Novel method for genotyping clinical herpes simplex virus type 1 isolates

Glück, Brigitte; Möbius, Susanne; Pfaff, Florian; Zell, Roland; Sauerbrei, Andreas

doi:10.1007/s00705-015-2568-y

Cited by 5 publications

(4 citation statements)

References 22 publications

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“…We additionally performed a genotyping analysis on our alignments to the reference sequence HSV-1 strain 17. Grouping of HSV-1 into three distinct genotypes (A, B, and C) is commonly based on intragenic SNPs in the glycoprotein genes US4 ( gG ) and US7 ( gI ) ( 65 ) and the more recent gene US2 ( 66 ). Because of low coverage at some genotyping coordinates, not all SNPs could be assessed in the ancient samples.…”

Section: Methodsmentioning

confidence: 99%

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

et al. 2022

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Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating from the 3rd to 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes, we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 to 5.65) ka. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60 to 6.12) ka, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

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Section: Methodsmentioning

confidence: 99%

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

et al. 2022

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“…Nucleotide sequence polymorphisms in glycoprotein G (gG, US4) and glycoprotein I (gI, US7) have been used to define three major genotypes termed A, B and C, that correlate to the three major geographic clades (Norberg, 2010; Norberg et al, 2004). A simpler assay to distinguished these genotypes based on digestion of an amplified segment of the US2 gene by the endonuclease EcoO109I has been proposed (Glück et al, 2015). However, this is uninformative when applied to the Patton genome, which in this limited region is identical to the sequences of North American/European (genotype B) strains H129 and F. Thus simple genotyping tests may not accurately assign all viruses and a combination of tests or better still, genome sequencing should be used.…”

Section: Resultsmentioning

confidence: 99%

“…Patton is indicated in blue. (B) In silico application of the US2 genotyping method (Glück et al, 2015), which is based on the presence or absence of two EcoO109I endonuclease cleavage sites (boxed) within the US2 coding region (nucleotides 134,151 to 134,256 of strain 17). Nucleotides that differ from the Patton sequence are indicated in white font and genotype designation follows the color scheme used in panel A.…”

Section: Figmentioning

confidence: 99%

Shared ancestry of herpes simplex virus 1 strain Patton with recent clinical isolates from Asia and with strain KOS63

Pourchet

Copin

Mulvey³

et al. 2017

Virology

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Herpes simplex virus 1 (HSV-1) is a widespread pathogen that persists for life, replicating in surface tissues and establishing latency in peripheral ganglia. Increasingly, molecular studies of latency use cultured neuron models developed using recombinant viruses such as HSV-1 GFP-US11, a derivative of strain Patton expressing green fluorescent protein (GFP) fused to the viral US11 protein. Visible fluorescence follows viral DNA replication, providing a real time indicator of productive infection and reactivation. Patton was isolated in Houston, Texas, prior to 1973, and distributed to many laboratories. Although used extensively, the genomic structure and phylogenetic relationship to other strains is poorly known. We report that wild type Patton and the GFP-US11 recombinant contain the full complement of HSV-1 genes and differ within the unique regions at only eight nucleotides, changing only two amino acids. Although isolated in North America, Patton is most closely related to Asian viruses, including KOS63.

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“…It is predicted to have a hydrophobic N-terminus [764]; it is non-essential in cell culture and not involved in the pathogenesis in the CNS of mice [765]. HSV-1 Us2 is not associated with any specific phenotype [766]; however, most research so far has been done on HSV-2 Us2. Initially, U S 2 was observed as discrete granules late during infection within and at the periphery of the nucleus [767].…”

Section: U Smentioning

confidence: 99%

“Non-Essential” Proteins of HSV-1 with Essential Roles In Vivo: A Comprehensive Review

Dogrammatzis

Waisner

Kalamvoki

2020

Viruses

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Viruses encode for structural proteins that participate in virion formation and include capsid and envelope proteins. In addition, viruses encode for an array of non-structural accessory proteins important for replication, spread, and immune evasion in the host and are often linked to virus pathogenesis. Most virus accessory proteins are non-essential for growth in cell culture because of the simplicity of the infection barriers or because they have roles only during a state of the infection that does not exist in cell cultures (i.e., tissue-specific functions), or finally because host factors in cell culture can complement their absence. For these reasons, the study of most nonessential viral factors is more complex and requires development of suitable cell culture systems and in vivo models. Approximately half of the proteins encoded by the herpes simplex virus 1 (HSV-1) genome have been classified as non-essential. These proteins have essential roles in vivo in counteracting antiviral responses, facilitating the spread of the virus from the sites of initial infection to the peripheral nervous system, where it establishes lifelong reservoirs, virus pathogenesis, and other regulatory roles during infection. Understanding the functions of the non-essential proteins of herpesviruses is important to understand mechanisms of viral pathogenesis but also to harness properties of these viruses for therapeutic purposes. Here, we have provided a comprehensive summary of the functions of HSV-1 non-essential proteins.

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Novel method for genotyping clinical herpes simplex virus type 1 isolates

Cited by 5 publications

References 22 publications

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Shared ancestry of herpes simplex virus 1 strain Patton with recent clinical isolates from Asia and with strain KOS63

“Non-Essential” Proteins of HSV-1 with Essential Roles In Vivo: A Comprehensive Review

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