| Literature DB >> 35446012 |
Luisa Zupin1, Francesco Fontana2, Libera Clemente2, Maurizio Ruscio2, Sergio Crovella3.
Abstract
The number of SARS-CoV-2 detection tests requested to the laboratories has dramatically increased together with an urgent need to release reliable responses in a very short time. The two options taken into consideration and analyzed in the current study were the point-of-care test (POCT) based on the nucleic acid amplification test (NAAT) and the Antigen (Ag) rapid test. The POCT-NAAT-based assay was compared with a rapid antigen test of nasopharyngeal swab samples. If the specimen tested positive, it was followed by viral load quantification and by the functional assessment of the residual infectivity. When the initial cycle threshold (Ct) was below 20 (100%), and in the range of 20-25 (92%) and of 25-30 (88%), a great concordance between the POCT-NAAT and the Ag test was observed. Moreover, the positivity of the antigen test was well correlated to a successful infection in vitro (78%), with greater concordance when the initial Ct below 20 or above 35 (100%) and in the range 20-25 (83%). Our findings showed that most of the swabs which tested positive using the antigen test were able to infect the cells in vitro, suggesting that probably only these samples hold residual infectivity and therefore an increased risk of virus transmission at the moment of being tested.Entities:
Keywords: Antigen test; Nucleic acid amplification test; SARS-CoV-2
Mesh:
Year: 2022 PMID: 35446012 PMCID: PMC9022615 DOI: 10.1007/s42770-022-00758-6
Source DB: PubMed Journal: Braz J Microbiol ISSN: 1517-8382 Impact factor: 2.214
The comparison of results from the four methodologies employed in the study
| RT-qPCR N gene (CDC) | Infection 7th day | STANDARD F COVID-19 Ag FIA (SD Biosensor) | Novel coronavirus (2019-nCoV) kit (Sansure Biotech) on iPonatic | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Swab | Ct | Viral copies/ml | Viral copies/ml | Positive/negative | Cutoff index | Positive/negative | ORF gene (Ct) | N gene (Ct) | RNase P gene (Ct) |
| 1 | 26.22 | 8.42 ⨯ 108 | 2.23 ⨯ 1014 | + | 31.77 | + | 36.86 | 28.13 | 27.09 |
| 2 | 31.45 | 2.54 ⨯ 106 | 2.62 ⨯ 1011 | + | 1.09 | + | 35.67 | 28.85 | 26.32 |
| 3 | 23.63 | 1.23 ⨯ 1009 | 1.03 ⨯ 1014 | + | 57.08 | + | 31.75 | 22.62 | 28.27 |
| 4 | 26.71 | 2.60 ⨯ 107 | 1.21 ⨯ 1014 | + | 9.44 | + | 36.09 | 27.38 | 26.87 |
| 5 | 18.85 | 4.85 ⨯ 1011 | 9.80 ⨯ 1013 | + | 58.09 | + | 32.13 | 20.18 | 27.72 |
| 6 | 18.58 | 6.76 ⨯ 1011 | 2.72 ⨯ 1013 | + | 58.01 | + | 28.76 | 20.27 | 22.77 |
| 7 | 24.3 | 5.26 ⨯ 108 | 9.35 ⨯ 1013 | + | 14.93 | + | 33.08 | 23.25 | 29.8 |
