Another swine flu virus

There is an old vaudeville joke where a man goes to the doctor complaining about pain in his arm:

Doctor: Have you ever had it before?
Man: Yes, once before.
Doctor: Well, you have it again.

CDC reported on their weekly FluView website on Friday that the Iowa Department of Public Health (IDPH) reported to CDC that in September a boy (age not stated) had a flu like illness from which he fully recovered and for which he hadn't required hospitalization. In November IDPH determined it was swine flu, but not the pandemic H1N1 but a swine-origin H3N2. According to CDC there was "no clear exposure" to swine, nor was there any evidence of sustained transmission. I checked the IDPH website and couldn't find any mention of this case so this is all the information we have. It sounds like CDC doesn't have much information, either. Ace flu reporter Helen Branswell was only able to get this out of CDC spokesperson, Tom Skinner:

He said the fact that the investigation turned up no other cases and that some time has since elapsed suggests there isn't any ongoing spread. "I think if there was other transmission going on associated with this case we would have picked it up and we haven't." (Helen Branswell, Canadian Press; hat tip Mike Coston at Avian Flu Diary and Crof at H5N1))

Well, maybe. This wasn't caught by the CDC NREVSS virologic surveillance system and was only noticed 2 months after the fact by public health officials in Iowa. We don't know exactly what IDPH and/or CDC did as a follow-up investigation, but the old saw "absence of evidence is not evidence of absence" springs immediately to mind. If this child really had no exposure to pigs (the phrase "no clear evidence" is ambiguous), then there was an intermediary host or vector between the pigs and the case.

Like the pandemic swine H1N1, which has a seasonal counterpart H1N1, this swine-origin H3N2 has a seasonal H3N2 counterpart. The big question for me is how transmissible is this virus? Lack of further documented cases isn't very persuasive when it sounds like they haven't been able to look very easily and the original case was not picked up by the virologic surveillance system. More details on how this was discovered would be useful. Let's suppose, though, that this virus did dead end in the child, that is, that there was no onward transmission to others. If it didn't come from a pig, where did it come from and how easily did this boy get infected? September was when pandemic H1N1 was being actively transmitted and circulating in the community, so one wonders what would have happened if this swine H3N2 had appeared 6 months earlier, in virgin soil, without any competition from H1N1. We still don't understand the mechanism whereby one subtype "crowds out" another, but we know it doesn't always happen. Is this one just hanging around out there at low levels, waiting for the right conditions to come out of hiding? Unfortunately we can't tell from the genetic analysis whether this, or any, flu virus is easily transmissible.

More generally, this is just another reason for urgent investment in human and animal surveillance for influenza and other zoonotic diseases (a zoonotic disease is one humans get from animals). Pigs and birds are natural reservoirs for influenza virus, but we haven't looked very hard in other species, especially livestock.

Maybe this is just another of the sporadic swine to human cases that have been reported in recent years. Of them, H1N1 swine flu is the only one that seems to have gotten a foothold in the population. It's hard to imagine it's the only one capable of it, though, and since we understand very little of what allows easy transmissibility, surveillance is our only early warning recourse.

More like this

As far as swine go, I do believe that Iowa is teh capital thereof. I had the disgusting experience of driving through Iowa during the spring thaw, in 1973. The stench has to be experienced to be believed. A boy (anyone, really) could be exposed to the virus unknowingly- those pigs are EVERYWHERE. The person who infected him might have had it, but with less severe symptoms due to being around the pigs all the time.

any H3N2 must come from humans >1968 probably >1990
and we should have some immunity.
And currently it's being outcrowded anyway

Interesting development indeed Revere, everyone has blamed Mexico and/or China, but I conjecture the real culprit is Giant US agribusiness interests shoving improperly tested viral or bacterial based genetically modified products eg. GM corn onto US/Canadian/Mexican farming soil for over a decade. As you already know, I'm a persistant freelance research analyst involved in healthcare (see edited email leter sent on Xmas day to Terry Redman, Western Australia's agriculture minister)

"[Dear agriculture minister] I'm writing to say, "All I want for Christmas is a GM free WA"! I'm hoping WA state government decides to make the sensible choice and not allow the commercial growing of GM canola in 2010...

I'm not a trained virologist and/or epidemiologist but I do have a basic understanding of both these disciplines as well as other health matters. The unstable nature and effects of genetically modified food vis a vis the recent -- and it is -- emergence of transgenic viruses such as SARS, swine H1N1/2009 and avian H5N1 influenzas, for example...

