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

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.

Genetic diversity of HHV8 subtypes in South Africa: A5 subtype is associated with extensive disease in AIDS‐KS

“…Six major subtypes (A, B, C, D, E, and F) and at least 13 different variants or clades based on genetic variability of ORF-K1 gene sequences, have been identified [Zong et al, 2002]. The different subtypes have been shown to have variable penetrance in various population groups and are distributed along broad geographic and ethnic lines, which may have arisen through ancient human migrations [Hayward, 1999;Zong et al, 1999;Zong et al, 2002]. Subtypes B and A5 have been found to predominate in sub-Saharan Africa [Cook et al, 1999;Hayward, 1999;Meng et al, 1999;Zong et al, 1999;Fouchard et al, 2000;Lacoste et al, 2000;Kajumbula et al, 2006].…”

Early childhood infection of Kaposi's sarcoma‐associated herpesvirus in Zambian households: A molecular analysis

“…Despite a high level of genomic conservation, KSHV contains a gene on the extreme left-hand end of the genome, K1, that is highly variable. 16 K1 is an 870-nucleotide gene that encodes a signal transducing, cell-surface glycoprotein important in transformation of KSHV-infected and surrounding cells as well as induction of inflammatory proteins and downregulation of the B-cell receptor. 17 The majority of K1 sequence variation is concentrated within two regions of the gene's extracellular domain, variable regions (VRs) 1 and 2, which are 40-and 38-nucleotides, respectively.…”

“…17 The majority of K1 sequence variation is concentrated within two regions of the gene's extracellular domain, variable regions (VRs) 1 and 2, which are 40-and 38-nucleotides, respectively. 16 Owing to its high variability, K1 is routinely used to classify KSHV into at least five different genotypes (A, B, C, D and E), and various subgenotypes. 16,18 Using molecular analysis of K1, we examined a longitudinal cohort of KSHV-seropositive children and all members of their households in the KSHV endemic country of Zambiamaking our study the first of its kind.…”

“…16 Owing to its high variability, K1 is routinely used to classify KSHV into at least five different genotypes (A, B, C, D and E), and various subgenotypes. 16,18 Using molecular analysis of K1, we examined a longitudinal cohort of KSHV-seropositive children and all members of their households in the KSHV endemic country of Zambiamaking our study the first of its kind. Here, we provide evidence that transmission of KSHV to children can occur from both within and outside the household and intrahousehold transmission may occur via nonmaternal sources.…”

Kaposi’s sarcoma: Etiology and pathogenesis, inducing factors, causal associations, and treatments: Facts and controversies

“…20 Sequence analysis of the highly variable ORF K1 region has allowed the identification of seven major HHV-8 subtypes (A, B, C, D, E, F, and Z), comprising each several sub-clades, whose distribution in the world parallels that of ORF 26 variants: HHV-8 subtype B predominates in Africa and F has been identified in Ugandan Bantu tribe, subtype D is present in the Pacific islands; subtype E clusters in ancient populations, like Brazilian Amerindians, whereas A and C predominate in Europe and the United States. [21][22][23][24][25] It is still unclear whether different genotypes may have different pathogenic and tumorigenic properties associated with inverse rates of disease progression. [26][27][28][29] The role of co-factors in KS pathogenesis Pathogen-related diseases do not have the same clinical outcome in all infected patients with a subset developing chronic infections and a smaller subset progressing to cancer, suggesting that cofactors are needed for the different evolution, including genetic and environmental determinants.…”