Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study

Abstract

Background Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of UL97 and UL54, target genes with mutations that confer GCV/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection. Methods Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV/VGCV. UL97 and UL54 genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations. Results Two drug resistance mutations (UL54 V823A and UL97 A594V) were found in one patient. Both mutations emerged after 6 months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV/VGCV treatment. Conclusions Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of UL97 and UL54 via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.

Congenital cytomegalovirus infection diagnostics and management

“…Although ganciclovir/valganciclovir resistance has only occasionally been reported in children with cCMV undergoing treatment, it is necessary to reassess the risk-benefit ratio for antiviral treatment, including the possibility of resistance onset, alongside improvement in SNHL and neurodevelopmental outcomes [55,56].…”

Optimizing Antiviral Dosing for HSV and CMV Treatment in Immunocompromised Patients

“…Immunocompromised patients are more likely than immunocompetent patients to develop therapy-resistant HSV or CMV infections [ 110 , 111 ]. Early detection of acyclovir-resistant HSV infections or ganciclovir-resistant CMV infections to optimize treatment regimens would benefit these patients.…”

An Update on Current Antiviral Strategies to Combat Human Cytomegalovirus Infection

“…In several cases of HCMV treated with GCV/VGCM, antiviral drug resistance has also been reported. Mutation in the viral protein kinase gene (UL97) and the DNA polymerase gene (UL54) confers resistance to GCV/VGCV ( Figure 1 ) [ 57 , 58 , 59 ]. Therefore, there is an urgent need to develop a new antiviral with higher efficacy and fewer side effects.…”