- van der Wijst, Monique GP;
- Vazquez, Sara E;
- Hartoularos, George C;
- Bastard, Paul;
- Grant, Tianna;
- Bueno, Raymund;
- Lee, David S;
- Greenland, John R;
- Sun, Yang;
- Perez, Richard;
- Ogorodnikov, Anton;
- Ward, Alyssa;
- Mann, Sabrina A;
- Lynch, Kara L;
- Yun, Cassandra;
- Havlir, Diane V;
- Chamie, Gabriel;
- Marquez, Carina;
- Greenhouse, Bryan;
- Lionakis, Michail S;
- Norris, Philip J;
- Dumont, Larry J;
- Kelly, Kathleen;
- Zhang, Peng;
- Zhang, Qian;
- Gervais, Adrian;
- Le Voyer, Tom;
- Whatley, Alexander;
- Si, Yichen;
- Byrne, Ashley;
- Combes, Alexis J;
- Rao, Arjun Arkal;
- Song, Yun S;
- Fragiadakis, Gabriela K;
- Kangelaris, Kirsten;
- Calfee, Carolyn S;
- Erle, David J;
- Hendrickson, Carolyn;
- Krummel, Matthew F;
- Woodruff, Prescott G;
- Langelier, Charles R;
- Casanova, Jean-Laurent;
- Derisi, Joseph L;
- Anderson, Mark S;
- Ye, Chun Jimmie;
- consortium, on behalf of the UCSF COMET;
- Abe-Jones, Yumiko;
- Alvarenga, Bonny;
- Asthana, Saurabh;
- Beagle, Alexander;
- Bhakta, Tanvi;
- Bhide, Sharvari;
- Cai, Cathy;
- Calvo, Maria;
- Carrillo, Sidney A;
- Chak, Suzanna;
- Collins, Zachary;
- Dandekar, Ravi;
- Darmanis, Spyros;
- Esmaili, Armond;
- Ghale, Rajani;
- Giberson, Jeremy;
- Glenn, Pat;
- Gonzalez, Ana;
- Jauregui, Alejandra;
- Jones, Norman;
- Ke, Serena;
- Lea, Tasha;
- Lee, Deanna;
- Lelidowicz, Aleskandra;
- Liu, Kathleen;
- Lota, Raphael;
- Matthay, Michael;
- Milush, Jeff;
- Nguyen, Viet;
- Nigam, Nishita;
- Ortiz, Gabe;
- Pierce, Logan;
- Prasad, Priya;
- Rajan, Jayant;
- Rashid, Ahmad Sadeed;
- Rodriguez, Nicklaus;
- Samad, Bushra;
- Scarlet, Diane;
- Shaw, Cole;
- Sigman, Austin;
- Sinha, Pratik;
- Spitzer, Matthew;
- Tang, Kevin;
- Altamirano, Luz Torres;
- Tumurbaatar, Erden;
- Willmore, Andrew;
- Wilson, Michael;
- Withers, Reese;
- Yee, Kimberly;
- Zamecnik, Colin;
- Zhan, Jenny;
- Zhou, Mingyue
Neutralizing autoantibodies against type I interferons (IFNs) have been found in some patients with critical coronavirus disease 2019 (COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the prevalence of these antibodies, their longitudinal dynamics across the disease severity scale, and their functional effects on circulating leukocytes remain unknown. Here, in 284 patients with COVID-19, we found type I IFN–specific autoantibodies in peripheral blood samples from 19% of patients with critical disease and 6% of patients with severe disease. We found no type I IFN autoantibodies in individuals with moderate disease. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 patients with COVID-19 and 26 non–COVID-19 controls revealed a lack of type I IFN–stimulated gene (ISG-I) responses in myeloid cells from patients with critical disease. This was especially evident in dendritic cell populations isolated from patients with critical disease producing type I IFN–specific autoantibodies. Moreover, we found elevated expression of the inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) on the surface of monocytes isolated from patients with critical disease early in the disease course. LAIR1 expression is inversely correlated with ISG-I expression response in patients with COVID-19 but is not expressed in healthy controls. The deficient ISG-I response observed in patients with critical COVID-19 with and without type I IFN–specific autoantibodies supports a unifying model for disease pathogenesis involving ISG-I suppression through convergent mechanisms.