biostudies-literatureGrant RANCATS NIH HHSNIA NIH HHSNIAID NIH HHSNHLBI NIH HHSNCI NIH HHSNIH HHSNIGMS NIH HHSCSRD VA635-641https://www.ebi.ac.uk/biostudies/studies/S-EPMC7987233biostudies-literatureUnknown590(7847)Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome¹ (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia². Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencNatureCircuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.PMC7987233R01 HL134800K07 CA216330F31 AG071225S10 OD011996UL1 TR001422R01 HL149883T32 AG020506K08 HL159356I01 CX001777T32 HL0761391S10OD011996-01HL134800P30 CA060553L30 CA153420HL147290P01 AG049665K99 AG068544HL147575R01 HL147290R01 HL154686K08 HL128867R01 HL153312R01 HL131745U19 AI135964GM129312R56 HL135124R01 HL145478HL14578R01 HL147575F32 HL151127R01 GM129312Fiala JASecunda KAren KPawlowski AEGoldberg IAZak TJGottardi CJKurihara CGrant RAMalsin ESPickens COPatel RGo PDGao CARidge KMSoulakis NDBudinger GRSBorkowski NSwaminathan SJain MCarns MWunderink RGLeibenguth EMColeman JDonnelly HKReyfman PAArgento ACNunes Amaral LALiu GYAbbott DASala MAOzer EAWang AASznajder JIArnold JMKhan NHChandel NSRen ZCooper PRHan SBartom ETWolfe ARCuttica MJSchroedl CJSchneider DKamp DWSeed PCGadhvi GTNU SCRIPT Study InvestigatorsSmith SBTodd KQuerrey MTran BMeza DShanes EDGuzman ERSaine MGatesy SWMMorimoto RIQi CLomasney JWRivas ORKim SSKihshen HMarkov NSLu ZWagh AAYeldandi AVNavarro HTDonayre AWalter JMHorvath CMStoeger TRosenbaum MLKandpal MMylvaganam RJLombardo TAKang MSichizya LPrickett MHWehbe FStarren JRussell SRGreen SJShilatifard ABharat ASporn PHSHauser ARLe JPoor TADematte JEMisharin AVGarza-Castillon RMorales-Nebreda LThakrar ANannapaneni PJoudi AMSinger BDThakkar SRosenberg SRTextor LNShamaly TPesce LLBen Maamar STomic RAbdala-Valencia HKruser JMDeters JSBailey JILevenson ARGradone LDRendleman EJPolitanska YWinter DRWolfe LFKalhan ROdell DDDu JCAlexander MJKlug ZMGates KLNozick SfalseCircuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome¹ (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia². Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequenc2021-01-01T00:00:00Z2021 Feb2026-04-30T17:12:54.376Z2022-02-10T18:55:01.513ZS-EPMC79872333342941810.1038/s41586-020-03148-w