REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-SARS-CoV-2 nucleoprotein monoclonal rabbit antibody	Sino Biological	Cat# 40143-R019; clone: 019; RRID:AB_2827973
Anti-CD68 monoclonal mouse antibody	Ventana Medical Systems	Cat# 790-2931; clone: KP-1; RRID:AB_2335972
Anti-CD163 monoclonal mouse antibody	Ventana Medical Systems	Cat# 760-4437; clone: MRQ-26; RRID:AB_2335969
Anti-TTF1 monoclonal mouse antibody	Cell Marque	Cat# 343M-96; clone: 8G7G3/1; RRID:AB_1158937
Anti-TGFß1 polyclonal rabbit antibody	Santa Cruz Biotechnology	Cat# SC-146; RRID:AB_632486
Anti-TGFß polyclonal rabbit antibody	Cell Signaling Technology	Cat# 3711; RRID:AB_2063354
Anti-LAG3 polyclonal rabbit antibody	Abcam	Cat# ab180187; clone: EPR4392(2); RRID:AB_2888645
Anti-C1q polyclonal rabbit antibody	Agilent	Cat# A0136; RRID:AB_2335698
Anti-GAPDH monoclonal rabbit antibody	Cell Signaling Technology	Cat# 2118; clone: 14C10; RRID:AB_561053
HRP-linked ECL Anti-Rabbit IgG	GE Healthcare	Cat# NA934; RRID:AB_772206
Dako REAL TM EnVision TM HRP rabbit/mouse detection-system	Agilent	Cat# K5007; RRID:AB_2888627
ultraView DAB detection-system	Roche	Cat# 760-500; RRID:AB_2753116
Bacterial and virus strains
SARS-CoV-2 strains from study	This study	N/A
Bacterial and fungal strains from study	This study	N/A
Biological samples
Autopsy tissue and body fluid samples	This study	N/A
Respiratory tract swabs	This study	N/A
Chemicals, peptides, and recombinant proteins
Thioglycollate broth	Oxoid	Cat# CM0173
OptiPro SFM medium	Gibco	Cat# 12309019
L-Glutamine	Gibco	Cat# 11539876
Penicillin-Streptomycin (10.000 U/ml)	Gibco	Cat# 11548876
TRIzol®	Invitrogen	Cat# 15596026
RIPA buffer	Sigma	Cat# R0278
Pefabloc	Roche	Cat# 11429868001
cOmpleteTM Mini	Merck	Cat# 11836153001
PhosSTOPTM	Roche	Cat# 4906845001
Laemmli buffer	Bio-Rad	Cat# 1610737EDU
Critical commercial assays
MagNA Lyser green beads tubes	Roche	Cat# 03358941001
Maxwell 16 LEV simplyRNA blood kit	Promega	Cat# AS1310
QIAamp Viral RNA Mini Kit	Qiagen	Cat# 221413
High-Capacity cDNA Reverse Transcription Kit with RNase inhibitor	Applied Biosystems	Cat# 4374966
SuperScript III One-Step RT-PCR System with Platinum Taq High Fidelity DNA Polymerase mastermix	ThermoFisher	Cat# 12574018
SYBR Green PCR Mastermix	Applied Biosystems	Cat# 4309155
Ampure XP beads	Beckman Coulter	Cat# A63881
NEBNext Fast DNA Fragmentation & Library Prep Set for Ion Torren kit	New England Biolabs	Cat# E6285L
KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® platforms	KAPABIOSYSTEMS	Cat# KR1351
16s Complete PCR Mastermix kit	Molzym	Cat# S-020-0250
QiaQick gel extraction kit	Qiagen	Cat# 28706X4
Ponceau S solution	Sigma	Cat# P7170
ECL Select Western Blot Reagent	Amersham	Cat# 12644055
RNAlater	ThermoFisher	Cat# AM7024
Deposited data
16S rRNA gene-, ITS- and RNAseq data	European nucleotide archive (ENA)	Acc. no. PRJEB45873
Experimental models: Cell lines
Vero CCL-81 cells	European Collection of Authenticated Cell Cultures	ECACC 84113001
Oligonucleotides
RdRp_SARSr-F GTGARATGGTCATGTGTGGCGG	(Corman et al., 2020)	N/A
RdRp_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGC-BBQ	(Corman et al., 2020)	N/A
RdRp_SARSr-R CARATGTTAAASACACTATTAGCATA	(Corman et al., 2020)	N/A
N_Sarbeco_F CACATTGGCACCCGCAATC	(Corman et al., 2020)	N/A
N_Sarbeco_P FAM-ACTTCCTCAAGGAACAACATTGCCA-BBQ	(Corman et al., 2020)	N/A
