Hidden Viral gene found in GMO Crops?

My conspiracy friends are sending me this story.
http://sustainablepulse.com/2013/01/...-fears-spread/

What truth, if any is behind these stories?

Not much. EFSA has answered some FAQ's in response to those stories.

http://www.efsa.europa.eu/en/faqs/faqinsertedfragmentofviralgeneingmplants.htm

1. Certain media reports have claimed a paper published in the academic journal GM Crops and Food: Biotechnology in Agriculture and the Food Chain had discovered a previously unknown viral gene in commercial GM crops that may present a hazard to human health. Is this claim true?

No, the data published in the paper ‘Possible Consequences of the overlap between the CaMV 35S promoter regions in the plant transformation vectors used in the viral gene VI in transgenic plants’ do not represent a new discovery of a viral gene nor do they indicate safety concerns in previously evaluated GMOs.

The following paper confirms the validity of EFSA's statements:

Gene transfer and cauliflower mosaic virus promoter 35S activity in mammalian cells.

Obtained data did not highlight evidences of dietary DNA transfer in mice. No CaMV35s transcriptional activity was detected in this experimental model. These findings emphasize the need for further studies and standardized methods.
 
The truth is:
1/ the gene is not "hidden" and it has been known about for years
2/ the study looked to see if any known toxins or allergens were produced by the gene - they could not find any that they recognised
3/ the study produced a "flowchart" to test whether ther might be any unforseen products of genes should you with to test for tehm at some time in the future.


Here is the abstract of the paper concerned


Abstract:
Multiple variants of the Cauliflower mosaic virus 35S promoter (P35S) are used to drive the expression of transgenes in genetically modified plants, for both research purposes and commercial applications. The genetic organization of the densely packed genome of this virus results in sequence overlap between P35S and viral gene VI, encoding the multifunctional P6 protein. The present paper investigates whether introduction of P35S variants by genetic transformation is likely to result in the expression of functional domains of the P6 protein and in potential impacts in transgenic plants. A bioinformatic analysis was performed to assess the safety for human and animal health of putative translation products of gene VI overlapping P35S. No relevant similarity was identified between the putative peptides and known allergens and toxins, using different databases. From a literature study it became clear that long variants of the P35S do contain an open reading frame, when expressed, might result in unintended phenotypic changes. A flowchart is proposed to evaluate possible unintended effects in plant transformants, based on the DNA sequence actually introduced and on the plant phenotype, taking into account the known effects of ectopically expressed P6 domains in model plants.
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