Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study

Human cytomegalovirus (HCMV) primary infections of pregnant women can lead to congenital infections of the fetus that could have severe impacts on the health of the newborn. Recent studies have shown that 10–100 billion DNA fragments per milliliter of plasma are circulating cell-free. The study of this DNA has rapidly expanding applications to non-invasive prenatal testing (NIPT). In this study, we have shown that we can detect viral specific reads in the massively parallel shotgun sequencing (MPSS) NIPT data. We have also observed a strong correlation between the viral load of calibration samples and the number of reads aligned on the reference genome. Based on these observations we have constructed a statistical model able to quantify the viral load of patient samples. We propose to use this new method to detect and quantify circulating DNA virus like HCMV during pregnancy using the same sequencing results as NIPT data. This method could be used to improve the NIPT diagnosis.