Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1—and, by extension, EBV—diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC).

IMPORTANCE Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The patterns of this mixing suggest that sequences can spread between strains (and also within the repeat) by copying sequence from another strain (or repeat unit) to repair DNA damage.

EB 病毒 (EBV) 是人类普遍存在的病原体，可引起多种类型的淋巴瘤和癌症。与其他疱疹病毒一样，EBV 通过与其宿主的共同进化以及病毒株之间的基因交换而实现多样化。由于病毒内重复区域的数量和长度巨大，因此 EBV 基因组的序列分析异常具有挑战性。在这里，我们描述了 70 多个毒株的 EBV 大型内部重复序列 1（IR1；也称为 BamW 重复序列）的序列组装和分析。潜伏蛋白 EBV 核抗原前导蛋白 (EBNA-LP) 的多样性主要存在于 IR1 下游的外显子内。超过 80% 的菌株保留了推定的 BWRF1 开放阅读框 (ORF) 的完整性，并且截短 IR1 的删除总是能保留 BWRF1。保守区域包括 IR1 潜伏启动子 (Wp) 以及 BWRF1 上游的一个区域和 BWRF1 内的两个区域。IR1 在 70% 的毒株中是异质的，这种异质性源于毒株之间的序列交换以及自发突变，其中毒株间重组在肿瘤来源的病毒中更为常见。这种基因交换通常包含 <1 kb 的区域，等位基因转换会改变重复区域内但不靠近侧翼的小区域的频率。这些观察结果表明，IR1（以及由此延伸的 EBV）通过重组和断点修复实现多样化，而 IR1 的协同进化是由小区域的基因转换驱动的。最后，原型 EBV 毒株 B95-8 在单个 IR1 重复单元内包含四个非共有变异，包括 EBNA-LP 基因中的终止密码子。修复 IR1 可提高 EBNA-LP 水平以及 B95-8 细菌人工染色体 (BAC) 的转化质量。

重要性爱泼斯坦-巴尔病毒 (EBV) 感染世界上大多数人口，但仅导致极少数人患病。然而，全世界超过 1% 的癌症是由 EBV 引起的。最近的测序项目调查了病毒多样性，以了解不同毒株是否具有不同的疾病影响，但排除了重复序列的区域，因为它们在技术上更具挑战性。在这里，我们分析了 EBV (IR1) 中最大重复的序列。我们首先表征了 IR1 编码的蛋白质序列的变异。在研究每个毒株重复序列中的变异时，我们在 EBV 主要实验室毒株中发现了一种损害病毒功能的突变，我们认为肿瘤相关病毒可能更可能含有两种毒株混合的 DNA。这种混合的模式表明，序列可以通过复制来自另一个菌株（或重复单元）的序列来修复 DNA 损伤，从而在菌株之间（以及重复序列内）传播。