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. 1999 May;73(5):4156-70.
doi: 10.1128/JVI.73.5.4156-4170.1999.

High-level variability in the ORF-K1 membrane protein gene at the left end of the Kaposi's sarcoma-associated herpesvirus genome defines four major virus subtypes and multiple variants or clades in different human populations

Affiliations

High-level variability in the ORF-K1 membrane protein gene at the left end of the Kaposi's sarcoma-associated herpesvirus genome defines four major virus subtypes and multiple variants or clades in different human populations

J C Zong et al. J Virol. 1999 May.

Abstract

Infection with Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) or human herpesvirus 8 (HHV8) is common in certain parts of Africa, the Middle East, and the Mediterranean, but is rare elsewhere, except in AIDS patients. Nevertheless, HHV8 DNA is found consistently in nearly all classical, endemic, transplant and AIDS-associated KS lesions as well as in some rare AIDS-associated lymphomas. The concept that HHV8 genomes fall into several distinct subgroups has been confirmed and refined by PCR DNA sequence analysis of the ORF-K1 gene encoding a highly variable glycoprotein related to the immunoglobulin receptor family that maps at the extreme left-hand end of the HHV-8 genome. Among more than 60 different tumor samples from the United States, central Africa, Saudi Arabia, Taiwan, and New Zealand, amino acid substitutions were found at a total of 62% of the 289 amino acid positions. These variations defined four major subtypes and 13 distinct variants or clades similar to those found for the HIV ENV protein. The B and D subtype ORF-K1 proteins differ from the A and C subtypes by 30 and 24%, respectively, whereas A and C differ from each other by 15%. In all cases tested, multiple samples from the same patient were identical. Examples of the B subtype were found almost exclusively in KS patients from Africa or of African heritage, whereas the rare D subtypes were found only in KS patients of Pacific Island heritage. In contrast, C subtypes were found predominantly in classic KS and in iatrogenic and AIDS KS in the Middle East and Asia, whereas U.S. AIDS KS samples were primarily A1, A4, and C3 variants. We conclude that this unusually high diversity, in which 85% of the nucleotide changes lead to amino acid changes, reflects some unknown powerful biological selection process that has been acting preferentially on this early lytic cycle membrane signalling protein. Two distinct levels of ORF-K1 variability are recognizable. Subtype-specific variability indicative of long-term evolutionary divergence is both spread throughout the protein as well as concentrated within two 40-amino-acid extracellular domain variable regions (VR1 and VR2), whereas intratypic variability localizes predominantly within a single 25-amino-acid hypervariable Cys bridge loop and apparently represents much more recent changes that have occurred even within specific clades. In contrast, numerous extracellular domain glycosylation sites and Cys bridge residues as well as the ITAM motif in the cytoplasmic domain are fully conserved. Overall, we suggest that rather than being a newly acquired human pathogen, HHV8 is an ancient human virus that is preferentially transmitted in a familial fashion and is difficult to transmit horizontally in the absence of immunosuppression. The division into the four major HHV8 subgroups is probably the result of isolation and founder effects associated with the history of migration of modern human populations out of Africa over the past 35,000 to 60,000 years.

