Genome-Wide Sequence Analysis of Kaposi Sarcoma-Associated Herpesvirus Shows Diversification Driven by Recombination.

BACKGROUND: Kaposi sarcoma-associated herpesvirus (KSHV) establishes lifelong infection in the human host and has been associated with a variety of malignancies. KSHV displays striking geographic variation in prevalence, which is highest in sub-Saharan Africa. The current KSHV genome sequences available are all tumor cell line-derived or primary tumor-associated viruses, which have provided valuable insights into KSHV genetic diversity. METHODS: Here, we sequenced 45 KSHV genomes from a Ugandan population cohort in which KSHV is endemic; these are the only genome sequences obtained from nondiseased individuals and of KSHV DNA isolated from saliva. RESULTS: Population structure analysis, along with the 25 published genome sequences from other parts of the world, showed whole-genome variation, separating sequences and variation within the central genome contributing to clustering of genomes by geography. We reveal new evidence for the presence of intragenic recombination and multiple recombination events contributing to the divergence of genomes into at least 5 distinct types. DISCUSSION: This study shows that large-scale genome-wide sequencing from clinical and epidemiological samples is necessary to capture the full extent of genetic diversity of KSHV, including recombination, and provides evidence to suggest a revision of KSHV genotype nomenclature

Comparison of Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus viral load in peripheral blood mononuclear cells and oral fluids of HIV-negative individuals aged 3-89 years from Uganda

We previously found that age, sex and malaria were associated with KSHV in individuals from Uganda. In this study, we have evaluated these same factors in relation to EBV in the same specimens. Overall, 74% (oral fluids) and 46% (PBMCs) had detectable EBV. This was significantly higher than observed for KSHV (24% oral fluids and 11% PBMCs). Individuals with EBV in PBMCs were more likely to have KSHV in PBMCs (P = 0.011). The peak age for detection of EBV in oral fluids was 3-5 years while that of KSHV was 6-12 years. In PBMCs, there was a bimodal peak age for detection of EBV (at 3-5 years and 66 + years) while for KSHV there was a single peak at 3-5 years. Individuals with malaria had higher levels of EBV in PBMCs compared to malaria-negative individuals (P = 0.002). In summary, our results show that younger age and malaria are associated with higher levels of EBV and KSHV in PBMCs suggesting malaria impacts immunity to both gamma-herpesviruses

Risk factors for Kaposi's sarcoma associated herpesvirus (KSHV) DNA in blood and in saliva in rural Uganda

INTRODUCTION: Detectable KSHV DNA in blood and increased antibody titres may indicate KSHV reactivation, while transmission of KSHV occurs via viral shedding in saliva. METHODS: We investigated risk factors for KSHV DNA detection by real-time PCR, in blood and viral shedding in saliva, in 878 people aged 3 to 89 years of both sexes in a rural Ugandan population cohort. Helminths were detected using microscopy and malaria parasitaemia was identified using rapid diagnostic tests. Regression modelling was used for statistical analysis. RESULTS: and discussion: KSHV viral load in blood did not correlate with viral load in saliva, suggesting separate immunological control within each compartment. The proportion of individuals with detectable virus in blood was 23% among children aged 3-5 years , 22% among 6-12 years old, thereafter reducing with increasing age. The proportion of individuals with detectable virus in saliva increased from 30% in 3-5 year old children to 45% in those aged 6-12 and decreasing subsequently with increasing age. Overall, 29% of males shed in saliva compared to 19% of females (p = 0.008). Together, these data suggest that young males may be responsible for much of the onward transmission of KSHV. Individuals with a current malaria infection had higher levels of viral DNA in blood (p = 0.031) compared to malaria uninfected individuals. This suggests that malaria may lead to KSHV reactivation, thereby increasing transmission and pathogenicity of the virus

Kaposi's sarcoma-associated herpesvirus T cell responses in HIV seronegative individuals from rural Uganda

T cell responses to Kaposi's sarcoma-associated herpesvirus (KSHV) are likely essential in the control of KSHV infection and protection from associated disease, but remain poorly characterised. KSHV prevalence in rural Uganda is high at >90%. Here we investigate IFN- γ T cell responses to the KSHV proteome in HIV-negative individuals from a rural Ugandan population. We use an ex-vivo IFN- γ ELISpot assay with overlapping peptide pools spanning 83 KSHV open reading frames (ORF) on peripheral blood mononuclear cells (PBMC) from 116 individuals. KSHV-specific T cell IFN- γ responses are of low intensity and heterogeneous, with no evidence of immune dominance; by contrast, IFN- γ responses to Epstein-Barr virus, Cytomegalovirus and influenza peptides are frequent and intense. Individuals with KSHV DNA in PBMC have higher IFN- γ responses to ORF73 (p = 0.02) and lower responses to K8.1 (p = 0.004) when compared with those without KSHV DNA. In summary, we demonstrate low intensity, heterogeneous T cell responses to KSHV in immune-competent individuals