Correia, S; Bridges, R; Wegner, F; Venturini, C; Palser, A; Middeldorp, JM; Cohen, JI; ... Farrell, PJ; + view all Correia, S; Bridges, R; Wegner, F; Venturini, C; Palser, A; Middeldorp, JM; Cohen, JI; Lorenzetti, MA; Bassano, I; White, RE; Kellam, P; Breuer, J; Farrell, PJ; - view fewer (2018) Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases. Journal of Virology , 92 (22) , Article e01132-18. 10.1128/JVI.01132-18.

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Abstract

One hundred thirty-eight new Epstein-Barr virus (EBV) genome sequences have been determined. One hundred twenty-five of these and 116 from previous reports were combined to produce a multiple-sequence alignment of 241 EBV genomes, which we have used to analyze variation within the viral genome. The type 1/type 2 classification of EBV remains the major form of variation and is defined mostly by EBNA2 and EBNA3, but the type 2 single-nucleotide polymorphisms (SNPs) at the EBNA3 locus extend into the adjacent gp350 and gp42 genes, whose products mediate infection of B cells by EBV. A small insertion within the BART microRNA region of the genome was present in 21 EBV strains. EBV from saliva of U.S. patients with chronic active EBV infection aligned with the wild-type EBV genome with no evidence of WZhet rearrangements. The V3 polymorphism in the Zp promoter for BZLF1 was found to be frequent in nasopharyngeal carcinoma cases from both Hong Kong and Indonesia. Codon usage was found to differ between latent and lytic cycle EBV genes, and the main forms of variation of the EBNA1 protein have been identified.

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