Nasopharyngeal carcinoma (NPC) has an elevated incidence in Southeast Asia and is influenced by a combination of risk factors, including host genetics, environmental exposures, and viral factors.¹ While genetic variants in Epstein-Barr virus (EBV) associated with NPC have been widely studied, findings regarding the most significant viral variants have varied.¹ Researchers from the LKS Faculty of Medicine of the University of Hong Kong (HKUMed) recently conducted a meta-analysis of genome-wide association studies (GWAS) of EBV genomes isolated from healthy donors and NPC biopsies, identifying a high-risk EBV lineage enriched in NPC of South China.¹ This EBV risk haplotype could aid in future studies of disease mechanisms, while the high-risk EBV lineage may be integrated into screening protocols for early NPC detection in the population.¹

Although NPC is a rare malignancy globally, it is endemic in specific populations, with more than 70% of new cases occurring in East and Southeast Asia and ranking as the fourth most common malignancy in Hong Kong.^2,3 While the ubiquitous EBV infects and persists latently in over 90% of the global population, the virus is associated with the later development of several malignancies, including NPC.² The carcinogenic mechanism of EBV remains unclear which could be due to abnormal interactions between the latent viral infection and existing precancerous genetic changes.³ At the same time, other risk factors include host genetic factors in the human leukocyte antigen (HLA) locus and NF-kB pathway, smoking, and consumption of preserved food.^1,3

In this study, comprehensive genomic analyses of EBV sequences from both NPC patients and healthy carriers in South China were conducted, consisting of previously published EBV genomes from Hong Kong (designated HK1), Guangdong and Guangxi (GZ), as well as 100 new EBV genomes isolated from 61 NPC patients and 39 healthy population controls in Hong Kong (HK2).¹ In total, 279 NPC biopsies and 227 control saliva samples were included in this meta-analysis of GWAS.¹ A high EBV genetic similarity in South China was determined through pairwise nucleotide diversity analysis, revealing low genomic variation between Hong Kong (HK) and Guangzhou (GZ) samples.¹

The study identified a 4-bp deletion downstream of EBER2 as the most significant variant associated with NPC.¹ EBER2 is a non-coding RNA that can interact with various cellular factors in EBV-infected cells, playing multiple roles including suppressing latent gene expression and regulating cytokine secretion.¹ 56 variants were found to have exceeded the genome-wide significance threshold in the meta-analysis, which were then grouped to identify 6 haplotypes, namely haplotypes I-IV, mixed haplotype, and risk haplotype.¹ NPC cases were enriched in the risk haplotype (case frequency=69.2%; control frequency=28.6%; OR=5.59; p<1.0x10^-9), suggesting that multiple EBV variants might be associated with NPC pathogenesis instead of a single variant.¹ Most of the healthy individuals carried low-frequency haplotypes that were grouped under “mixed haplotypes” (47.1%) and haplotype IV (15.4%).¹ The haplotype frequencies in NPC cases and controls were also similar across locations (HK and GZ).¹

Additionally, previous studies have reported that certain EBV subpopulations are preferentially enriched in NPC.¹ Population structure and phylogenetic analyses further identified a high-risk EBV lineage for NPC which could be characterized by 38 single nucleotide polymorphisms (SNPs), including those in the EBER2 and BALF2 loci.¹ Using linkage disequilibrium clumping and feature selection algorithm, the 38 SNPs could be narrowed down to 9 SNPs which could accurately detect the high-risk EBV lineage and achieve similar screening efficiency for NPC with fewer markers.¹

In conclusion, this meta-analysis of GWAS identified a risk haplotype of EBV associated with NPC for further functional investigations and characterized a high-risk EBV lineage marked by 9 SNPs, which could be useful for developing population screening programs for NPC in endemic areas.¹