Contributors: COVID-19 Host Genetics Initiative; DeCOI Host Genetics Group; GEN-COVID Multicenter Study (Italy); Mount Sinai Clinical Intelligence Center; GEN-COVID consortium (Spain); GenOMICC Consortium; Japan COVID-19 Task Force; Regeneron Genetics Center; Apollo - University of Cambridge Repository; Butler-Laporte, Guillaume; Povysil, Gundula; Kosmicki, Jack A.; Cirulli, Elizabeth T.; Drivas, Theodore; Furini, Simone; Saad, Chadi; Schmidt, Axel; Olszewski, Pawel; Korotko, Urszula; Quinodoz, Mathieu; Çelik, Elifnaz; Kundu, Kousik; Walter, Klaudia; Jung, Junghyun; Stockwell, Amy D.; Sloofman, Laura G.; Jordan, Daniel M.; Thompson, Ryan C.; Del Valle, Diane; Simons, Nicole; Cheng, Esther; Sebra, Robert; Schadt, Eric E.; Kim-Schulze, Seunghee; Gnjatic, Sacha; Merad, Miriam; Buxbaum, Joseph D.; Beckmann, Noam D.; Charney, Alexander W.; Przychodzen, Bartlomiej; Chang, Timothy; Pottinger, Tess D.; Shang, Ning; Brand, Fabian; Fava, Francesca; Mari, Francesca; Chwialkowska, Karolina; Niemira, Magdalena; Pula, Szymon; Kenneth Baillie, J; Stuckey, Alex; Salas, Antonio; Bello, Xabier; Pardo-Seco, Jacobo; Gómez-Carballa, Alberto; Rivero-Calle, Irene; Martinón-Torres, Federico; Ganna, Andrea; Karczewski, Konrad J.; Veerapen, Kumar; Bourgey, Mathieu; Bourque, Guillaume; JM Eveleigh, Robert; Forgetta, Vincenzo; Morrison, David; Langlais, David; Lathrop, Mark; Mooser, Vincent; Nakanishi, Tomoko; Frithiof, Robert; Hultström, Michael; Lipcsey, Miklo; Marincevic-Zuniga, Yanara; Nordlund, Jessica; Schiabor Barrett, Kelly M.; Lee, William; Bolze, Alexandre; White, Simon; Riffle, Stephen; Tanudjaja, Francisco; Sandoval, Efren; Neveux, Iva; Dabe, Shaun; Casadei, Nicola; Motameny, Susanne; Alaamery, Manal; Massadeh, Salam; Aljawini, Nora; Almutairi, Mansour S.; Arabi, Yaseen M.; Alqahtani, Saleh A.; Al Harthi, Fawz S.; Almutairi, Amal; Alqubaishi, Fatima; Alotaibi, Sarah; Binowayn, Albandari; Alsolm, Ebtehal A.; El Bardisy, Hadeel; Fawzy, Mohammad; Cai, Fang; Soranzo, Nicole; Butterworth, Adam; Host Genetics Initiative, COVID-19; Host Genetics Group, Decoi; Multicenter Study (Italy), GEN-COVID; Daga, Sergio; Meloni, Ilaria; Sinai Clinical Intelligence Center, Mount; consortium (Spain), GEN-COVID
Abstract: Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75–10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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