COVID-19 severity may link to weak spots in immune system — Genome study

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People infected by the novel coronavirus can have symptoms that range from mild to deadly. Now, two new analyses suggest that some life-threatening cases can be traced to weak spots in patients’ immune systems. At least 3.5% of study patients with severe COVID-19, the disease caused by the novel coronavirus, have mutations in genes involved in antiviral defence. And at least 10 percent of patients with severe disease create “auto-antibodies” that attack the immune system, instead of fighting the virus.

The results identify some root causes of life-threatening COVID-19, says study leader Jean-Laurent Casanova, a Howard Hughes Medical Institute investigator at The Rockefeller University.

Seeing these harmful antibodies in so many patients – 101 out of 987 – was “a stunning observation,” he says. “These two papers provide the first explanation for why COVID-19 can be so severe in some people, while most others infected by the same virus are okay.”

The work has immediate implications for diagnostics and treatment, Casanova says. If someone tests positive for the virus, they should “absolutely” be tested for the auto-antibodies, too, he adds, “with medical follow-up if those tests are positive.” It’s possible that removing such antibodies from the blood could ease symptoms of the disease. Casanova’s team, in collaboration with clinicians around the world, first began enrolling COVID-19 patients in their study in February. At the time, they were seeking young people with severe forms of the disease to investigate whether these patients might have underlying weaknesses in their immune systems that made them especially vulnerable to the virus.

The plan was to scan patients’ genomes – in particular, a set of 13 genes involved in interferon immunity against influenza. In healthy people, interferon molecules act as the body’s security system. They detect invading viruses and bacteria and sound the alarm, which brings other immune defenders to the scene.

Casanova’s team has previously discovered genetic mutations that hinder interferon production and function. People with these mutations are more vulnerable to certain pathogens, including those that cause influenza. Finding similar mutations in people with COVID-19, the team thought, could help doctors identify patients at risk of developing severe forms of the disease. It could also point to new directions for treatment, he says.

In March, Casanova’s team was aiming to enrol 500 patients with severe COVID-19 worldwide in their study. By August, they had more than 1,500, and they now have over 3,000. As the researchers began analysing patient samples, they started to uncover harmful mutations, in people young and old. The team found that 23 out of 659 patients studied carried errors in genes involved in producing antiviral interferons.

Without a full complement of these antiviral defenders, COVID-19 patients wouldn’t be able to fend off the virus, the researchers suspected. That thought sparked a new idea. Maybe other patients with severe COVID-19 also lacked interferons – but for a different reason. Maybe some patients’ bodies were harming these molecules themselves. As in autoimmune disorders such as type 1 diabetes and rheumatoid arthritis, some patients might be making antibodies that target the body. “That was the eureka moment for us,” Casanova says.

The team’s analysis of 987 patients with life-threatening COVID-19 revealed just that. At least 101 of the patients had auto-antibodies against an assortment of interferon proteins. “We said, ‘bingo’!” Casanova remembers. These antibodies blocked interferon action and were not present in patients with mild COVID-19 cases, the researchers discovered.

“It’s an unprecedented finding,” says study co-author Isabelle Meyts, a paediatrician at the University Hospitals KU Leuven, in Belgium, who earlier this year helped enrol patients in the study, gather samples, and perform experiments. By testing for the presence of these antibodies, she says, “you can almost predict who will become severely ill.”

The vast majority – 94% – of patients with the harmful antibodies were men, the team found. Men are more likely to develop severe forms of COVID-19, and this work offers one explanation for that gender variability, Meyts says.

Casanova’s lab is now looking for the genetic driver behind those auto-antibodies. They could be linked to mutations on the X chromosome, he says. Such mutations might not affect women, because they have a second X chromosome to compensate for any defects in the first. But for men, who carry only a single X, even small genetic errors can be consequential.

Looking ahead Clinically, the team’s new work could change how doctors and health officials think about vaccination distribution strategies, and even potential treatments. A clinical trial could examine, for instance, whether infected people who have the auto-antibodies benefit from treatment with one of the 17 interferons not neutralised by the auto-antibodies, or with plasmapheresis, a medical procedure that strips the antibodies from patients’ blood. Either method could potentially counteract the effect of these harmful antibodies, Meyts says.

In addition to the current work, Meyts, Casanova, and hundreds of other scientists involved with an international consortium called the COVID Human Genetic Effort are working to understand a second piece of the coronavirus puzzle. Instead of hunting for factors that make patients especially vulnerable to COVID-19, they’re looking for the opposite – genetic factors that might be protective. They’re now recruiting people from the households of patients with severe COVID-19 – people who were exposed to the virus but did not develop the disease. “Our lab is currently running at full speed,” Casanova says.

Abstract 1
Interindividual clinical variability in the course of SARS-CoV-2 infection is immense. We report that at least 101 of 987 patients with life-threatening COVID-19 pneumonia had neutralizing IgG auto-Abs against IFN-ω (13 patients), the 13 types of IFN-α (36), or both (52), at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1,227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 were men. A B cell auto-immune phenocopy of inborn errors of type I IFN immunity underlies life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men.

