Complete Genome Sequence of Pig-Tailed Macaque Rhadinovirus 2 and Its Evolutionary Relationship with Rhesus Macaque Rhadinovirus and Human Herpesvirus 8/Kaposi's Sarcoma-Associated Herpesvirus

Abstract

Two rhadinovirus lineages have been identified in Old World primates. The rhadinovirus 1 (RV1) lineage consists of human herpesvirus 8, Kaposi's sarcoma-associated herpesvirus (KSHV), and closely related rhadinoviruses of chimpanzees, gorillas, macaques and other Old World primates. The RV2 rhadinovirus lineage is distinct and consists of closely related viruses from the same Old World primate species. Rhesus macaque rhadinovirus (RRV) is the RV2 prototype, and two RRV isolates, 26-95 and 17577, were sequenced. We determined that the pig-tailed macaque RV2 rhadinovirus, MneRV2, is highly associated with lymphomas in macaques with simian AIDS. To further study the role of rhadinoviruses in the development of lymphoma, we sequenced the complete genome of MneRV2 and identified 87 protein coding genes and 17 candidate microRNAs (miRNAs). A strong genome colinearity and sequence homology were observed between MneRV2 and RRV26-95, although the open reading frame (ORF) encoding the KSHV ORFK15 homolog was disrupted in RRV26-95. Comparison with MneRV2 revealed several genomic anomalies in RRV17577 that were not present in other rhadinovirus genomes, including an N-terminal duplication in ORF4 and a recombinative exchange of more distantly related homologs of the ORF22/ORF47 interacting glycoprotein genes. The comparison with MneRV2 has revealed novel genes and important conservation of protein coding domains and transcription initiation, termination, and splicing signals, which have added to our knowledge of RV2 rhadinovirus genetics. Further comparisons with KSHV and other RV1 rhadinoviruses will provide important avenues for dissecting the biology, evolution, and pathology of these closely related tumor-inducing viruses in humans and other Old World primates. IMPORTANCEThis work provides the sequence characterization of MneRV2, the pig-tailed macaque homolog of rhesus rhadinovirus (RRV). MneRV2 and RRV belong to the rhadinovirus 2 (RV2) rhadinovirus lineage of Old World primates and are distinct but related to Kaposi's sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma. Pig-tailed macaques provide important models of human disease, and our previous studies have indicated that MneRV2 plays a causal role in AIDS-related lymphomas in macaques. Delineation of the MneRV2 sequence has allowed a detailed characterization of the genome structure, and evolutionary comparisons with RRV and KSHV have identified conserved promoters, splice junctions, and novel genes. This comparison provides insight into RV2 rhadinovirus biology and sets the groundwork for more intensive next-generation (NextGen) transcript and genetic analysis of this class of tumor-inducing herpesvirus. This study supports the use of MneRV2 in pigtailed macaques as an important model for studying rhadinovirus biology, transmission and pathology. K aposi's sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV) was first detected in 1994 in Kaposi's sarcoma (KS) lesions of individuals with human immunodeficiency virus (HIV)-...

Conservation of the glycoprotein B homologs of the Kaposi׳s sarcoma-associated herpesvirus (KSHV/HHV8) and old world primate rhadinoviruses of chimpanzees and macaques

“…We previously cloned and sequenced the gB genes of RV1 rhadinovirus species from pig-tailed macaques, including RFHVMn-M78114 from the Washington National Primate Research Center (WaNPRC) (Bruce et al, 2013) and RFHVMn-442N from the NIH primate facility, and RFHVMm-YN91 from a rhesus macaque at the Yerkes National Primate Research Center (Rose et al, 2003). We have also cloned and sequenced the gB gene of the pigtailed macaque RV2 rhadinovirus (MneRV2-J97167) from the WaNPRC (Bruce et al, 2015). The sequence of the gB gene of an additional pig-tailed macaque RV2 rhadinovirus (PMRV-98126) was sequenced from a pig-tailed macaque at the New England National Primate Research Center (NENPRC) (Auerbach et al, 2000).…”

ORF73 LANA homologs of RRV and MneRV2 contain an extended RGG/RG-rich nuclear and nucleolar localization signal that interacts directly with importin β1 for non-classical nuclear import

“…The complete genome sequences have been determined for KSHV (Russo et al, 1996), RFHVMn (Bruce et al, 2013), MneRV2 (Bruce et al, 2015) and RRV strains 17577 (Searles et al, 1999) and 26–95 (Alexander et al, 2000). The RFHV genome is colinear with the KSHV genome with strong sequence homology to the corresponding KSHV genes, lacking homologs of only 3 genes ORF11, K5 and K6, which are duplications of other genes in the genome (Bruce et al, 2013).…”

“…The RFHV genome is colinear with the KSHV genome with strong sequence homology to the corresponding KSHV genes, lacking homologs of only 3 genes ORF11, K5 and K6, which are duplications of other genes in the genome (Bruce et al, 2013). While the RRV and MneRV2 genomes are co-linear and highly homologous to each other, they exhibit multiple differences with the RV1 rhadinoviruses, including the absence of ORFs K3, K4.1, K4.2, K4.3, K5, K6, K7, K10, K10.5 and K11, the insertion and replication of seven homologs of ORFK9, and the recapture and reposition of a dihydrofolate reductase homolog (Bruce et al, 2015). Additional genetic differences have been detected between the RV1 and RV2 rhadinoviruses, including the unique presence in the RV1 rhadinoviruses of an “RGD” motif in the major virion ORF8 glycoprotein B, which functions to bind the critical integrin αVβ3 entry receptor (Garrigues et al, 2014, 2008; Rose, 1999) and a large central repetitive region within the ORF73 LANA (Bruce et al, 2013), which plays a critical role in episome persistence (De Leon Vazquez and Kaye, 2011).…”

Japanese Macaque Rhadinovirus Encodes a Viral MicroRNA Mimic of the miR-17 Family

“…Similarly to what is observed for RRV and predicted for other rhadinoviruses, including RFHVMn and MneRV2 (4,(23)(24)(25), a KSHV miR-K10a/miR-142-3p seed homolog, miR-J15-3p, was identified for JMRV (Fig. 2E).…”

“…Viruses of the rhadinovirus 1 (RV1) lineage include the only known human rhadinovirus (Kaposi's sarcoma-associated herpesvirus [KSHV]) and retroperitoneal fibromatosis-associated herpesvirus (RFHV), which infects Old World nonhuman primates. The rhadinovirus 2 (RV2) lineage includes JMRV; rhesus macaque (RM) rhadinovirus (RRV), which infects RM (Macaca mulatta); and Macaca nemestrina rhadinovirus 2 (MneRV2), which infects pig-tailed macaques (Macaca nemestrina) (2,4,5). JMRV is most closely related to RRV at the genetic level; the genomes are colinear, and the majority of viral open reading frames (ORFs) are homologous to a few unique ORFs that are specific to JMRV (2).…”