Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U_L and U_S regions from genital swabs collected from 3 continents.

ABSTRACT:

Introduction

Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines.

Methods

Genital lesion swabs containing ≥ 10⁷log₁₀ copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (U_L_U_S) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction.

Results

Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated U_L

SUBMITTER: Johnston C 

PROVIDER: S-EPMC5565707 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature