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Swine Flu Natural?

May 1, 2009 5 comments
Proper avian flu mask.

Proper avian flu mask.

The Swine Flu has been covered ad nauseam in the media, with many aspects addressed, however little has been elucidated on the first (and most important) question I had when this strain broke loose:

How can three virus strains combine, in nature, to form a single, viable virus?

To answer this question we need to look at a little bit of background information on the Influenza A virus (in brief). It is an RNA virus, a genus of the Orthomyxoviridae family. The virus itself lacks most of the needed equipment (enzymes and so forth) for replication and depends on the body’s own cells, which it enters on contact with outer membranes. The protective viral coat breaks open inside the cell, with the RNA being fed to the cell’s protein making “factories” to reproduce the viral coat which protects the virus and enables its further spread, and also the enzymes necessary to replicate the virus’ RNA (RNA Polymerase). The completed virus particle either continues to reproduce inside the cell, or is expelled by the cell itself, where, if successful, it survives long enough to infect another cell.

The replication process itself is very error prone (much more so than that for human DNA), such that many of the viral copies fail. Some errors work, however. This may result in a more “successful” viral particle. This system of natural selection means that, over time (sometimes a very short time), a virus adapts to its host, which can be a good or bad thing:

  1. The virus might develop a slower replication rate, so that the symptom free phase is longer, allowing it to spread to more hosts. This would make it a better virus than one which kills its host so quickly that it has never had a chance to spread to a new host.
  2. The virus might develop into a more benign form, so that it can spread happily without the host minding too much. This could be an advantage for the virus, for example, if the sickest individuals were quarantined (or dead), rendering that viral trait undesirable and selecting for less severe traits.
  3. The virus might develop into one which can survive a longer time in the atmosphere, increasing its infectiousness. It could be said that the universal wearing of surgical masks, for example, might mean that the virus will be pressured into learning how to spread in more extreme conditions (past the mask), making it more virulent.

Many of the symptoms of flu virus are deliberate, such as mucous membrane irritation which causes people to sneeze and cough, or develop diarrhoea. These aide the spread of the virus, which is why hand washing and the wearing of masks is advocated by authorities. On the other hand, measures to stop the virus can promote a super-strain which can make matters worse.

The important point, to answer the question, is that the Viral RNA is not presented as a single strand but, in the case of Influenza, eight separate segments. These float around near the nucleus of the cell relatively freely until they are repackaged. Thus, it is possible (either in a laboratory or in nature) for a cell to be infected by two different virus strains simultaneously, resulting in any number of random combinations of the Viral RNA segments, any of which may potentially result in a successful virus particle. Most of the time, however, it can be expected that recombinations would fail.

The combination of two virus strains can easily occur in nature. Three is less likely.

However, it should take a long time for three viruses to combine into one coat. Long enough for a precursor to have spread widely, causing animals to get sick so that they get tested, perhaps to the point that the new genome is detected in a laboratory, before a third virus is incorporated into the new strain. It should also be possible to find a virus having a combination of two of the three RNA strains somewhere else in the wild. This may have occurred already in pigs in Ohio (2007). There are doubts, however, that the Ohio outbreak is not a red herring, as is covered well here.

Yet it is now reported by wired magazine that the viral genome is entirely made up of elements from pigs only and only from two, pre-existent strains, a claim that needs further corroboration. But if this is true, then the almost-pandemic A/H1N1 virus can safely be viewed as one having developed entirely naturally, but precursors still need to be found.

Swine Flu A Natural Occurrence?

The current outbreak of Swine Flu is probably a natural occurrence, but the work necessary to show this is incomplete. The question, as at 1/5/2009, remains unanswered, and thus, the theory that the outbreak was no accident, cannot yet be discounted as just another of the flighty ideas of a paranoid lunatic.

(As this stage, we won’t be covering any more of this epidemic, unless something new and meaningful is learned of the virus itself. Instead, we intend on concentrating on other, more pressing matters.)

Swine Flu Less Scary Than Expected

April 29, 2009 Leave a comment
Oink

...Oink?

In the Australian news, a succinct update on the flu is given (where it says that one baby in Texas has died of the virus):

There were no further details about the death in the US, most of whose 65 confirmed cases of swine flu have proved mild.

Nearly a week after the threat of the pandemic emerged in Mexico, that country remains the hardest hit, with up to 159 people killed – although the number of confirmed deaths in Mexico sits at seven.

The facts, then, are that of roughly 2,500 cases in Mexico, there are really only 7 deaths (presumably confirmed at autopsy), giving a mortality rate of 0.28%. That’s less than Spanish flu (up to 20%) by 100 times! It’s probably not as benign as that, but the statistics coming out in the media are wildly fluctuating at the moment. Dividing the media faeces from the clay is not proving to be very easy.

I think at this point this flu looks like it’s got its wings clipped.

May 11 Update:

Today it was reported that the U.S. has 2254 H1N1 cases, with 3 deaths. Mortality rate for the U.S. (almost a first world country) is 0.12%, or just over one per thousand infections. How, then, does this differ from normal influenza? Not by much.

Categories: health Tags: , ,

Swine Flu got Legs

April 25, 2009 1 comment

Swine Flu

Swine Flu

This could be the big one.