Many folk, who comprehended the unstable technology of genetically modified organisms in the 1990s (including myself), are not exactly surprised by the recent evolution of swine and avian influenza. The viral or bacterial based technology used to splice many different genes together in a modified crop seed line which will grow when planted has been proven unstable by scientists.

For me, the "backstory" to swine flu"begins with the underreported evolutionary tragedy (and it is) of accelerated "horizontal gene transfer and homologous recombination" arrising from the 1990s to present American agribusiness release of unstable genetically modified organisms (GMOs) within the global environment.

I discussed this theory further with a sceptic in recent reader postings @ Crof's H5N1 Blog -- Offline again (June 22, 2009)

The horror-story probability of a high pathogenic transgenic zoonotic virus -- a cross-species disease easily moving back and forth between different species -- is what propelled me into this study-work in the first place. Pandemic swine flu is such a disease, currently in a state of internal genetic evolutionand mutation [eg. Ukraine-style Eastern European changes to the original antigenic clades used as vaccine templates by world manufacturers ie. A/Mexico/4108/2009 E1, A/California/4/2009(H1N1)swl, A/California/7/2009(H1N1)swl, and A/California/08/2009 E2].

For an understanding of the scope of this scenario -- a scenario still yet to be explained in a sensible and logical fashion by authorities -- refer to the recent Institute of Medicine and National Research Councilâs 2009 report "Sustaining Global Surveillance and Response to Emerging Zoonotic Diseases". And also see Recombinomics Commentary 03:38, "Lab Confirmed H1N1 in New York Dog" December 22, 2009.

In 2006, I got off my ass and contacted the UK Department of Health for simple answers. I then received a written acknowledgement of a "possible link between genetically modified food and avian flu":

Date: Friday, March 10, 2006

Our ref: TO00000073916
10 March 2006

Dear Mr Singleton,

Thank you for your email of 5 January to the Home Office about avian flu. As this is a health related matter, your email has been passed to the Department of Health for response. I have been asked to reply.

With regard to a possible link between genetically modified food and avian flu, may I suggest that you address your concerns to the Food Standards Agency as they are best placed to comment on this matter...

I hope the above information has been helpful and thank you again for writing.

Yours sincerely,

Hazel Mendonca
Customer Service Directorate
[UK] Department of Health

By Jonathon Singleton (not verified) on 18 Jan 2010 #permalink

Wow, jonathan s. Regardless of the validity or otherwise of your theory, that reply was purest bullshit.

Shorter beaurocratese:
Your question has been passed to us as most appropriate to answer. Our answer is you should ask someone else.


Up here in Quebec we now have few H3N2 Perth version.


BTW, Last week on the radio show, I just heard the beginning of your answer on my question about where we should invest in priority considering the psychological, physical and economical contexts.

Seems your answered has created a technical problem at the radio station, lol

I you could summary-se it would be appreciated.

Again Thank you


By Snowy Owl (not verified) on 18 Jan 2010 #permalink

The GM reference is pure speculation and, in my professional opinion, an unlikely source of swine virus. However, 'giant agribusiness' does indeed have a hand in the spread of swine influenza to susceptible humans in Iowa and other states, through manure spreading operations that can and do contaminate soils water (surface and groundwater) supply; distribution by fine dust is also quite possible, although demonstrated for HPAI (BC Canada case a few years ago), wind carriage of contaminated barn bedding from a poultry farm.

Absolutely not surprised to read of this case, if you know 'the rest of the story'. This virus probably doesn't have the SNPs necessary to sustain spread (HTH contact).

It's a cautionary tale that deserves mention and discussion.

The swine flu is possibly "the mildest pandemic on record" ( news about swine flu)

I live in Iowa. Always have.

In the old days, when I was a kid ('73 time frame) Spring was the time of two things.

1. The Spring Thaw and
2. Preparation for planting

The thaw often activated the thermally "dormant" bacteria which kicked up the smell factor a notch or two. Winter was no time to spread manure for two reasons. First, the ground was frozen (as was the manure). Precipitation was also frozen so that manure wasn't going anywhere once it was spread on the field. It would just lay on top of the ground when spread onto the farm fields. The purpose of spreading manure is to use the Nitrogen contained within, to fertilize the crops. Though methods vary, it's typical to fertilize prior to planting. So, farmers spread poo in the Spring. The combined thaw and spreading of the fertilizer, caused some smell in the Spring back then. We were used to it and it's only temporary.

As a farm kid....I saw and participated in fertilizing in this manner. It was done with fertilizer spreaders (called "manure spreaders") that literally flung the waste into the air and distributed it somewhat evenly on the ground, where it laid for days, until it broke down and was eventually incorporated into the soil by rain. In heavy rains, the poo could be carried to nearly streams by runoff.

