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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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.
1. Bradley RK, et al. 2009. Fast statistical alignment. PLoS Comp. Biol.
2. Cai WZ, Schaffer PA. 1989. Herpes simplex virus type 1 ICP0 plays a
tion of viral DNA. J. Virol. 63:4579–4589.
3. Chou J, Roizman B. 1990. The herpes simplex virus 1 gene for ICP34.5,
which maps in inverted repeats, is conserved in several limited-passage
isolates but not in strain 17. J. Virol. 64:1014–1020.
4. Hill JM, Rayfield MA, Haruta Y. 1987. Strain specificity of spontaneous
Received 13 March 2012 Accepted 15 March 2012
Address correspondence to Stuart J. Macdonald, firstname.lastname@example.org, or David J.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
June 2012 Volume 86 Number 11 Journal of Virology p. 6371–6372 jvi.asm.org
and adrenergically induced HSV-1 ocular reactivation in latently infected
rabbits. Curr. Eye Res. 6:91–97.
5. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and
memory-efficient alignment of short DNA sequences to the human ge-
nome. Genome Biol. 10:R25.
6. Luker KE, Schultz T, Romine J, Leib DA, Luker GD. 2006. Transgenic
reporter mouse for bioluminescence imaging of herpes simplex virus 1
infection in living mice. Virology 347:286–295.
7. Negatsch A, Mettenleiter TC, Fuchs W. 2011. Herpes simplex virus type
1 strain KOS carries a defective US9 and a mutated US8A gene. J. Gen.
8. Otto TD, Dillon GP, Degrave WS, Berriman M. 2011. RATT: Rapid
Annotation Transfer Tool. Nucleic Acids Res. 39:e57.
KOS strain ICP34.5 gene in place of the McKrae ICP34.5 gene have McK-
rae-like spontaneous reactivation but non-McKrae-like virulence. J. Gen.
10. Roizman R, Knipe DM, Whitley RJ. 2007. Herpes simplex viruses, p
2501–2601. In Knipe DM Howley PM (ed), Fields virology, vol 2. Lippin-
cott Williams & Wilkins, New York, NY.
11. Schaffer PA, Aron GM, Biswal N, Benyesh-Melnick M.1973. Temperature-
12. Smith KO. 1964. Relationship between the envelope and the infectivity of
herpes simplex virus. Proc. Soc. Exp. Biol. Med. 115:814–816.
13. Szpara ML, Parsons L, Enquist LW. 2010. Sequence variability in clinical
14. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read
assembly using de Bruijn graphs. Genome Res. 18:821–829.
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