In-utero Exposure to Zidovudine-containing Antiretroviral Therapy and Clonal Hematopoiesis in HIV-exposed Uninfected Newborns

Shu-Hong Lin; Youjin Wang; Stephen W. Hartley; Danielle M. Karyadi; Olivia W. Lee; Bin Zhu; Weiyin Zhou; Derek W. Brown; Erin Beilstein-Wedel; Rohan Hazra; Deborah Kacanek; Ellen G. Chadwick; Carmen J. Marsit; Miriam C. Poirier; Sean S. Brummel; Stephen J. Chanock; Eric A. Engels; Mitchell J. Machiela


AIDS. 2021;35(10):1525-1535. 

In This Article

Abstract and Introduction


Objective: Zidovudine (ZDV) has been extensively used in pregnant women to prevent vertical transmission of HIV but few studies have evaluated potential mutagenic effects of ZDV during fetal development.

Design: Our study investigated clonal hematopoiesis in HIV-exposed uninfected (HEU) newborns, 94 of whom were ZDV-exposed and 91 antiretroviral therapy (ART)-unexposed and matched for potential confounding factors.

Methods: Utilizing high depth sequencing and genotyping arrays, we comprehensively examined blood samples collected during the first week after birth for potential clonal hematopoiesis associated with fetal ZDV exposure, including clonal single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural copy number or copy neutral alterations.

Results: We observed no statistically significant difference in the number of SNVs and indels per person in ZDV-exposed children (adjusted ratio [95% confidence interval, CI] for expected number of mutations = 0.79 [0.50--1.22], P = 0.3), and no difference in the number of large structural alterations. Mutations in common clonal hematopoiesis driver genes were not found in the study population. Mutational signature analyses on SNVs detected no novel signatures unique to the ZDV-exposed children and the mutational profiles were similar between the two groups.

Conclusion: Our results suggest that clonal hematopoiesis at levels detectable in our study is not strongly influenced by in-utero ZDV exposure; however, additional follow-up studies are needed to further evaluate the safety and potential long-term impacts of in-utero ZDV exposure in HEU children as well as better investigate genomic aberrations occurring late in pregnancy.


Zidovudine (ZDV) was the first approved antiretroviral medication used for preventing the transmission of HIV from mother to child.[1] The availability of ZDV, especially as part of combination antiretroviral therapy (ART), has dramatically reduced vertical transmission of HIV.[2] However, the long-term safety of in-utero exposure to antiretroviral medications in HIV-exposed uninfected (HEU) children remains a concern.

ZDV is a nucleoside reverse transcriptase inhibitor (NRTI), which competitively inhibits HIV reverse transcriptase and is incorporated into viral DNA, resulting in DNA chain termination.[3] NRTIs can also become incorporated into human nuclear and mitochondrial DNA.[4] Previous studies have shown potential impact of in-utero exposure to ZDV and other NRTIs. For instance, Le Chenadec et al.[5] observed transiently lower hemoglobin, which disappeared within 3 months and reduction in neutrophil, lymphocyte, and platelet counts, which persisted from birth to at least 18 months in the French Perinatal Study. The European Collaborative Study reported that reduced neutrophil count could be observed in children exposed to ART even after 8 years.[6] Finally, Pacheco et al.[7] demonstrated that changes in platelet and lymphocyte counts in children exposed to ART persisted 2 years after birth. In-vitro studies also suggest ZDV could have genotoxic effects.[8,9] Furthermore, evidence from animal studies suggests ZDV could have transplacental effects and cause genetic abnormalities and genotoxicity.[10–12] Finally, aneuploidy rate in cord blood cells as well as expression of genes related to DNA repair have been shown to be altered in children with exposure to ZDV.[13,14]

These hematologic and genotoxic effects have raised concerns regarding the long-term risk of cancer in HEU children exposed in utero to ZDV. The International Agency for Research on Cancer has classified ZDV as a probable carcinogen for humans (class 2A agent).[15] As the population of surviving HEU children expands and ages, knowledge of potential genotoxic and carcinogenic effects of early-life exposure to ZDV is essential for weighing potential risks and benefits of in-utero antiretroviral regimens that include ZDV or other NRTIs.

Clonal hematopoiesis refers to clonal expansion of a subset of leukocytes carrying somatic mutations.[16] These mutations range in size from a single nucleotide variant (SNV) to large somatic copy number alterations (SCNAs) at the chromosomal scale. The detection of clonal hematopoiesis relies on the size of event: SNVs require next-generation sequencing whereas SCNAs are better detected by virtual karyotyping methods using single nucleotide polymorphism (SNP) genotyping arrays. In addition to being a characteristic of myelodysplastic syndromes as well as leukemia,[17,18] clonal hematopoiesis has been found to be associated with cardiovascular disease,[19] Alzheimer disease,[20] and cancer.[21–23] Previous studies on clonal hematopoiesis have also found associations with chemotherapy,[24] cigarette smoking,[16,25] and air pollution[26] suggesting that clonal hematopoiesis can serve as a biomarker reflecting environmental exposure to a carcinogen or mutagen. However, no study has characterized potential adverse effects of ZDV exposure on fetal clonal hematopoiesis using currently available genomic technologies.

In this study, we investigate clonal hematopoiesis as a marker of genomic damage detected in peripheral blood mononuclear cell samples obtained from ZDV-exposed and, for comparison, ART-unexposed neonates during the first week after birth. We utilize high-depth DNA sequencing and SNP genotype array-based methods to comprehensively identify clonal SNVs, small insertions and deletions (indels), and large acquired SCNAs.