The Cell-Free DNA Virome of 108,349 Dutch Pregnant Women

Pregnancy increases the body's vulnerability to infectious disease, and current guidelines during pregnancy include minimizing possible exposure to viral infection. In cases where viral infection does occur, these can cause mild to severe complications in both mother and fetus; many viruses that result in such complications are DNA viruses. Current diagnosis technology for DNA viruses relies largely on polymerase chain reaction (PCR), which is very sensitive but generally targeted at a specific virus and so tends to not be very comprehensive. In addition, this testing is normally performed only on those who are at high risk or expressing symptoms. To more fully understand the effect and prevalence of DNA viruses in pregnancy, this study used noninvasive prenatal testing (NIPT) that captures cell-free DNA (cfDNA) to examine the DNA virome in pregnant women between 2017 and 2020. Data included deidentified NIPT results for 108,349 individuals, and DNA sequences were used to screen for 224 DNA viruses. Viruses that were genetically similar were differentiated based on taxonomy through a meticulous decision tree to avoid generalized errors in categorizing them. The most commonly detected virus was parvovirus B19, occurring in approximately 1 in 3000 cfDNA reads. High viral loads were also observed for hepatitis B, Bocaparvovirus, papillomavirus, adenovirus, adeno-associated virus, Epstein-Barr virus (EBV)/herpesvirus 4, cytomegalovirus (CMV), herpesvirus 6, and torque teno virus. A cross-examination of demographic and pregnancy factors revealed many associations, most of which remained significant after adjustments for multiple comparisons. Available characteristics included maternal age, body mass index (BMI), gestational age, fetal fraction, and the number of sequenced reads with the presence of viral DNA in the samples. Detection of viral DNA was associated with lower BMI, along with a lower concentration of cfDNA and a higher fetal fraction. When individual viruses were analyzed, CMV had the most significant relationship with gestational age and maternal age. Results additionally showed that low fetal fraction was associated with lower detection of viral DNA for specific viruses. These results show that it is feasible to detect viral DNA in NIPT samples. If viral DNA can be detected, there is potential to diagnose infection and to possibly prevent complications due to the virus. Current clinical practice does not use NIPT as a diagnostic tool for viral infection, but there is potential for this in the future. Further research should focus on clinical utility, sensitivity, specificity, and accuracy, as well as the relationship of viral DNA with low fetal fraction.