ArticleInvestigative ophthalmology & visual science2011
Multiplex sequencing of seven ocular herpes simplex virus type-1 genomes: phylogeny, sequence variability, and SNP distribution.
Article in Investigative ophthalmology & visual science, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 41 citations in OpenAlex.
- Genotypic Characterization of Herpes Simplex Virus Type 1 Isolates in Immunocompromised Patients in Rio de Janeiro, Brazil.PloS one · 2015Trial
- Phylogenetic and Genomic Characterization of Whole Genome Sequences of a Herpes Simplex Virus Type 1 Isolate Identified Genomic Variant Characteristics in a Human Subject with Fulminant Hepatitis.International journal of molecular sciences · 2026Article
- Herpes simplex virus genomes from an under-sampled population in Namibia reveal novel genetic diversity.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Phylogenetic and Genomic Characterization of Whole Genome Sequences of Ocular Herpes Simplex Virus Type 1 Isolates Identifies Possible Virulence Determinants in Humans.Investigative ophthalmology & visual science · 2023Article
- Dysregulated metabolism of the late herpes simplex virus 1 transcriptome through the vhs-VP22 axis uncouples virus cytopathic effect and virus production.PLoS pathogens · 2023Article
- Surveillance for feline herpesvirus type 1 mutation and development of resistance in cats treated with antiviral medications.Frontiers in veterinary science · 2023Article
- Viral and Prion Infections Associated with Central Nervous System Syndromes in Brazil.Viruses · 2021Review
- Article
- Genomic analysis for virulence determinants in feline herpesvirus type-1 isolates.Virus genes · 2020Article
- Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses.Virus evolution · 2020Article
- Review
- Comparison of Herpes Simplex Virus 1 Strains Circulating in Finland Demonstrates the Uncoupling of Whole-Genome Relatedness and Phenotypic Outcomes of Viral Infection.Journal of virology · 2019Article
- Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.BMC genomics · 2018Article
- Genomic, Recombinational and Phylogenetic Characterization of Global Feline Herpesvirus 1 Isolates.Virology · 2018Article
- Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution.Journal of virology · 2018Review
- Molecular Evolution of Herpes Simplex Virus 2 Complete Genomes: Comparison between Primary and Recurrent Infections.Journal of virology · 2017Article
- Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 UVirology · 2017Article
- Ancient Recombination Events between Human Herpes Simplex Viruses.Molecular biology and evolution · 2017Article
- HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.Journal of neurovirology · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
purposeLittle is known about the role of sequence variation in the pathology of HSV-1 keratitis virus. The goal was to show that a multiplex, high-throughput genome-sequencing approach is feasible for simultaneously sequencing seven HSV-1 ocular strains.
methodsA genome sequencer was used to sequence the HSV-1 ocular isolates TFT401, 134, CJ311, CJ360, CJ394, CJ970, and OD4, in a single lane. Reads were mapped to the HSV-1 strain 17 reference genome by high-speed sequencing. ClustalW was used for alignment, and the Mega 4 package was used for phylogenetic analysis (www.megasoftware.net). Simplot was used to compare genetic variability and high-speed sequencing was used to identify SNPs (developed by Stuart Ray, Johns Hopkins University School of Medicine, Baltimore, MD, http://sray.med.som.jhml.edu/SCRoftware/simplot).
resultsApproximately 95% to 99% of the seven genomes were sequenced in a single lane with average coverage ranging from 224 to 1345. Phylogenetic analysis of the sequenced genome regions revealed at least three clades. Each strain had approximately 200 coding SNPs compared to strain 17, and these were evenly spaced along the genomes. Four genes were highly conserved, and six were more variable. Reduced coverage was obtained in the highly GC-rich terminal repeat regions.
conclusionsMultiplex sequencing is a cost-effective way to obtain the genomic sequences of ocular HSV-1 isolates with sufficient coverage of the unique regions for genomic analysis. The number of SNPs and their distribution will be useful for analyzing the genetics of virulence, and the sequence data will be useful for studying HSV-1 evolution and for the design of structure-function studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.