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.