Universal Screening of Cytomegalovirus Viral Load by Low-Pass Whole-Genome Sequencing in First-Trimester Pregnancy:...

Congenital cytomegalovirus (cCMV) infection is a leading cause of sensorineural hearing loss in children. Recent evidence that high-dose valacyclovir reduces vertical transmission following primary maternal infection has renewed the urgency for screening. We investigated the utility of quantifying cell-free CMV DNA from noninvasive prenatal screening (NIPS) data to identify pregnancies at risk for primary CMV infection and cCMV.

In this retrospective study, we analyzed NIPS data from 22 333 unselected pregnancies at 12 weeks gestation. CMV-aligned reads were quantified from low-pass whole-genome sequencing data and validated against quantitative PCR (qPCR) for viral load, maternal serology for infection status and systematic newborn screening for cCMV.

CMV read counts demonstrated good correlation with qPCR-measured viral loads (rs = 0.76; 95%CI: 0.68-0.81). Presence of ≥1 CMV read count (2.1% of pregnancies) was highly predictive of cCMV [likelihood ratio (LR) = 21.1; 95% confidence interval (CI): 14.9-30.1]. CMV read counts showed good diagnostic accuracy for primary infection [area under the receiver operator characteristic curve (AUROC) = 0.77; 95% CI: 0.72-0.82] and for cCMV (AUROC = 0.82; 95% CI: 0.76-0.86). A threshold of ≥4 read counts identified a subgroup with significantly elevated risk for primary infection (LR = 7.8; 95% CI: 4.3-14.2) and cCMV (LR = 6.0; 95% CI: 3.3-10.8), achieving positive predictive value for cCMV of 51.7%.

Quantification of CMV DNA during NIPS is an accurate and sensitive method for CMV viral load. This approach effectively stratifies risk for both primary maternal infection and cCMV, enabling identification of pregnancies that may benefit from antiviral therapy.