Paul Bastard, indsey B Rosen, Qian Zhang, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Yu Zhang, Karim Dorgham, Quentin Philippot, Jérémie Rosain, Vivien Béziat, Jérémy Manry, Elana Shaw, Liis Haljasmägi, Pärt Peterson, Lazaro Lorenzo, Lucy Bizien, Sophie Trouillet-Assan, Kerry Dobbs, Adriana Almeida de Jesus, Alexandre Belot, Anne Kallaste, Emilie Catherinot, Yacine Tandjaoui-Lambiotte, Jeremie Le Pen, Gaspard Kerner, Benedetta Bigio, Yoann Seeleuthner, Rui Yang, Alexandre Bolze, András N Spaan, Ottavia M Delmonte, Michael S Abers, Alessandro Aiuti, Giorgio Casari, Vito Lampasona, Lorenzo Piemonti, Fabio Ciceri, Kaya Bilguvar, Richard P. Lifton, Marc Vass, David M Smadja, Mélanie Migaud, Jérome Hadjadj, Benjamin Terrier, Darragh Duffy, Lluis Quintana-Murci, Diederik van de Beek, Lucie Roussel, Donald C Vinh, Stuart G Tangye, Filomeen Haerynck, David Dalmau, Javier Martinez-Picado, Petter Brodin, Michel C Nussenzweig, Stéphanie Boisson-Dupuis, Carlos Rodríguez-Gallego, Guillaume Vogt, Trine H Mogensen, Andrew J Oler, Jingwen Gu, Peter D Burbelo, Jeffrey Cohen, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angio, Paolo Bonfanti, Patrick Rossignol, Julien Mayaux, Frédéric Rieux-Laucat, Eystein S Husebye, Francesca Fusco, Matilde Valeria Ursini, Luisa Imberti, Alessandra Sottini, Simone Paghera, Eugenia Quiros-Roldan, Camillo Rossi, Riccardo Castagnoli, Daniela Montagna, Amelia Licari, Gian Luigi Marseglia, Xavier Duval, Jade Ghosn, John S Tsang,Raphaela Goldbach-Mansky, Kai Kisand, Michail S Lionakis, Anne Puel,Shen-Ying Zhang,Steven M Holland,Guy Gorochov,Emmanuelle Jouanguy, Charles M Rice, Aurélie Cobat, Luigi D Notarangelo, Laurent Abel, Helen C Su, Jean-Laurent Casanova


Abstract 2
Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.

Qian Zhang, Paul Bastard, Zhiyong Liu, Jérémie Le Pen, Marcela Moncada-Velez, Jie Chen, Masato Ogishi, Ira KD Sabli, Stephanie Hodeib, Cecilia Korol, Jérémie Rosain, Kaya Bilguvar, Junqiang Ye, Alexandre Bolze,Benedetta Bigio,Rui Yang, Andrés Augusto Arias, Qinhua Zhou, Yu Zhang, Fanny Onodi, Sarantis Korniotis, Léa Karpf, Quentin Philippot, Marwa Chbihi, Lucie Bonnet-Madin, Karim Dorgham, Nikaïa Smith, William M Schneider, Brandon S Razooky, Hans-Heinrich Hoffmann, Eleftherios Michailidis, Leen Moens, Ji Eun Han, Lazaro Lorenzo, Lucy Bizien, Philip Meade, Anna-Lena Neehus, Aileen Camille Ugurbil, Aurélien Corneau, Gaspard Kerner,Peng Zhang, Franck Rapaport, Yoann Seeleuthner, Jeremy Manry, Cecile Masson, Yohann Schmitt, Agatha Schlüter, Tom Le Voyer, Taushif Khan, Juan Li, Jacques Fellay, Lucie Roussel, Mohammad Shahrooei, Mohammed F. Alosaimi, Davood Mansouri, Haya Al-Saud, Fahd Al-Mulla, Feras Almourfi, Saleh Zaid Al-Muhsen, Fahad Alsohime, Saeed Al Turki, Rana Hasanato, Diederik van de Beek, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angio, Paolo Bonfanti, Luisa Imberti, Alessandra Sottini, Simone Paghera, Eugenia Quiros-Roldan, Camillo Rossi, Andrew J Oler, Miranda F Tompkins, Camille Alba, Isabelle Vandernoot, Jean-Christophe Goffard, Guillaume Smits, Isabelle Migeotte, Filomeen Haerynck, Pere Soler-Palacin, Andrea Martin-Nalda, Roger Colobran, Pierre-Emmanuel Morange, Sevgi Keles, Fatma Çölkesen, Tayfun Ozcelik, Kadriye Kart Yasar, Sevtap Senoglu, Şemsi Nur Karabela, Carlos Rodríguez Gallego, Giuseppe Novelli, Sami Hraiech, Yacine Tandjaoui-Lambiotte, Xavier Duval, Cédric Laouénan, Andrew L Snow, Clifton L Dalgard, Joshua Milner, Donald C Vinh, Trine H. Mogensen, Nico Marr, András N Spaan, Bertrand Boisson, Stéphanie Boisson-Dupuis, Jacinta Bustamante, Anne Puel, Michael Ciancanelli, Isabelle Meyts, Tom Maniatis, Vassili Soumelis, Ali Amara, Michel Nussenzweig, Adolfo García-Sastre, Florian Krammer, Aurora Pujol, Darragh Duffy, Richard Lifton, Shen-Ying Zhang, Guy Gorochov, Vivien Béziat, Emmanuelle Jouanguy, Vanessa Sancho-Shimizu, Charles M Rice, Laurent Abel, Luigi D Notarangelo, Aurélie Cobat, Helen C Su, Jean-Laurent Casanova


Howard Hughes Medical Institute material


Science abstract 1


Science abstract 2

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