Saturday, December 25, 2010

The (Swine) Influenza Reassortment Puzzle



# 5177



cafo puzzle



With this week’s release of Helen Branswell’s SciAm article called Flu Factories (see Branswell: Podcast On Flu Factories) and a small (but potentially important) change to the CDC’s webpage on recent SOIV (Swine Origin Influenza Viruses) cases, influenza reassortment in pigs is bound to be a hot topic over the next few days.


First, the change to the CDC’s webpage (and for spotting this, a big hat tip goes to IronOreHopper):


Reported Human Infections with Swine Origin Influenza Viruses (SOIV) in the United States since 2005

As of December 17, 2010, 19 cases of human infection with swine origin influenza viruses (SOIV) have been reported in the United States. These are viruses that normally infect pigs. Like human influenza viruses, there are different subtypes and strains of swine origin influenza viruses. The main swine viruses circulating in U.S. pigs in recent years are swine triple reassortant (tr) H1N1 influenza virus, trH3N2 virus and trH1N2 virus.


Of the 19 human cases reported since 2005, 12 have been trH1N1 viruses, six have been trH3N2 viruses and one has been a trH1N2 virus. All 19 persons infected with swine viruses recovered from their illness. Twelve cases occurred in children (persons younger than 19) and 7 cases occurred in adults. In 15 cases, exposure to swine has been identified.


Although no person-to-person transmission of swine influenza viruses has been laboratory confirmed in the investigation of these cases to date, some cases reported only exposure to ill persons and no exposure to live pigs.  Thus, limited person-to-person is likely to have occurred.


The section in red was added sometime over the past few days, replacing `No person-to-person transmission of these viruses has been documented in the investigation of these cases to date.


Before anyone starts heading down to the bunker, let me state that this change wasn’t completely unexpected, nor is it particularly alarming.


We were already aware that there were some cases with no apparent exposure to pigs, and that the CDC was continuing to investigate how these people may have acquired the virus.


As I said, I find none of this particularly alarming.  But it is, I believe, worthy of perhaps a modicum of concern.


As I’ve pointed out before (including here and here) we occasionally will see a novel swine influenza virus jump to humans. Although the 2009 swine flu pandemic was an exception, most of the time this turns out to be a one-off dead-end transmission, and goes no further. 


The key phrase being `most of the time’.


Since only a tiny fraction of influenza flu viruses are ever sequenced, we really don’t know how often these types of novel infections occur.


It’s probably more often than we think.


But surveillance systems must be incredibly lucky, or wait until a novel virus has made sufficient inroads into the population, before they are apt to start picking up cases.


The 2009 Swine flu epidemic was undoubtedly spreading stealthily in humans for several months before the folks at the Naval Health Research Center (NHRC) in San Diego first isolated the strain on April 16th of last year.


By then, thousands had been infected.  


It is likely that limited transmission of novel influenza reassortments occur with some frequency, all over the world.  But only rarely are these novel viruses `biologically fit’ enough to compete with fully human adapted strains.


So most turn out to be evolutionary dead-ends, die out of their own accord, and are never detected.   We don’t hear about them, so we don’t tend to worry about them.  


But each novel virus that jumps to a human host is another opportunity for the virus to adapt to human physiology.  And as 2009 showed us, once that happens, a virus can spread around the world in a matter of months.


If you’ve not already read Helen Branswell’s excellent article on Flu Factories, or listened to the SciAm Podcast, I would invite you to do so.


When you return, I’ll have more.


Over the past 5 years, we’ve revisited the subject of influenza reassortment dozens of times.   Just a few recent examples include:


Virology Journal: Receptor Cells In Minor Poultry Species
mBio: A/H1N1 Potential For Mutation
Study: The Continuing Evolution Of Avian H9N2
EID Journal: Co-Infection By Influenza Strains
EID Journal: Swine Flu Reassortants In Pigs
If You’ve Seen One Triple Reassortant Swine Flu Virus . . .


Influenza viruses change, evolve, or mutate over time via two well established routes; Antigenic drift and Antigenic Shift (reassortment).


Antigenic drift causes small, incremental changes in the virus over time.   Drift is the standard evolutionary process of influenza viruses, and often come about due to replication errors that are common with single-strand RNA viruses.


Shift occurs when one virus swap out chunks of their genetic code with gene segments from another virus.  This is known as reassortment. While far less common than drift, shift can produce abrupt, dramatic, and sometimes pandemic inducing changes to the virus.


For shift to happen, a host (human, swine, bird) must be infected by two influenza viruses at the same time.  While that is relatively rare, as any virologist will tell you . . . Shift happens.



mixing vessel


Although avian influenzas had captured the headlines up until a couple of years ago, since the outbreak of pandemic H1N1 in 2009 - which circulated under-the-radar in pigs for about 10 years – scientists are looking at pigs, and swine influenzas with keener interest today.



Source: FAO


With global pig production growing rapidly to meet the demands of a hungry world, each year we add millions more `mixing vessels’ to natures laboratory.   And the bulk of the predicted growth in hog farming is expected in developing countries.


While limited viral surveillance in pig farms may be found in some parts of the developed world - for much of the globe - that simply doesn’t happen.


Unfortunately, some hog farmers here in the US are  reluctant to allow their herds to be tested (see Swine Flu: Don’t Test, Don’t Tell) out of fears that the discovery of a new swine flu virus would depress pork sales.


Some will only consent to anonymous testing, which limits the CDC’s ability to investigate cases.




Diseases that might never have caught fire fifty years ago - when Old McDonald had a half dozen sows on his farm -  have a far better opportunity to spread and mutate when introduced into a CAFO (Concentrated Animal Feeding Operation) with thousands of pigs or hundreds of thousands of chickens.



Photo Credit (Wikipedia)


For more perspective on this, you might wish to read Dr. Michael Greger’s Bird Flu: A Virus Of Our Own Hatching (available free, online) and watch his Humane Society video on Flu Factories (online here).



And for even more background, you might want to check out David Brown’s terrific piece in the Washington Post from October of 2009.



Back where virus started, new scrutiny of pig farming

By David Brown

Washington Post Staff Writer
Sunday, October 25, 2009



As you can see, concern over reassortment in pigs (and other hosts) is hardly new, although we are learning more about the threat’s potential with each passing day. 


And the change in the CDC’s SOIV webpage indicating that `limited person-to-person is likely to have occurred’ isn’t really a surprise.


It basically just confirms what many observers have assumed all along.


The reality is, Nature’s laboratory is open 24/7, and it performs billions of random genetic experiments each day.   As the supply of `test animals’ increases, so do the opportunities for a new virus to emerge.


Another pandemic is all but inevitable.  It could start tomorrow, or it might not happen for decades.


Which is why we need better viral surveillance, both among the human population, and on the farm.



It is, after all, to our advantage to detect any emerging virus as early as possible. 


That may allow us to contain or slow its spread using antivirals and other methods, and that would hopefully buy us precious time to develop, manufacture, and distribute a protective vaccine.


Because - while the 2009 H1N1 virus turned out to be a less virulent strain than first feared - the next time . . . we may not be nearly so lucky.