Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture

Author:

Greninger Alexander L.12,Roychoudhury Pavitra12,Xie Hong1,Casto Amanda3,Cent Anne12,Pepper Gregory12,Koelle David M.12345,Huang Meei-Li12,Wald Anna1236,Johnston Christine23,Jerome Keith R.12

Affiliation:

1. Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA

2. Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA

3. Department of Medicine, University of Washington, Seattle, Washington, USA

4. Department of Global Health, University of Washington, Seattle, Washington, USA

5. Benaroya Research Institute, Seattle, Washington, USA

6. Department of Epidemiology, University of Washington, Seattle, Washington, USA

Abstract

Herpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding the global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

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