Furthermore, livestock lots (or in particular, hog lots) weren't cleaned very often. It's hard work and it has to be done prior to planting or right after harvest. So the manure buildup would often run off into streams, ditches, whatever.

Todays "commercial" livestock producers have done nothing to help the small family farmer. But I do think they've done much to help clean the environment. Modern hog facilities contain the manure in well designed cement holding pits until it's ready to be pumped out. And then it's applied to the farming soil by being "knifed in" or incorporated directly into the soil. Rarely is it laid on top and exposed to runoff. Do some Nitrates leech into ground water? Probably yes, but the runoff of higher concentrations is much less than the old days because it's knifed directly into the soil at precise levels optimized for fertilizing.

So.......where am I going with all this? I could go on and on about disease containment as well. I've come a long way around, but basically, I'm trying to say that corporate farmers (or large family farms) today are doing a much better job of containing disease (and dealing with manure) than they EVER did in the past.

Large confinements may indeed make huge mixing vessels for disease (although it wasn't much different than hog houses on the family farm). But those confinements are also contained and fairly well quarantined from other confinements.

I live here. I see it. And I smell it. I don't "drive through" and profess to know it.

To: "India's Environment Minister, Jairam Ramesh"

To: "Food Standards Australia New Zealand (FSANZ)"

Monday, January 25, 2010


Recently I referenced on EM, a major US science and public health blog, an edited email leter sent by me on Xmas day to Terry Redman, Western Australia's agriculture minister... The subject was (and is) the health and safety issues related to the unstable technology of genetically modified organisms (GM crops and food) released into the environment.

I've reached a point, quite frankly, where I am beyond caring about my own existence vis a vis the activities I enact in attempting to communicate with Australian government agencies "bitched" by corporate interests. My life has, over the last decade, degenerated into a very violent parody of "shoot the questioner/messenger". The system itself is at fault, not clever and questioning citizens, violently abused by state and federal government agencies for the "crime" of intuiting, researching and then analyzing information and joining the final dots -- "dots" such as transgenic zoonotic pathogens like pandemic swine flu and bird flu...

Indeed, it is beyond strange that the government agency, FSANZ, carries out GM food safety assessments on a case-by-case basis when it is obvious to anyone who has been involved with this issue for the past decade, the unstable technology itself is questionable. FSANZ are behaving somewhat oddly, as if the cigarette were not dangerous and the many smoking tobacco products sold ought to be reviewed on a case by case basis:*(

What is worse, FSANZ believe "it is the responsibility of companies that have developed GM foods to demonstrate the safety of that food and to supply FSANZ with the raw data from scientific studies to prove this..." Again, the methodology is odd, when it is routine for companies to manipulate and censor data contained in "scientific studies" (see linked ISIS reports, below).

Getting back to reader posting #3 by: Jonathon Singleton | January 18, 2010 on EM blog. I received several anonymous responses to my posting. One from a chap called Eddie who found it incredibly hilarious a question to the UK Department of Health re: GM food and bird flu connection, resulted in me being shunted off to the British version of FSANZ (who utilize science data from GM crop/food producers, also:*) The other anonymous response was a "professional" believing "the GM reference is pure speculation and an unlikely source [or contributing factor to the recent evolution] of swine virus..."

The response from the professional was odd given at least two different research teams have confirmed that the CaMV 35S promoter (used in the majority of GM crops/food) is currently active in animal and human cells and can enhance horizontal gene transfer and recombination -- the evolutionary paradigm most likely at work in the genesis of new viral and bacterial pathogens ie. pandemic swine flu (see research in European food Research and Technology 2006, 222, 185-93 and Environ Biosafety Res 2004, 3, 91-7. linked below in ISIS Report 15/06/09).

So, these are the days of our lives where government agencies behave like Monty Python parodies -- I can see John Cleese performing the role now, "No, your parent died of cancer, which has absolutely nothing to do with the carcinogenic effects of smoking tobacco. Now please go away so I can dream about saving up and buying a new four wheel drive and yet another investment property."

Cheers Then -- Jonathon Singleton

ISIS Report 15/06/09 -- "New Evidence Links CaMV 35S Promoter to HIV Transcription"

ISIS Report 13/07/06 -- "GM Egg Plant [Brinjal] Contains Bt Toxin Linked to Hundreds of Allergy Cases and Thousands of Sheep Deaths"

By Jonathon Singleton (not verified) on 24 Jan 2010 #permalink