That blogger is interesting. I have never seen his blog before, and although this is all not his field of expertise, he makes a few good points and definitely found the very few reliable sources of information out there. As opposed to the heaps of confusion, irrelevancy and misinformation out there.

But watch out: some remarks are already outdated


http://www.synthesis.cc/2009/04/con...-nonesense.html



Confusion over genetic origin of Mexican "Swine Flu" and assorted press nonesense.

By Rob Carlson on April 28, 2009 9:52 PM | No Comments | No TrackBacks
There appears to be uncertainty over just which genes are in the H1N1 genome now causing illness.

(Update: Must read for anyone interested in the present situation: the CIDRAP Swine Influenza Overview.)

As of the evening of Tuesday, 28 April, CNN is reporting that:

The new virus has genes from North American swine influenza, avian influenza, human influenza and a form of swine influenza normally found in Asia and Europe, said Nancy Cox, chief of the CDC's Influenza Division.

However, today's ProMED mail contained a the following exchange.

From Professor Roger Morris, at Massey University, New Zealand, a whole bunch of really good questions:

For those of us who are involved in international work on influenza epidemiology and control and responding to the many media enquiries, there is a very large information gap in relation to diagnosis and epidemiology of the Mexican influenza. What is known of the genetic structure of this virus? It has been called a swine flu, but no evidence has been put forward to allow this statement to be evaluated. I have received information that it is a reassortant, which has genetic components from 4 different sources, but nothing official has been released on this. Where does it fit phylogenetically? Is there any genetic variation of significance among the isolates investigated? Would this help to explain the difference in severity of disease between Mexico and other countries?

It is also stated that it should be diagnosed by RT-PCR, without clarifying which PCR. I have received information that the standard PCR for H1 does not reliably detect this virus. Is this true? What is an appropriate series of diagnostic steps for samples from suspect cases? Could we have an authoritative statement on these issues from one of the laboratories, which has been working with the virus?

In response, here is Professor Paul Rabadan, of Columbia University College of Physicians and Surgeons, who is digging into the flu genome sequences filed at NCBI and finds that the sequence appears to be solely of swine (swinian?) origin:

In relation to the questions posed by Prof. Morris: My group and I are analyzing the recent sequences from the isolates in Texas and California of swine H1N1 deposited in National Center for Biotechnology Information (NCBI) (A/California/ 04/2009(H1N1), A/California/05/2009(H1N1), A/California/ 06/2009(H1N1), A/California/07/2009(H1N1), A/California/09/2009(H1N1), A/Texas/04/2009(H1N1) and A/Texas/05/2009(H1N1).

The preliminary analysis using all the sequences in public databases (NCBI) suggests that all segments are of swine origin. NA and MP seem related to Asian/European swine and the rest to North American swine (H1N2 and H3N2 swine viruses isolated since 1998). There is also interesting substratification between these groups, suggesting a multiple reassortment.

We are puzzled about sources of information that affirm that the virus is a reassortment of avian, human and swine viruses. It is true that the H3N2 swine virus from 1998 and 1999 is a triple reassortant, but all the related isolates are found since then in swine.

In lay English: the virus is composed of pieces of other viruses found in pigs. While the structure of the genome is curious, in that it appears the different viruses exchanged chromosomes multiple times, there isn't any sign that the present genome of concern contains elements of avian or human flu viruses.

(Update: I just stumbled over a 21 April CDC briefing that describes the genomes of H1N1 viruses in pediatric cases in California as entirely of swine origin.)

So it isn't at all clear why the press (and government officials) keep repeating the assertion that the new virus is some sort of amazing Frankenstein strain. The message containing Professor Rabadan's comments also notes that a mess of new sequences from clinical isolates were filed today in the GISAID database. Analysis of those sequences should help clarify the origin -- or at least the composition of the genome -- of the virus in the coming days.

The press also continues to bray about flies as the vector, when there is no evidence I can find in any literature, anywhere, that suggests flies have ever been associated with transmitting the flu. If this particular bug did figure out how to hitch a ride of flies, that would be some seriously scary evolutionary juju. Intelligent design, even. We would all be in deep trouble. But, as there is no evidence to support these assertions other than repeating what other reporters are saying, my recommendation to all you in the press would be simply this: STOP.