N_Sarbeco_R GAGGAACGAGAAGAGGCTTG	(Corman et al., 2020)	N/A
2019-nCoV_N1-F GACCCCAAAATCAGCGAAAT	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
2019-nCoV_N1-R TCTGGTTACTGCCAGTTGAATCTG	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
2019-nCoV_N2-F TTACAAACATTGGCCGCAAA	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
2019-nCoV_N2-R GCGCGACATTCCGAAGAA	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
2019-nCoV_N3-F GGGAGCCTTGAATACACCAAAA	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
2019-nCoV_N3-R TGTAGCACGATTGCAGCATTG	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
RP-F AGATTTGGACCTGCGAGCG	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
RP-R GAGCGGCTGTCTCCACAAGT	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
GAPDH_f CCTCCACCTTTGACGCT	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
GAPDH_r TTGCTGTAGCCAAATTCGTT	https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html	N/A
CoV_gen_f1 TAAAGGTTTATACCTTCCCAGG	This study	N/A
CoV_gen_r1 CAGATGTGAACATCATAGCATC	This study	N/A
CoV_gen_f2 AAAGAGCTATGAATTGCAGACACC	This study	N/A
CoV_gen_r2 GGAGGGTAGAAAGAACAATACA	This study	N/A
CoV_gen_f3 GATGCTATGATGTTCACATCTG	This study	N/A
CoV_gen_r3 CAGAATCTGGATGAAGATTGCCAT	This study	N/A
CoV_gen_f4 TGTATTGTTCTTTCTACCCTCC	This study	N/A
CoV_gen_r4 CTCCATCCAAATAAGTTGGACCAA	This study	N/A
CoV_gen_f5 ATGGCAATCTTCATCCAGATTCTG	This study	N/A
CoV_gen_r5 CACATCACCATTTAAGTCAGGGAA	This study	N/A
CoV_gen_f6 TTGGTCCAACTTATTTGGATGGAG	This study	N/A
CoV_gen_r6 CACTCTGCAACTAAGCCAAA	This study	N/A
CoV_gen_f7 TTCCCTGACTTAAATGGTGATGTG	This study	N/A
CoV_gen_r7 GCCAGTAACTTCTATGTCAGATTG	This study	N/A
CoV_gen_f8 TTTGGCTTAGTTGCAGAGTG	This study	N/A
CoV_gen_r8 CACTAGTAGATACACAAACACCAG	This study	N/A
CoV_gen_f9 CAATCTGACATAGAAGTTACTGGC	This study	N/A
CoV_gen_r9 CCAGCCTGTACCAAGAAATTA	This study	N/A
CoV_gen_f10 CTGGTGTTTGTGTATCTACTAGTG	This study	N/A
CoV_gen_r10 CCAACCATGTCATAATACGCAT	This study	N/A
CoV_gen_f11 TAATTTCTTGGTACAGGCTGG	This study	N/A
CoV_gen_r11 CCAACTTACGTTGCATGGCTG	This study	N/A
CoV_gen_f12 ATGCGTATTATGACATGGTTGG	This study	N/A
CoV_gen_r12 GGATGATCTATGTGGCAACGG	This study	N/A
CoV_gen_f13 CAGCCATGCAACGTAAGTTGG	This study	N/A
CoV_gen_r13 GGTGGTATGTCTGATCCCAATATT	This study	N/A
CoV_gen_f14 CCGTTGCCACATAGATCATCC	This study	N/A
CoV_gen_r14 GCATGTTAGGCATGGCTCTATCA	This study	N/A
CoV_gen_f15 AATATTGGGATCAGACATACCACC	This study	N/A
CoV_gen_r15 GGTCGTAACAGCATTTACAA	This study	N/A
CoV_gen_f16 TGATAGAGCCATGCCTAACATGC	This study	N/A
CoV_gen_r16 GTCTCAGGCAATGCATTTAC	This study	N/A
CoV_gen_f17 TTGTAAATGCTGTTACGACC	This study	N/A
CoV_gen_r17 GCTTCTCTAGTAGCATGACACCC	This study	N/A
CoV_gen_f18 GTAAATGCATTGCCTGAGAC	This study	N/A
CoV_gen_r18 CACATGGACTGTCAGAGTAATAGA	This study	N/A
CoV_gen_f19 GGGTGTCATGCTACTAGAGAAGC	This study	N/A
CoV_gen_r19 CACTTAGATGAACCTGTTTGCGC	This study	N/A
CoV_gen_f20 TCTATTACTCTGACAGTCCATGTG	This study	N/A
CoV_gen_r20 GACTAGAGACTAGTGGCAATAA	This study	N/A
CoV_gen_f21 GCGCAAACAGGTTCATCTAAGTG	This study	N/A
CoV_gen_r21 GCAAATCTGGTGGCGTTAAA	This study	N/A
CoV_gen_f22 TTATTGCCACTAGTCTCTAGTC	This study	N/A
CoV_gen_r22 GAGGAGAATTAGTCTGAGTCT	This study	N/A
CoV_gen_f23 TTTAACGCCACCAGATTTGC	This study	N/A
CoV_gen_r23 GCTCTGATTTCTGCAGCTCTAATT	This study	N/A
CoV_gen_f24 AGACTCAGACTAATTCTCCTC	This study	N/A
