title: Diversity of naturally occurring Epstein-Barr virus revealed by nucleotide sequence polymorphism in hypervariable domains in the BamHI K and N subgenomic regions.
abstract: The extent of nucleotide sequence microheterogeneity varies among subgenomic regions of Epstein-Barr virus (EBV). We examined, in EBV-carrying lymphoid cell lines, the extent of polymorphism in EBV DNA fragments amplified from the BamHI E, K, N and Z regions, and then investigated the diversity of the more hypervariable regions in tissues and body fluids. In cell lines, sequence dissimilarities in a genotype-specifying fragment of the EBNA-3C gene varied from < 1-4% within each genotype; dissimilarities in the first intron of the BZLF- 1 gene were < 2% within each genotype. By contrast, dissimilarities in a C-terminal unique domain of the EBNA-1 gene, and in a fragment that encompasses and is upstream of the LMP-1 start codon, varied between 2 and 7% and were not genotype-specific. The sequence diversity in BamHI K and N regions was then examined in tissues and body fluids by single-strand conformation polymorphism (SSCP) analysis and cycle sequencing. Extensive inter-host diversity was observed, whether the host was co-infected by human immunodeficiency virus (HIV) or not. In the oral cavity of HIV-infected patients, inter-compartmental EBV diversity could be demonstrated, even between sites that were anatomically proximate. Studies of BamHI K clones derived from EBV in oral lesions revealed infection by multiple variants. Identification of hypermutable loci within the EBV genome such as those located in the BamHI K and N regions should permit fine discrimination of individual EBV variants.
authors.affiliation: Virus Reference Division, Central Public Health Laboratory, London, UK.
authors.forename: D
authors.initials: D
authors.lastname: Triantos
authors.forename: A W
authors.initials: AW
authors.lastname: Boulter
authors.forename: J C
authors.initials: JC
authors.lastname: Leao
authors.forename: L
authors.initials: L
authors.lastname: Di Alberti
authors.forename: S R
authors.initials: SR
authors.lastname: Porter
authors.forename: C M
authors.initials: CM
authors.lastname: Scully
authors.forename: W
authors.initials: W
authors.lastname: Birnbaum
authors.forename: N W
authors.initials: NW
authors.lastname: Johnson
authors.forename: C G
authors.initials: CG
authors.lastname: Teo
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral