Genotypic analysis of two hypervariable human cytomegalovirus genes

Abstract

Most human cytomegalovirus (HCMV) genes are highly conserved in sequence among strains, but some exhibit a substantial degree of variation. Two of these genes are UL146, which encodes a CXC chemokine, and UL139, which is predicted to encode a membrane glycoprotein. The sequences of these genes were determined from a collection of 184 HCMV samples obtained from Africa, Australia, Asia, Europe, and North America. UL146 is hypervariable throughout, whereas variation in UL139 is concentrated in a sequence encoding a potentially highly glycosylated region. The UL146 sequences fell into 14 genotypes, as did all previously reported sequences. The UL139 sequences grouped into 8 genotypes, and all previously reported sequences fell into a subset of these. There were minor differences among continents in genotypic frequencies for UL146 and UL139, but no clear geographical separation, and identical nucleotide sequences were represented among communities distant from each other. The frequent detection of multiple genotypes indicated that mixed infections are common. For both genes, the degree of divergence was sufficient to preclude reliable sequence alignments between genotypes in the most variable regions, and the mode of evolution involved in generating the genotypes could not be discerned. Within genotypes, constraint appears to have been the predominant mode, and positive selection was detected marginally at best. No evidence was found for linkage disequilibrium. The emerging scenario is that the HCMV genotypes developed in early human populations (or even earlier), becoming established via founder or bottleneck effects, and have spread, recombined and mixed worldwide in more recent times.

Figure 1

Phylogenetic analysis of UL139.A:Alignment (CLUSTAL W) of amino acid sequences representing the eight genotypes. Predicted signal peptide and transmembrane sequences are highlighted in gray. Completely conserved residues are indicated in the consensus row (con). Below this is the CCMV sequence, which is included to illustrate conservation of the SETTTGTSSNSS motif (underlined). The CCMV sequence [Davison et al., 2003] provided is theC–terminal portion (final 12 residues not shown) of a larger protein, the N–terminal portion of which lacks a counterpart in HCMV but is related to a protein (encoded by gene rh174) in rhesus cytomegalovirus. B: Unrooted neighborjoining tree for the HCMV amino acid sequences shown in (A), computed using Mega4.0 (Poisson correction method with gaps removed). Bootstrap values (out of 100) are shown, and values below 70 indicate regions of unresolved branching order. The scale bar indicates the number of amino acid substitutions per site.