The evolving Swine Flu story

This afternoon CDC held a "media availability" on the evolving swine flu cases. Evolving is an understatement. There are now more recognized cases, although not all cases are "new," with some cases retrospectively recognized now that more intense investigation is occurring. The total is now seven cases. Two occurred in San Antonio, Texas, two sixteen year old boys in the same school. Three more were found in California (in addition to the initial two cases), including a father - daughter pair. All California cases are in San Diego and neighboring Imperial counties, the location of the initial cases. Those counties are also where there has been the most intense looking. CDC expects more cases to be recognized with the ramped up index of suspicion. They promise to update the situation daily at 3 pm on its website. None of the cases gives a history of contact with pigs, so together with the two "doubles" (the schoolmates and family pair), this strongly suggests active person to person spread. Moreover, the initial two viruses have been completely sequenced and are very similar. Partial information on some of the additional viruses from California are also similar, which reinforces the idea that the virus is in active circulation. How widely we don't yet know. But this isn't all the news.

It turns out this virus is highly unusual, a quadruple reassortant. The genes of a flu virus are packaged in eight discrete segments. When two flu viruses infect the same host cell, the segments of each are copied and repackaged, 8 at a time, in new viral particles which then bud off from the infected cell. They then may infect a new host cell. In this repackaging process the segments of the two different viruses may mix and match, so that new virus particle will have segments from two different viruses. The new virus is, in a sense, not just a swine flu virus. It does have viral segments characteristic of two different families of swine flu, one typical of North America, where swine flu is endemic, and one typical of pig flu viruses from Europe and Asia. But we learned today that it also has viral segments seen in North American birds and in human seasonal influenza. Which of the segments is a bird segment and which is humans wasn't discussed in today's briefing, but the fact that the genetic sources comprise widely different geographies and species is highly unusual -- unusual at least as far as we know. We have little systematic information on swine viruses, so how common this really is we don't know for sure, nor do we know how recent. The virus is resistant to the older adamantane antivirals but sensitive to both oseltamivir (Tamilfu) and zanamivir (Relenza).

Whatever this is, it isn't seasonal influenza. The reported cases range from 9 years old to 54 years old, 3 females, 4 males. All have recovered and only one required hospitalization. The earliest case is from late March, the most recent just days ago. Symptoms are typical for influenza-like illness except that there seems to be a greater prominence of gastrointestinal symptoms (nausea, vomiting, diarrhea) along with the respiratory symptoms and fever. CDC emphasized they were in an active investigation mode and will keep sharing information as it develops. Clearly there is a lot more to learn about this.

Could this be the harbinger of an influenza pandemic? A pandemic is a global sized outbreak from a single strain of influenza. We believe that there are several necessary conditions for this to happen with influenza. One is the ability of the viral strain to infect humans (there are many influenza viruses but most don't infect humans). Another is the ability to be transmitted from person to person. While bird flu can infect humans, it still has not acquired the ability to spread easily from person to person. Yet another is an influenza virus which is sufficiently different that there is little natural immunity in the human population. As far as I can tell, this virus seems to have all of these characteristics. The most important part, though, is what the virulence of the virus is. Virulence doesn't refer to the ability to cause disease, but the ability to cause severe disease it does cause. We don't yet know how virulent infections with this virus are because there aren't enough cases to make that judgment. But if most cases are relatively mild, like all so far reported, then even if this becomes a pandemic it isn't the kind of global catastrophe that would ensue if H5N1 became pandemic at any where near its current virulence (H5N1 has a case fatality ratio in excess of 60%, versus a case fatality ratio, so far, of 0% for this virus). When asked if this event is causing any change in pandemic warning levels, CDC said it was not.

Finally, reports have been circulating of severe respiratory disease in central and southern Mexico. A question was asked at the briefing whether these two events might be related. CDC could only say that they were in contact with their counterparts in Mexico and at the Pan American Health Organization (PAHO, the WHO regional entity). In other words, CDC left the door open to the possibility, although they seemed to have no specific information one way or the other.

That's what we know at this point. We can all continue to follow it through CDC's daily updates on their website.