Similarly, the notion that at this early date anyone could possibly have identified the index case ("Patient 0") as a young boy in some village in Mexico is -- let me choose my words very carefully here -- COMPLETE PIGSHIT. With so little molecular forensics done on the virus, and no real map of who is actually sick, who has been sick, nor when or where they were sick, publishing the name of an innocent four-year old boy based on cribbing from some other reporter's story is the height of irresponsible journalism. Where the **** are the editors?

(Update: The New York Times is still repeating this nonesense: "...The Mexican government has identified a young boy as the first person in the country infected with swine flu...". Waaay down in the story it acknowledges that the village the boy is from "may not, in the end, be found to be the source of anything" and then goes on to describe earlier potential cases. Oy.)

Perhaps reporters should try a little, oh, I don't know, reporting. Visit ProMED mail. Check out CIDRAP and Effect Measure. Stop reading what other reporters write, and think for yourseves. We will all be better off. 

OT... but wasn't there a study we discussed here (maybe Japanese) showing that flies COULD carry influenza virus on their legs?

Found it...
http://www.curevents.com/vb/showthread.php?t=17242


MomCares 

From Helen Branswell's Twitter...

genetic sequences for NZ isolates in GISAID database 

That link goes to a thread without an article but a link to agonist.

We discussed that fly (non stinging house flies) nonsense issue before here: there simply is ZERO evidence and ZERO in articles that ever showed that flies transmitt influenza (it is extremely unlikely anyway). 

Oooops... maybe I linked to the wrong thread... I was thinking of this one about the Blowfly research from Japan... I have no idea if it's possible for flies to spread flu, I just remembered having seen mention of the research some years ago.

http://www.curevents.com/vb/showthr...light=Blowflies


Am J Trop Med Hyg. 2006 Aug;75(2):327-332.

DETECTION AND ISOLATION OF HIGHLY PATHOGENIC H5N1 AVIAN INFLUENZA A VIRUSES FROM BLOW FLIES COLLECTED IN THE VICINITY OF AN INFECTED POULTRY FARM IN KYOTO, JAPAN, 2004.

Sawabe K, Hoshino K, Isawa H, Sasaki T, Hayashi T, Tsuda Y, Kurahashi H, Tanabayashi K, Hotta A, Saito T, Yamada A, Kobayashi M.

Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan; Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan; Department of Virology III, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan.

During the outbreak of highly pathogenic avian influenza that occurred in Tamba Town, Kyoto Prefecture in 2004, a total of 926 flies were collected from six sites within a radius of 2.3 km from the poultry farm. The H5 influenza A virus genes were detected from the intestinal organs, crop, and gut of the two blow fly species, Calliphora nigribarbis and Aldrichina grahami, by reverse transcription-polymerase chain reaction for the matrix protein (M) and hemagglutinin (HA) genes. The HA gene encoding multiple basic amino acids at the HA cleavage site indicated that this virus is a highly pathogenic strain. Based on the full-length sequences of the M, HA, and neuraminidase (NA) segments of virus isolates through embryonated chicken eggs, the virus from C. nigribarbis (A/blow fly/Kyoto/93/2004) was characterized as H5N1 subtype influenza A virus and shown to have > 99.9% identities in all three RNA segments to a strain from chickens (A/chicken/Kyoto/3/2004) and crows (A/crows/Kyoto/53/2004) derived during this outbreak period in Kyoto in 2004. Our results suggest it is possible that blow flies could become a mechanical transmitter of H5N1 influenza virus.

PMID: 16896143 [PubMed - as supplied by publisher] 

I remember that one. They found it in the intestines of blow fly. So? Still they are only speculating of possible transmission, as it has not been shown to infect anything or anyone with flu. There were plenty of stupid fly speculation threads here, in my view a total non issue.

Unless people have a hobby of fly inhalation, they have much bigger problems in this possible pandemic. You know that proven big fat sneezing coughing carrier who sheds thousands of virii very efficient: humans. 

The more you think you know which data is reliable, the more conflicting data you find from reliable sources.

ProMed reports the OP article from Highflyer then goes on to post 3 entries repeating the human/avian/pig/pig assortment. [correction: reports on a source within the OP article]

Dr Niman still posts that the 1918 virus was a swine human reassortment while most current literature reports it was a direct avian mutation.

It's bad enough almost every news account has some bad information, but when the information is this inconsistent from presumably reliable sources, that makes it very hard to have confidence in one's own assessment of which facts are most accurate. 

