Swine flu: genetics of the novel virus

Last week another expedited-review paper appeared in the high profile journal Science, this one summarizing the genetics of the novel H1N1 influenza A virus causing the current outbreak cum pandemic. This time there is quite a bit of interesting material in this paper for non-virologist scientists with a strong interest in knowing what we are dealing with. And the first conclusion is that we are indeed dealing with swine influenza, whatever else you want to call it. Here is a short summary of the paper, which can be found here.

Influenza was identified as a viral disease in 1930 when it was isolated from a pig by Shope. We now believe pigs either got it from humans at the time of the 1918 pandemic or both pigs and humans got it from a common source, probably birds, the natural reservoir for most influenza A viruses. The subtype of swine influenza from 1918 on, H1N1, was the same as the subtype that circulated in people until 1957. During that period the pig virus remained relatively stable while the antigenic (immunologic) character of the human H1N1 drifted so that by the 1950s the human and pig H1N1s differed substantially. While several new subtypes displaced H1N1 in people -- H2N2 in 1957, H3N2 replacing H2N2 in 1968 and H1N1 returned to co-circulate with H3N2 in 1977 -- the pig H1N1 continued to be stable and unlike any H1N1 circulating in people, sufficiently so that the only people infected by classical H1N1 swine flu were people in close contact with pigs and even then documented infection was very rare. During this period the human flu virus was changing frequently, sometimes substituting entirely new subtypes and from 1977 to 2009 there were eight H1N1 vaccine updates because of antigenic drift caused by viral mutation. By contrast, there was relatively little change in the North American swine virus in the period from 1930 to the 1990s.

The situation changed suddenly in 1998 when the swine virus suddenly reassorted with a human and a bird influenza virus to make a triple reassortant. Thus began a period of instability for the swine virus, with the appearance of H3N2, H1N1 and H1N2 reassortants, each again a triple reassortant containing a human HA or NA segment and two internal gene segments derived from one or more North American birds (so far not identified as to donor host or viral subtype). After the triple reassortant appeared swine viruses diverged antigenically in a few short years to the point that if they were human viruses, a new vaccine would have been required for some.

In April 2009 a new swine flu virus appeared that not only infected people who weren't in close contact with pigs, but transmitted with ease from person to person. It is this virus that is the cause of the current outbreak. It is a descendent of the 1998 triple reassortant swine flu virus but has a number of novel features. Like other triple reassortants it contains segments that have long been part of the North American swine flu make-up (HA, NP, NS), but also two segments (NA, M) from birds that got into Eurasian swine flu viruses at least as far back as 1979. These genes have not been seen outside of Europe and Asia before, so they are a new ingredient for a North American swine flu virus (North American genes have been seen in Eurasian viruses but not the other way around). A human PB1 segment and the two bird segments (PB2, PA) from the triple reassortant round out the picture. In summary, this is a version of the genetically labile triple reassortant 1998 swine flu virus that has swapped two North American swine flu segments for two swine flu segments that 30 years ago somehow got into pigs in Europe and Asia from birds.

We don't know where all this swapping and exchanging came from:

Given the history of reassortment events of swine influenza, it is likely that additional reassortant viruses have emerged but have not been sampled. The poor surveillance for swine influenza viruses and the observation that the closest ancestral gene for each of the eight gene segments is of swine origin suggests that this virus might have been circulating undetected among swine herds somewhere in the world. Several scenarios exist, including reassortment in Asia or the Americas, for the events that have led to the genesis of the 2009 A(H1N1) virus. Where the reassortment event(s) most likely happened is currently unclear.
(Garten et al., "Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans," ScienceExpress)

There are some interesting observations about this virus, 76 isolates of which have been sequenced in whole or in part (17 from Mexico, 59 from the US). Of most interested are what they don't have: any of the markers suspected to be of importance for pathogenicity, virulence and transmissibility in humans on the basis of the reconstructed 1918 virus or H5N1 ("bird flu"). This was spun as "good news" ("we do not see the genetic markers we believe made the 1918 virus so virulent"), but it has a flip side, something flu scientists knew but often didn't emphasize when talking to the public about the latest "breakthrough" unlocking the secret of the 1918 virus: we still don't know how to go from the genetic sequence to the biology. Said another way, we still can't tell from looking at the genetic sequence of a flu virus whether it will infect humans and then cause serious disease and be easily transmitted.

For example, the E627K mutation in the former bird PB2 (substituting a K [lysine] for an E [glutamic acid] at position 627 of PB2) has been put forward as a sign that an avian virus is mutating to one adapted to humans. This virus retains E at 627 but is happily adapted to humans. Several other changes thought to be related to human adaptation are not present, either. The authors conclude the obvious:

Together these data suggest that other previously unrecognized molecular determinants are responsible for the ability of the 2009 A(H1N1) virus to replicate and transmit in humans.