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Susan: One of the two Calif. cases traveled to Dallas but the Texas cases were in San Antonio and there was no apparent link. That's the only travel we know about at this point, but they are working hard on this and this is only interim info. It's also true that the surveillance at the border is more intense. So we may find out this virus is all over. Or not.

One possible outcome is that this event puts an end to the apathy towards the threat from novel influenza viruses.

Thanks for the summary, the CDC website was not up earlier today. CDC does seem to be taking this seriously, is this more than just an opportunity to test drive the pandemic flu plan?

What I want to know is whether, should this swine flu (or any other similar virus) become the new pandemic, there is any reason to believe H5N1 will necessarily NOT go pandemic as well? Isn't it possible if a milder flu goes pandemic that it could co-infect one or more people in Egypt or Indo or China that happened to have H5N1 at the same time, and then have another reassortment event that conferred some of the H5N1's lethality onto the swine flu's transmissability?? There's that, or the other possibility which is that we could have two different pandemic viruses going at the same time? As far as I can see, one does not preclude the other, and if one strain has any effect on the pandemic potential of the other it would be to increase it, not negate it.

By mary in hawaii (not verified) on 23 Apr 2009 #permalink

Hi Mary,

Regarding the potential for a H5N1 to go pandemic. The guidance from OIE and WHO remains the same. H5N1 remains mainly an animal disease with an occasional zoonotic potential (i.e. occasionally is able to pass on to human). All data to date indicates that the infectious dose for humans is high requiring relativelly intimate contact between humans and infected animals. There are very very few cases described of human to human transmission and even this was associated with intimate contact. On top of that you have to remember that there is now a worldwide focus on the control and eradication of this disease which is starting to give results reducing incidence in poultry. Obviously there is little we can do control the circulation of the virus in wildlife but as long as we are able to keep there, then there is litle potential for re-assortment of the virus with other starins more adapted to in fect mammals and particularly Humans. So my bottom line is: no, I honestly do not think that these new cases do not increase significantly the risks associated with H5N1. If anything it lowers it as the biggest problem with Influenza virus so far has been when multiple strains are allowed to circulate simultaneusly in silently in susceptible animal populations. If awareness is increased it will not circulate silently.

Hi Revere,

bumped to this blog by accident, excelent work, will definatly become regular visitor. Regarding your comments about the virulence of this particular recombinant strain, they are all fair. I would add that considering what has happened so far my bet is that the lab will confirm that it is a strain of low virulence. Let us not forget that children as young as 9 years old have been affected with only mild symptoms. Young children are a naturally imunossupressed segment of the population and should be particularly vulnerable. Do you have any information about coordinated action between CDC and veterinary authorities in California (or any other state for that matter) about this outbreak?


By Lowlander (not verified) on 23 Apr 2009 #permalink

Also MSM are starting to connect the dots between Mexico, So Cal, Texas and Canada.

@Mary - yes, if the new swine H1N1 goes pandemic and goes around the world, the interaction between it and H5N1 in Egypt or Indonesia can potentially produce something more transmissible than current H5N1 but not necessarily less lethal. CDC analysis shows that the novel swine H1N1 has already exchanged bits of its genetic code with an avian virus, and it can do it again.

maybe it's only single reassortant and the avian and human segments are just what the American swine acquired earlier in ~1998 ? Typical American Swine H1N1 had avian,human
segments the last years

Is there any possibility that this new swine flu is the result of laboratory manipulation? In other words, could this be a terrorist or criminal attack?

Based on conversations with neighbors and folks at the coffee shop, there is something going around that is affecting children and adults...the symptoms reported match those linked to the swine flu reports. Some adults insist they have had a bad case of food poisoning but it sounds like swine flu. Whatever it is, it seems to be spreading fast. I am in northern California where no cases have been reported, but there are plenty here.

By Sharon Rickard (not verified) on 24 Apr 2009 #permalink

"Is there any possibility that this new swine flu is the result of laboratory manipulation? In other words, could this be a terrorist or criminal attack?"

