PMC

Phylogenetic trees for the Gammaherpesvirinae. Panel A shows the phylogenetic tree as obtained by BMCMC (equivalent to the top-scoring tree from the NJ-ML analysis). The root position was determined by analyses using alpha- and betaherpesvirus sequences to provide an out-group. Three closely related viruses (rhesus monkey rhadinovirus 2695, Macaca fascicularis rhadinovirus 1 [MfasRHV-1], and MfasRHV-2) are shown together as rhesus monkey rhadinovirus (RRV) isolates. The major lineages are indicated with numbers 1 to 11. Panel B shows the same tree collapsed to form multifurcations at four locations of uncertainty in the NJ-ML analysis. The divergence scale at the bottom, indicating the number of substitutions per site, applies to both panels. EBV, Epstein-Barr virus; RLV, rhesus monkey lymphocryptovirus; CalHV-3, callitrichine herpesvirus 3; OvHV-2, ovine herpesvirus 2; RrupGHV-1, Rupicapra rupicapra gammaherpesvirus 1; CpRHV-2, caprine rhadinovirus 2; AlHV-1, alcelaphine herpesvirus 1; PLHV-1, porcine lymphotropic herpesvirus 1; HlibGHV-1, Hexaprotodon liberiensis gammaherpesvirus 1; McerRHV-1, Mus cervicolor rhadinovirus 1; BsavRHV-1, Bandicota savilei rhadinovirus 1; CcroGHV-1, Crocuta crocuta gammaherpesvirus 1; EzebGHV-1, Equus zebra gammaherpesvirus 1; EHV-2, equine herpesvirus 2; BadHV, badger herpesvirus; SaraGHV-1, Sorex araneus gammaherpesvirus 1; HVA, herpesvirus ateles; TbelGHV-1, Tupaia belangeri gammaherpesvirus 1; PtroRHV-1, Pan troglodytes rhadinovirus 1; GgorRHV-1, Gorilla gorilla rhadinovirus 1; BoHV-4, bovine herpesvirus 4; DbicGHV-1, Diceros bicornis gammaherpesvirus 1; BbabRHV-1, Babyrousa babyrussa rhadinovirus 1; SbarRHV-1, Sus barbatus rhadinovirus 1; PleoGHV-1, Panthera leo gammaherpesvirus 1; AflaRHV-1, Apodemus flavicollis rhadinovirus 1; BindRHV-4, Bandicota indica rhadinovirus 4; CglaRHV-1, Clethrionomys glareolus rhadinovirus 1; SsciGHV-2, Saimiri sciureus gammaherpesvirus 2.

RHVP is most closely related to rodent rhadinoviruses. Concatenated amino acid sequences corresponding to glycoprotein B and DNA polymerase from various gammaherpesviruses were aligned, and phylogenetic analysis was performed using the neighbor-joining method with 1,000 bootstrap replicates. The corresponding sequence from the betaherpesvirus murine cytomegalovirus (MCMV) was included for comparison. Subclassifications of the gammaherpesviruses are indicated, and bootstrap values over 65% are shown. Abbreviations: BoHV-4, bovine herpesvirus 4; EHV-2, equine herpesvirus 2; BsavRHV1, Bandicota savilei rhadinovirus 1; MmusRHV1, Mus musculus rhadinovirus 1; McerRHV1, Mus cervicolor rhadinovirus 1; AlHV-1, alcelaphine herpesvirus 1; PLHV-1, porcine lymphotropic herpesvirus 1; EBV, Epstein-Barr virus; CalHV-3, callitrichine herpesvirus 3; RHVP, rat herpesvirus Peru; BindRHV4, Bandicota indica rhadinovirus 4; γHV68, murine gammaherpesvirus 68; AflaRHV1, Apodemus flavicollis rhadinovirus 1; AsylRHV1, Apodemus sylvaticus rhadinovirus 1; MglaRHV1, Myodes glareolus rhadinovirus 1; MagrRHV1, Microtus agrestis rhadinovirus 1; KSHV, Kaposi's sarcoma-associated herpesvirus; RRV, rhesus monkey rhadinovirus; HVS, herpesvirus saimiri; HVA, herpesvirus ateles; MCMV, murine cytomegalovirus.

Phylogenetic tree of primate rhadinoviruses based on partial DNA polymerase (DPOL) sequences. The tree was derived from a 510 bp alignment using Neighbor-joining in Genious v.7.0.6 with outgroup provided by EBV (Human gammaherpesvirus 4, HHV-4). Numbers at each node indicate the percentage of bootstrap samples (out of 100) in which the cluster to the right is supported. Sequences published in Genbank used to construct this tree included: Gorilla beringei beringei rhadinovirus 1 (GbbRV1, sequence submitted), Gorilla gorilla cytomegalovirus 1.1 (GgorCMV-1.1, FJ538492), Gorilla gorilla cytomegalovirus 2.1 (GgorCMV-2.1, FJ538490), Human herpesvirus 4 (HHV-4, LN827558), Retroperitoneal fibromatosis-associated herpesvirus Macaca nemestrina (RFHVMn, AF005478), Chimpanzee rhadinovirus 1b (PanRHV1b, AF250881), Gorilla gorilla rhadinovirus 1 (GgorRHV-1, AY177144), Kaposi sarcoma associated herpesvirus (HHV-8, AF148805), Chimpanzee rhadinovirus 1 (PanRHV1, AY138585), Chimpanzee rhadinovirus 1a (PanRHV1a, AF250879), Mandrill rhadinovirus 2 (MndRHV2, AF282937), Chimpanzee rhadinovirus 2 (PanRHV2, AF246488).

Alignment of rhadinovirus CBP sequences. An alignment was constructed of CBP amino acid sequences from RRV17577 (accession no. AF083501), RRV26-95, KSHV (accession no. U75698), and HVS (accession no. X64346) by using CLUSTAL W software. The first 293 aa of RRV17577 CBP sequences did not align with the other rhadinovirus CBP sequences depicted here. Conserved cysteines are shaded in black. Deletion polymorphisms between sequences starting at amino acid 294 of RRV17577 CBP are indicated with dashes.