Early Pregnancy CMV Screening: How NIPS and Viral DNA Testing Detect Congenital Cytomegalovirus Risk

Congenital cytomegalovirus (cCMV) is the most common congenital infection worldwide and a leading non-genetic cause of hearing loss and developmental delays in infants. Detecting CMV infection early in pregnancy is critical because interventions, such as antiviral therapy with high-dose valacyclovir, can significantly reduce the risk of transmission from mother to fetus. Traditionally, CMV screening has relied on maternal blood tests, but recent advances in noninvasive prenatal screening (NIPS) and viral DNA analysis provide a new, high-precision approach for early detection.

In this article, we explore how low-pass whole-genome sequencing from NIPS data can identify CMV viral load in first-trimester pregnancies and how this method improves risk stratification for congenital CMV.

What Is Congenital Cytomegalovirus (cCMV)?

CMV is a common herpesvirus that can infect individuals of all ages. While most infections in healthy adults are asymptomatic, CMV can be dangerous during pregnancy. When a mother experiences a primary CMV infection in the first trimester, the risk of passing the virus to the developing fetus can range from 30 to 40 percent.

Infants with cCMV may develop:

• Sensorineural hearing loss
• Vision impairment
• Neurodevelopmental delays
• Cognitive and motor deficits

Approximately 20 percent of infants with congenital CMV will experience long-term complications, highlighting the importance of early detection and preventive care.

Traditional CMV Screening Methods

Historically, CMV screening relied on serological testing, including:

• CMV IgG: Indicates past exposure
• CMV IgM: Suggests recent infection
• IgG avidity testing: Helps distinguish primary infection from reactivation

While these tests can identify primary maternal infection, they have limitations:

• Interassay variability may lead to inconsistent results
• Nonprimary infections, such as reactivation or reinfection, may go undetected
• Screening is often performed at a single time point, which can miss early or transient infections

Because of these challenges, universal CMV screening has not been widely implemented, especially before the availability of effective interventions like antiviral therapy.

The Role of Noninvasive Prenatal Screening (NIPS)

NIPS is commonly used to detect fetal chromosomal abnormalities using cell-free DNA (cfDNA) circulating in maternal blood. Recent research has shown that NIPS data can also be leveraged to detect viral DNA fragments, including CMV.

How It Works

1. Blood Sample Collection: Maternal blood is collected in the first trimester.
2. Low-Pass Whole-Genome Sequencing: Millions of DNA fragments are sequenced, primarily to screen for fetal chromosomal anomalies.
3. Viral DNA Analysis: Sequences that do not match the human genome are compared to the CMV reference genome.
4. Read Count Quantification: The number of CMV-specific DNA fragments, or “reads,” is measured to determine viral load.

This approach provides a noninvasive, high-throughput method to detect CMV in early pregnancy while simultaneously performing routine NIPS.

Clinical Validation of NIPS-Based CMV Screening

A landmark study published in Clinical Chemistry in 2026 evaluated NIPS-based CMV screening in 22,333 consecutive pregnancies at 12 weeks gestation. Researchers analyzed CMV read counts and correlated the results with:

• Quantitative PCR (qPCR) viral loads
• Maternal CMV serology
• Systematic newborn cCMV screening

Key Findings

• Prevalence: CMV DNA was detected in 2.1 percent of pregnancies.
• Correlation with qPCR: CMV read counts strongly correlated with viral load (rs = 0.76).
• Prediction of Primary Infection: Read counts ≥4 were highly predictive of primary maternal infection (likelihood ratio = 7.8).
• Prediction of cCMV: Read counts ≥4 corresponded to a 51.7 percent positive predictive value for congenital infection.
• Sensitivity: Even low read counts (1–3) provided useful information for risk stratification, although some infections occurring later in pregnancy may be missed.

These results demonstrate that NIPS-derived CMV read counts are an effective and sensitive method to identify pregnancies at risk for congenital CMV.

