I'm surprised that someone "leaked" the full text of the paper, in
violation of the very simple and minimal requests made by the authors
that I am sure accompanied
every pre-print.  

But given that it is out, I will translate from "Paper" into "Beekeeper"
below, as it is important to know the difference between what the data
says, and what
the paper tries to say, despite the data.

Paper: 
"Recently, an unprecedented 'metagenomic' approach was used to detect
parasites and pathogens in bees associated with CCD...
One striking result was the tight correlation between Israeli Acute
Paralysis Virus (IAPV), an unclassified Dicistroviridae virus, and CCD."

Beekeeper:
But our 'tight correlation' is blown out of the water by the years of
apparently healthy colonies with IAPV, 10% of what we sampled.
But we have an strategy - position this as a minor finding, speculate
even further to avoid retracting anything, and publish in ABJ, which is
read by about 0% of those who read "Science".  In short, 'bury' the
contradictory results.


Paper:
"IAPV isolates. can be split into four distinct clusters supported with
bootstrap statistical values > 55%"

Beekeeper:
We found very minor differences between US samples.


Paper:
"Israeli samples, including the strain first named as IAPV, are not
distinct from the U.S. isolates as a group."

Beekeeper:
Israeli Versions of IAPV aren't at all different from US versions, so we
can't explain why IAPV killed bees and brood in mere days in Israel, but
not in the US.


Paper:
"These three complete genomes, when compared to the definitive (Israeli)
IAPV genome sequence, show 4.2 -4.7% divergence at the RNA level."

Beekeeper:
We have no idea of the implications of a 4.2% difference, if any, but
4.7% is a bigger number, and might have even bigger implications.


Paper:
"Genetic heterogeneity across the studied 5' region is interesting in
that this region is involved in the initiation of protein translation,
and genetic variability of this region may lead to different
pathogenicities."

Beekeeper:
We looked at the 'prelude' section of the gene, before the gene settles
down and does any actual coding, and speculate that differences here
MIGHT explain how Israel's version of IAPV can be more virulent than the
US version, but the US version can cause CCD when the Israeli version
does not. WE COULD also speculate that freckled people might be
vampires, using the same sound, rational approach of 'different could be
deadly'.
We are hoping that the reader won't glance back to where we said that
Israeli samples are NOT distinct from the US isolates as a group, as we
are now speculating that there are significant differences, and that
they matter.


Paper:
"Nevertheless, we caution that much work is still needed to absolve or
implicate this virus, or specific imports, in CCD."

Beekeeper:
Rather than honestly admitting that too much speculation about too
little data was done in the last paper on CCD, we will speculate our way
even further out on a limb, in an attempt to explain away these new
findings rather than admit to speculating the first time. 


Paper:
"Further analyses are needed to explore the implications of these and
other genome sequences for virulence traits of IAPV."

Beekeeper:
We will also seek additional funding to look for other reasons to not
change our initial highly speculative theory in light of this new,
compelling, and very surprising evidence.


Now that we've wiped the lipstick off the pig, we can look at
implications.
Long story short, every claim made in the much-ballyhooed paper in
"Science" about CCD appears to have been wrong.

1) IAPV is clearly not "a significant marker" for CCD. In 2002-2005,
neither CCD nor any other unusual symptoms were observed, yet IAPV had
infected roughly 10% of the bees sampled in those years.

2) IAPV was claimed to have been found in bees imported from Australia,
which were "tested as potential sources of pathogens". It was also noted
that CCD appeared only after Australian bees were imported to the US.
The finding of IAPV in years prior to the first bee imports indicate
that Australian bees may have been wrongly accused of being "sources" of
pathogens.

2a) But Australia is not out of the equation just yet.  IAPV in the USA
was explained in Bee Culture's October issue as being something that
could have easily come via Canada during the "border closure" days.
http://bee-quick.com/reprints/world.pdf
   
3) But IAPV may or may not have anything at all to do with CCD, given
all those years that US bees had IAPV without showing CCD symptoms,
which is the important
message that the authors of this new paper go to even further
speculative lengths to avoid admitting.

4) The claim that the work leading to the first paper was a "model to
establish a strategy for investigating epidemics of unexplained
infectious disease" is called into question. The work clearly suffered
from the small number of samples, due to the high cost per sample for
this new technology. So, claims were made and inferences were drawn
beyond those firmly supported by the limited sample set. Ironically, the
samples from years well before CCD appeared in the US would have made
excellent "controls", and were readily available.

Jay did a nice job of doing his best to soft-pedal the findings, but I'm
not the only one who know things like what the 5' end of a gene is, so
the attempt was partly based upon the assumption that no one would
notice something published in ABJ, and may have also been based upon the
assumption that beekeepers would not see the misdirection.

But make no mistake, this data is a retraction of the "Science" paper as
a whole.
Not a single assertion made in the first paper survives this.

...and "IAPV in the USA" should be sung to the tune of the John Cougar
Melencamp classic "R.O.C.K. in he USA".

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