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Figures

FIG. 1
FIG. 1
Organization of the left-hand end of the HHV8 genome encompassing the ORF-K1 gene. (A) Map of the genomic location of HHV8 (BCBL-R) lambda clone λD-S1 relative to other LHS clones and major features of the HHV8 DNA molecule. DL and DR, duplicated 1-kb ORI-like regions (left and right, respectively) at genomic coordinates 23 kb and 119 kb. (B) Organization and orientation of ORFs and terminal repeat unit sequences within an expanded area across the LHS TTR-unique region boundary encompassed within the 3.5-kb BamHI-BamHI fragment in plasmid subclone pDJA61 (genomic coordinates −1600 to +1885). Nucleotide positions of the initiator and terminator codons in the unique region are given above the ORFs (open arrows), and those of the TTR sequences are given above the different repeat unit fragments (solid arrows). (C) Predicted domain structure and key features of the highly variable 289-amino-acid ORF-K1 membrane receptor-like protein encoded between genomic nucleotide coordinates 105 and 974. Hatched bars denote signal peptide and transmembrane (TM) domains with amino acid boundaries indicated. Predicted N-glycosylation sites (NXS/NXT) (solid triangles) and the 12 conserved Cys residues (solid circles) are indicated. Cytopl, cytoplasmic. (Lower panel) Locations of highly variable VR1 and VR2 domains and the proposed hypervariable A subtype VR* domain and summary listing of major subtype amino acid difference values both within and outside of the VR blocks.
FIG. 2
FIG. 2
Amino acid alignment of the ORF-K1 proteins of 63 distinct HHV8 genomes. The complete amino acid sequence is given only for HHV8 (BCBL-R) on the top line, with amino acid identities indicated by dashes for the other genomes. Deletions in VR2 are indicated by gaps in parentheses, and subtype designations are given to the far right. The A1, A2, A3, B, and D2 subtype ORF-K1 proteins consist of 289 amino acids, whereas the A4 subtype has 285 amino acids, the C3 and C2 subtypes have 284 amino acids, the C1 subtype has 282 amino acids, and the single example of subtype D1 has 302 amino acids. The conserved Cys residues (∧) surrounding the predicted VR* loop and key amino acids in the predicted ITAMs (★) are highlighted. ∼, potential N-glycosylation site; +, BCBL or PEL tumor or cell line; C, classic or endemic non-HIV-associated KS; R, renal transplant-associated iatrogenic KS; A, patient lived in or was a direct immigrant from Africa; P, Pacific Islander; F, aggressive KS from Florida. Blanks indicate incomplete data for AKS4, ST1, and JKS20, for which insufficient original DNA was available. All samples designated as members of the A1, A4, A2, A3, C3, C2, C1, B, and D variants are grouped together. AKS, AIDS KS from Maryland; BKS, samples from Texas and Tennessee; OKS, AIDS KS samples from Tanzania or Florida; RKS, AIDS KS samples from Zambia; SKS, renal transplant KS from Saudi Arabia; TKS, samples from Taiwan; ZKS, samples from New Zealand. Note that the data for HBL6 (BCBL cell line) and WKS1 (KS) are identical to the published sequence for the BC1 cell line (59). Similarly, our results for the BCBL1 cell line and BKS14 KS are identical to each other and to published data for BCBL1 (35). Finally, the data for the BCBL-B cell line and for the BKS10 KS samples from different patients are also identical. KS-F shows data reported by Neipel et al. (48) for an AIDS KS sample from Germany.
FIG. 2
FIG. 2
Amino acid alignment of the ORF-K1 proteins of 63 distinct HHV8 genomes. The complete amino acid sequence is given only for HHV8 (BCBL-R) on the top line, with amino acid identities indicated by dashes for the other genomes. Deletions in VR2 are indicated by gaps in parentheses, and subtype designations are given to the far right. The A1, A2, A3, B, and D2 subtype ORF-K1 proteins consist of 289 amino acids, whereas the A4 subtype has 285 amino acids, the C3 and C2 subtypes have 284 amino acids, the C1 subtype has 282 amino acids, and the single example of subtype D1 has 302 amino acids. The conserved Cys residues (∧) surrounding the predicted VR* loop and key amino acids in the predicted ITAMs (★) are highlighted. ∼, potential N-glycosylation site; +, BCBL or PEL tumor or cell line; C, classic or endemic non-HIV-associated KS; R, renal transplant-associated iatrogenic KS; A, patient lived in or was a direct immigrant from Africa; P, Pacific Islander; F, aggressive KS from Florida. Blanks indicate incomplete data for AKS4, ST1, and JKS20, for which insufficient original DNA was available. All samples designated as members of the A1, A4, A2, A3, C3, C2, C1, B, and D variants are grouped together. AKS, AIDS KS from Maryland; BKS, samples from Texas and Tennessee; OKS, AIDS KS samples from Tanzania or Florida; RKS, AIDS KS samples from Zambia; SKS, renal transplant KS from Saudi Arabia; TKS, samples from Taiwan; ZKS, samples from New Zealand. Note that the data for HBL6 (BCBL cell line) and WKS1 (KS) are identical to the published sequence for the BC1 cell line (59). Similarly, our results for the BCBL1 cell line and BKS14 KS are identical to each other and to published data for BCBL1 (35). Finally, the data for the BCBL-B cell line and for the BKS10 KS samples from different patients are also identical. KS-F shows data reported by Neipel et al. (48) for an AIDS KS sample from Germany.
