In silico analysis of human herpes virus-8 genome: a comparison of the K1, VR1, and VR2 regions for genotyping and global geographical distribution

Abstract

Abstract Investigations of the K1 gene revealed six main genotypes clustered according to geography. Here, the global distribution and HHV8 genotyping using the K1 gene and two hypervariable regions (VR1 and VR2) were evaluated. We searched GenBank for 6,889 HHV8-K1 genes via various keywords, selecting sequences longer than 730 bp. Afterwards, the VR1 and VR2 regions were derived from the K1 genes, and genotyping of the K1, VR1, and VR2 sequences was performed by applying phylogenetic tree and BioAfrica methods. The K1 genotyping result was most similar to that of VR1, followed by VR2. The most common genotypes and subtypes in the three regions studied were A (A2) and C (C3), which are found in Africa, America, and Asia. Although the A and C genotypes are more predominant, the other genotypes, B, D, E, and F, are more ancient and are commonly found in America, Asia, and Oceania. K1 is commonly used for HHV8 genotyping, but VR1 can be a reliable alternative when long-term PCR amplification is not possible. The genotyping and subtyping results of both methods were very similar (92%), and it can be inferred that both procedures can be applied for HHV-8 genotyping.

Keywords

• Human herpesvirus-8
• K1
• Genotyping
• Distribution
• VR1
• VR2