Evaluation of global clustering patterns and strain variation over an extended ORF26 gene locus from Kaposi's sarcoma herpesvirus.

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. OBJECTIVES: We evaluated the nature, extent and source of nucleotide sequence variability among a large and diverse set of known KSHV-positive DNA samples. STUDY DESIGN: 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.

Genotypic analysis at multiple loci across Kaposi's sarcoma herpesvirus (KSHV) DNA molecules: clustering patterns, novel variants and chimerism.

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. OBJECTIVES: 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. STUDY DESIGN: 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. RESULTS AND 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.

Obesity and gender differences in the risk of type 2 diabetes mellitus in Uganda.

OBJECTIVE: We assessed the severity of type 2 diabetes in urban and rural communities of Uganda and characterized this disease according to sex, obesity, and hypertension. METHODS: A total of 440 subjects was tested for high blood and urine glucose levels with the respective glucometers and sample strips. Body mass index and hypertension were determined by measuring height, weight, and blood pressure. RESULTS: In a random study conducted in the communities of the districts of Kampala and Mokono, the prevalence of type 2 diabetes was found to be about 8.1% (n = 148). An association between obesity, hypertension, and risk of type 2 diabetes was found among the women, of whom nearly 80% were overweight. However, the men, who were primarily lean, did not exhibit this same correlation. CONCLUSIONS: These epidemiologic data suggest a variance from the strong correlation of type 2 diabetes and obesity seen in Western countries and most of Europe. Specifically, the etiology of this disease in Uganda is different between men and women. The reasons for this phenomenon are not well elucidated, but it is likely that a long history of obesity in women may genetically or environmentally predispose them to this disease.

Ugandan Kaposi's sarcoma-associated herpesvirus phylogeny: evidence for cross-ethnic transmission of viral subtypes.

OBJECTIVE: The aim of this study was to test the relationship between Kaposi's sarcoma-associated herpesvirus (KSHV) phylogeny and host ethnicity at the within-country scale. METHODS: KSHV genomic DNA samples were isolated from 31 patients across eleven Ugandan ethnic groups. Amino acid sequences of the ORF-K1 gene were used to construct a neighbor-joining phylogenetic tree. RESULTS: A5 and B1 variants predominated with no evidence of distinct ethnic or geographic distribution. A new K1 subtype (F) was identified in a member of the Bantu Gisu tribe and a new subtype B variant (B3) among members of the Bantu Ganda tribe. CONCLUSIONS: The phylogeny may yet be structured by host ethnicity if members of Ugandan groups have convoluted biological origins, even as they identify with single tribes. An alternative possibility is that KSHV subtype evolution may have preceded major diversification of sub-Saharan Africans into ethnicities as we know them today, with ethnic groups beginning their histories already hosting multiple subtypes. A third alternative is that horizontal transmission of multiple KSHV subtypes may have broken up vertical lineages of the virus passed down within Ugandan populations.