The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses

Herpesviridae is a diverse family of large and complex pathogens whose genomes are extremely difficult to sequence. This is particularly true for clinical samples, and if the virus, host, or both genomes are being sequenced for the first time. Although herpesviruses are known to occasionally integrate in host genomes, and can also be inherited in a Mendelian fashion, they are notably absent from the genomic fossil record comprised of endogenous viral elements (EVEs). Here, we combine paleovirological and metagenomic approaches to both explore the constituent viral diversity of mammalian genomes and search for endogenous herpesviruses. We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi's sarcoma-associated virus. We also identify 58 genes of Pan paniscus lymphocryptovirus 1, the bonobo equivalent of human Epstein-Barr virus. For each of the viruses, we postulate gene function via comparative analysis to known viral relatives. Most notably, the evidence from gene content and phylogenetics suggests that the aye-aye sequences represent the most basal known rhadinovirus, and indicates that tumorigenic herpesviruses have been infecting primates since their emergence in the late Cretaceous. Overall, these data show that a genomic fossil record of herpesviruses exists despite their extremely large genomes, and expands the known diversity of Herpesviridae, which will aid the characterization of pathogenesis. Our analytical approach illustrates the benefit of intersecting evolutionary approaches with metagenomics, genetics and paleovirology.

疱疹病毒科（Herpesviridae）是一类兼具多样性的大型复杂病原体类群，其基因组测序难度极高。临床样本更是如此，若为首次对病毒、宿主或二者的基因组开展测序时，这一难题尤为突出。尽管已知疱疹病毒偶尔会整合至宿主基因组，且可通过孟德尔式方式遗传，但在由内源性病毒元件（endogenous viral elements, EVEs）构成的基因组化石记录中，疱疹病毒却明显缺失。本研究结合古病毒学与宏基因组学方法，既探究哺乳动物基因组中蕴含的病毒多样性，也搜寻内源性疱疹病毒。我们首次从菲律宾跗猴的基因组中鉴定出一株内源性疱疹病毒，该病毒隶属于玫瑰病毒属（Roseolovirus），并对其整合入宿主基因组且两侧带有明确宿主DNA序列的高度缺陷型基因组进行了特征分析。我们通过指狐猴基因组的草图组装，借助生物信息学工具揭示了一段超过100,000碱基对的新型兔疱疹病毒属（Rhadinovirus）序列——这是首株被发现的狐猴源γ疱疹病毒，与卡波西肉瘤相关疱疹病毒（Kaposi's sarcoma-associated virus, KSHV）亲缘关系密切。我们还鉴定出了倭黑猩猩淋巴细胞病毒1型（Pan paniscus lymphocryptovirus 1）的58个基因，该病毒是与人类EB病毒（Epstein-Barr virus, EBV）对应的倭黑猩猩相关病毒。针对每一株病毒，我们通过与已知亲缘病毒的比较分析，推测了其基因功能。最值得注意的是，来自基因组成与系统发育学的证据表明，指狐猴的相关序列是目前已知的最原始兔疱疹病毒属病毒；同时该证据也证实，致瘤性疱疹病毒自灵长类动物在白垩纪晚期出现以来，便一直在感染灵长类。总体而言，本研究数据表明，尽管疱疹病毒基因组体量极大，但仍存在其专属的基因组化石记录；同时本研究拓展了人们对疱疹病毒科（Herpesviridae）多样性的认知，这将有助于相关致病机制的解析。我们的分析方法也证实，将进化生物学方法与宏基因组学、遗传学及古病毒学相结合具有显著优势。