Olp Landon N, Jeanniard Adrien, Marimo Clemence, West John T, Wood Charles
Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
Department of Pathology and Microbiology, University of Zambia School of Medicine, Lusaka, Zambia.
J Virol. 2015 Dec;89(24):12299-308. doi: 10.1128/JVI.01712-15. Epub 2015 Sep 30.
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 since 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 16 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 16 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.
Our results represent the largest number of KSHV whole-genomic sequences published to date and the first time that multiple genomes have been sequenced from sub-Saharan Africa, a geographic area where KS is highly endemic. Based on our new sequence data, it is apparent that whole-genome KSHV diversity is greater than previously appreciated and differential phylogenetic clustering exists between viral genomes of Zambia and Western countries. Furthermore, individual genes may be insufficient for KSHV genetic characterization. Continued investigation of the KSHV genetic landscape is necessary in order to effectively understand the role of viral evolution and sequence diversity on KSHV gene functions and pathogenesis.
卡波西肉瘤相关疱疹病毒（KSHV）是卡波西肉瘤（KS）的病原体。KSHV和KS在撒哈拉以南非洲地区均为地方病，全球约84%的KS病例发生在该地区。然而，KSHV的全基因组测序仅使用来自西方国家（KS并非地方病流行区）的分离株完成。由于尚不清楚基因组多样性是否在KSHV发病机制中起作用，因此缺乏来自撒哈拉以南非洲这一临床上最重要地理区域的KSHV全基因组序列数据是一个重要差距。我们推测，与西方国家相比，撒哈拉以南非洲地区可能存在不同的KSHV基因型。我们采用针对KSHV的富集方案，随后进行Illumina深度测序，生成并分析了16个来自赞比亚KS患者的独特KSHV基因组。我们将KSHV DNA相对于细胞DNA富集了1851至18235倍。富集提供了高达24740倍的覆盖水平，因此支持高度可靠的多态性分析。对16个新测序的KSHV基因组进行多重比对显示，整个中央保守区域的变异性较低。这种变异性导致赞比亚KSHV基因组序列与来自西方国家的序列之间出现明显的系统发育聚类。重要的是，无论是否纳入高度可变基因K1和K15，赞比亚序列与西方序列在系统发育上都存在分离。我们还表明，KSHV基因组更保守区域内的四个基因含有多态性，这些多态性部分但并非完全导致了赞比亚KSHV独特的全基因组系统发育结构。综上所述，我们的数据表明，为了准确进行病毒特征鉴定，应考虑整个KSHV基因组。
我们的结果代表了迄今为止发表的数量最多的KSHV全基因组序列，并且首次从KS高度流行的撒哈拉以南非洲地区对多个基因组进行了测序。基于我们的新序列数据，很明显KSHV全基因组多样性比之前认为的更大，并且赞比亚和西方国家的病毒基因组之间存在不同的系统发育聚类。此外，单个基因可能不足以进行KSHV基因特征鉴定。为了有效理解病毒进化和序列多样性对KSHV基因功能和发病机制的作用，有必要继续研究KSHV的遗传图谱。