Highflyer --

FWIW, it's my impression that most of the current discussion about whether flies could be any sort of vector does NOT relate to whether one could currently get swine flu from a fly, but rather whether reported swarms of flies near a huge pig factory-farm in Mexico could have played any role in initially spreading virus in the small town of La Gloria.

Btw... I totally agree that there have been some wildly speculative threads here over the years.


MomCares 

The flies are likely a red herring. The pig farm, not so much.

The local people focused on the flies but those same people are untrained observers. People have a tendency to draw conclusions that make sense to them, but which often bear no resemblance to reality.

This is a topic I am as familiar with as I am with infectious disease epidemiology. My other forum life and hobby is on the JREF skeptic's forum which promotes critical thinking skills. I think some of the CurEvents forum community would enjoy the JREF group. But I digress.

The point is, one would expect the local population faced with a new threat (to them a mysterious disease) to look for answers and the pig farms are dirty, smelly, and not 'one of them' so to speak. That's an obvious target to blame. It makes sense then that knowing flies spread other disease, the public would latch on to the flies as an explanation for the 'mystery' disease that infected the town.

But I would bet if you visited La Gloria you'd find lots of human-pig interfacing. People from the town must work there. The kids may play there. All sorts of pollution issues are associated with large pig farms in terms of concentrated animal waste. Mexico is not big on following worker or food safety rules. Corruption is rampant and ingrained in their way of life. I remember being taken aback by someone cutting in line in a travel agent's office. I mean, in the market in the line for toilet paper there was a shortage of, sure. But in an office where people were nicely dressed and at least middle class if not better off?

The officials at CDC, and the experts such as the ProMed moderator are refusing to suggest the pig farm as the location of the reassortment event because of the ignorance that follows of people being afraid to eat pork. I can understand their position and who cares if they don't make public what they are investigating until there is actual evidence. But my bet is going on a reassortment event on the pig farm and direct transmission to farm workers who then brought it home to their families.

That's where the current evidence points. Pig farm workers are known to have antibodies to swine flu viruses just as poultry workers often have various avian flu virus antibodies. It makes sense then, that with a new reassortment a farm worker with related therefore partial immunity (from previous infection with a related strain) would have a mild case of the new Mexican swine flu. But a child in that household with little influenza immunity let alone immunity to a new strain would not be so lucky.

From there the infected child plays with other kids and the fire is lit.

I don't expect this information to be made public by investigators until it is confirmed. But I would wager that within a couple weeks, we hear about the antibodies or the virus being found in the La Gloria pigs.


Edited to add: Rather than the identified patient zero, Edgar Martinez, the 5yr old from La Gloria, being the real pt. zero, the infection probably smoldered a while in La Gloria beforehand.

Attention turns to La Gloria in search to determine swine flu source

From Édgar, 5, Coughs Heard Round the World

Mexican Officials Hope Early Swine Flu Case Can Yield Clues 

??? What OP article??


By the way momcares, I do not talk about any current articles about the swine flu in any combination with flies, for heavens sake. The blogger mentioned some fly issues and you started talking about it in a general way. Had nothing to do with swine flu for you or me - no idea what the blogger meant as I just read it very fast. So stop twisting and turning a non issue. 

Skeptigal -- totally agreed. I only remembered the fly research wrt the comment about no fly research in the OP and thought I'd mention it, but perhaps it's taken the thread needlessly OT.

Back to our regularly-scheduled "Genetic origin of Mexican "Swine Flu"" topic... 

The blog you cited.

Here's the ProMed related story:
ProMed, 04/29/09

From the blog's link to CIDRAP:

Swine Influenza in Humans: 2009 Situation


The blog you linked to refers to Professor Rabadan's letter to ProMed. 

Translated for clarity: You are a nurse (or nurse practioner?) by your own saying long ago. With some infectious disease / hygiene specialisation.
That is good, this board needs all and any expertise. 

ARNP, FNP, COHN-S, CIC.

That is nurse practitioner, certified in occupational health and infection control.

I've had a private practice in occupational infectious disease for 19 years now.

Thanks for the (re)welcome.  

Here are the URLs for items talking about bird/human/swine reassortments:

http://www.promedmail.org/pls/otn/f...L_ID:1000,77207

http://www.cidrap.umn.edu/cidrap/co...09swineflu.html

http://www.cidrap.umn.edu/cidrap/co...r2109swine.html

http://www.msnbc.msn.com/id/30386163/ 

http://www.promedmail.org/pls/otn/f...L_ID:1000,77265

 

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