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This was further supported by analysis of effective number of codons (ENc), codon adaptation index (CAI) and mRNA structural variation. RESULTS Patients with HCMV-associated CNS were found to have significant variations in many studied parameters compared with controls. The majority of clinical strains formed a separate phylogenetic cluster defining them as somewhat distinct from standard reference strains, which was supported by the other analyses. CONCLUSION This study defined parameters for monitoring cases of HCMV-associated CNS, wh