Extremelly unlikely. Influenza viruses have the natural ability of re-assorting their genomics as they replicate in cells. This a their natural mechanism of survival as it allows the virus to ilude the immune system of the viruses hosts. In a way it is similar to what HIV but through a different process and slower. This is why we are able to produce vaccines against human flu every year and why we have to come up with something new every year too.
Aditionally this virus is not very portable because it is very fragile outside its host which does not make of it a good candidate for bio-weaponry and anyway, because of its natural tendency to change as time goes on is not a "stable weapon", its virulence (i.e. ability to produce serious clinical signs) fluctuates through time as it re-assorts itself.

By Lowlander (not verified) on 24 Apr 2009 #permalink

Would it be feasible to use a pandemic rapid containment plan using tamiflu?

Chris: I think CDC has been pretty good so far. They had an extensive briefing late yesterday. They promise daily updates at a defined time. They may have to increase the frequency as events move forward, but I don't think it's fair to characterize them as a total lack of communication. The link you cite is based on what they said.

Al: Before doing that, we need to know what we are dealing with. Tamiflu blankets are unlikely to work in this situation anyway. There is really no way to bottle up efficiently transmitting flu.

I don't know how long it takes to get results back from the sample testing, but based on the high-level of response so far, can't we assume that the WHO, etc., already know that the Mexican cases are H1N1 and they're just waiting for the sequencing to be completed to see if there's a match to the US swine flu cases? And if there is a match, how concerned should we be?

Hi Chris, I read that WHO policy is to do mass blanket of Tamiflu. Apparently H1N1 is suspectible to tamiflu. I suppose that it depends on the reproductive rate also.

Karen: We should be very concerned...

Hope this swine virus is not the real deal considering the USA has a 80 % stockpile of a useless drug in its arsenal.

Tell me why this was allowed to happen. Sorry I know the answer !! Just ask Glaxo Smith Kline.

"maybe it's only single reassortant and the avian and human segments are just what the American swine acquired earlier in ~1998 ? Typical American Swine H1N1 had avian,human
segments the last years

Posted by: anon | April 24, 2009 6:31 AM"

The trick is this H1N1 has European and Asian swine flu bits, but NOT North American.

Were the victims vaccinated for flu recently or around people who were?

liberty: Neither of the two cases reported on Tuesday by MMWR (the first two) were vaccinated. No info on the rest.

I guess culling is pointless since it's a swine-Avian hybrid from Europe and Asia. I assume tracking the farm (or wild pigs in Mexico?) vector and tracking recent Mexican poultry and/or pig imports is of lesser importance right now. I assume a ban on Mexican birds and hogs is being considered.

When samples are sent to Winnipeg or Atlanta for analysis and results come back in a few days, will the results be specific enough from early cases to say, cases from a week later, to determine conclusively the flu has not further mutated while spreading among humans? Can this be known conclusively that it is all the same general flu blueprint or is the state of knowledge of "sample analysis expression" not that advanced yet?
To be blunt, can we use time-series sample analysis to determine if it is mutating?

By Phillip Huggan (not verified) on 24 Apr 2009 #permalink

Any evidence that there would be partial protection against the swine flu for those who were vaccinated this year due to the n1 component?

My daughter's school in Boston (Wellesley) had some kind of outbreak that had her home a couple of weeks ago.

They cancelled classes.

5 will get you 10 that it's the same virus, as that is an extremely rare event. Anyone know if Harvard cancelled the same week?

I've got a 92 year old Mom who is already in late-stage dementia - I think I'll start thinking of a future without her.

Well, it is natural fact; all must die. Sadness though.

John/Fort Wayne


I may be wrong re Wellesley - I looked for it, it might have been an old post in her blog.

Here's new stuff - from citing a promed source:

[The "swine" influenza A(H1N1) virus associated with current outbreaks of
respiratory illness in the southern region of the USA and in Mexico appears
to be a complex reassortant containing genome components from avian, human,
and swine virus sources. Such a virus is unique and it is too early to
conclude that this virus has originated in swine.

