Cook, Rachelle; (2002) Molecular epidemiology of Kaposi’s sarcoma-associated herpesvirus in an endemic country. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

The molecular epidemiology of Kaposi's sarcoma-associated herpesvirus (KSHV) was investigated in family groups in Malawi, a region of high KSHV endemicity. It was hypothesised that: KSHV transmission may not only occur along intra-familial routes, as seroepidemiologic studies suggest, but also extra-familially; and that a host living in an endemic region may carry multiple KSHV strains. KSHV DNA in mouth rinse samples was frequently detected in study individuals (n=89 from 22 families) suggesting that saliva was a potential source of infection. Molecular sequences were compared between members of the same family by sequence analysis of hypervariable domains of opening reading frame (ORF) K1 PCR products generated from blood and oral samples. Phylogenetic analysis revealed that in some families (n=5), identical sequences in the variable region 1 were present. In others (n=4), dissimilar sequences were recovered (range of nucleotide sequence divergence: approximately 0.5% to 27%). While sequence similarity between family members is consistent with familial KSHV transmission, sequence dissimilarity and sequence clustering point to extra-familial transmission of closely related viral variants as having taken place. A PCR-based restriction fragment length polymorphism (RFLP) procedure to screen for sequence variation in the internal repeat domain of ORF 73 was then adapted to complement the ORF K1 nucleotide sequencing studies. RFLP patterns were unique for each individual and could be compared between family members. The PCR-RFLP findings broadly corroborated with the sequencing data. Intra-host KSHV sequence variation was investigated using denaturing gel gradient electrophoresis to screen multiple ORF K1 clones derived from oral samples. While intra-sample clonal diversity was observed, further investigation using KSHV infected cell lines revealed that such diversity could be attributed to Taq polymerase nucleotide misincorporation. Therefore, no firm evidence for KSHV viral diversity within single individuals could be found.

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