Systematic analysis of Kaposi's sarcoma (KS)‐associated herpesvirus genomes from a KS case‐control study in Cameroon: Evidence of dual infections but no association between viral sequence variation and KS risk

Abstract

In sub‐Saharan Africa, Kaposi's sarcoma‐associated herpesvirus (KSHV) is endemic, and Kaposi's sarcoma (KS) is a significant public health problem. Until recently, KSHV genotype analysis was performed using variable gene regions, representing a small fraction of the genome, and thus the contribution of sequence variation to viral transmission or pathogenesis are understudied. We performed near full‐length KSHV genome sequence analysis on samples from 43 individuals selected from a large Cameroonian KS case‐control study. KSHV genomes were obtained from 21 KS patients and 22 control participants. Phylogenetic analysis of the K1 region indicated the majority of sequences were A5 or B1 subtypes and all three K15 alleles were represented. Unique polymorphisms in the KSHV genome were observed including large gene deletions. We found evidence of multiple distinct KSHV genotypes in three individuals. Additionally, our analyses indicate that recombination is prevalent suggesting that multiple KSHV infections may not be uncommon overall. Most importantly, a detailed analysis of KSHV genomes from KS patients and control participants did not find a correlation between viral sequence variations and disease. Our study is the first to systematically compare near full‐length KSHV genome sequences between KS cases and controls in the same endemic region to identify possible sequence variations associated with disease risk.

Sequencing of Kaposi’s Sarcoma Herpesvirus (KSHV) genomes from persons of diverse ethnicities and provenances with KSHV-associated diseases demonstrate multiple infections, novel polymorphisms, and low intra-host variance

“…In comparison, genes with high sequence conservation of ≥ 99.4% across all study genomes included K6, K7, ORF6, ORF35, ORF40, ORF42, ORF61, and ORF67A ( Fig 4A ). Many previously reported polymorphisms were observed, including early stop codons in the K4.2 and K8 genes and variations within ORF47 and vIRF2 (K11) ( Fig 4B ) [ 12 , 19 , 20 ]. Of note, a sequence inversion involving an 80 bp area between ORF9 and ORF10, which includes two deletions (11 bp and 4 bp) and an insertion (3 bp) was identified in five K1 B subtype genomes ( Fig 5A ).…”

“…Three factors could result in samples falsely appearing as harboring multiple-infection: (1) Index-hopping, (2) contamination during sample processing and library preparation, and (3) sequencing error. For 11 of 14 identified multiple infections, validation was performed at the molecular level via Sanger sequencing using subtype-specific primers, as previously described [ 12 , 15 ]. Areas distinguishing the subtypes were identified for forward primer design while a conserved region was used for the reverse primer ( S3 Table ).…”

“…In our recent Cameroon KS case-control study, where we observed predominantly B1 and A5 K1 subtypes in whole blood and oral fluids, we were unable to identify sequence variations associated with the risk of KS. However, we observed evidence of multiple infections in three individuals [ 12 ].…”

Next-generation sequencing survey of acute febrile illness in Senegal (2020–2022)

“…HHV-8 is endemic in sub-Saharan Africa and may cause fever upon primary infection or be latently reactivated (possibly resulting in sarcoma) in certain scenarios (Andreoni, 2002). Its genome was found to be 99% identical at the nucleotide level to strains recently recovered from Cameroonians (Marshall et al, 2022). Saffold virus (SAFV), recently discovered in 2007, was also detected in a single specimen from Bounkiling from a patient with fever and respiratory symptoms such as cough.…”

Malignancy and viral infections in Sub-Saharan Africa: A review

“…Conversely, analysis of KSHV genomes from patients and controls in Cameroon revealed that recombination is common, suggesting multiple KSHV infections can occur. Yet sequence variation did not correlate with disease risk ( 344 ). A Ugandan study of KSHV genomes from tumors and oral swabs found that genomes were identical at the point mutation level within individuals but intra-host tumor-associated KSHV mutations and genome sequences impacting protein coding were present ( 345 ).…”