FIG. 2
FIG. 2
Amino acid alignment of the ORF-K1 proteins of 63 distinct HHV8 genomes. The complete amino acid sequence is given only for HHV8 (BCBL-R) on the top line, with amino acid identities indicated by dashes for the other genomes. Deletions in VR2 are indicated by gaps in parentheses, and subtype designations are given to the far right. The A1, A2, A3, B, and D2 subtype ORF-K1 proteins consist of 289 amino acids, whereas the A4 subtype has 285 amino acids, the C3 and C2 subtypes have 284 amino acids, the C1 subtype has 282 amino acids, and the single example of subtype D1 has 302 amino acids. The conserved Cys residues (∧) surrounding the predicted VR* loop and key amino acids in the predicted ITAMs (★) are highlighted. ∼, potential N-glycosylation site; +, BCBL or PEL tumor or cell line; C, classic or endemic non-HIV-associated KS; R, renal transplant-associated iatrogenic KS; A, patient lived in or was a direct immigrant from Africa; P, Pacific Islander; F, aggressive KS from Florida. Blanks indicate incomplete data for AKS4, ST1, and JKS20, for which insufficient original DNA was available. All samples designated as members of the A1, A4, A2, A3, C3, C2, C1, B, and D variants are grouped together. AKS, AIDS KS from Maryland; BKS, samples from Texas and Tennessee; OKS, AIDS KS samples from Tanzania or Florida; RKS, AIDS KS samples from Zambia; SKS, renal transplant KS from Saudi Arabia; TKS, samples from Taiwan; ZKS, samples from New Zealand. Note that the data for HBL6 (BCBL cell line) and WKS1 (KS) are identical to the published sequence for the BC1 cell line (59). Similarly, our results for the BCBL1 cell line and BKS14 KS are identical to each other and to published data for BCBL1 (35). Finally, the data for the BCBL-B cell line and for the BKS10 KS samples from different patients are also identical. KS-F shows data reported by Neipel et al. (48) for an AIDS KS sample from Germany.
FIG. 2
FIG. 2
Amino acid alignment of the ORF-K1 proteins of 63 distinct HHV8 genomes. The complete amino acid sequence is given only for HHV8 (BCBL-R) on the top line, with amino acid identities indicated by dashes for the other genomes. Deletions in VR2 are indicated by gaps in parentheses, and subtype designations are given to the far right. The A1, A2, A3, B, and D2 subtype ORF-K1 proteins consist of 289 amino acids, whereas the A4 subtype has 285 amino acids, the C3 and C2 subtypes have 284 amino acids, the C1 subtype has 282 amino acids, and the single example of subtype D1 has 302 amino acids. The conserved Cys residues (∧) surrounding the predicted VR* loop and key amino acids in the predicted ITAMs (★) are highlighted. ∼, potential N-glycosylation site; +, BCBL or PEL tumor or cell line; C, classic or endemic non-HIV-associated KS; R, renal transplant-associated iatrogenic KS; A, patient lived in or was a direct immigrant from Africa; P, Pacific Islander; F, aggressive KS from Florida. Blanks indicate incomplete data for AKS4, ST1, and JKS20, for which insufficient original DNA was available. All samples designated as members of the A1, A4, A2, A3, C3, C2, C1, B, and D variants are grouped together. AKS, AIDS KS from Maryland; BKS, samples from Texas and Tennessee; OKS, AIDS KS samples from Tanzania or Florida; RKS, AIDS KS samples from Zambia; SKS, renal transplant KS from Saudi Arabia; TKS, samples from Taiwan; ZKS, samples from New Zealand. Note that the data for HBL6 (BCBL cell line) and WKS1 (KS) are identical to the published sequence for the BC1 cell line (59). Similarly, our results for the BCBL1 cell line and BKS14 KS are identical to each other and to published data for BCBL1 (35). Finally, the data for the BCBL-B cell line and for the BKS10 KS samples from different patients are also identical. KS-F shows data reported by Neipel et al. (48) for an AIDS KS sample from Germany.
FIG. 2
FIG. 2