Examination of the immunological reaction of this virus to ferret antisera raised against a variety of swine and human H1N1 viruses also underscores our ignorance. With the available assays, the new virus looks to our immune systems most like the classical swine flu and the North American triple reassortant of 1998, neither of which were prone to cause disease in humans. But there is something different about this virus that allow ready human infection and facile transmission. What it is, we don't know.

It is always possible that this could become a viral Rosetta Stone that unlocks the secrets of what makes an animal flu virus dangerous to humans. Let's hope so. Because at the moment, we don't seem to have a clue.


More like this

It seems difficult to get a firm grip on the epidemiology here. It spreads very well in certain areas like schools but then seems to peter out in 2nd and 3rd level transmission. It seems to behave somewhat intermediate to say a norovirus and an influenza virus. Also the incubation period seems long like it has trouble getting going in humans despite most being immunologically naive. It seems possible for both these factors to pick up steam with the traditional transmission and replication factors that we know somewhat about. Just by becoming more transmissible/replicatable not mentioning more virulent this virus could become more of a threat. That is picking up from human H1N1 something like better upper airway binding and perhaps the mammalian PB2. This could shorten the incubation period and cause faster development of high viral loads which may be more difficult to fend off. And then there are virulence factors such as PB1-F2 and NS variants that would inhibit interferon.

By medmatters (not verified) on 26 May 2009 #permalink

Medmatters, don't forget that we're outside of flu season right now. That could explain the virus' ambivalence. In that case, the virus will pick up steam once flu season returns. I'm not looking forward to seeing this virus spread even faster in schools, though.

This is another very interesting paper and it is great to see this and the other recent publications dealing with A/H1N1 getting rapid publication in peer reviewed journals. It usually takes many months to get a scientific paper published and the authors, reviewers and editors all deserve our thanks for expeditiously bringing these important works to print so quickly.


By The Doctor (not verified) on 26 May 2009 #permalink

Revere-To date, with little or no pneumonia in these cases so far and actually living by email with the bug, is there a direct cause of death in most of these people. I have been told that the exact cause is specific when they do go. E.g. pneumonias, renal failure, or "underlying causes" to what have you but it seems that this stuff is doing something unique. Daedalus posted on it like three weeks ago but so far (and its likely not provable right now) there isnt a lungful of snot, 20 cases of a single renal failure or anything like that. Pregnancy as you said did have something to do with it, as did being under the age of 25. But nothing we can point the finger at like H5N1 which is pretty much lack of oxygen from pneumonia.

Is there anything along these lines that has been seen? So far the stuff I am reading and its every day that the fatalities seem to just shut down. By the time someone makes it to the hospital its mostly too late. Hence the term "mild" is relative to the situation. If you have it and you start to turn and it was initially mild, you may have just shot yourself in the head for not showing up at the ER.

Is there anything beyond killer fever thats a signal?

By M. Randolph Kruger (not verified) on 26 May 2009 #permalink

Randy: A specific immediate cause of death is required on the death certificate. I haven't seen any breakdown of that, although I would expect it would be things like pneumonia or sepsis. There have been only 12 deaths in the US so it's not a lot to go on. I haven't seen any Mexican data and I don't know how reliable their cause of death data are (ours are not that reliable, either, as most deaths have no autopsy in the US; don't know about Mexico).

So far it sounds like influenza, which is a disease that deserves great respect. Garden variety flu kills a lot of people every year, the exact number is unknown and it varies greatly from year to year (the 36,000 deaths number is an average over some 30 flu seasons and since the number of excess deaths per year is multimodal is a very uninformative number).

None of the authors are from USDA. USDA has no swine influenza surveillance. Farmers prevail. Mad cow and e. coli scare the beef industry enough to take steps. You would expect the prospect of 1918 would bring hog farmers to the table.

By Dave Sencer (not verified) on 26 May 2009 #permalink


Where are the autopsy results?

We have had a dozen "confirmed" deaths in the US as of today. There are many more "confirmed" cases in Mexico and some in Canada but there are no, as far as I know published autopsy reports. Are they classified or something and if so why? The only reason I can think of to explain why the autopsy reports might not be revealed may relates to privacy concerns under HIPPA, which are important and valid.

However, given the risk pandemic presents to humankind as a whole, it seems to me that privacy interests as enshrined by the HIPPA law in the US should not rule the day. The families of the victims could authorize there release. But even if they did not, the details of the cases could be provided in such a way to shield the patient's identity to some degree. If presented at all though, it should be done formally with respect and published in a proper medical outlet. ProMed comes to mind as a venue.

