Molecular Diagnosis of Congenital Cytomegalovirus Infection among Neonates in Tertiary Health Institutions in Jos: A Cross-Sectional Study

Background: Congenital cytomegalovirus (CMV) infection is considered the most common congenital viral infection worldwide and a leading cause of neurodevelopmental abnormalities, including sensorineural hearing loss, microcephaly and developmental delay in neonates. Transmission occurs primarily through vertical maternal–foetal infection in early pregnancy. However, most infected neonates are asymptomatic at birth; a significant proportion develops long-term neurological sequelae. In low- and middle-income countries, including Nigeria, routine screening for congenital CMV is practically not done, and molecular epidemiological data remain limited. Aim: To determine the molecular prevalence and characterise congenital CMV infection among neonates attending tertiary health institutions in Jos, Nigeria. Materials and Methods: A cross-sectional molecular study was conducted among neonates aged ≤21 days, recruited from three tertiary hospitals in Jos, between January 2021 and December 2022. Buccal swab samples were collected and tested for CMV DNA using standardised in-house polymerase chain reaction. Positive samples were sequenced using Sanger sequencing, and phylogenetic analysis was performed. Data were analysed descriptively, and molecular prevalence was reported with exact 95% confidence intervals (CIs). Results: A molecular prevalence of 0.6% (95% CI: 0.02%–3.1%) was obtained. The single CMV-positive sample was subjected to Sanger sequencing. Basic local alignment search tool analysis revealed 98.9% nucleotide sequence similarity to human herpesvirus 5 strain HAN22. The sequence was assigned the GenBank accession number PV668598. Phylogenetic analysis showed clustering with previously reported African isolates. The CMV-positive neonate presented with microcephaly and was small for gestational age. Conclusion: Congenital CMV infection was rare in this cohort; however, molecular detection and genomic characterisation contribute valuable data to the limited CMV epidemiology in Nigeria and underscore the importance of continued surveillance and early diagnosis.