Fig 2: Changes in myeloid populations associated with COVID-19 severity, related to Figure 4(A-C) Single cell mass cytometry. (A) Mean metal intensity (MMI) of HLA-DR, CD33 and CD11c for classical monocytes (cMono) by patient group. (B) Representative plot of Ki67+ expression and 191Iridium (DNA) labeling in a healthy volunteer and a COVID19 patient; two distinct population of Ki67+ proliferating cells were identified, one containing the same amount of DNA as Ki67- cells (Ki67+DNAlow) and a rarer population containing double the amount of DNA (Ki67+DNAhigh) which likely comprises proliferating cells in S, G2 and M phase. The boxplots describe the frequencies of Ki67+DNAlow and Ki67+DNAhigh across different disease states. (C) Myeloid cell population frequencies by patient group. (D-G) CITE-seq PBMC myeloid cell clusters. (D) Differential abundance analysis with boxplots of cell cluster frequency by patient group where abundance significantly differs relative to healthy volunteers and (E) scRNA-seq MSigDB hallmark gene set enrichment for cMono, ncMono and DC. (F,G) Differential gene expression in classical monocytes comparing (F) critical COVID-19 patients versus healthy volunteers and (G) COVID-19 community cases versus healthy volunteers with volcano plots showing significant genes (FDR < 0.01 and logFC > 2) in red. (H-K) scATAC-seq with cell lysis, nuclear extraction and tagmentation on viability sorted PBMC prior to single nuclei capture and sequencing. Data shown for 42,000 cells post QC (ArchR pipeline) for 8 COVID-19 samples (paired acute and convalescent) and 2 healthy volunteers with (H) label transfer (unconstrained method) to assign cell clusters based on CITE-seq, (I) comparison of chromatin accessibility (scATAC-seq peaks linked to genes) to CITE-seq gene expression, (J) differential chromatin accessibility in myeloid cells comparing acute COVID-19 versus healthy volunteers, and (K) scATAC-seq tracks at FGFRL1 locus comparing cell populations and condition (healthy, COVID-19 acute and convalescent). All boxplots show median, first and third quartiles; whiskers show 1.5x interquartile range. Abbreviations for CITE-seq (panels D-G). cDC: classical dendritic cell; cMono: classical monocytes; DC: dendritic cell; hi: high; MT, mitochondrial; ncMono: non-classical monocyte; pDC: plasmacytoid dendritic cell. Comparator group abbreviations. HV: healthy volunteer; CM: COVID-19 in-patient mild; CS: COVID-19 in-patient severe; CC: COVID-19 in-patient critical; CComm: COVID-19 community case in the recovery phase (never admitted to hospital); CConv: COVID-19 convalescence (survivors from 28 days after discharge); Flu: influenza in-patient critical; Sepsis: in-patient severe and critical sepsis; SeConv: sepsis convalescence.Comparator group abbreviations HV: healthy volunteer; CM: COVID-19 in-patient mild; CS: COVID-19 in-patient severe; CC: COVID-19 in-patient critical; CComm: COVID-19 community case in the recovery phase (never admitted to hospital); CConv: COVID-19 convalescence (survivors from 28 days after discharge); Flu: influenza in-patient critical; Sepsis: in-patient severe and critical sepsis; SeConv: sepsis convalescence.