Effect of interstrain variation on diagnostic DNA amplification of the cytomegalovirus major immediate-early gene region

The immediate-early region exon 4 sequences of six clinical cytomegalovirus strains were determined and compared with those of laboratory strains AD169 and Towne. Of 407 codons in exon 4, 33 (8.1%) showed interstrain variation at the peptide level and 74 (18%) showed interstrain variation at the nucleotide level. Variation occurred sporadically throughout the exon, and no grouping of strains was apparent. Published oligonucleotide primers proposed for diagnostic detection of cytomegalovirus by polymerase chain reaction have often been based on exon 4 sequences. Some of these primers show sequence mismatches with strains sequenced here. Amplification sensitivity for mismatched strains was reduced up to 100-fold. More-uniform detection sensitivity was achieved with primers of conserved sequence.