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,Virology

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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
Virology ( IF 2.8 ) Pub Date : 2017-07-13 , DOI: 10.1016/j.virol.2017.06.031
Christine Johnston ₁ , Amalia Magaret ₂ , Pavitra Roychoudhury ₃ , Alexander L Greninger ₃ , Anqi Cheng ₄ , Kurt Diem ₃ , Matthew P Fitzgibbon ₅ , Meei-Li Huang ₃ , Stacy Selke ₃ , Jairam R Lingappa ₆ , Connie Celum ₇ , Keith R Jerome ₈ , Anna Wald ₉ , David M Koelle ₁₀

Affiliation

Department of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Department of Laboratory Medicine, University of Washington, USA; Department of Biostatistics, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Department of Laboratory Medicine, University of Washington, USA.
Department of Biostatistics, University of Washington, USA.
Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, USA.
Department of Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Department of Pediatrics, University of Washington, USA.
Department of Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Department of Global Health, University of Washington, USA.
Department of Laboratory Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA; Benaroya Research Institute, Seattle, WA, USA.

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 ≥ 10⁷ log₁₀ 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.

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