Amino acid alignment of the ORF-K1 proteins of 63 distinct HHV8 genomes. The complete amino acid sequence is given only for HHV8 (BCBL-R) on the top line, with amino acid identities indicated by dashes for the other genomes. Deletions in VR2 are indicated by gaps in parentheses, and subtype designations are given to the far right. The A1, A2, A3, B, and D2 subtype ORF-K1 proteins consist of 289 amino acids, whereas the A4 subtype has 285 amino acids, the C3 and C2 subtypes have 284 amino acids, the C1 subtype has 282 amino acids, and the single example of subtype D1 has 302 amino acids. The conserved Cys residues (∧) surrounding the predicted VR* loop and key amino acids in the predicted ITAMs (★) are highlighted. ∼, potential N-glycosylation site; +, BCBL or PEL tumor or cell line; C, classic or endemic non-HIV-associated KS; R, renal transplant-associated iatrogenic KS; A, patient lived in or was a direct immigrant from Africa; P, Pacific Islander; F, aggressive KS from Florida. Blanks indicate incomplete data for AKS4, ST1, and JKS20, for which insufficient original DNA was available. All samples designated as members of the A1, A4, A2, A3, C3, C2, C1, B, and D variants are grouped together. AKS, AIDS KS from Maryland; BKS, samples from Texas and Tennessee; OKS, AIDS KS samples from Tanzania or Florida; RKS, AIDS KS samples from Zambia; SKS, renal transplant KS from Saudi Arabia; TKS, samples from Taiwan; ZKS, samples from New Zealand. Note that the data for HBL6 (BCBL cell line) and WKS1 (KS) are identical to the published sequence for the BC1 cell line (59). Similarly, our results for the BCBL1 cell line and BKS14 KS are identical to each other and to published data for BCBL1 (35). Finally, the data for the BCBL-B cell line and for the BKS10 KS samples from different patients are also identical. KS-F shows data reported by Neipel et al. (48) for an AIDS KS sample from Germany.
FIG. 3
FIG. 3
Summary of ORF-K1 subtype and clade patterns compared with disease type and geographic origins. The diagram includes a listing of the clinical characteristics and geographic source of each of the 63 individual HHV8 samples included in Fig. 2 together with the evolutionary relationships between the various ORF-K1 clades. ∗, prototype A, B, and C samples collected in 1984; +, AIDS-associated, HIV-positive patients; X, patients from which multiple independent samples were sequenced (all proved to be identical). KS, lesion biopsy, autopsy, or archival paraffin block samples; PEL, PEL tumor samples; BCBL, established lymphoblastoid cell lines; Classic and Endem, non-HIV-associated KS patients; Renal, iatrogenic renal transplant KS. Solid circles denote those genomes that have M rather than P alleles of the ORF-K15 gene (53). $, data from Neipel et al. (48).
FIG. 4
FIG. 4
Predicted phylogenetic relationships among the 63 HHV8 ORF-K1 protein subtypes and variants examined here. The diagrams were generated by PHYLIP, PRODIST, and NEIGHBOR program analysis by Raphael Viscidi of the Department of Pediatrics, Johns Hopkins School of Medicine, based on estimated PAM distances and variances for each pair of the intact protein sequences. In-frame deletions and insertions in the VR2 block are not taken into account. (A and B) Linear (A) and radial (B) unrooted phylogenetic dendrograms with the SKS1 sequence as an outgroup. The length of each branch indicates genetic distance with the size scale for 0.1 (10% difference) indicated. Confidence levels (percent) from bootstrap analysis at major branch points are given. Not all samples have been labelled in the radial diagram because of space constraints.
FIG. 5
FIG. 5
Homology between ORF-K1 and the variable region of immunoglobulin (IG) light chains. (Top panel) Typical variations seen within the major subtypes of ORF-K1 in the vicinity of the immunoglobulin homology. Dashes indicate matches to the ORF-K1 subtype A sequence (top line). The conserved Cys at position 117 in ORF-K1 is indicated in a black box. (Center panel) Amino acid alignments between the N termini of mature and unprocessed immunoglobulin lambda chains (positions 7 to 35 and 21 to 56, respectively), a Bence Jones protein, and a BCR protein with positions 86 to 140 of ORF-K1 subtype A. Dashes indicate spaces, asterisks denote identities to the ORF-K1A version, and vertical bars denote similarities. (Bottom panel) Homologies among different lambda chain variable region subtypes compared to the ORF-K1 (A) immunoglobulin homology region. The numbering used represents that of amino acid positions in the mature immunoglobulin forms lacking the signal peptide. FRI, flanking region I; CDR1, complementarity-determining region I. Other symbols are the same as for the center panel above.
FIG. 6
FIG. 6
Summary of amino acid substitutions found within the predicted Cys-bridged VR* loop segment within the extracellular domain of HHV8 ORF-K1. The diagram lists all alternative amino acids found within VR1 between amino acids 52 and 76 of the A, C, B, and D subtypes, together with an overall summary of all substitutions within this region among the 63 distinct HHV8 ORF-K1 genes studied here. ∗, conserved probable Cys-bridging residue; ^, conserved N-glycosylation site (NXS/T); ∼, potential N-glycosylation site.

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