{"id":755,"date":"2016-01-06T09:29:44","date_gmt":"2016-01-06T09:29:44","guid":{"rendered":"http:\/\/www.virologyhighlights.com\/?p=755"},"modified":"2018-05-25T08:30:11","modified_gmt":"2018-05-25T08:30:11","slug":"herpes-simplex-virus-sequencing-shows-stability-in-the-genomes-and-variability-in-the-technology","status":"publish","type":"post","link":"https:\/\/www.elsevierblogs.com\/virology\/herpes-simplex-virus-sequencing-shows-stability-in-the-genomes-and-variability-in-the-technology\/","title":{"rendered":"Herpes Simplex Virus sequencing shows stability in the genomes and variability in the technology"},"content":{"rendered":"

Read the full article on ScienceDirect<\/a><\/h3>\n

This research article is dedicated to the late Priscilla Shaffer<\/h2>\n

Text by Robin Colgrove<\/em><\/h4>\n

 <\/p>\n

Though well-known to those slogging deep in the genome-sequencing trenches, less-appreciated aspects of NextGen sequencing merit wider exposure among general audiences. Technological advances have made \u201ceasy\u201d sequences, well, easy -and rendered \u201cdifficult\u201d sequences doable- but announcement that some genome is \u201csequenced\u201d now often means mostly<\/em> sequenced: the hard bits left for \u201clater\u201d. Also, advanced methods can now look back<\/em> at sequences and isolates derived using \u201ctraditional\u201d techniques to see if we really have what we thought. Finally, phenotypic data from strains characterized before current modalities can now be mined to better understand the links between genotype and phenotype.<\/h4>\n

 <\/p>\n

Here, we employed a combination of meticulous, old-fashioned, pre-kit techniques for virus production, isolation and genome purification then NextGen sequencing and manual finishing of \u201cdifficult\u201d herpes simplex virus genomes, whose abundant repeated sequences and high-GC content previously frustrated attempts at obtaining fully \u201cpolished\u201d genomes. The KOS strain of HSV-1 and its derivatives have rich histories, both in the circumstances involved in their isolation and in the body of subsequent laboratory research on these standards. We describe these here and see what lessons can be drawn from a detailed look at the genomes.<\/h4>\n

 <\/p>\n

KOS was isolated from a lip lesion by and from Kendall O. Smith at Baylor in 1964, selected for its attractive PFU\/virion ratio. Phylogenetic analysis, though, suggests an Asian origin for the strain, perhaps from Dr. Smith\u2019s military service in Korea.\u00a0 It was established as a standard by the late Priscilla Shaffer, to whom our paper is dedicated and who supported our earlier efforts. KOS1.1 was picked over a decade and rounds of plaquing later by Hughes and Munyon in Buffalo, screening for growth at elevated temperature, demonstrating markedly reduced neurovirulence. Despite this, we see a striking lack of inter-strain variation: only five coding changes out of seventy-odd genes.\u00a0 The few changes are intriguing, like the R->H mutation in the major glycoprotein, gB, in a region potentially influencing re-folding from pre- to post-fusion states. In contrast, comparison with Strain 17, the first reference HSV-1 genome sequence, shows numerous differences, such as short \u201cframeshifts\u201d, which in context were likely sequence errors from older technology.<\/h4>\n

 <\/p>\n

Bringing together the history of standard viral strains with what is gleaned through modern techniques has interest in its own light and also helps understand both the promise and the limitations of our methods.<\/h4>\n

 <\/p>\n

\"Table<\/a><\/p>\n

Image legend<\/strong><\/h3>\n

In contrast to the strikingly few coding changes between KOS and KOS1.1, comparison with the original HSV-1 reference sequence, Strain 17, published in 1988, shows multiple biologically unlikely short regions of amino acid sequence divergence due to paired, compensating \u201cpseudo-frameshifts\u201d at the nucleotide level, \u00a0likely resulting from base-calling off the old autoradiograms.<\/h4>\n

Introducing the author<\/strong><\/h3>\n

\"Robin<\/a><\/p>\n

First author Robin Colgrove<\/h4>\n

About the research<\/strong><\/h3>\n

History and genomic sequence analysis of the herpes simplex virus 1 KOS and KOS1.1 sub-strains<\/a><\/h3>\n

Robert C. Colgrove, Xueqiao Liu, Anthony Griffiths, Priya Raja, Neal A. Deluca, Ruchi M. Newman, Donald M. Coen, David M. Knipe<\/h4>\n

Virology<\/em>, Volume 487, January 2016, Pages 215\u2013221<\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

Read the full article on ScienceDirect This research article is dedicated to the late Priscilla Shaffer Text by Robin Colgrove   Though well-known to those slogging deep in the genome-sequencing trenches, less-appreciated aspects of NextGen sequencing merit wider exposure among general audiences. Technological advances have made \u201ceasy\u201d sequences, well, easy -and rendered \u201cdifficult\u201d sequences doable- Read More…<\/a><\/p>\n","protected":false},"author":1,"featured_media":756,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,634,633],"tags":[510,511,507,506,512,508,513,509],"class_list":["post-755","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-highlighted-article","category-virus-evolution","category-virus-structure","tag-herpes-simplex-virus","tag-hsv","tag-hsv-genome-sequence","tag-hsv-history","tag-kos","tag-kos-sequence","tag-kos1-1","tag-kos1-1sequence"],"_links":{"self":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/755","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/comments?post=755"}],"version-history":[{"count":2,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/755\/revisions"}],"predecessor-version":[{"id":759,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/posts\/755\/revisions\/759"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/media\/756"}],"wp:attachment":[{"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/media?parent=755"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/categories?post=755"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.elsevierblogs.com\/virology\/wp-json\/wp\/v2\/tags?post=755"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}