Genome sequence of herpes simplex virus 1 strain KOS.
ABSTRACT Herpes simplex virus type 1 (HSV-1) strain KOS has been extensively used in many studies to examine HSV-1 replication, gene expression, and pathogenesis. Notably, strain KOS is known to be less pathogenic than the first sequenced genome of HSV-1, strain 17. To understand the genotypic differences between KOS and other phenotypically distinct strains of HSV-1, we sequenced the viral genome of strain KOS. When comparing strain KOS to strain 17, there are at least 1,024 small nucleotide polymorphisms (SNPs) and 172 insertions/deletions (indels). The polymorphisms observed in the KOS genome will likely provide insights into the genes, their protein products, and the cis elements that regulate the biology of this HSV-1 strain.
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ABSTRACT: Herpes simplex virus 2 is an important human pathogen as the causative agent of genital herpes, neonatal herpes, and increased risk of HIV acquisition and transmission. Nevertheless, the only genomic sequence that has been completed is the attenuated HSV-2 HG52 laboratory strain. In this study we defined the genomic sequence of the HSV-2 SD90e low passage clinical isolate and a plaque-purified derivative, SD90-3P. We found minimal sequence differences between SD90e and SD90-3P. However, in comparisons with the HSV-2 HG52 reference genome sequence, the SD90e genome ORFs contained numerous point mutations, 13 insertions/deletions (indels), and 9 short compensatory frameshifts. The indels were true sequence differences, but the compensatory frameshifts were likely sequence errors in the original HG52 sequence. Because HG52 virus is less virulent than other HSV-2 strains and may not be representative of wildtype HSV-2 strains, we propose that the HSV-2 SD90e genome serve as the new HSV-2 reference genome.Virology 01/2014; s 450–451:140–145. · 3.35 Impact Factor
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ABSTRACT: The aim of this study was to evaluate the use of RNA interference to inhibit herpes simplex virus type-1 replication in vitro. For herpes simplex virus type-1 gene silencing, three different small interfering RNAs (siRNAs) targeting the herpes simplex virus type-1 UL39 gene (sequence si-UL 39-1, si-UL 39-2, and si-UL 39-3) were used, which encode the large subunit of ribonucleotide reductase, an essential enzyme for DNA synthesis. Herpes simplex virus type-1 was isolated from saliva samples and mucocutaneous lesions from infected patients. All mucocutaneous lesions' samples were positive for herpes simplex virus type-1 by real-time PCR and by virus isolation; all herpes simplex virus type-1 from saliva samples were positive by real-time PCR and 50% were positive by virus isolation. The levels of herpes simplex virus type-1 DNA remaining after siRNA treatment were assessed by real-time PCR, whose results demonstrated that the effect of siRNAs on gene expression depends on siRNA concentration. The three siRNA sequences used were able to inhibit viral replication, assessed by real-time PCR and plaque assays and among them, the sequence si-UL 39-1 was the most effective. This sequence inhibited 99% of herpes simplex virus type-1 replication. The results demonstrate that silencing herpes simplex virus type-1 UL39 expression by siRNAs effectively inhibits herpes simplex virus type-1 replication, suggesting that siRNA based antiviral strategy may be a potential therapeutic alternative.The Brazilian journal of infectious diseases: an official publication of the Brazilian Society of Infectious Diseases 05/2014; · 1.04 Impact Factor
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ABSTRACT: Abstract Purpose: To determine the relative importance of viral glycoproteins gK, gM, gE and the membrane protein UL11 in infection of mouse corneas and ganglionic neurons. Methods: Mouse eyes were scarified and infected with herpes simplex virus (HSV)-1(F), gE-null, gM-null, gK-null, or UL11-null viruses. Clinical signs of ocular disease were monitored daily. Virus shedding was determined at 24, 48 and 72 h post infection. Viral DNA within trigeminal ganglia (TG) was quantified by quantitative PCR at 30 d post infection. Results: The gE-null virus replicated as efficiently as the parental virus and formed viral plaques approximately half-the-size in comparison with the HSV-1(F) wild-type virus. The UL11-null and gM-null viruses replicated approximately one log less efficiently than the wild-type virus, and formed plaques that were on average one-third the size and one-half the size of the wild-type virus, respectively. The gK-null virus replicated more than 3-logs less efficiently than the wild-type virus and formed very small plaques (5-10 cells). Mice infected with the wild-type virus exhibited mild clinical ocular symptoms, while mice infected with the mutant viruses did not show any significant ocular changes. The wild-type virus produced the highest virus shedding post infection followed by the gM-null, gE-null and UL11-null viruses, while no gK-null virus was detected at any time point. All TG collected from mice infected with the wild-type virus and 6-of-10 of TG retrieved from mice infected with the UL11-null virus contained high numbers of viral genomes. The gE-null and gM-null-infected ganglia contained moderate-to-low number of viral genomes in 4-of-10 and 2-of-10 mice, respectively. No viral genomes were detected in ganglionic tissues obtained from gK-null eye infections. Conclusions: The results show that gK plays the most important role among gM, gE and UL11 in corneal and ganglionic infection in the mouse eye model.Current eye research 04/2014; · 1.51 Impact Factor
Genome Sequence of Herpes Simplex Virus 1 Strain KOS
Stuart J. Macdonald,aHeba H. Mostafa,aLynda A. Morrison,band David J. Davidoa
Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA,aand Department of Molecular Microbiology and Immunology, Saint Louis University
School of Medicine, St. Louis, Missouri, USAb
linear double-stranded DNA genome (10) which contains ?80
genes. Infection by HSV-1 can result in cold, ocular, and genital
variance is probably due to base substitutions leading to amino
acid or cis regulatory changes (3, 7, 13). One HSV-1 strain, KOS,
was originally isolated from a human labial lesion and is fre-
(11, 12). KOS is less virulent than other HSV-1 strains, such as
led us to sequence the genome of strain KOS.
KOS genomic DNA (passage 12) was isolated from infected
Vero (African green monkey kidney) cells using standard proto-
cols (2), and an unpaired 42-bp Illumina library was generated
and run at Genome Technology Access Center, Washington Uni-
versity. Since viral DNA was isolated from Vero cells, potential
contaminating host reads that matched the Rhesus macaque
and/or human genomes were removed using Bowtie (5). The re-
Velvet de novo assembler (14). The resulting contigs that were
?100 bp were assembled against the reference HSV-1 strain 17
genome (GenBank accession number NC_001806) with SeqMan
Pro (DNASTAR, Inc.). Because the HSV-1 genome includes two
pairs of inverted repeat regions, TRL/IRL and IRS/TRS, contigs
assembling into one of the repeat units were reverse comple-
mented and also placed into the other repeat unit.
The final KOS genome is 152,011 bp and has 13 gaps, exclu-
sively at variable number tandem repeat (VNTR) regions, to-
taling 1,582 bp in length. In the GenBank annotation, the se-
quence and length of each VNTR was copied from strain 17.
Using Bowtie to align the filtered reads against the de novo
erage for the KOS genome was 4,257?. Gene annotations were
transferred from the strain 17 genome using Rapid Annotation
Transfer Tool (RATT) (8).
KOS and 17, we aligned the genomes using fast statistical align-
from strain 17 by 1,024 single nucleotide polymorphisms (SNPs),
reading frames. In addition, we identified previously reported
herpesvirinae subfamily of the Herpesviridae family and has a
mutations in the US9 and US8A genes (7). The two genomes also
differ by 172 insertion/deletion events (indels), most of which are
insertions or deletions of single bases in noncoding regions; how-
ever, 26 indels are in-frame additions or removals of codons. Fu-
HSV-1 strains will allow us to identify the genetic attributes of
KOS that contribute to its pathogenesis.
Nucleotide sequence accession number. The HSV-1 strain
KOS genome sequence has been deposited in GenBank under ac-
cession number JQ673480.
We thank the Genome Technology Access Center in the Department of
Genetics at Washington University School of Medicine for help with se-
This work was supported in part by National Institutes of Health
(NIH) grants R01AI72357 (D.J.D.), R21EY019739 (L.A.M. and D.J.D.),
R01RR024862 and R01GM085260 (S.J.M.), and R21NS070417 (S.J.M.
and E. Lundquist). The Genome Technology Access Center is partially
supported by NCI Cancer Center Support grant no. P30 CA91842 to the
the National Center for Research Resources (NCRR), a component of the
NIH, and NIH Roadmap for Medical Research. Support provided by the
The content is solely the responsibility of the authors and does not
necessarily represent the official views of the NIH.
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Received 13 March 2012 Accepted 15 March 2012
Address correspondence to Stuart J. Macdonald, email@example.com, or David J.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
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