Comparative Analysis of Epstein-Barr Virus (Ebv) Latent Gene and Microrna Sequences among AKATA, B95.8, AG876 And GD1 EBV Genomes

Abstract

Akata cell line is an Epstein-Barr virus (EBV)-producing line established from a Japanese patient with EBV-positive Burkitt lymphoma. It is extensively used in EBV-related studies in the published literature. Yet the existing DNA sequences of the Akata EBV genome in NCBI Entrez and other public genome databases are very scanty and do not include the polymorphic latent gene regions. In this study, we PCR-amplified and sequenced all latent genes and microRNA regions of Akata EBV genome. The Akata EBV DNA sequences were then compared with those of corresponding EBV genetic loci in prototype cell lines, B95.8 (type 1 EBV) and AG876 (type 2 EBV), and in GD1 (type 1 EBV DNA sequence of a Chinese patient with nasopharyngeal carcinoma). Type-specific sequence divergence was observed at the EBNA2, EBNA3A, -3B and -3C loci of Akata EBV with >95% homology to those of B95.8 and GD1 but only 86% homology to that of AG876. Thirty-bp deletion and four 11- amino acid repeat sequences were present in the C-terminus of LMP1 gene of Akata EBV. LMP1, -2A and -2B loci, which do not correlate with type 1 or type 2 status, showed significant genetic diversity between Akata EBV and the prototype sequences. MicroRNA regions, miR-BART cluster 2 and miR-BHRF1, have >99% homology among Akata, AG876 and GD1 genomes. The single nucleotide change (A>T, 146466) at the hinge region of miRBART7 did not affect the microRNA folding (as predicted by MFold software). The data supported the idea that EBV microRNAs are highly conserved throughout evolution. Genetic variations of LMP1, LMP2A, LMP2B, EBNA1, EBER and miR-BART cluster 1 among Akata and the prototype EBV genomes will be further analyzed for potential functional polymorphisms.