Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses

ABSTRACT Herpes simplex virus (HSV) is a widespread pathogen that causes epithelial lesions with recurrent disease that manifests over a lifetime. The lifelong aspect of infection results from latent viral infection of neurons, a reservoir from which the virus reactivates periodically. Recent work h...

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Autores principales:	Lance R. Parsons, Yolanda R. Tafuri, Jacob T. Shreve, Christopher D. Bowen, Mackenzie M. Shipley, L. W. Enquist, Moriah L. Szpara
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/354933c588384ba7bc1677f731eb0419
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spelling	oai:doaj.org-article:354933c588384ba7bc1677f731eb04192021-11-15T15:41:33ZRapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses10.1128/mBio.02213-142150-7511https://doaj.org/article/354933c588384ba7bc1677f731eb04192015-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02213-14https://doaj.org/toc/2150-7511ABSTRACT Herpes simplex virus (HSV) is a widespread pathogen that causes epithelial lesions with recurrent disease that manifests over a lifetime. The lifelong aspect of infection results from latent viral infection of neurons, a reservoir from which the virus reactivates periodically. Recent work has demonstrated the breadth of genetic variation in globally distributed HSV strains. However, the amount of variation or capacity for mutation within one strain has not been well studied. Here we developed and applied a streamlined new approach for assembly and comparison of large DNA viral genomes such as HSV-1. This viral genome assembly (VirGA) workflow incorporates a combination of de novo assembly, alignment, and annotation strategies to automate the generation of draft genomes for large viruses. We applied this approach to quantify the amount of variation between clonal derivatives of a common parental virus stock. In addition, we examined the genetic basis for syncytial plaque phenotypes displayed by a subset of these strains. In each of the syncytial strains, we found an identical DNA change, affecting one residue in the gB (UL27) fusion protein. Since these identical mutations could have appeared after extensive in vitro passaging, we applied the VirGA sequencing and comparison approach to two clinical HSV-1 strains isolated from the same patient. One of these strains was syncytial upon first culturing; its sequence revealed the same gB mutation. These data provide insight into the extent and origin of genome-wide intrastrain HSV-1 variation and present useful methods for expansion to in vivo patient infection studies. IMPORTANCE Herpes simplex virus (HSV) infects more than 70% of adults worldwide, causing epithelial lesions and recurrent disease that manifests over a lifetime. Prior work has demonstrated that HSV strains vary from country to country and between individuals. However, the amount of variation within one strain has not been well studied. To address this, we developed a new approach for viral genome assembly (VirGA) and analysis. We used this approach to quantify the amount of variation between sister clones of a common parental virus stock and to determine the basis of a unique fusion phenotype displayed by several variants. These data revealed that while sister clones of one HSV stock are more than 98% identical, these variants harbor enough genetic differences to change their observed characteristics. Comparative genomics approaches will allow us to explore the impacts of viral inter- and intrastrain diversity on drug and vaccine efficacy.Lance R. ParsonsYolanda R. TafuriJacob T. ShreveChristopher D. BowenMackenzie M. ShipleyL. W. EnquistMoriah L. SzparaAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 2 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Lance R. Parsons Yolanda R. Tafuri Jacob T. Shreve Christopher D. Bowen Mackenzie M. Shipley L. W. Enquist Moriah L. Szpara Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
description	ABSTRACT Herpes simplex virus (HSV) is a widespread pathogen that causes epithelial lesions with recurrent disease that manifests over a lifetime. The lifelong aspect of infection results from latent viral infection of neurons, a reservoir from which the virus reactivates periodically. Recent work has demonstrated the breadth of genetic variation in globally distributed HSV strains. However, the amount of variation or capacity for mutation within one strain has not been well studied. Here we developed and applied a streamlined new approach for assembly and comparison of large DNA viral genomes such as HSV-1. This viral genome assembly (VirGA) workflow incorporates a combination of de novo assembly, alignment, and annotation strategies to automate the generation of draft genomes for large viruses. We applied this approach to quantify the amount of variation between clonal derivatives of a common parental virus stock. In addition, we examined the genetic basis for syncytial plaque phenotypes displayed by a subset of these strains. In each of the syncytial strains, we found an identical DNA change, affecting one residue in the gB (UL27) fusion protein. Since these identical mutations could have appeared after extensive in vitro passaging, we applied the VirGA sequencing and comparison approach to two clinical HSV-1 strains isolated from the same patient. One of these strains was syncytial upon first culturing; its sequence revealed the same gB mutation. These data provide insight into the extent and origin of genome-wide intrastrain HSV-1 variation and present useful methods for expansion to in vivo patient infection studies. IMPORTANCE Herpes simplex virus (HSV) infects more than 70% of adults worldwide, causing epithelial lesions and recurrent disease that manifests over a lifetime. Prior work has demonstrated that HSV strains vary from country to country and between individuals. However, the amount of variation within one strain has not been well studied. To address this, we developed a new approach for viral genome assembly (VirGA) and analysis. We used this approach to quantify the amount of variation between sister clones of a common parental virus stock and to determine the basis of a unique fusion phenotype displayed by several variants. These data revealed that while sister clones of one HSV stock are more than 98% identical, these variants harbor enough genetic differences to change their observed characteristics. Comparative genomics approaches will allow us to explore the impacts of viral inter- and intrastrain diversity on drug and vaccine efficacy.
format	article
author	Lance R. Parsons Yolanda R. Tafuri Jacob T. Shreve Christopher D. Bowen Mackenzie M. Shipley L. W. Enquist Moriah L. Szpara
author_facet	Lance R. Parsons Yolanda R. Tafuri Jacob T. Shreve Christopher D. Bowen Mackenzie M. Shipley L. W. Enquist Moriah L. Szpara
author_sort	Lance R. Parsons
title	Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
title_short	Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
title_full	Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
title_fullStr	Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
title_full_unstemmed	Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses
title_sort	rapid genome assembly and comparison decode intrastrain variation in human alphaherpesviruses
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/354933c588384ba7bc1677f731eb0419
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Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses

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