Dataset Information

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_}U_S segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids.

Conclusions

Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.

SUBMITTER: Johnston C

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

REPOSITORIES: biostudies-literature

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Publications

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U<sub>L</sub> and U<sub>S</sub> regions from genital swabs collected from 3 continents.

Johnston Christine C Magaret Amalia A Roychoudhury Pavitra P Greninger Alexander L AL Cheng Anqi A Diem Kurt K Fitzgibbon Matthew P MP Huang Meei-Li ML Selke Stacy S Lingappa Jairam R JR Celum Connie C Jerome Keith R KR Wald Anna A Koelle David M DM

Virology 20170713

<h4>Introduction</h4>Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines.<h4>Methods</h4>Genital lesion swabs containing ≥ 10<sup>7</sup>log<sub>10</sub> 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<sub ...[more]

PMID: 28711653

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Dataset Information

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.

Introduction

Methods

Results

Conclusions

Publications

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U<sub>L</sub> and U<sub>S</sub> regions from genital swabs collected from 3 continents.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

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

Introduction

Methods

Results

Conclusions

Publications

Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U<sub>L</sub> and U<sub>S</sub> regions from genital swabs collected from 3 continents.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

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.