Characterization of two divergent lineages of macaque rhadinoviruses related to Kaposi's sarcoma-associated herpesvirus

Abstract

We have cloned and characterized the entire DNA polymerase gene and flanking regions from Kaposi's sarcoma-associated herpesvirus (KSHV) and two closely related macaque homologs of KSHV, retroperitoneal fibromatosis-associated herpesvirus-Macaca nemestrina (RFHVMn) and -Macaca mulatta (RFHVMm). We have also identified and partially characterized the corresponding genomic region of another KSHV-like herpesvirus, provisionally named "M. nemestrina rhadinovirus type 2 (MneRV-2)," with close similarity to rhesus rhadinovirus (RRV). A sequence comparison of these four macaque viruses and two KSHV-like gammaherpesviruses recently identified in African green monkeys, Chlorocebus rhadinovirus types 1 and 2 (ChRV-1 and ChRV-2) reveals the presence of two distinct lineages of KSHV-like rhadinoviruses in Old World primates. The first rhadinovirus lineage consists of KSHV and its closely related homologs RFHVMn, RFHVMm, and ChRV-1, while the second more distantly related lineage consists of RRV, MneRV-2, and ChRV-2. Our findings raise the possibility of the existence of another human KSHV-like herpesvirus belonging to the second rhadinovirus lineage.

FIG. 1

CODEHOPs PCR cloning strategy. The expected linear arrangement of the glycoprotein B (ORF 8), DNA polymerase (ORF 9), and ORF 10 homologs in the KSHV-like gammaherpesviruses is indicated. The positions and orientation of CODEHOPs derived from conserved sequence motifs are shown. The name of the CODEHOPs indicates conserved amino acids within the motif, and the terminal A or B indicates sense or antisense orientation, respectively. The positions of the conserved DNA polymerase regions are indicated for reference (see reference 22).

FIG. 2

Comparison of the nucleotide and encoded amino acid sequences of the 3′ end of the glycoprotein B gene (ORF 8), the entire DNA polymerase gene (ORF 9), and the 5′ end of the ORF 10 gene for RFHVMm (top line) and RRV (bottom line). Asterisks indicate the positions of identical nucleotide sequences. The positions of identical amino acids are indicated within the RRV sequence with a · , and gaps are indicated with a -. The position of a potential TATA box in the promoter region of the DNA polymerase genes is indicated in boldface and underlined.

FIG. 2

Comparison of the nucleotide and encoded amino acid sequences of the 3′ end of the glycoprotein B gene (ORF 8), the entire DNA polymerase gene (ORF 9), and the 5′ end of the ORF 10 gene for RFHVMm (top line) and RRV (bottom line). Asterisks indicate the positions of identical nucleotide sequences. The positions of identical amino acids are indicated within the RRV sequence with a · , and gaps are indicated with a -. The position of a potential TATA box in the promoter region of the DNA polymerase genes is indicated in boldface and underlined.

FIG. 2

Comparison of the nucleotide and encoded amino acid sequences of the 3′ end of the glycoprotein B gene (ORF 8), the entire DNA polymerase gene (ORF 9), and the 5′ end of the ORF 10 gene for RFHVMm (top line) and RRV (bottom line). Asterisks indicate the positions of identical nucleotide sequences. The positions of identical amino acids are indicated within the RRV sequence with a · , and gaps are indicated with a -. The position of a potential TATA box in the promoter region of the DNA polymerase genes is indicated in boldface and underlined.

FIG. 3

Amino acid sequence comparison of the DNA polymerases of the KSHV-like gammaherpesviruses. The positions of gaps and cysteine residues are boxed, and the general nucleotide polymerase conserved regions are indicated (see reference 22). Positions with identities with the KSHV sequence are shown as a · , and the unidentified N-terminal region of MneRV-2 is indicated. The numbering refers to the KSHV sequence. The source of the sequences is given in Table 2.

FIG. 4

Comparison of the amino acid sequences encoded within the 5′ end of the cloned ORF 10 homologs of HVS and the KSHV-like gammaherpesviruses. Highly conserved amino acids are boxed, and the position of the GDWE sequence motif from which the ORF 10 CODEHOPs were derived is highlighted (shaded area), with known sequences in uppercase and presumed sequences in lowercase.

FIG. 5

Phylogenetic tree of the gammaherpesviruses. Phylogenetic trees were generated by maximum-parsimony analysis using the amino acid sequences of the DNA polymerases shown in Fig. 3 and Table 2. The branch points of the ChRV-1 and ChRV-2 sequences were derived from analyses of smaller sequence sets due to limited sequence data and are indicated with dotted lines. Bootstrap values derived from 100 replicates are shown for each branch point. The EBV (gamma-1) and HVS (gamma-2) prototypes (γ1 and γ2) and the proposed rhadinovirus genogroups RV-1 and RV-2 are indicated.