Juanese asked about viruses, nosema in failing bee colonies.
Yes, its all available in our PLOS ONE paper, Iridovirus and Microsporidian
Linked to Honey Bee Colony Decline, October, 2010.
As you know, we have had some very vocal critics, but we're now publishing
a rebuttal that says in essence - we did it right, the others have it
wrong. This rebuttal has taken some time due to false claims that we had to
deal with over past two years. Our data has now been carefully examined by
two independent groups and found to be solid and complete and appropriately
analyzed. That took some time.
There is a paper by another research group who looked at 3 of our samples
and state that they did not find nosema nor evidence of a DNA,
iridescent-like virus. Problem is, they got our samples without our knowledge..
Army sent raw data for three samples to one group, who without asking
permission, passed them to another group, who then re-analyzed and published a
quick paper, making over-stated claims that their analysis differed, and as
such, we (Army) was shown to be wrong, and that their paper should serve as a
warning.
Here's our summary, which is a very small part of our full rebuttal:
Army sent out three samples as per request of another group, who passed
them on. These samples were carefully picked and sent as blind samples -
the recipients had no knowledge of the provenance.
One sample by Army ABOID analysis had no Nosema and no IIV-like virus (it
was a true control)
One sample had very small amounts of Nosema and IIV-like virus (it served
to test analysis detection limits,
Only one sample had both pathogens (it was the positive control - they
should have found both pathogens)
They re-analyzed these 3, got their paper published, without asking about
the nature of the three samples that they re-examined.
They then wrote a paper saying - no nosema, no IIV virus. They then
alleged that they were right, Army was wrong.
Interestingly, they did not dispute all of the small, RNA viruses that we
found -they also found them.
Again, they claimed none of the samples had Nosema or an IIV-like virus.
They claimed in their paper that we failed to look at bee proteins, which
is patently untrue - we looked at all bee proteins and a wide array of honey
bee, insect, and plant pathogens, which was clearly stated in our article.
We chose not to include the bee body proteins in our statistical
analysis, choosing instead to focus on the pathogens. Its not that we didn't look
at them - they were inappropriate for the analysis.
There was no reason to include the proteins of the bee host in a
statistical analysis of pathogen proteins in CCD colonies. There may be another
paper there, if we chose to see if somehow the host's proteins were altered by
the pathogens, but that wasn't out purpose.
Where they went wrong is:
1) analyzing samples and writing a paper without asking about the nature of
the three samples - which they said represented all of our samples, which
is incorrect - they got carefully picked samples to test whether others
could properly classify them (it was an intentional test by Army and they took
the bait)
2) stating that they neither found the IIV-like virus or Nosema Here's
where they went over the cliff.
We confirmed the Nosema by both PCR and microscopy, in the two of the three
samples that had Nosema,
To be clear, we knew other groups did not agree with our finds. Army
chose to hand-pick three samples to sent to anyone wanting to re-analyze.
These were NOT picked to represent out full data set, they were sent to
determine whether the other groups could properly categorize the proteins in the
three samples. One blank or control, one very low level infection that
would test limits of detection, and one sample with both pathogens, the only
sample that Army expected anyone else to find Nosema and virus in.
So their abstract proclaims that the three samples had no Nosema, no
IIV-like virus, and that these three samples were representative of our CCD
samples - wrong on all accounts - too bad they can't read.
There is no doubt that two of the three samples had Nosema. Army
proteomics, MSU PRC, and MSU and UM microscopy confirmed. In other words, two labs
confirmed the Nosema using non-proteomics analysis. As you all know, one
can see Nosema spores under a microscope, and adding PCR brings a genomic
analysis to bear on the question. Nosema in two of the three samples were
confirmed by three independent methods and two different institutions. There
is no doubt that those samples had Nosema, and if they had Nosema, then a
proteomics analysis should have found proteins from Nosema. Army's
proteomics did, theirs didn't.
If they couldn't find Nosema proteins, then they have no justification
for claiming that Army analysis was wrong. Their approach either lacked
the sensitivity or specificity to detect, not Army's. If they can't find
Nosema, then any claims about whether IIV was present is mute. It like being
so blind as to not see the elephant in the room, but arguing that since
they couldn't see the elephant, there certainly couldn't have been a mouse in
the opposite corner. If you can't see the elephant, you can't see the
mouse. If others can see the elephant, you have to accept there may have been
a mouse in the room.
3) assuming that analysis algorithm they used was comparable to the custom
ABOID software developed
by the Army, and licensed last year to Sage-N-Research for intensively
computational protein analysis. Sage-N-Research and Army conducted many tests
of the accuracy of the Army software over past few years. They were
engaged in this testing when our paper emerged. Sage-N licensed Army ABOID
software based on its unique capabilities and proven ability to detect microbes
and Id to strain, not just species.
So, our formal rebuttal verifies our original results and points out why
our detractors failed to find the same results.
That said, we have seen a lot of viruses in collapsing bees plus nosema
ceranae, some nosema apis, but varroa only in a subset of the samples we
analyzed over several years.
Jerry
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