Development and validation of a next-generation sequencing assay with open-access analysis software for detecting resistance-associated mutations in CMV

Human Cytomegalovirus (HCMV) Genetic Diversity, Drug Resistance Testing and Prevalence of the Resistance Mutations: A Literature Review

Human cytomegalovirus (HCMV) is a pathogen with high prevalence in the general population that is responsible for high morbidity and mortality in immunocompromised individuals and newborns, while remaining mainly asymptomatic in healthy individuals. The HCMV genome is 236,000 nucleotides long and encodes approximately 200 genes in more than 170 open reading frames, with the highest rate of genetic polymorphisms occurring in the envelope glycoproteins. HCMV infection is treated with antiviral drugs such as ganciclovir, valganciclovir, cidofovir, foscarnet, letermovir and maribavir targeting viral enzymes, DNA polymerase, kinase and the terminase complex. One of the obstacles to successful therapy is the emergence of drug resistance, which can be tested phenotypically or by genotyping using Sanger sequencing, which is a widely available but less sensitive method, or next-generation sequencing performed in samples with a lower viral load to detect minority variants, those representing approximately 1% of the population. The prevalence of drug resistance depends on the population tested, as well as the drug, and ranges from no mutations detected to up to almost 50%. A high prevalence of resistance emphasizes the importance of testing the patient whenever resistance is suspected, which requires the development of more sensitive and rapid tests while also highlighting the need for alternative therapeutic targets, strategies and the development of an effective vaccine.

Next-generation sequencing for cytomegalovirus genotypic antiviral resistance testing

Sanger-based sequencing has long served as the gold standard for detecting cytomegalovirus (CMV) resistance mutations. However, next-generation sequencing (NGS) offers a highly multiplexed and sensitive approach. Clinical implementation of NGS-antiviral resistance testing requires thorough validation. In this issue of the Journal of Clinical Microbiology, M. A. Mallory, W. C. Hymas, K. E. Simmon, M. T. Pyne, et al. (J Clin Microbiol 61:e00829-23, 2023, https://doi.org/10.1128/jcm.00829-23) detail a validation of a targeted NGS-based assay for multiple genomic regions that confer resistance to CMV antivirals and share their bioinformatics analysis and reporting pipeline. This validation can serve as guidance for laboratories wishing to develop similar methodologies.