Medhat:

Despite there is a different take on nosema if it kills bees or not by various researchers, under our climatic conditions nosema is a serious disease. It kills bees

 
We also find Nosema to be associated with bee kills, sometimes severe, and often producing low honey yield, bees reducing foraging, going off feed, and at times catastrophic population drops.  

Since 2006, we have conducted several controlled experiments whereby we've dosed full-size colonies with Nosema, then introduced virus.  Nosema kills a percentage of the colony following the Koch method - introduce, induce, verify.  Same is true with some of the viruses we employed; a percentage of the colonies die.  Add the two pathogens together, and we get rapid and severe losses.  

Problem is, USDA denies existence of one of the viruses we employ, despite Camazine having found it in US varroa as far back as the Canadian/NE US colony collapses in the Peace River area and NY in the 1990s.  We can't get the funding to do the genomic characterization of the subspecies or variant of the DNA virus that the Army lab found, nor to conduct the Nosema/Virus studies at the scale we'd like to really address the issue.  So when we get a summer student, we do another experiment, as we slowly tease this issue apart.

If we are wrong about Nosema + virus and bee losses, not much is lost, except some colonies - and the student gets some research experience.

If we are right, then the bee industry has been dealing with a bee loss factor that hasn't been properly addressed since 2006.  

My bias -  if we keep Nosema under control + good nutrition, our annual losses are low.  Let either Nosema or viral loads get high, our annual colony loss goes up.  Nosema + virus is usually lethal.  We think this could be an interaction of one or more viruses. 

It may not have to be any one specific virus - although we know one virus that is really bad for bees - again, it's the DNA virus that we found, but that USDA says doesn't exist.  

Without funding to get the exact genomics of the DNA variant that we saw in US bees, we have had to use a closely related, but different strains of the virus for  our testing -  strains of the DNA virus that are  found in several other insects and that occur world-wide.  These are generalist viruses in terms of hosts, and their effect can be as bad for bees as for the beetles and moths that are endemic hosts.  Strains of the IIV-6 virus can cause  death by itself in bees, beetles, and moths, and we find that it is even more potent when combined with Nosema.

For more than three years after publishing of the 2010 paper, both Army and we were challenged by critics who claimed  that the US Army used the wrong proteomics data base that there was no DNA virus, these same critics failed to realize that the Army used not one, but multiple microbial databases and that the Army lab used their own, unique, microbial agent identification proteomics analysis software - in other words the ARMY did not use the wrong database, or only one database; and the Army stated this in the original article.

At the time of publication in 2010, the Army software was near the end of a ten year  development period and DoD was conducting round robin tests for several potential clients for licensing of this software (2010).  The DoD software was not available to the critics at that time.  And because Army was negotiating licensing their software, Army knew that their potential clients had access to far more rigorous data and testing than did  any of the critics.  In other words,  the critics could say and do what they wanted, Army was focused on getting the software thoroughly tested, verified, and licensed.

In fact, at the time, some of  the most severe critics were competing with DoD in terms of licensing proteomics identification software to these same instrumentation software and instrumentation manufacturing companies.  One group in particular showed up with a copy of their software in hand, waving a copy of their own paper and press releases aimed at refuting the Army's findings.  Needless to say, these critics did not disclose their conflict of interest; although Army and their  potential client found it to be amusing. 

The good news is that the microbial ID software developed by the Army has now been licensed by DoD for use by the research community, and it is being employed in several labs using state-of-the-art instruments.  Also, Dr. Charles Wick, who lead the Army proteomics software development effort, as well as the development of the IVDS (viral detection) instrument used by the Army, has now published two books on these subjects. 

Following the Army nosema/virus in bee publication in 2010, not only did critics claim that Army used the wrong proteomics data base, but some  critics said they could not find evidence of either the DNA virus or Nosema in three samples data sets that they obtained from the Army.  What these critics did not know is that Army deliberately provided them samples with and without Nosema and with and without the DNA virus.  

The critics saw neither the virus nor the nosema.  In fact, they saw no differences in the samples at all. 

The critics made a very big issue of this in papers and articles- if there was no nosema, then there probably wasn't any DNA virus - both had to be false positives, the Army lab was wrong!  They even published the 'fact' that they didn't see the virus or the nosema.  We believe these negative findings to be a consequence of limitations of their identification software.   

There are two important points to consider:  1) The DNA virus variant that DoD found had not been seen before - as such, Army understood why others might not be able to detect it, especially if they didn't have the same proteomics software.  But the inability of the critics to identify nosema in the samples raised a giant red flag.  The absence of detection of nosema didn't mean that Army was also wrong regarding Nosema.  What the critics did not know, of the samples that DoD provided,  we (at UM and MSU) had verified the presence of Nosema in the samples by PCR and microscopy.  Nosema was definitely in some of those samples.  Army proteomics analysis found it, the critics did not.

If the critics couldn't find any Nosema in any of the samples, it was probably because their software and analysis methods were either too insensitive to detect the nosema (which was actually at a relatively high level in the bee samples) or their approach was incapable of detecting Nosema.  If they couldn't find Nosema, then they really couldn't say that the DNA virus didn't exist in the samples.

2) More specifically, in a series of double blind trials that were being conducted at the time of publication of the Army results (2010)  as part of the software licensing negotiations, the  DoD proteomics software was being tested on mixtures of microbes made up by independent labs.   DOD was able to ID all of the microbes, most to strain level, getting perfect scores. The software most commonly employed by adamant Army critics, when used to analyze these controlled, spiked samples (containing known compositions and amounts of microbial agents), could not identify any of the microbes to strain, completely missed at least one microbe, and misidentified another.  We've documented all of this, and both UM and DoD have full documentation of all methods, findings, and results.  

As you  might imagine,  while critics were saying Army's Proteomics Analysis used the wrong database, the client who ended up licensing the proteomics software from Army, realized that this dispute clearly underscored the need for better proteomics algorithms.  Their independent testing found the clear winner - it was the Army's software.   And that software is now available and is being used outside of Army labs.

Regardless of whether one believes the Army findings of a DNA virus in US bees, we have observed the following about Nosema.  Climate certainly is an issue.  Geographic location may be another - how else to explain Rich Fell finding a complete reversal of seasonality of nosema infection lows and peaks from what we see.  Virulence may be another - Robert Cramer who worked with us on Nosema and viruses suspected different strains of Nosema by area and year, just like human flu.  And if one is only looking for Nosema and does not include tests to determine presence of viruses, viral diversity and viral loads,  our data says one will see big differences in researcher conclusions about whether Nosema does or does not kill bees.  


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