CoV_gen_r24 CCTTGGAGAGTGCTAGTTGCC	This study	N/A
CoV_gen_f25 AATTAGAGCTGCAGAAATCAGAGC	This study	N/A
CoV_gen_r25 GGCATAGGCAAATTGTAGAAGACA	This study	N/A
CoV_gen_f26 GGCAACTAGCACTCTCCAAGG	This study	N/A
CoV_gen_r26 GTGAAACTGATCTGGCACGTAACT	This study	N/A
CoV_gen_f27 TGTCTTCTACAATTTGCCTATGCC	This study	N/A
CoV_gen_r27 CCATAGGGAAGTCCAGCTTCTG	This study	N/A
CoV_gen_f28 AGTTACGTGCCAGATCAGTTTCAC	This study	N/A
CoV_gen_r28 GTCCTCCCTAATGTTACACA	This study	N/A
CoV_gen_f29 CAGAAGCTGGACTTCCCTATGG	This study	N/A
CoV_gen_r29 TTTGTATGCGTCAATATGCTT	This study	N/A
CoV_gen_f30 TGTGTAACATTAGGGAGGAC	This study	N/A
CoV_gen_r30 TTTGTCATTCTCCTAAGAAGC	This study	N/A
16S_515_f TGCCAGCAGCCGCGGTAA	(Maiwald 2011)
16S_806_r GGACTACCAGGGTATCTAAT	(Maiwald 2011)
ITS1 TCCGTAGGTGAACCTGCGG	(Halwachs et al., 2017)
ITS2 GCTGCGTTCTTCATCGATGC	(Halwachs et al., 2017)
Software and algorithms
R (v4.1)	https://www.R-project.org/	N/A
GISAID SARS-CoV-2 (hCoV-19) database	GISAID	https://www.gisaid.org
clustalw (v2.1)	(Larkin et al., 2007)	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
figtree (v1.4.4)		http://tree.bio.ed.ac.uk/software/figtree/
STAR	(Dobin et al., 2013)	https://github.com/alexdobin/STAR
bowtie2-2.4.1	(Langmead and Salzberg 2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
HTSeq (v0.12.4)	G Putri, S Anders, PT Pyl, JE Pimanda, F Zanini Analysing high-throughput sequencing data in Python with HTSeq 2.0 https://doi.org/10.1093/bioinformatics/btac166(2022)	https://htseq.readthedocs.io/en/master/
xCell	(Aran et al., 2017)	https://github.com/dviraran/xCell
edgeR	(Robinson et al., 2010)	https://bioconductor.org/packages/release/bioc/html/edgeR.html
Gene set enrichment analysis online tool	(Subramanian et al., 2005)	https://www.gsea-msigdb.org/gsea/msigdb/annotate.jsp
Single-cell atlas database SCovid	(Qi et al., 2022)	http://bio-annotation.cn/scovid/
MetaPhlAn2 (v2.6.0)	(Segata et al., 2012)	https://github.com/biobakery/MetaPhlAn2
Pathseq (GATK v4.1.0.0)	(Kostic et al., 2011)	https://github.com/broadinstitute/gatk
QIIME2 (v. 2020.6)	(Bolyen et al., 2019)	https://qiime2.org/
LEfSe	(Segata et al., 2011)	https://www.bioconductor.org/packages/release/bioc/html/lefser.html
DADA2	(Callahan et al., 2016)	https://bioconductor.org/packages/release/bioc/html/dada2.html
UNITE reference database	(Nilsson et al., 2018) Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K. 2018. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, https://doi.org/10.1093/nar/gky1022	https://unite.ut.ee/
SILVA reference database	(Quast et al., 2013)	https://www.arb-silva.de/
bcftools (v1.3.1)		http://github.com/samtools/bcftools
Incscape (v0.92)		https://inkscape.org/de/release/inkscape-0.92/
fastx (v0.0.13)		http://hannonlab.cshl.edu/fastx_toolkit/
seqclean		https://sourceforge.net/projects/seqclean/
samtools	(Danecek et al., 2021)	http://www.htslib.org/
GraphPad PrismTM		https://www.graphpad.com/scientific-software/prism/
ImageJ		https://imagej.nih.gov/ij/index.html
BioRender		https://biorender.com/
Other
eSwab	Copan	Cat# 80490CEA
Inform EBER Epstein Barr Virus early RNA kit	Ventana	Cat# 800-2824
ISH invers blue detection-system	Ventana	Cat# 800-092
Genbox anaer	bioMérieux	Cat# 45534
Blood agar	BD Diagnostics	Cat# 256506
MacConkey agar	BD Diagnostics	Cat# 215197
Chocolate agar	BD Diagnostics	Cat# 257456