Human Cytomegalovirus UL144 Open Reading Frame: Sequence Hypervariability in Low-Passage Clinical Isolates

Abstract

Human cytomegalovirus (HCMV) infects a number of organs and cell types in vivo, leading to the hypothesis that HCMV disease and tissue tropism may be related to specific sequence variants. A potential component of HCMV variant strains is the UL144 open reading frame (ORF), which encodes a homologue of the herpesvirus entry mediator, HveA, a member of the tumor necrosis factor receptor superfamily. Sequence analysis of the UL144 ORF in 45 low-passage clinical isolates demonstrated significant strain-specific variability. In individual isolates, nucleotide substitutions occur at up to 21% of the 531 positions, resulting in approximately the same percentage of substitutions in the predicted 176-amino-acid sequence. Phylogenetic analysis indicated that the nucleotide and amino acid sequences diverge into three major groups. For genotypic comparison, the known hypervariable region encompassing the proteolytic cleavage site of the glycoprotein B (gB) gene was also sequenced. All of the isolates could be typed according to the four known gB groups; however, the gB and UL144 sequence groups appeared to be phylogenetically unlinked. The predicted UL144 product homology with tumor necrosis factor receptor family members, along with the unexpectedly high level of sequence variability of the UL144 ORF, suggests that the predicted product may play a role in HCMV infectivity and subsequent host disease.

Genetic polymorphisms among human cytomegalovirus (HCMV) wild‐type strains

“…Arav-Boger et al [54] also detected clustered polymorphisms in UL144 from HCMV clinical isolates, which they denoted major genotypes A, B and C. Two minor patterns were also detected: the chimeras A/B and A/C. The correspondence of UL144 genotypes indicated with figures 1, 2 and 3 [53] or with capital letters A, B, C [54] is as follows: Group 1 comprises the genotypes A and the recombinant A/B; Group 2 corresponds to genotype C; Group 3 corresponds to genotype B.…”

“…This ORF (531 nt) belongs to the genomic region lacking in laboratory strains, but found in Toledo and other low passage clinical strains. It encodes a homologue of the herpes simplex virus entry mediator, a member of the tumour necrosis factor (TNF)--like receptor superfamily [53]. Therefore, this evidence evoked speculation that the locus may play an important role in determining the biological behaviour of wild-type HCMV strains.…”

“…Lurain et al [53] showed a significant strain-specific sequence variability for UL144, with the majority of the nucleotide changes in the 5' half of the gene. Phylogenetic analysis indicated that the nucleotide and the amino acid sequences diverge into three major groups, denoted group 1, group 2 and group 3, with group 1 showing three distinct subgroups (A, B and C).…”

“…The product of UL146 has been demonstrated to be a functional -chemokine [91]. Some reports referred to clustered sequence variability and high divergence within these loci [53,[91][92][93], but nothing has been published to date.…”

“…In vitro passaging of virus is another documented phenomenon described as co-responsible for strain selection [115]. Studies on UL73 and UL144 polymorphisms reported that sequence adaptation during passage in cell culture is unlikely [38,53]. However, in vitro propagation of virus may affect isolation of strains, so that some variants may be overlooked.…”