Detection of Retroviral Super-Infection from Non-Invasive Samples
Publication Date
May 08, 2012
Journal
PLOS ONE
Authors
Adeelia S. Goffe, Anja Blasse, Roger Mundry, Fabian H. Leendertz, et al
Volume
7
Issue
5
Pages
e36570
DOI
https://dx.plos.org/10.1371/journal.pone.0036570
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0036570
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22590569
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348140
Europe PMC
http://europepmc.org/abstract/MED/22590569
Web of Science
000305335500018
Scopus
84860701910
Mendeley
http://www.mendeley.com/research/detection-retroviral-superinfection-noninvasive-samples
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/331007", "https://ndownloader.figshare.com/files/331053", "https://ndownloader.figshare.com/files/331073", "https://ndownloader.figshare.com/files/331133", "https://ndownloader.figshare.com/files/331209", "https://ndownloader.figshare.com/files/331272"], "description"=>"<div><p>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, <em>i.e.,</em> 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 (<em>Pan troglodytes</em>). 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.</p> </div>", "links"=>[], "tags"=>["detection", "retroviral", "super-infection", "non-invasive", "samples"], "article_id"=>125348, "categories"=>["Molecular Biology", "Cancer", "Genetics", "Biotechnology"], "users"=>["Adeelia S. Goffe", "Anja Blasse", "Roger Mundry", "Fabian H. Leendertz", "Sébastien Calvignac-Spencer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036570.s001", "https://dx.doi.org/10.1371/journal.pone.0036570.s002", "https://dx.doi.org/10.1371/journal.pone.0036570.s003", "https://dx.doi.org/10.1371/journal.pone.0036570.s004", "https://dx.doi.org/10.1371/journal.pone.0036570.s005", "https://dx.doi.org/10.1371/journal.pone.0036570.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Detection_of_Retroviral_Super_Infection_from_Non_Invasive_Samples/125348", "title"=>"Detection of Retroviral Super-Infection from Non-Invasive Samples", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-08 01:29:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/641284"], "description"=>"<p>Individuals are ordered such that first four individuals with a single infection (as determined by EPD-PCR) are shown (B2, B3, B4 and T3; above the bar) followed by individuals with super-infections (below the bar). Plots are paired for each individual with the EPD-PCR dataset on the left and the bulk-PCR clone dataset on the right. EPD-PCR distributions are black; bulk-PCR clone distributions identified as unimodal (ΔAICc<2) are green; bulk-PCR clone distributions identified as bimodal are purple (ΔAICc>2).</p>", "links"=>[], "tags"=>["analyses", "epd-pcr", "clone"], "article_id"=>311774, "categories"=>["Virology", "Molecular Biology", "Genetics", "Biotechnology"], "users"=>["Adeelia S. Goffe", "Anja Blasse", "Roger Mundry", "Fabian H. Leendertz", "Sébastien Calvignac-Spencer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036570.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mismatch_distribution_analyses_of_EPD_PCR_and_clone_sequence_datasets_/311774", "title"=>"Mismatch distribution analyses of EPD-PCR and clone sequence datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:29:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/641482"], "description"=>"<p>(a) Probability to detect bimodality (<i>i.e.</i>, super-infection) in the frequency distribution of the number of mismatches per pair of sequences as a function of the number of bulk-PCR products analysed and for subjects for which EPD-PCR revealed a super-infection (n = 6); (b) Probability to detect bimodality in the frequency distribution of the number of mismatches per pair of sequences as a function of the number of bulk-PCR products analysed and for subjects for which EPD-PCR revealed a single infection (n = 4). Shown are median, quartiles, minimum and maximum, of the respective probabilities per subject.</p>", "links"=>[], "tags"=>["negativity", "positivity", "bulk-pcr", "products"], "article_id"=>311973, "categories"=>["Virology", "Molecular Biology", "Genetics", "Biotechnology"], "users"=>["Adeelia S. Goffe", "Anja Blasse", "Roger Mundry", "Fabian H. Leendertz", "Sébastien Calvignac-Spencer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036570.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_False_negativity_and_positivity_as_a_function_of_the_number_of_bulk_PCR_products_analysed_/311973", "title"=>"False negativity and positivity as a function of the number of bulk-PCR products analysed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:32:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/641564"], "description"=>"<p>As in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036570#pone-0036570-g001\" target=\"_blank\">Figure 1</a>, the networks are ordered by infection status. Within each network, node size is proportional to the frequency of sequence occurrence (total n = 25 for each individual). Branch lengths are directly related to the number of mutations between sequences, with values noted for differences greater than two base pairs. Clone haplotypes a–f (as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036570#pone-0036570-t001\" target=\"_blank\">Table 1</a>) are noted within or adjacent to their corresponding node. Networks generated using TCS were highly similar (data not shown).</p>", "links"=>[], "tags"=>["joining", "pcr", "clone"], "article_id"=>312060, "categories"=>["Virology", "Molecular Biology", "Genetics", "Biotechnology"], "users"=>["Adeelia S. Goffe", "Anja Blasse", "Roger Mundry", "Fabian H. Leendertz", "Sébastien Calvignac-Spencer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036570.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_network_of_bulk_PCR_product_clone_sequences_/312060", "title"=>"Median joining network of bulk PCR product clone sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-08 00:34:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/641637"], "description"=>"<p>All EPD-PCR haplotypes are presented, while only those haplotypes getting OP values above the minimum value are shown for bulk-PCR clone sequences. Assumed founder sequences are highlighted in bold. # origin of sequences refer to the bulk-PCR products from which they originate (<i>e.g.</i>, if haplotype <i>a</i> appeared two times in PCR product B and once in PCR product C, then 2<b>×</b>B and 1<b>×</b>C will appear in this column) * individuals for which statistical parsimony analyses produced two separated networks; here the sum of all OPs will be greater than one as OPs will be calculated independently for each network.</p>", "links"=>[], "tags"=>["sequences", "epd-pcr", "bulk-pcr", "clone"], "article_id"=>312130, "categories"=>["Virology", "Molecular Biology", "Genetics", "Biotechnology"], "users"=>["Adeelia S. Goffe", "Anja Blasse", "Roger Mundry", "Fabian H. Leendertz", "Sébastien Calvignac-Spencer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036570.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_founder_sequences_from_EPD_PCR_and_bulk_PCR_clone_sequence_alignments_/312130", "title"=>"Identification of founder sequences from EPD-PCR and bulk-PCR clone sequence alignments.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-08 00:35:30"}

PMC Usage Stats | Further Information

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Relative Metric

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