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Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics.

Houldcroft, CJ; Breuer, J; (2015) Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front Microbiol , 6 , Article 188. 10.3389/fmicb.2015.00188. Green open access

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Abstract

Herpesviruses are ubiquitous double-stranded DNA viruses infecting many animals, with the capacity to cause disease in both immunocompetent and immunocompromised hosts. Different herpesviruses have different cell tropisms, and have been detected in a diverse range of tissues and sample types. Metagenomics-encompassing viromics-analyses the nucleic acid of a tissue or other sample in an unbiased manner, making few or no prior assumptions about which viruses may be present in a sample. This approach has successfully discovered a number of novel herpesviruses. Furthermore, metagenomic analysis can identify herpesviruses with high degrees of sequence divergence from known herpesviruses and does not rely upon culturing large quantities of viral material. Metagenomics has had success in two areas of herpesvirus sequencing: firstly, the discovery of novel exogenous and endogenous herpesviruses in primates, bats and cnidarians; and secondly, in characterizing large areas of the genomes of herpesviruses previously only known from small fragments, revealing unexpected diversity. This review will discuss the successes and challenges of using metagenomics to identify novel herpesviruses, and future directions within the field.

Type: Article
Title: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics.
Location: Switzerland
Open access status: An open access version is available from UCL Discovery
DOI: 10.3389/fmicb.2015.00188
Publisher version: http://dx.doi.org/10.3389/fmicb.2015.00188
Language: English
Additional information: © 2015 Houldcroft and Breuer. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords: de novo assembly, herpesviruses, metagenomics, next-generation sequencing, virus discovery
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
URI: https://discovery.ucl.ac.uk/id/eprint/1465810
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