KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Saliva samples from healthy humans | Taylor et al., 2021 | N/A |
| Oropharyngeal, nasopharyngeal, and endotracheal aspirate samples subjects hospitalized with COVID-19 |
Merenstein et al., 2021 | N/A |
| Oropharyngeal, nasopharyngeal, and endotracheal aspirate samples from medical intensive care unit patients | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Phi29 polymerase | New England BioLabs | Cat#M0269 |
| Critical commercial assays | ||
| TaqMan Fast Universal PCR Master Mix | Thermo Fisher | Cat#4352042 |
| TaqMan Fast Virus 1-Step Master Mix | Thermo Fisher | Cat#5555532 |
| PowerUp SYBR Green Mix | Thermo Fisher | Cat#A25741 |
| DNeasy Blood and Tissue Kit | Qiagen | Cat#69504 |
| QIAamp DNA Mini Kit | Qiagen | Cat#51304 |
| SuperScript First-Strand Synthesis System Kit | Thermo Fisher | Cat#18080051 |
| Scientific Kwik-Diff™ Staining Kit | Thermo Fisher | Cat#9990700 |
| Phusion High-Fidelity PCR Kit | New England BioLabs | Cat#E0553S |
| Monarch DNA Gel Extraction Kit | New England BioLabs | Cat#T1020S |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC1311024 |
| Deposited data | ||
| Raw metagenomic sequencing reads | NCBI | Accession #: PRJNA858476 |
| Raw shotgun sequencing reads | NCBI | Accession #: PRJNA858476 |
| Redondovirus (RV-30956) genome | GenBank | Accession #: ON986208 |
| Experimental models: Organisms/strains | ||
| E. gingivalis | ATCC | ATCC-30956 |
| Oligonucleotides | ||
| qPCR, redondovirus Cap ORF (F: 5’-GGATGCCATGAAACTTTGATAC-3’; R: 5’TCTTCCTCCTTATTTGTATGGC-3’; probe: 5’-CCCATACTTACGCCGGTTACCTGC-3’) | Integrated DNA Technologies | N/A |
| qPCR, E. gingivalis 18S rRNA gene (F: 5’-TACCATACAAGGAATAGCTTTGTGAATAA-3’; R: 5’-ACAATTGTAAATTTGTTCTTTTTCT-3’) | Integrated DNA Technologies | N/A |
| Whole-genome PCR, redondovirus (Set A F: 5’CCTTTGGTCTCGAAATCTTCCTATACTGG-3’; Set A R: 5’-AGGCCTCTCTCCCTTCCATTTGG-3’; Set B F: 5’-GGTTATCGTTCATTTGATCATGCATTAGTACC-3’; Set B R: 5’-ACCAAGATGTTTAAGCCCTTTAGTTAATGTTTC-3’) | Integrated DNA Technologies | N/A |
| qPCR, human GAPDH (F: 5’-GGTGGTCTCCTCTGACTTCAACA-3’; R: 5’CCAGCCACATACCAGGAAATG-3’; probe: 5’CTGGCATTGCCCTCAACGACCAC-3’) | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| pUC57 | BioBasic | Addgene 4509 |
| Software and algorithms | ||
| BLASTn v2.9.0 | Altschul et al., 1990 | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
| PhyML v3.0 | Guindon et al., 2010 | https://github.com/stephaneguindon/phyml |
| RaxML v8.2 | Stamatakis et al., 2005 | https://github.com/stamatak/standard-RAxML |
| MUSCLE v3.8.31 | Edgar, 2004 | https://github.com/rcedgar/muscle |
| iTOL v6 | Letunic and Bork, 2019 | https://itol.embl.de/ |
| VipTree v3.1 | Nishimura et al., 2017 | https://www.genome.jp/viptree/ |
| hisss v3.0 | Abbas et al., 2019 | https://github.com/louiejtaylor/hisss |
| IGV v2.9.0 | Robinson et al., 2011 | https://software.broadinstitute.org/software/igv/ |
| CAP3 v3.0 | Huang and Madan, 1999 | http://doua.prabi.fr/software/cap3 |
| MEGAHIT v1.2.9 | Li et al., 2015 | https://github.com/voutcn/megahit |
| FastQC v0.11.9 | Andrews, 2010 | https://github.com/s-andrews/FastQC |
| Trimmomatic v0.39 | Bolger et al., 2014 | https://github.com/usadellab/Trimmomatic |
| Sunbeam v2.1.0 | Clarke et al., 2019 | https://github.com/sunbeam-labs/sunbeam |
| Kraken2 v2.1.2 | Wood et al., 2019 | https://github.com/DerrickWood/kraken2 |
| R version v4.0.4 | Ihaka and Gentleman, 1996 | https://www.r-project.org/ |
| Snakemake v7.16.0 | Köster and Rahmann, 2012 | https://github.com/snakemake/snakemake |
| SAMtools v1.9 | Li et al., 2009 | http://samtools.sourceforge.net/ |
| BEDtools v2.30.0 | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |