High-throughput analysis of human cytomegalovirus genetic diversity reveals variation in coding capacity and extensive recombination

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that causes serious sequelae in immunocompromised patients and newborns. The coding capacity and diversity of its 235 kbp genome is still not fully comprehended and there is a pressing need to characterize genomic contents in clinically representative strains. We therefore have developed a procedure for the high-throughput generation of full genome sequences from minimally passaged clinical isolates. This procedure relies on low number passaging of clinical strains on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA. After multiple displacement amplification, highly pure viral DNA was generated. Validation experiments have shown that the consensus sequences derived from these extracts using different next-generation sequencing platforms are representative for the virus population present in the original clinical material. Full genome analysis of 100 clinical isolates has revealed extensive genetic variability in several regions of the HCMV genome. In addition, gene-disrupting mutations were identified in a set of 21 genes, including the viral interleukin-10 encoding gene UL111A. Consequently, HCMV coding capacity seems to be variable among clinical isolates and this variation could have clinical significance. Finally, phylogenetic analysis highlighted the predominant role of recombination in the evolution of HCMV genetic diversity, which provides the virus with a very powerful mechanism of adapting to its changing environment through the exchange of alleles.status: publishe