Detection of retroviral super-infection from non-invasive samples.

While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has rem...

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Autores principales:	Adeelia S Goffe, Anja Blasse, Roger Mundry, Fabian H Leendertz, Sébastien Calvignac-Spencer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/87ecd5dff77240f988d319a9b28c6d81
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spelling	oai:doaj.org-article:87ecd5dff77240f988d319a9b28c6d812021-11-18T07:19:24ZDetection of retroviral super-infection from non-invasive samples.1932-620310.1371/journal.pone.0036570https://doaj.org/article/87ecd5dff77240f988d319a9b28c6d812012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22590569/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has remained largely neglected. In particular, methods possibly allowing the investigation of super-infection from samples collected non-invasively (such as faeces) have never been properly compared. Here, we fill in this gap by assessing the costs and benefits of end-point dilution PCR (EPD-PCR) and multiple bulk-PCR cloning, as applied to a case study focusing on simian foamy virus super-infection in wild chimpanzees (Pan troglodytes). We show that, although considered to be the gold standard, EPD-PCR can lead to massive consumption of biological material when only low copy numbers of the target are expected. This constitutes a serious drawback in a field in which rarity of biological material is a fundamental constraint. In addition, we demonstrate that EPD-PCR results (single/multiple infection; founder strains) can be well predicted from multiple bulk-PCR clone experiments, by applying simple statistical and network analyses to sequence alignments. We therefore recommend the implementation of the latter method when the focus is put on retroviral super-infection and only low retroviral loads are encountered.Adeelia S GoffeAnja BlasseRoger MundryFabian H LeendertzSébastien Calvignac-SpencerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 5, p e36570 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adeelia S Goffe Anja Blasse Roger Mundry Fabian H Leendertz Sébastien Calvignac-Spencer Detection of retroviral super-infection from non-invasive samples.
description	While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has remained largely neglected. In particular, methods possibly allowing the investigation of super-infection from samples collected non-invasively (such as faeces) have never been properly compared. Here, we fill in this gap by assessing the costs and benefits of end-point dilution PCR (EPD-PCR) and multiple bulk-PCR cloning, as applied to a case study focusing on simian foamy virus super-infection in wild chimpanzees (Pan troglodytes). We show that, although considered to be the gold standard, EPD-PCR can lead to massive consumption of biological material when only low copy numbers of the target are expected. This constitutes a serious drawback in a field in which rarity of biological material is a fundamental constraint. In addition, we demonstrate that EPD-PCR results (single/multiple infection; founder strains) can be well predicted from multiple bulk-PCR clone experiments, by applying simple statistical and network analyses to sequence alignments. We therefore recommend the implementation of the latter method when the focus is put on retroviral super-infection and only low retroviral loads are encountered.
format	article
author	Adeelia S Goffe Anja Blasse Roger Mundry Fabian H Leendertz Sébastien Calvignac-Spencer
author_facet	Adeelia S Goffe Anja Blasse Roger Mundry Fabian H Leendertz Sébastien Calvignac-Spencer
author_sort	Adeelia S Goffe
title	Detection of retroviral super-infection from non-invasive samples.
title_short	Detection of retroviral super-infection from non-invasive samples.
title_full	Detection of retroviral super-infection from non-invasive samples.
title_fullStr	Detection of retroviral super-infection from non-invasive samples.
title_full_unstemmed	Detection of retroviral super-infection from non-invasive samples.
title_sort	detection of retroviral super-infection from non-invasive samples.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/87ecd5dff77240f988d319a9b28c6d81
work_keys_str_mv	AT adeeliasgoffe detectionofretroviralsuperinfectionfromnoninvasivesamples AT anjablasse detectionofretroviralsuperinfectionfromnoninvasivesamples AT rogermundry detectionofretroviralsuperinfectionfromnoninvasivesamples AT fabianhleendertz detectionofretroviralsuperinfectionfromnoninvasivesamples AT sebastiencalvignacspencer detectionofretroviralsuperinfectionfromnoninvasivesamples
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Detection of retroviral super-infection from non-invasive samples.

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