Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from Southeast Asia

Abstract

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.

FIG. 1.

Maximum-likelihood phylogenies of EBV isolates for three regions of the LMP1 gene: (a) N terminus, (b) transmembrane, and (c) C terminus. (d) Concatenated alignment of isolates for which all three regions were sequenced. See the text for details of phylogeny estimation. Each tree shows distinct clustering of isolates from different geographical regions: southeast Asia, Africa, Australia, and Papua New Guinea (PNG). Note that these trees are unrooted and so cannot be used to determine which regional group is basal. Isolates from NPC patients are shown in grey shading.

FIG. 2.

Maximum-likelihood phylogeny of LMP1 sequences from the southeast Asian isolates. All three gene regions—C terminus, transmembrane, and N terminus—were included in the alignment on which this tree is based, although not all three sequences were available for all isolates. Isolates from NPC patients are shown with grey shading.

FIG. 3.

C-terminal alignment, with the putative positively selected sites shown. Sites for which P is >99% are shown in bold yellow letters on a blue background, while sites for which P is >50% but less than 99% are shown as red letters on a yellow background. The repeat region is shown as a red box. The CTAR domains and JAK3 motif are also indicated. For more details on the analysis, see the text and Table 3.