title: Genotypic analysis at multiple loci across Kaposi's sarcoma herpesvirus (KSHV) DNA molecules: clustering patterns, novel variants and chimerism.
abstract: BACKGROUND
  The genomes of human Kaposi's sarcoma-associated herpesvirus (KSHV) display several levels of DNA sequence heterogeneity and subgrouping that show distinctive clustering patterns in related human populations. The four major subtype patterns for the hypervariable ORF-K1 protein correlate closely with the principal diasporas resulting from the migration of modern humans out of East Africa and suggest that KSHV is an ancient human virus that is transmitted primarily in a familial fashion with consequent very low recombination rates. However, chimeric genomes have also been detected, especially with regard to the presence of P versus M alleles of the ORF-K15 gene.
  
  
  OBJECTIVE
  To understand further the genetic organization and evolutionary history of KSHV, especially with regard to possible new subtypes, recombinant genomes, constant region loci and clustering in particular ethnic groups or among classic versus epidemic cases in the same geographic area.
  
  
  METHODS
  Direct PCR DNA sequencing was carried out on the ORF-K1 and ORF-K15 genes at the extreme left and right hand sides, as well as on six other internal loci of diagnostic samples collected from 70 new KSHV-positive patients in Israel, South Korea, Sicily, Scandinavia, Brazil, Uganda, South Africa and the US.
  
  
  CONCLUSIONS
  Our overall results from more than 135 KSHV genomes from many different human population groups now provides evidence for seven distinct subtypes of KSHV genomes (referred to as A/P, B/P, C/P, D/P, M, N and Q). However, the two most closely related subtypes (A/P and C/P) are only differentiated at the LHS side of the genome, and the three most distantly related forms (M, N and Q) appear to exist only as small chimeric segments that are remnants from the RHS of more ancient forms of the virus. By analyzing multiple conserved loci across the B subtype genomes that predominate in sub-Saharan Africa, we can also now recognize three to four distinct B genome subgroups with varying patterns of inter and intratypic mosaicism. Analysis of classic KS genomes from Israel has revealed that the ORF-K1 clade referred to as A1' predominates in Ashkenazi Jewish immigrants from Russia, whereas C2 and C6 variants predominate in North African Sephardi Jews. A variety of chimeric genomes containing C2 or C3 ORF-K1 genes are disseminated among classic KS cases throughout Europe and Asia including Israel, Sicily, Scandinavia, South Korea, and Taiwan. Comparison of the genomes from classic versus AIDS-associated KSHV in the US indicates that it was derived originally by reactivation and spread of a subset of the endogenous viruses carried by descendants of immigrants from endemic areas of Northern and Eastern Europe, the Mediterranean and sub-Saharan Africa.
authors.affiliation: Molecular Virology Laboratories, Department of Oncology, The Johns Hopkins University School of Medicine, 1650 Orleans Street, CRB 3M09, Baltimore, MD 21205, USA.
authors.forename: Jianchao
authors.initials: J
authors.lastname: Zong
authors.forename: Dolores M
authors.initials: DM
authors.lastname: Ciufo
authors.forename: Raphael
authors.initials: R
authors.lastname: Viscidi
authors.forename: Lee
authors.initials: L
authors.lastname: Alagiozoglou
authors.forename: Stephen
authors.initials: S
authors.lastname: Tyring
authors.forename: Peter
authors.initials: P
authors.lastname: Rady
authors.forename: Jan
authors.initials: J
authors.lastname: Orenstein
authors.forename: William
authors.initials: W
authors.lastname: Boto
authors.forename: Henry
authors.initials: H
authors.lastname: Kalumbuja
authors.forename: Nino
authors.initials: N
authors.lastname: Romano
authors.forename: Mads
authors.initials: M
authors.lastname: Melbye
authors.forename: Gyeong H
authors.initials: GH
authors.lastname: Kang
authors.forename: Chris
authors.initials: C
authors.lastname: Boshoff
authors.forename: Gary S
authors.initials: GS
authors.lastname: Hayward
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000150:complications / Q000821:virology; D000352:Africa, Northern; D000483:Alleles; D000595:Amino Acid Sequence; D005060:Europe; D016679:Genome, Viral; D005838:Genotype; D019288:Herpesvirus 8, Human / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007723:Korea; D008565:Membrane Proteins / Q000145:classification / Q000235:genetics; D008877:Middle East; D008969:Molecular Sequence Data; D009656:North America; D016366:Open Reading Frames; D010802:Phylogeny; D011995:Recombination, Genetic; D012514:Sarcoma, Kaposi / Q000821:virology; D016415:Sequence Alignment; D014759:Viral Envelope Proteins / Q000145:classification / Q000235:genetics; D014764:Viral Proteins
chemical_list: D008565:Membrane Proteins; D014759:Viral Envelope Proteins; C111600:K1 protein, Human herpesvirus 8; D014764:Viral Proteins