Whole-genome sequencing of KSHV from Zambian Kaposi’s sarcoma biopsies reveals unique viral diversity

Authors

Landon N. Olp, University of Nebraska-LincolnFollow
Adrien Jeanniard, University of Nebraska-Lincoln
Clemence Marimo, University of Zambia School of Medicine, Lusaka, Zambia
John T. West, University of Nebraska-LincolnFollow
Charles Wood, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

9-30-2015

Citation

JVI Accepted Manuscript Posted Online 30 September 2015 J. Virol. doi:10.1128/JVI.01712-15

Comments

Copyright © 2015, American Society for Microbiology. All Rights Reserved. Used By Permission.

Abstract

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent for Kaposi’s sarcoma (KS). Both KSHV and KS are endemic in sub-Saharan Africa where approximately 84% of global KS cases occur. Nevertheless, whole-genome sequencing of KSHV has only been completed using isolates from Western countries—where KS is not endemic. The lack of whole-genome KSHV sequence data from the most clinically important geographical region, sub-Saharan Africa, represents an important gap as it remains unclear whether genomic diversity has a role on KSHV pathogenesis. We hypothesized that distinct KSHV genotypes might be present in sub-Saharan Africa compared to Western countries. Using a KSHV-targeted enrichment protocol followed by Illumina deep-sequencing, we generated and analyzed sixteen unique Zambian, KS-derived, KSHV genomes. We enriched KSHV DNA over cellular DNA 1,851 to 18,235-fold. Enrichment provided coverage levels up to 24,740-fold; therefore, supporting highly confident polymorphism analysis. Multiple alignment of the sixteen newly sequenced KSHV genomes showed low level variability across the entire central conserved region. This variability resulted in distinct phylogenetic clustering between Zambian KSHV genomic sequences and those derived from Western countries. Importantly, the phylogenetic segregation of Zambian from Western sequences occurred irrespective of inclusion of the highly variable genes K1 and K15. We also show that four genes within the more conserved region of the KSHV genome contained polymorphisms that partially, but not fully, contributed to the unique Zambian KSHV whole-genome phylogenetic structure. Taken together, our data suggest that the whole KSHV genome should be taken into consideration for accurate viral characterization.