REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
QIAseq FX DNA Library Kit	QIAGEN	180473
Quick-RNA Viral 96 Kit	Zymo Research	R1041
QIAseq SARS-CoV-2 Primer Panel	QIAGEN	333895
NEB Next Ultra II Directional RNA Library kit	New England Biolabs	E7760S
Deposited Data
Raw data	This Study	Sequence Read Archive- BioProject SRA: PRJNA745169 (https://www.ncbi.nlm.nih.gov)
Healthy Nasal Microbiome	http://journal.frontiersin.org/article/10.3389/fmicb.2017.02372/full	European Nucleotide Archive - study number ENA: PRJEB23057 (https://www.ebi.ac.uk/ena/browser)
Oligonucleotides
16S rRNA gene 515F forward primer 5′-GTGYCAGCMGCCGCGGTAA-3′	https://doi.org/10.1111/1462-2920.13023	N/A
16S rRNA gene 806R reverse primer 5′-GGACTACNVGGGTWTCTAAT-3′	https://doi.org/10.3354/ame01753	N/A
SARS-CoV-2 nucleoprotein qPCR forward primer 5′-GGGGAACTTCTCC TGCTAGAAT-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
SARS-CoV-2 nucleoprotein qPCR reverse primer 5′-CAGACATTTTG CTCTCAAGCTG-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
SARS-CoV-2 nucleoprotein qPCR probe 5′-FAMTTGCTGCTGCTTG ACAGATT-BHQ1-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
Human RNaseP qPCR forward primer 5′-AGATTTGGACCTGCGAGCG-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
Human RNaseP qPCR reverse primer 5′-GAGCGGCTGTCTCCACAAGT-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
Human RNaseP qPCR probe 5′-FAM-TTCTGACCTGAAGGC TCTGCGCG–BHQ1-3′	https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf	N/A
Software and algorithms
Quantitative Insights Into Microbial Ecology 2 (QIIME2)(2019.10) Built in tools: Dada2, mafft, sklearn, FastTree 2	http://www.nature.com/articles/s41587-019-0209-9	https://qiime2.org
GraphPad Prism 8	GraphPad Software Inc	http://www.graphpad.com:443
Metascape	10.1038/s41467-019-09234-6	https://metascape.org/
R software (v4.0.2) R packages: vegan (v2.5-7), SystemPipeR (v1.26.3), edgeR (v3.34.0), ggplot2 (v3.3.3)	R Foundation	https://www.r-project.org
GitHub of commands used in data analysis	This Study	https://github.com/NickRhoades/COVID-19_nasal_microboime