| 8 | 20.44 | 6.64 ⨯ 1010 | 6.80 ⨯ 1013 | + | 26.13 | + | 30.36 | 19.2 | 25.09 |
| 9 | 21.92 | 1.02 ⨯ 1011 | 1.40 ⨯ 1014 | + | 24.83 | + | 29.09 | 20.79 | 28.4 |
| 10 | 25.73 | 1.55 ⨯ 109 | 6.16 ⨯ 1013 | + | 15.03 | + | 27.5 | 20.42 | 27.94 |
| 11 | 18.94 | 2.69 ⨯ 1012 | 1.52 ⨯ 1014 | + | 58 | + | 24.99 | 18.52 | 26.91 |
| 12 | ND | ND | ND | - | 0.37 | - | 39.48 | 36.12 | 33.15 |
| 13 | 28.41 | 8.20 ⨯ 107 | 9.21 ⨯ 1013 | + | 1.29 | + | 33.2 | 25.4 | 27.61 |
| 14 | 33.11 | 4.67 ⨯ 105 | 4.35 ⨯ 1013 | + | 2.65 | + | 37.05 | 30.74 | 27.46 |
| 15 | 34.37 | 4.62 ⨯ 104 | 2.27 ⨯ 1013 | + | 0.39 | - | 37.44 | 32.04 | 29.82 |
| 16 | 22.44 | 3.22 ⨯ 1010 | 1.74 ⨯ 1013 | + | 56.48 | + | 32.43 | 25.59 | 25.25 |
| 17 | 27.18 | 1.54 ⨯ 108 | ND | - | 1.43 | + | 36.45 | 28.55 | 27.21 |
| 18 | 28.37 | 4.02 ⨯ 107 | 4.69 ⨯ 1013 | + | 1.9 | + | 32.72 | 25.86 | 28.02 |
| 19 | 19.14 | 1.34 ⨯ 1012 | 3.54 ⨯ 1013 | + | 58.11 | + | 23.45 | 17.34 | 28.2 |
| 20 | 23.78 | 7.10 ⨯ 109 | 2.46 ⨯ 1013 | + | 58.23 | + | 27.01 | 18.16 | 24.36 |
| 21 | 36.87 | 2.73 ⨯ 103 | ND | - | 0.84 | - | 39.24 | 33.91 | 26.1 |
| 22 | 31.21 | 1.78 ⨯ 106 | ND | - | 0.65 | - | 40.61 | 31.39 | 26.65 |
| 23 | 27.49 | 1.11 ⨯ 108 | ND | - | 4.18 | + | 39.16 | 27.49 | 21.86 |
| 24 | 37.61 | 5.52 | ND | - | 0.72 | - | ND | 35.81 | 29.84 |
| 25 | ND | ND | ND | - | 0.39 | - | 38.34 | 32.69 | 29.14 |
| 26 | 29.69 | 2.25 ⨯ 105 | 4.67E ⨯ 1013 | + | 0.43 | - | 32.71 | 26.06 | 28.19 |
| 27 | 18.57 | 6.64 ⨯ 1011 | 8.41 ⨯ 1013 | + | 51.32 | + | 22.17 | 15.48 | 26.32 |
| 28 | 18.78 | 5.00 ⨯ 1011 | 2.31 ⨯ 1013 | + | 50.99 | + | 22.28 | 14.96 | 26.54 |
| 29 | 22.5 | 3.43 ⨯ 109 | 8.98 ⨯ 1013 | + | 51.22 | + | 25.59 | 19.43 | 29.5 |
| 30 | 37.23 | 9.18 | ND | - | 0.85 | - | ND | 34.25 | 26.33 |
| 31 | 27.66 | 3.42 ⨯ 106 | 1.30⨯ 1014 | + | 1.96 | + | 33.64 | 27.15 | 27.07 |
| 32 | 25.54 | 5.86 ⨯ 107 | 1.84⨯ 1012 | + | 4.09 | + | 34.69 | 26.04 | 28.48 |
| 33 | 26.75 | 1.15 ⨯ 107 | 7.43⨯ 1013 | + | 2.61 | + | 31.68 | 24.24 | 27.25 |
| 34 | 36.74 | 4.45 ⨯ 102 | 2.03⨯ 1014 | + | 0.61 | - | 42.18 | 34.65 | 30.34 |
| 35 | ND | ND | 2.79⨯ 1014 | + | 0.09 | - | 40.4 | 34.92 | 28.78 |
| 36 | 18.25 | 4.54 ⨯ 1012 | 1.31⨯ 1014 | + | 51.15 | + | 29.02 | 20.62 | 25.86 |
| 37 | 30.49 | 1.08 ⨯ 106 | ND | - | 0.97 | - | 37.43 | 28.96 | 28.89 |
| 38 | 21.79 | 5.54 ⨯ 1010 | 7.84⨯ 10 13 | + | 50.41 | + | 29.24 | 21.03 | 24.14 |
| 39 | 33.33 | 3.11 ⨯ 104 | ND | - | 2.61 | + | 33.72 | 27.5 | 25.24 |
| 40 | 26.86 | 9.97 ⨯ 107 | ND | - | 15.5 | + | 34.2 | 27.24 | 25.04 |
| 41 | 24.92 | 1.12 ⨯ 109 | ND | - | 12.17 | + | 29.02 | 20.57 | ND |
| 42 | 28.01 | 2.37 ⨯ 107 | 7.53 ⨯ 1012 | + | 12.46 | + | 35.46 | 28.52 | 26.18 |
| 43 | 27.21 | 3.07 ⨯ 107 | 1.70 ⨯ 1014 | + | 42.58 | + | 30.18 | 23.65 | 30.27 |
