New research suggests non-invasive prenatal screening using a low-cost form of whole genome sequencing can detect pregnant mothers at risk of transmitting cytomegalovirus which can cause permanent hearing loss to their developing babies.
The test is commonly used during pregnancy in Australia as a highly accurate, optional, private-pay test for detecting chromosomal conditions such as Down syndrome.
Cytomegalovirus (CMV) is a common herpes infection that can trigger neurodevelopmental delays and other irreversible problems in up to 20% of infants born with it. The infection occurs in about one in 150 live births globally.
The findings were published on 6 January 2026 in the Association for Diagnostics & Laboratory Medicine’s Clinical Chemistry journal.
Researchers said the findings could help doctors identify which pregnant patients would benefit from receiving antiviral treatment, preventing mother-to-foetus virus transmission.
Despite its prevalence, guidelines do not recommend prenatal screening for CMV mainly because no effective therapies have been available to treat it.
The researchers said that in 2020, research showed the antiviral drug valacyclovir could reduce CMV transmission by more than 70% when given to infected women in their first trimester of pregnancy.
While the Food and Drug Administration has not formally approved valacyclovir for this use, many doctors prescribe it to pregnant patients known to have CMV, they said.
They said the new study provided powerful evidence that non-invasive prenatal screening (NIPS) can gauge CMV infection in mother and baby.
Researchers from Belgium led by Dr Geert Martens analysed NIPS data from 22,333 pregnancies at 12–14 weeks’ gestation between November 2019 and January 2025.
NIPS was done using a cost-effective method called low-pass whole genome sequencing, which assesses a patient’s genetic blueprint. The researchers evaluated blood samples found to include genetic material from non-human sources such as viruses and bacteria for free-floating fragments of DNA (called cell-free DNA) from CMV.
They found CMV DNA in 2.1% (462) of pregnancies studied. The researchers divided those patients’ blood samples into four groups based on the amount of viral DNA detected, ranging from least to most.
They validated the information by comparing it to results gleaned using PCR, the gold-standard method for measuring DNA.
Results found NIPS-derived CMV data showed good diagnostic accuracy for maternal and newborn CMV infections. A positive CMV result was a strong indicator of infection among mothers (confirmed by antibody testing) and their newborns (confirmed through a systematic screening program).
The risk for maternal and newborn (or congenital) CMV infection was highest in blood samples from pregnancies with the most CMV DNA.
“Crucially, our study is the first to directly link NIPS-derived CMV read counts to both maternal serostatus and confirmed cCMV [congenital CMV] outcomes from a systematic newborn screening program, in a real-world high-volume setting of first-tier cell-free foetal DNA screening,” the researchers said.
They said more research was needed to flesh out the clinical significance of the findings but the results are promising.
“Given its low cost and high throughput, [the integration of CMV DNA testing] into routine aneuploidy screening is a powerful complement to serology, poised to improve the identification of pregnancies that may benefit from antiviral therapy to prevent cCMV,” they said.
NIPS screening, also referred to as aneuploidy screening, checks for an incorrect number of chromosomes (too many or too few) in a foetus, commonly for Down (Trisomy 21), Edwards (Trisomy 18), or Patau (Trisomy 13) syndromes.
