A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension

Abstract

Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV‐8) allows the identification of six major subtypes (A–F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV‐8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV‐8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294‐bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV‐8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the ‘gold standard’ method in all analysed samples. This method can reliably identify HHV‐8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low‐cost screening method for viral genotyping in a single tube, particularly samples with low‐quality DNA, and with easy data interpretation.

An innovative single‐base extension method for synchronous detection of point mutations and MSI status in colorectal cancer

“…In this study, on the basis of the standard pipeline of single‐base extension assay for mutation detection, 14 , 15 we implanted two procedures to detect MSI: PCR amplification of MSI loci and fluorescently labeling of MSI loci. To fluorescently label MSI loci using single‐base extension that has been applied to label mutation sites, we designed the extension primer for MSI detection as the template and the DNAs of MSI loci were extended using fluorescently labeled ddNTPs.…”