| 44 | 26.58 | 7.10 ⨯ 107 | 7.05 ⨯ 1013 | + | 0.25 | - | 28.98 | 22.6 | 27.28 |
| 45 | 27.77 | 1.47 ⨯ 107 | 5.60 ⨯ 1013 | + | 10.25 | + | 34.2 | 27.65 | 28.96 |
| 46 | 25.06 | 5.29 ⨯ 108 | ND | - | 51.1 | + | 40.03 | 26.82 | 27.07 |
In the table are reported the data from
• the custom reverse transcription-quantitative (RT-q) PCR for the SARS-CoV-2 N (nucleocapsid) gene (with CDC primers and probe) on the 7500 Applied Biosystem Real-Time PCR instrument
• the RT-PCR performed by employing the Novel Coronavirus (2019-nCoV) kit (Sansure Biotech) for the ORF1ab and N genes on the iPonatic device
• the antigen rapid immunofluorescence lateral flow test (STANDARD F COVID-19 Ag FIA, SD Biosensor)
• the infection in the in vitro model of Vero E6 cells of the samples analyzed
Ct, cycle threshold; RT-qPCR, reverse transcription PCR; ND, not detected
The comparison of results from the novel coronavirus (2019-nCoV) kit (Sansure Biotech) on iPonatic device, the rapid antigen immunofluorescence lateral flow assay (STANDARD F COVID-19 Ag FIA), and the infection in the in vitro model of Vero E6 cells based on the Cycle threshold (Ct) data from the iPonatic
| Ct | 2019-nCoV kit (Sansure Biotech) on iPonatic device | Culture positive | Antigen immunofluorescence test (STANDARD F COVID-19 Ag FIA) | Concordance culture/antigen test | Concordance culture/antigen test | Concordance 2019-nCoV kit (Sansure Biotech) on iPonatic device/antigen test |
|---|---|---|---|---|---|---|
| < 20 | 7 | 7 | 7 | 7 | 100% | 100% |
| 20–25 | 12 | 11 | 11 | 10 | 83% | 92% |
| 25–30 | 17 | 11 | 15 | 11 | 65% | 88% |
| 30–35 | 8 | 4 | 1 | 5 | 63% | 13% |
| > 35 | 2 | 0 | 0 | 2 | 100% | 0% |
Ct, cycle threshold; RT-qPCR, reverse transcription PCR; ND, not detected
Limit of detection of the rapid antigen immunofluorescence lateral flow assay (STANDARD F COVID-19 Ag FIA) with previously isolated SARS-CoV-2. The data from the reverse transcription-quantitative (RT-q)—PCR and the plaque-forming unit (PFU) assay are reported
| RT-qPCR N gene (CDC primers and probe) | PFU assay | STANDARD F COVID-19 Ag FIA | ||||
|---|---|---|---|---|---|---|
| SARS-CoV-2 standard | Ct | Viral copies/ml | Infection in vitro | PFU/ml | Cutoff index (COI) | Positive/negative |
| Dilution-1 | 18.98 | 2.57 ⨯ 1012 | + | 25,000 | 57.42 | + |
| Dilution-2 | 22.54 | 4.94 ⨯ 1010 | + | 2500 | 56.06 | + |
| Dilution-3 | 25.25 | 2.45 ⨯ 109 | + | 250 | 7.26 | + |
| Dilution-4 | 30 | 1.26 ⨯ 107 | + | 25 | 1.13 | + |
| Dilution-5 | 32.37 | 9.04 ⨯ 105 | - | 2 | 0.62 | - |
| Dilution-6 | 36.77 | 6.90 ⨯ 103 | - | 0.25 | 0.84 | - |
Ct, cycle threshold; RT-qPCR, reverse transcription PCR; PFU, plaque-forming unit