Benefits of Early CMV Detection Using NIPS

Integrating CMV viral load analysis into NIPS offers several advantages:

1. Noninvasive: No additional procedures are required beyond standard NIPS blood collection.
2. Early Detection: Identifies infections before seroconversion, providing a broader therapeutic window for antiviral intervention.
3. High Sensitivity: Can detect low-level DNA fragments that may not be measurable by traditional PCR.
4. Risk Stratification: Read count thresholds enable clinicians to categorize pregnancies into high- and low-risk groups.
5. Complementary to Serology: Enhances traditional serological screening and identifies cases that serology alone may miss.

Clinical Implications

Pregnancies with high CMV read counts may benefit from targeted interventions, including:

• High-dose valacyclovir therapy: Proven to reduce vertical transmission in first-trimester primary infections.
• Confirmatory PCR testing: To verify viral load and guide treatment decisions.
• Ongoing monitoring: Follow-up serology or amniocentesis when clinically indicated.

By identifying high-risk pregnancies early, clinicians can implement strategies to reduce fetal exposure and improve neonatal outcomes.

Limitations and Considerations

While NIPS-based CMV screening is promising, it is important to note the following:

• Some infections may occur after the NIPS blood draw, so ongoing monitoring is still necessary.
• Low read counts may represent either early infection or transient viral DNAemia, requiring careful interpretation.
• Laboratory variability in serology testing and sequencing pipelines can affect results.
• Prospective studies are needed to validate outcomes and optimize clinical protocols.

Future Directions

Research suggests several opportunities for improving early CMV detection:

• Earlier NIPS Testing: Performing NIPS at 10 weeks could expand the window for effective intervention.
• Enhanced Bioinformatics: Refining read mapping and filtering could reduce false positives.
• Integration with Other Pathogen Screening: NIPS could become a multi-pathogen platform for early prenatal infection detection.
• Personalized Treatment Algorithms: Combining viral load, serology, and maternal risk factors could guide individualized antiviral therapy.

Conclusion

Early detection of CMV in pregnancy is critical to prevent congenital infections that can lead to hearing loss and developmental delays. Noninvasive prenatal screening, combined with viral DNA quantification, provides a sensitive, scalable, and low-cost method for first-trimester CMV screening. By analyzing CMV read counts from NIPS data, clinicians can identify high-risk pregnancies and offer timely interventions such as antiviral therapy. This approach complements traditional serology, improving early detection and risk stratification for congenital CMV.

Key Takeaways

• CMV is a common congenital infection with serious long-term effects.
• Traditional serology has limitations in early and nonprimary infection detection.
• NIPS-based CMV screening detects viral DNA fragments in maternal plasma.
• CMV read counts correlate with viral load and can predict primary maternal infection and cCMV.
• High-risk pregnancies (≥4 reads) may benefit from early antiviral therapy.

References

1. Herroelen PH, Swaerts K, Descheemaeker P, et al. Universal Screening of Cytomegalovirus Viral Load by Low-Pass Whole-Genome Sequencing in First-Trimester Pregnancy: Clinical Validation. Clin Chem. 2026;72(1):173–182.
2. Kenneson A, Cannon MJ. Review and meta-analysis of the epidemiology of congenital cytomegalovirus infection. Rev Med Virol. 2007;17(4):253–276.
3. Revello MG, Gerna G. Diagnosis and management of CMV infection in pregnancy. Curr Opin Infect Dis. 2010;23(3):259–264.
4. Revello MG, et al. Valacyclovir therapy in primary maternal CMV infection. N Engl J Med. 2015;372:933–943.
5. Sweeney TE, Wong H, et al. Cell-free DNA detection of viral infections in pregnancy. Genome Med. 2020;12:45.

Disclaimer

This blog is for informational purposes only and is based on published research. It is not a substitute for professional medical advice. Clinical decisions regarding CMV screening or treatment should be made in consultation with qualified healthcare providers.