By John Hubertz (not verified) on 25 Apr 2009 #permalink

could you share with us your opinion about the difference in virulence of the swine flu in US ( zero mortality ) vs the mortality of appr. 80 out of 1000 infected case in Mexico. The reassortment seems very complex and could this be a lab. designed bio-weapon. BTY, global pandemic is likely judging from the effective human to human transmission mode. Do you agree?

By Ernest Lee (not verified) on 25 Apr 2009 #permalink

Ernest: Click on Swineflu in the categories in the sidebar or up top under the post title and you'll find numerous posts discussing the virulence difference. Short answer: we don't know.

I think they should seriously think about implementing some more effective ways to contain this from the public.
I read that Mexico may be thinking of a new strategy for containment.

SwineFlu: What you describe is not containment, is what is called non-pharmceutical intervention to manage spead. Containment means locking up the outbreak within a geographci area. That's no longer possible.

I have been trying to find more information from the blogosphere, that routes round MSM and govt. gatekeepers. So far I got a 'cynical left' blogger with anecdotes about how the situation in mexico is much worse than the official line.

Take it with as much salt as you need but I'd appreciate anyone else with access to info not filtered through MSM. Maybe you doctors/biologists have contacts in hospitals/universities in the affected reas?

Salutations Revere,

Via the Canadian Program of Research in Ethics in a Pandemic, CanPrep, I have been immerge by the wave from Mexico and it evque in me the need to focus and act accordingly.

Sorry for the conspiracies, they are too many, I have to Focus on an apparent pandemic virus.

After taking knowledge of Pandemic Preparedness for six years, I aremember.

I remember that my Oath is to reduce morbidity and mortality in a Public Health crisis.

The priority that many agreed tacitely was the continuity of Humanitarian Governance as the First Priority.
I feel secure after the US Declaration today.

Since Security Forces are covered, here comes the First Responders as tacitelly agreed.

Today I manage to get up todate and adapt to the context, an Interim Protocol For First Responders in Preventive and Protective Mesures, I foubd most swift and apparently precise Protocols in the Health Ministry of Alberta, Canada.

Communications enshrine itself and with its Ethics.

WHO release today a pdf doc called
Pandemic influenza preparedness and response
WHO guidance document released Apr 26 2009
at, Keiiji Fukuda is omnipresent in it IMHO.

I post its summary at

Then there was Forecast of Grattan Woodson, 270 millions of deaths.

I had it for awhile and I had to ponder before responding him,
told him I agree that if it is a mild first wave we will have more time to produce pragmatic solutions in an eventual second wave.

DemfromCt does not agree with The Doctor.

In fact there are so many factors and contexts, I step back and remember my priorities.

Snowy Owl an OjibWay Achak

I was following this with interest, but a healthy grain of salt until I read some posts from Mexico on a BBC page.
To quote one; I'm a specialist doctor in respiratory diseases and intensive care at the Mexican National Institute of Health. There is a severe emergency over the swine flu here. More and more patients are being admitted to the intensive care unit. Despite the heroic efforts of all staff (doctors, nurses, specialists, etc) patients continue to inevitably die. The truth is that anti-viral treatments and vaccines are not expected to have any effect, even at high doses. It is a great fear among the staff. The infection risk is very high among the doctors and health staff.

There is a sense of chaos in the other hospitals and we do not know what to do. Staff are starting to leave and many are opting to retire or apply for holidays. The truth is that mortality is even higher than what is being reported by the authorities, at least in the hospital where I work it. It is killing three to four patients daily, and it has been going on for more than three weeks. It is a shame and there is great fear here. Increasingly younger patients aged 20 to 30 years are dying before our helpless eyes and there is great sadness among health professionals here.

The problem with "unfiltered" is that I don't know if the poster is real, a doctor, or even in Mexico.

The problem with "unfiltered" is that I don't know if the poster is real, a doctor, or even in Mexico.

Dave C: Quite, and I read a comment elsewhere (not on a news site; it was a comment on someone's blog post) from someone who claims to live in Mexico City who says it's not nearly as bad as is being reported. As with the one you cite, there's no way to verify what they're saying, but they do point out that there are other forms of flu besides this one, and not every person who turns up sick necessarily has this strain.