TABLE 8.
Characteristics of nucleic acid amplification tests for laboratory diagnosis of MERSa
| Diagnostic method (target gene) | Clinical specimen(s) | Recommended use | Technical LOD | Remarks | Reference(s) |
|---|---|---|---|---|---|
| upE assay (upstream of E gene) | Respiratory swab, sputum, and endotracheal aspirate | Screening | 1.6 to 3.4 RNA copies/reaction | Most widely used test globally | 310 |
| ORF1a assay (ORF1a gene) | BAL fluid, NPA | Confirmatory for upE-positive samples | 4.1 RNA copies/reaction | As sensitive as upE assay | 62, 69 |
| RealStar MERS-CoV RT-PCR kit 1.0 | Aspiration tube flushed with PBS, BAL fluid, mouth exudates, nose exudates, stool, urine, CVC flushed with PBS | Screening | upE assay, 5.3 copies/reaction; ORF1a assay, 9.3 copies/reaction | As sensitive as the in-house upE and 1A assays; rapid and less labor-intensive than the in-house assays | 321 |
| ORF1b assay (ORF1b gene) | Respiratory swab, sputum, and endotracheal aspirate | Confirmatory for upE-positive samples | 64 RNA copies/reaction | Less sensitive than upE and 1A assays; no overlap with those of known pan-CoV assays | 310 |
| RdRpSeq assay (RdRp gene and sequencing) | BAL fluid, NPA | Screening (pan-CoV RT-PCR) and confirmatory (sequencing) | 0.3 to 3.0 PFU/ml | May cross-react with other βCoVs as the gene target is highly conserved | 62, 69 |
| NSeq assay (N gene and sequencing) | BAL fluid, NPA | Screening (RT-PCR) and confirmatory (sequencing) | 0.03 to 0.3 PFU/ml | Highly sensitive and specific for MERS-CoV; may have deletion or mutation in the amplified fragment | 62, 69 |
| N2 assay (N gene) | URT, LRT, serum, stool | Screening with upE to enhance sensitivity and specificity | 5 to 10 RNA copies/reaction | As sensitive as upE assay | 322 |
| N3 assay (N gene) | URT, LRT, serum, stool | Confirmatory for upE- or N2-positive samples | 5 to 10 RNA copies/reaction | As sensitive as upE assay | 322 |
| RT-RPA assay (N gene) | No clinical specimen; culture supernatant | Field use (point-of-care test) | 10 RNA copies/reaction | As sensitive as RT-PCR, faster TAT (≤30 min), and mobile | 199 |
| RT-LAMP | Medium containing pharyngeal swabs (healthy adults) mixed with MERS-CoV | Field use | 3.4 RNA copies/reaction | As sensitive as upE and ORF1a assays, faster TAT(≤30 min) | 200 |
a
Abbreviations: BAL, bronchoalveolar lavage; CoV, coronavirus; CVC, central venous catheter; Ig, immunoglobulin; LOD, lower limit of detection; LRT, lower respiratory tract; N, nucleocapsid; NPA, nasopharyngeal aspirate; ORF, open reading frame; RdRp, RNA-dependent RNA polymerase; RT-LAMP, reverse transcription loop-mediated isothermal amplification; RT-PCR, reverse transcription-PCR; RT-PRA, reverse transcription isothermal recombinase polymerase amplification; TAT, turnaround time; URT, upper respiratory tract.