Christine Johnston1, Amalia Magaret2, Pavitra Roychoudhury3, Alexander L Greninger3, Anqi Cheng4, Kurt Diem3, Matthew P Fitzgibbon5, Meei-Li Huang3, Stacy Selke3, Jairam R Lingappa6, Connie Celum7, Keith R Jerome8, Anna Wald9, David M Koelle10. 1. Department of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA. Electronic address: cjohnsto@uw.edu. 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 (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.
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.
Authors: Aaron W Kolb; Marie Adams; Eric L Cabot; Mark Craven; Curtis R Brandt Journal: Invest Ophthalmol Vis Sci Date: 2011-11-25 Impact factor: 4.799
Authors: Sonia Burrel; Emiliana P Abrao; Nathalie Désiré; Sophie Seang; Eric Caumes; Henri Agut; David Boutolleau Journal: J Clin Virol Date: 2013-04-05 Impact factor: 3.168
Authors: Robert Colgrove; Fernando Diaz; Ruchi Newman; Sakina Saif; Terry Shea; Sarah Young; Matt Henn; David M Knipe Journal: Virology Date: 2013-12-31 Impact factor: 3.616
Authors: Robert B Belshe; Peter A Leone; David I Bernstein; Anna Wald; Myron J Levin; Jack T Stapleton; Iris Gorfinkel; Rhoda L Ashley Morrow; Marian G Ewell; Abbie Stokes-Riner; Gary Dubin; Thomas C Heineman; Joann M Schulte; Carolyn D Deal Journal: N Engl J Med Date: 2012-01-05 Impact factor: 91.245
Authors: Mark Shlapobersky; Joshua O Marshak; Lichun Dong; Meei-Li Huang; Qun Wei; Alice Chu; Alain Rolland; Sean Sullivan; David M Koelle Journal: J Gen Virol Date: 2012-03-07 Impact factor: 3.891
Authors: R Wim Roest; Jeroen Maertzdorf; Marius Kant; Willem I van der Meijden; Albert D M E Osterhaus; Georges M G M Verjans Journal: J Infect Dis Date: 2006-09-08 Impact factor: 5.226
Authors: Daniel B Reeves; Amalia S Magaret; Alex L Greninger; Christine Johnston; Joshua T Schiffer Journal: J R Soc Interface Date: 2018-02 Impact factor: 4.118
Authors: Meena S Ramchandani; Lichen Jing; Ronnie M Russell; Tran Tran; Kerry J Laing; Amalia S Magaret; Stacy Selke; Anqi Cheng; Meei-Li Huang; Hong Xie; Eric Strachan; Alex L Greninger; Pavitra Roychoudhury; Keith R Jerome; Anna Wald; David M Koelle Journal: J Infect Dis Date: 2019-03-15 Impact factor: 5.226
Authors: Christine Johnston; Amalia Magaret; Pavitra Roychoudhury; Alexander L Greninger; Daniel Reeves; Joshua Schiffer; Keith R Jerome; Cassandra Sather; Kurt Diem; Jairam R Lingappa; Connie Celum; David M Koelle; Anna Wald Journal: PLoS Med Date: 2017-12-27 Impact factor: 11.069
Authors: Mackenzie M Shipley; Daniel W Renner; Mariliis Ott; David C Bloom; David M Koelle; Christine Johnston; Moriah L Szpara Journal: J Infect Dis Date: 2018-07-13 Impact factor: 5.226
Authors: Lisa N Akhtar; Christopher D Bowen; Daniel W Renner; Utsav Pandey; Ashley N Della Fera; David W Kimberlin; Mark N Prichard; Richard J Whitley; Matthew D Weitzman; Moriah L Szpara Journal: mSphere Date: 2019-02-27 Impact factor: 4.389
Authors: Alexander L Greninger; Giselle M Knudsen; Pavitra Roychoudhury; Derek J Hanson; Ruth Hall Sedlak; Hong Xie; Jon Guan; Thuy Nguyen; Vikas Peddu; Michael Boeckh; Meei-Li Huang; Linda Cook; Daniel P Depledge; Danielle M Zerr; David M Koelle; Soren Gantt; Tetsushi Yoshikawa; Mary Caserta; Joshua A Hill; Keith R Jerome Journal: BMC Genomics Date: 2018-03-20 Impact factor: 3.969
Authors: Alexander L Greninger; Pavitra Roychoudhury; Hong Xie; Amanda Casto; Anne Cent; Gregory Pepper; David M Koelle; Meei-Li Huang; Anna Wald; Christine Johnston; Keith R Jerome Journal: mSphere Date: 2018-06-13 Impact factor: 4.389