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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 (UL_US) 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 UL_US 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
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]