(See also: Swine Flu and the Dreaded Lurgi and Swine Flu Less Scary Than Expected)

Health alerts have spread through Australia’s government institutions, in particular hospitals, advising of the risk of Swine Flu. It affects young adults, has a high probability of mortality, and is described by the World Health Organization as an emergency having the potential to reach pandemic proportions rapidly. In Mexico, it is said that over 1000 people at the present time have been infected, of which over 60 (27/4/09 – now 80) have died – a fatality rate of (roughly) 6%. Schools, museums and other public gathering places have been closed to try to prevent further spread. The virus has already spread to California, Texas, with at least seven confirmed infections.

The number of fatalities outside of Mexico currently equals 1, a 23 month old in the US.

Specifically, the virus belongs to the H1N1 group of influenza A viruses. This particular strain is novel; its discovery occurred as recently as 2 days ago (23/4/2009). Its genetic profile is such that the conventional flu vaccines offered to hospital workers and the community are unlikely to offer protection. It is said to be sensitive to the drugs zanamivir (Relenza, owned by GSK) and oseltamivir (Tamiflu, owned by Roche). Supplies of this drug in Australia are probably adequate to manage the early stages of an outbreak, but clearly, in developing countries, this is definitely not the case.

The lethality of this infection is similar to that during the Spanish Flu pandemic (1918-1920) which had a mortality rate of 2 to 20%. It too was a subtype of the H1N1 influenza A virus.

One of the most common questions being asked by the public are about the presentation of the illness and how to avoid getting infected. In general, the symptoms and signs of the infection are nothing out of the ordinary. They include:

  1. All the usual flu symptoms, such as fever, lethargy, lack of appetite and coughing (respiratory tract), sometimes runny nose and sore throat.
  2. Other body systems can also be involved, such the gut (nausea and vomiting, diarrhoea)

These are the same symptoms that can happen in pneumonia, the common cold, even urinary tract infection in some people. This is not very helpful, because it can now be expected that, very often, a person with even the slightest runny nose, or food poisoning or whatever, will think he or she has swine flu. The rule of thumb is, if you are more sick than your usual, see a doctor. If you have a reason to avoid being sick at all (such as being on drugs which decrease your immunity), see a doctor.

As for avoiding infection, well there are more myths than facts around. If you managed to avoid catching a cold over the last five years, then you are doing something right, but the fact is that most people are forced to go to public places, shop, go to school, work and so forth. Like every virus, the flu will have an incubation period (even if it’s just a couple of days) where a person is infected, is infectious, but is feeling perfectly well.

Of the few things that have been proven to work, careful and consistent hand washing after human contact, isolation of the sick, vaccines (by no means a panacea), and being otherwise healthy, well slept and well fed, are the best thing. If you are worried about dying, but smoke, drink too much, go to fast food restaurants and drive too fast, then fix those before you worry about the flu!

The coming weeks will reveal whether this virus manages to spread faster than the ability of researchers to design a vaccine in order to produce herd immunity, especially in major cities. In the meantime, governments around the world will be placing their institutions on alert for symptoms and putting in place treatment protocols and the like. There is no doubt that everybody will do whatever is feasible to curtail the spread of this organism.

There are oddities about this organism, however, as reported in the Wall Street Journal:

The flu virus mutates promiscuously, and this strain is no exception: Officials said that, in addition to genetic material associated with North American swine flu, the strain has gene segments associated with European and Asian swine flu, North American avian flu and human flu.

Most surgical masks do not offer protection.

Most surgical masks do not offer protection.

Three strains in one! It’s not unreasonable to ask questions about just how probable (or improbable) such a mutation is in the wild. In laboratories, however, mixtures of multiple viral RNA fragments can be combined to yield a successful result. Biological weapons research has not ceased either, but has continued quietly out of the public limelight. We can expect to hear of many different explanations about this particular virus.

It is useful to keep an open mind about the outbreak. It is currently assumed that the virus is a natural occurrence. Indeed, there have been warnings about this for years now. The thing is, though, that warnings do not change the probabilities. Many people are rightly wondering whether the virus was engineered in a laboratory or is merely a coincidental mutation among a herd of pigs. If it is a man-made virus, then its release into the wild could represent the greatest act of mass murder in history. This question, therefore, is not to be shirked at and must be answered.

The influenza viruses, however, are known for their unstable genetics and rapid rate of mutation, hence the tendency for new strains to emerge each year, and even during a seasonal outbreak. It would be interesting to tease out the probabilities that this particular strain would have spontaneously emerged. Also, we can expect this outbreak, if it does spread as predicted, to rapidly mutate into multiple strains, making containment even more difficult.

On the topic of containment, it needs to be said that ordinary surgical masks do little to prevent the spread of influenza. It’s all just for show. During the first few minutes of wearing a surgical mask, the device performs to manufacturer specifications, but after that the mask is damp and warm and cannot offer the same protection. A paper mask cannot form a tight seal around the face so that air is always entrained on inhalation. If you are sneezed on, or are in contact with an infected person, you are going to get infected. Mask wearing is by and large a waste of time – as good as placebo. But people will do it anyway, of course.

Whatever its origins, this virus is already showing an ability to spread extremely rapidly. Within days we will know whether this is indeed the flu pandemic of the century.