DNA sequence analysis of intrastrain variants of herpes simplex virus-type 2

Abstract

PCR products from intrastrain variants of HSV-1 vary in size. The length of the gene product determines the length of protein, and hence the number of Proline-Alanine-Threonine (PAT) repeats that are present. Some strains of HSV-2 have a 13 nucleotide (13-mer) repeat, which are unlike the 9-mer repeats found in HSV-1. The repeat sequence of the 12-mer would cause the end of the ICP34.5 gene in HSV-2 to be out of frame such that the encoded protein will be different. One possibility is that the repeat is deleted in the messenger RNA (mRNA). Another possibility is that there is a three-fold repeat in the number of 13-mer copies, which would then result in a gene that continues in frame. In this project, the reasons why the 13-mer in HSV-2 does not affect the ICP34.5 gene and cell infection are investigated. The size and sequence of genetic DNA and the cDNA obtained from PCR will be compared. Amino acid sequences deduced from genes with the 13-mer repeats are also determined for the following HSV-2 strains- 333,414, 427, 443, 471, 519, 564, HSV-3, 392, 472 and MS.