Clinical performance evaluation of a high-throughput real-time PCR platform for congenital cytomegalovirus screening on saliva swabs with quantitative reporting thresholds.

BACKGROUND

Congenital cytomegalovirus (cCMV) is typically diagnosed using nucleic acid amplification testing on saliva followed by urine confirmation if positive. Major challenges in saliva screening include low positive predictive value (PPV) and throughput constraints. We validated the cobas CMV assay on the cobas 8800 high-throughput real-time polymerase chain reaction (PCR) platform as a lab-developed test for newborn saliva swabs and urine, and evaluated its clinical performance characteristics for cCMV screening.

METHODS

From April 2023 to January 2026, saliva swabs and urine from infants ≤ 21 days were tested in a cCMV screening program. Qualitative results were reported, with viral loads recorded offline. Urine PCR served as the reference standard to classify saliva results.

RESULTS

CMV PCR was positive in 50/6559 (0.76%) saliva swabs meeting study inclusion criteria, with 29 (58%) confirmed by urine. Among 28 saliva-negative infants who had urine testing, all were negative. Median saliva viral load was significantly lower in false-positives than true-positives (below lower limit of quantitation at <35 IU/mL vs. 4.09 × 106 IU/mL, p < 0.001). Using urine PCR as the gold standard, saliva PCR performance varied by reporting threshold (from detected at any value up to 100 IU/mL) with sensitivity 93.1-100%, specificity 57.1-100%, PPV 58.0-100%, and negative predictive value (NPV) 96.1-100%.

CONCLUSION

The cobas CMV assay as validated in our laboratory demonstrated acceptable clinical performance characteristics for saliva-based cCMV screening. Clinical specificity and PPV are further improved through application of a viral load threshold for positivity reporting or an "equivocal" range.