{"doi":"10.1101/2021.06.28.450153","title":"Myeloid cell interferon responses correlate with clearance of SARS-CoV-2","abstract":"Abstract The emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. While studies have reported immune profiling using single cell RNA sequencing in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. We performed longitudinal single-cell RNA sequencing of bronchoalveolar lavage (BAL) cell suspensions from adult rhesus macaques infected with SARS-CoV-2 (n=6) to delineate the early dynamics of immune cells changes. The bronchoalveolar compartment exhibited dynamic changes in transcriptional landscape 3 days post-SARS-CoV-2-infection (3dpi) (peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline). We observed the accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I IFN response was highly induced in the plasmacytoid dendritic cells. The presence of a distinct HLADR + CD68 + CD163 + SIGLEC1 + macrophage population exhibiting higher angiotensin converting enzyme 2 (ACE2) expression was also observed. These macrophages were significantly recruited to the lungs of macaques at 3dpi and harbored SARS-CoV-2, while expressing a strong interferon-driven innate anti-viral gene signature. The accumulation of these responses correlated with decline in viremia and recovery. The recruitment of a myeloid cell-mediated Type I IFN response is associated with the rapid clearance of SARS-CoV-2 infection in macaques.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":225537,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9498,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":817279,"name":"Ekaterina Aladyeva","orcid":"0000-0002-3483-6944","position":1,"is_corresponding":false},{"id":246480,"name":"Shibali Das","orcid":"0000-0003-1263-8178","position":2,"is_corresponding":false},{"id":245262,"name":"Bindu Singh","orcid":"0000-0003-2974-1737","position":3,"is_corresponding":false},{"id":109967,"name":"Ekaterina Esaulova","orcid":"0000-0001-9806-662X","position":4,"is_corresponding":false},{"id":246482,"name":"Amanda Swain","orcid":"0000-0003-0683-368X","position":5,"is_corresponding":false},{"id":245277,"name":"Mushtaq Ahmed","orcid":"0000-0002-6296-7626","position":6,"is_corresponding":false},{"id":248291,"name":"Journey Cole","orcid":null,"position":7,"is_corresponding":false},{"id":248553,"name":"Chivonne Moodley","orcid":null,"position":8,"is_corresponding":false},{"id":282266,"name":"Smriti Mehra","orcid":"0000-0001-9923-8745","position":9,"is_corresponding":false},{"id":245289,"name":"Larry S. Schlesinger","orcid":"0000-0002-7177-8421","position":10,"is_corresponding":false},{"id":52958,"name":"Maxim N. Artyomov","orcid":"0000-0002-1133-4212","position":11,"is_corresponding":false},{"id":225184,"name":"Shabaana A. Khader","orcid":"0000-0002-9545-4982","position":12,"is_corresponding":false},{"id":245291,"name":"Deepak Kaushal","orcid":"0000-0003-3521-1257","position":13,"is_corresponding":false},{"id":245261,"name":"Dhiraj Kumar Singh","orcid":"0000-0001-5507-1197","position":0,"is_corresponding":true}],"reference_count":81,"raw_metadata":null,"created_at":"2026-07-18T23:54:26.581453Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}