title: Evaluation of global clustering patterns and strain variation over an extended ORF26 gene locus from Kaposi's sarcoma herpesvirus.
abstract: BACKGROUND
  Small 233-bp or 330-bp DNA fragments of the ORF26 gene of human Kaposi's sarcoma herpesvirus (KSHV) have been used extensively to identify KSHV by PCR in clinical samples; to associate KSHV with novel diseases and to correlate KSHV strain differences with pathogenicity.
  
  
  OBJECTIVE
  We evaluated the nature, extent and source of nucleotide sequence variability among a large and diverse set of known KSHV-positive DNA samples.
  
  
  METHODS
  Direct DNA PCR sequencing was carried out on 136 distinct Kaposi's sarcoma and primary effusion lymphoma-related samples from different geographic locations.
  
  
  RESULTS
  The presence of 26 diagnostic nucleotide polymorphisms across an expanded 965-bp PCR locus define eight distinct ORF26E genotypes, three being of Eurasian origin, one from the Pacific Rim, and five from Sub-Saharan Africa. Previous ambiguities between some genotype patterns in the 330-bp locus data are fully resolved.
  
  
  CONCLUSIONS
  This analysis provides an expanded database for understanding and evaluating ORF26 polymorphisms. In particular, the eight genotype clusters correlated with specific ethnic and geographic origins of the patients. Furthermore, the very low level of additional sporadic nucleotide variation found permits detection of spurious sequence errors or contamination present in some published data.
authors: Viral Oncology Program, Department of Oncology, Blunting Blaustein Cancer Research Building, Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21231-1000, United States.
authors: Jian-Chao
authors: JC
authors: Zong
authors: Henry
authors: H
authors: Kajumbula
authors: William
authors: W
authors: Boto
authors: Gary S
authors: GS
authors: Hayward
mesh_terms: D017088:AIDS-Related Opportunistic Infections / Q000821:virology; D001483:Base Sequence; D016000:Cluster Analysis; D003710:Demography; D016679:Genome, Viral; D005838:Genotype; D006566:Herpesviridae Infections / Q000453:epidemiology* / Q000821:virology; D019288:Herpesvirus 8, Human / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011110:Polymorphism, Genetic; D012514:Sarcoma, Kaposi / Q000453:epidemiology* / Q000821:virology
references: J Gen Virol. 2004 Jan;85(Pt 1):155-63
references: 14718630
references: Science. 1994 Dec 16;266(5192):1865-9
references: 7997879
references: Lancet. 1995 Mar 18;345(8951):722-3
references: 7885137
references: Lancet. 1995 Mar 25;345(8952):759-61
references: 7891487
references: N Engl J Med. 1995 May 4;332(18):1181-5
references: 7700310
references: N Engl J Med. 1995 May 4;332(18):1186-91
references: 7700311
references: Blood. 1995 Aug 15;86(4):1276-80
references: 7632932
references: Lancet. 1995 Sep 23;346(8978):799-802
references: 7674745
references: J Clin Microbiol. 1996 Oct;34(10):2635-8
references: 8880542
references: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14862-7
references: 8962146
references: J Virol. 1997 Jan;71(1):839-42
references: 8985427
references: J Virol. 1997 Mar;71(3):2505-11
references: 9032391
references: Am J Epidemiol. 1998 Feb 1;147(3):217-21
references: 9482495
references: J Virol. 1999 May;73(5):4156-70
references: 10196312
references: J Virol. 1999 Aug;73(8):6646-60
references: 10400762
references: Intervirology. 2006;49(3):133-43
references: 16428889
references: Curr Top Microbiol Immunol. 2007;312:1-42
references: 17089792
references: J Gen Virol. 2000 Aug;81(Pt 8):2029-38
references: 10900042
references: J Immunol. 2000 Aug 15;165(4):2077-83
references: 10925292
references: J Clin Virol. 2007 Sep;40(1):1-8
references: 17698410
references: J Natl Cancer Inst. 2001 Feb 7;93(3):194-202
references: 11158187
references: J Clin Virol. 2002 Jan;23(3):119-48
references: 11595592
references: J Med Virol. 2002 Feb;66(2):235-40
references: 11782933