Within-Host Human Cytomegalovirus (HCMV) Genotype Dynamics in Congenital Infection Across Neonatal and Follow-Up Specimens

Human cytomegalovirus (HCMV) exhibits substantial genetic diversity, but within-host genotype dynamics in congenital infection remain incompletely characterized. We investigated HCMV genotype distribution, saliva–urine concordance, and longitudinal genotype changes in 12 congenitally infected infants. Thirty-three specimens were analyzed, including 21 specimens collected within the first 21 days of life and 12 follow-up urine specimens obtained from eight infants up to 36 months. Seven polymorphic loci were genotyped: glycoprotein B (gB/UL55) and glycoprotein H (gH/UL75) using genotype-specific real-time polymerase chain reaction (PCR), and glycoprotein N (gN/UL73), glycoprotein O (gO/UL74), UL6, UL139, and UL146 using amplicon-based next-generation sequencing. In neonatal urine, a single genotype at each locus was detected in 11 of 12 infants, whereas one infant showed mixed infection at multiple loci. Among nine infants with paired neonatal saliva and urine specimens, genotype concordance was observed in seven. During follow-up, additional genotypes became detectable at one or more loci in six of eight infants. These findings indicate that congenital HCMV infection is often characterized by a predominant genotype pattern early in life, while additional genotypes may become detectable over time. Larger longitudinal studies with multi-compartment sampling are needed to clarify the biological and clinical significance of these dynamics.