The New England Journal of Medicine followed a similar ethical standard citing exigent pandemic circumstances for why they were publishing case reports of Mexican Flu victims. They pointed out that HIPPA concerns regarding privacy are clearly trumped by the threat pandemic influenza posed to all of humanity. In the authors and editors opinions the importance of getting this information in the hands of treating physicians was paramount.

In Mexico, initial unconfirmed but probably reliable reports published on the BBC wed site from resident physicians serving in Mexico City hospitals in late April were that there were at least 2000+ deaths. Where are the autopsy reports from these patients?


Where is the autopsy report for http://www.nytimes.com/imagepages/2009/05/23/nyregion/23baby.inlineB.re…
the 16 month old infant Johnathan who died on May 19th in Queens, New York?

This information is very important because it will reveal exactly why these people died. Clinicians taking care of the victims of Mexican Flu need this information to be able to take better care of their patients with this illness.

An old saw in medicine goes something like this "the pathologist always knows why the patient died but just too late to save them". This is the point. Treating physicians need to know the cause of death from those succumbing to Mexican Flu. This information needs to be released ASAP given the current situation.

Grattan Woodson, MD

By The Doctor (not verified) on 26 May 2009 #permalink

Doctor: Most deaths in the US have no autopsy. Unless it is a Medical Examiner case (e.g., unattended or unexplained death) in many jurisdictions there is no requirement there be an autopsy. I don't know how many of these deaths had autopsies, and, as you point out, it is not obvious that this is public information. It certainly isn't "classified" or "secret" in the usual sense, but it may either not exist or private/confidential.

I don't know if it is true in all states, but in California, every patient who dies in a hospital is entitled to an autopsy free of charge if the family wants it.

I used to present the option to families in this way, rather than saying 'do you want an autopsy', since most families think that it will appear as a line-item on their hospital bill.

Also, presenting it as a 'right' tends to make families want it, where if you present it as something 'science' wants, they tend to feel it is invasive.

In any case the results are confidential unless tabulated with others as statistics such that individuals cannot be identified. When you only have 10-12 individuals in the sample (and that is if they *all* opted for autopsy), its a bit difficult to hide who is who. So unless the families of the deceased all decide they want that information public...

I expect it will be awhile before we get much of that kind of data.

This is good. It means that people aren't dying.

By Lisa the GP (not verified) on 26 May 2009 #permalink

Thanks for your response Revere.

It would seem to me to be a public health priority to autopsy every patient who died of Mexican Flu for the reasons mentioned in my post above.

I had the honor of completing a categorical internal medicine training program at a hospital that made it a practice to autopsy virtually every in-patient death (M.I.Basset Hospital, Cooperstown, NY 1980-83).

The ward team was routinely called down to the autopsy suite to view the results and the pathologist's findings. The cases of note were presented as a formal CPC every Saturday morning in the hospital library.

What I can tell you from this humbling experience is that the value of having autopsy results on patients within your care who pass away can not be underestimated.


By The Doctor (not verified) on 26 May 2009 #permalink

Gratt: I think most doctors feel as you do about the value of the autopsy, but most families don't. Last I looked the percentage of US deaths with autopsies was somewhere down around 12%. I think there are legal standards that vary by state about which cases must be Medical Examiner cases, but outside of that it probably also depends on the state whether an autopsy can be compelled. Maybe a lawyer-reader knows the answer to this.

It is amazing how fast information about this virus has been disseminated. It makes you realize that even though people weren't looking at swine for the next pandemic influenza virus researchers really did learn a lot about the genetics of influenza viruses.

It is unfortunate that surveillance data from swine is still missing. Like Dave pointed out, there are no authors from USDA. But then again, the pork lobby is scary and powerful - Are we allowed to call it swine flu again? Even though this is a swine virus and we've known it's a swine virus since the start of the outbreak (Check out the MMWR April 23).

Interesting post on Nature about this paper, the speed of publication and how fast people have made data available. They even have a link to a previous post from Revere.


Dave Sencer: "None of the authors are from USDA. USDA has no swine influenza surveillance. Farmers prevail. Mad cow and e. coli scare the beef industry enough to take steps. You would expect the prospect of 1918 would bring hog farmers to the table."

This is exactly what I have concerned also. Not only the situation in the United States is lacking the surveillance system on animal production, but also on global scale- FDA's future role and responsibility on preventing bird flu and swine flu, etc.

Indeed, the public health sector is becoming the most critical stakeholder of animal production; the voice needs to heard clearly.

I don't believe HIPPA applies to cases such as this. In matters of public health we are allowed to collect data and present it in an aggregate or anonymous form. People often see HIPPA as having more power than it actually does. The CDC is certainly collecting epidemiological and pathology data on each death. Hopefully, we'll have a better picture of its mechanisms before the fall wave comes.

By EDobrinen (not verified) on 01 Jul 2009 #permalink