrera-Marante, Sheila, Carcel, Paola, Carrera, Giorgio, Casari, Khalil, Chaïbi, Roger, Colobran, Antonio, Condino-Neto, Laura E, Covill, Loubna, El Zein, Carlos, Flores, Peter K, Gregersen, Marta, Gut, Filomeen, Haerynck, Rabih, Halwani, Selda, Hancerli, Lennart, Hammarström, Nevin, Hatipoğlu, Adem, Karbuz, Sevgi, Keles, Christèle, Kyheng, Rafael, Leon-Lopez, Jose Luis, Franco, Davood, Mansouri, Javier, Martinez-Picado, Ozge Metin, Akcan, Isabelle, Migeotte, Pierre-Emmanuel, Morange, Guillaume, Morelle, Andrea, Martin-Nalda, Giuseppe, Novelli, Antonio, Novelli, Tayfun, Ozcelik, Figen, Palabiyik, Qiang, Pan-Hammarström, Rebeca, Pérez de Diego, Laura, Planas-Serra, Daniel E, Pleguezuelo, Carolina, Prando, Aurora, Pujol, Luis Felipe, Reyes, Jacques G, Rivière, Carlos, Rodriguez-Gallego, Julian, Rojas, Patrizia, Rovere-Querini, Agatha, Schlüter, Mohammad, Shahrooei, Ali, Sobh, Pere, Soler-Palacin, Yacine, Tandjaoui-Lambiotte, Imran, Tipu, Cristina, Tresoldi, Jesus, Troya, Diederik, van de Beek, Mayana, Zatz, Pawel, Zawadzki, Saleh Zaid, Al-Muhsen, Hagit, Baris-Feldman, Manish J, Butte, Stefan N, Constantinescu, Megan A, Cooper, Clifton L, Dalgard, Jacques, Fellay, James R, Heath, Yu-Lung, Lau, Richard P, Lifton, Tom, Maniatis, Trine H, Mogensen, Horst, von Bernuth, Alban, Lermine, Michel, Vidaud, Anne, Boland, Jean-François, Deleuze, Robert, Nussbaum, Amanda, Kahn-Kirby, France, Mentre, Sarah, Tubiana, Guy, Gorochov, Florence, Tubach, Pierre, Hausfater, Isabelle, Meyts, Shen-Ying, Zhang, Anne, Puel, Luigi D, Notarangelo, Stephanie, Boisson-Dupuis, Helen C, Su, Bertrand, Boisson, Emmanuelle, Jouanguy, Jean-Laurent, Casanova, Qian, Zhang, Laurent, Abel, Aurélie, Cobat
Rok vydání: 2022
Předmět:
Zdroj: Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
medRxiv
Popis: BackgroundWe previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and auto-antibodies against type I IFN in another 15-20% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants wasTLR7, with an OR of 27.68 (95%CI:1.5-528.7,P=1.1×10−4), in analyses restricted to 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). Adding the recently reportedTYK2COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4];P=3.4×10−3). When these 14 loci andTLR7were considered, all individuals hemizygous (n=20) or homozygous (n=5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0],P=4.7×10−7), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9],P=0.02). Finally, the patients with pLOF or 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).ConclusionsRare 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.
Databáze: OpenAIRE
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