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

Christine Johnston; Amalia Magaret; Pavitra Roychoudhury; Alexander L Greninger; Anqi Cheng; Kurt Diem; Matthew P Fitzgibbon; Meei-Li Huang; Stacy Selke; Jairam R Lingappa; Connie Celum; Keith R Jerome; Anna Wald; David M Koelle

doi:10.1016/j.virol.2017.06.031

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

Virology. 2017 Oct:510:90-98. doi: 10.1016/j.virol.2017.06.031. Epub 2017 Jul 13.

Authors

Affiliations

¹ Department of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA. Electronic address: [email protected].
² 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.
³ Department of Laboratory Medicine, University of Washington, USA.
⁴ Department of Biostatistics, University of Washington, USA.
⁵ Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, USA.
⁶ Department of Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Department of Pediatrics, University of Washington, USA.
⁷ Department of Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Department of Global Health, University of Washington, USA.
⁸ Department of Laboratory Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
⁹ 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.
¹⁰ 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.

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.

Keywords: Genital herpes; Genomics; Herpes simplex virus type 2; Sequencing.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Africa
Cluster Analysis
Conserved Sequence*
Genes, Viral*
Genetic Variation*
Genitalia / virology
Herpes Genitalis / virology*
Herpesvirus 2, Human / classification*
Herpesvirus 2, Human / genetics*
High-Throughput Nucleotide Sequencing
Phylogeny
Sequence Homology
South America
United States

Abstract

Publication types

MeSH terms

Grants and funding