Table 1.
Sample Type |
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---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NP Swab | BAL | Sputum | Plasma | CSF | Stool** | PBS | VTM/UTM | HBSS (Hanks') | |||||||||||
Target | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | N1 | N2 | At LoD |
Dilution | 1e-5 | 2e-5 | 1e-5 | 2e-5 | 1e-5 | 1e-5 | 5e-4 | 1e-5 | 1e-5 | 1e-6 | 1e-5 | 1e-5 | 1e-5 | 1e-5 | 1e-5 | 1e-5 | 1e-5 | 1e-5 | |
Copies/ Reaction* | 10 | 5 | 10 | 5 | 10 | 10 | 20 | 10 | 10 | 1 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | |
Mean CT | 33.8 | 35.1 | 33.8 | 35.4 | 34.5 | 35.4 | 34.4 | 34.9 | 35.5 | 36 | 35.7 | 36.2 | 35 | 34.8 | 34.6 | 34 | 34.8 | 34.8 | |
Pos. Detected | 20/20 | 20/20 | 20/20 | 20/20 | 19/20 | 19/20 | 20/20 | 20/20 | 19/20 | 20/20 | 20/20 | 20/20 | 20/20 | 20/20 | 20/20 | 20/20 | 20/20 | 20/20 | |
Dilution | 2e-5 | 5e-5 | 2e-5 | 5e-5 | 1e-6 | 1e-6 | 1e-5 | 2e-5 | 2e-5 | 1e-7 | 1e-6 | 1e-6 | 2e-5 | 2e-5 | 1e-6 | 1e-6 | 1e-6 | 1e-6 | Beyond LoD |
Copies/ Reaction* | 5 | 2 | 5 | 2 | 1 | 1 | 10 | 5 | 5 | 0.1 | 1 | 1 | 5 | 5 | 1 | 1 | 1 | 1 | |
Mean CT | 35.9 | 36.4 | 35.6 | 36.9 | 36.5 | 37.2 | 35.4 | 36.5 | 36.5 | 38.3 | 37.1 | 37.8 | 35.7 | 36.4 | 37.2 | 37.5 | 36.5 | 36.1 | |
Pos. Detected | 18/20 | 17/20 | 18/20 | 16/20 | 8/20 | 14/20 | 17/20 | 18/20 | 14/20 | 1/20 | 5/20 | 8/20 | 18/20 | 18/20 | 7/20 | 14/20 | 17/20 | 18/20 | |
Unique Specimens | 77 | 104 | 47 | 100 | 100 | 60 | N/A | N/A | N/A | Specificity | |||||||||
Unique Respiratory Pos. | 20 | 25 | 16 | N/A | N/A | N/A | N/A | N/A | N/A |
Abbreviations: NDET, Not detected; CT, cycle threshold; NP nasopharyngeal; BAL, bronchoalveolar lavage; PBS, phosphate buffered saline; VTM, viral transport medium; UTM, universal transport medium; HBSS, Hanks’ balanced buffer solution; CSF, cerebral spinal fluid; rxn, reaction.
Conversion of copies/rxn to copies/mL is a factor of 50.
*Estimated copies/rxn were quantified using digital droplet PCR of SARS-CoV-2 dilutions series in duplicates.
**Stool serial dilutions are adjusted as 20 uL of stool sample was already diluted with 180uL STAR buffer for extraction (1:10 dilution).