KSHV Genome in Saliva, Whole Blood and Kaposi's Sarcoma Biopsy Specimens in Republic of Congo: Phylogenetic Analysis and an APOBEC3B Mutational Signature.

Kaposi's sarcoma-associated herpesvirus (KSHV) has been associated with a variety of diseases and is endemic in Sub-Saharan Africa. We performed KSHV-whole-genome analysis and search for APOBEC-editing to describe genetic diversity in samples issued from an endemic region. We included 15 Congolese samples including 12 saliva and whole blood samples of people living with HIV and 3 KS biopsies samples, to perform KSHV qPCR and NGS Illumina followed by KSHV typing on ORFs K1 and K15. Furthermore, we looked for APOBEC3B-mutations in KSHV-whole-genome sequences. KSHV viral load was detectable in all samples and ranged from 374 to 72799 copies/106 cells. NGS allowed us to have 8 full sequences out of the 15 samples analyzed. Phylogenetic analysis on KSHV-whole-genome resulted in distinct phylogenetic clustering between the genomic sequences of Congolese KSHV and those derived from Western countries. KSHV ORF-K1 subtypes A5, B and C were identified. On KSHV ORF-K15, only the P subtype was observed. We found virtually no APOBEC3B-induced mutations in KSHV genome. KSHV sequences from Congo samples present phylogenetic particularities but remain close to the whole genome sequences found in Sub-Saharan Africa. We were able to observe, using bioinformatics tools, only very few mutations due to APOBEC3B on KSHV genome.