The Swine Flu thing...

[geokr]

Hopefully it's something as minor as a change in the type of aircraft.

With all the cancellations and postponements the number of people going on any day is hard to predict so I think they're putting the right aircraft on when they know the loads both going and coming. I went down May 2nd on a 737 with only 9 passengers, came back on a 757 3/4 full. The United next to us at the gate in Coz came in with 2 passengers. I called Continental when I boarded to go after seeing so few passengers worried (sort of) that my flight back was going to be cancelled. They said they were sending them down empty and bringing them back full. I wouldn't worry about the aircraft type - it'll get straightened out eventually.

 

[Hamradiopaul]

The swine flu does not exist in Cozumel - it was perfect - we ate everything and drank the local water and no problems. We had the whole island to ourselves and when we went diving with Victor Brito - we were the only boat on the reefs. It was like a private dive site - no crowds - just fish! And turtles.

Paul

 

[lamont]

Did you just write all of that yourself? If so I'm impressed! Or are parts copied from other sources?

I referenced wikipedia for the specific genes. I don't have those memorized off the top of my head... =)

Not starting anything but just wondering. Do you really not dive as your sig says?

No, I dive. I'll be in MX diving the caves next month.

...

Interesting bit of Swine Flu News in the past 24h is that Australia has confirmed its first case. Normal flu season is about to start there, and that is when we'll see how this flu is going to compare to normal influenza. It is going to have an easier time spreading and infecting people, and it will have a larger chance of reassortment with existing circulating human viruses. Over the next 2-4 months in the southern hemisphere, we'll get a much better idea of what the real ultimate impact of this virus is going to be, and if it will do anything unexpected.

 

[lamont]

I keep wondering why people keep repeating this, H1N1 Influenza A, is NOT new. It has been around for a while, in fact as recently as 5 months ago, results were being published about it's resistance to Tamiflu:

So i just pulled the protein sequences of the HA and NA envelope proteins of A/Solomon Islands/3/2006 (the 2007-2008 northern hemisphere H1N1 vaccine component), A/Brisbane/59/2007 (the 2008-2009 northern hemisphere H1N1 vaccine component), and A/California/14/2009 (somewhat non-scientifically picked out of the dozens of 'swine flu' sequences, but based on sequence length it seems 'typical'). I ran them (somewhat non-scientifically) through diff -u and counted the number of differences that resulted, which should be close to 2x the number of 'mutations' in the envelope protein (it double counts a change as one subtraction and one addition) -- regardless it produces an easy measure of the delta between two sequences.

Between the two circulating virus strains for the two years (2008 vaccine to 2009 vaccine), there was 16 changes in the HA protein and 35 changes in the NA protein. That makes for about (16/2) / 565 = 1.4% of the HA sequence changing and about (35/2) / 457 = 3.8% of the NA sequence changing. That much change year-to-year is sufficient so that people who caught the flu last season don't have a sufficient immune response to the next seasons flu to provide immunity.

Between the 2009 vaccine virus and the Swine Flu there were 221 changes in the HA protein, and 177 changes in the NA protein. That makes for about (221/2) / 565 = 20% of the HA sequence changing and about (177/2) / 462 = 19% of the NA sequence changing. That is an order of magnitude difference compared to the year-to-year changes and I'd say that its a 'new' virus and that the response of our immune system to it cannot be determined without seeing how it behaves in the human population.

Here's the search interface for influenza sequences:

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/select.cgi

 

[DandyDon]

The Novel H1N1 virus that mutated into a new infection in Mexico is surely constantly mutating as it makes its way around the world. The infections in various countries and even with countries will vary somewhat, may have a lot in common - subject to changes. Here is an article that explains virus mutations with links to more info. The Hereford cattle we raise in the US have little in common with the original cattle of Herefordshire England, but viruses are wild, unpredictable, don't even need breeding mates, and change much faster than cattle.

With all the cancellations and postponements the number of people going on any day is hard to predict so I think they're putting the right aircraft on when they know the loads both going and coming. I went down May 2nd on a 737 with only 9 passengers, came back on a 757 3/4 full. The United next to us at the gate in Coz came in with 2 passengers. I called Continental when I boarded to go after seeing so few passengers worried (sort of) that my flight back was going to be cancelled. They said they were sending them down empty and bringing them back full. I wouldn't worry about the aircraft type - it'll get straightened out eventually.

That's gotta suck. Flying 9 passengers on $300 RT tickets with a crew of 4 plus ground crews, phone agents, etc. Yeah they come back with a 3/4 full plane but they're committed to coming back for you too. Cont irritates me occassionally, but usually I'm impressed at how well they treat people. Hope you had a good trip.

 

[lamont]

I just compared Brisbane/2007 vs. California/2009 ("swine flu") vs. USSR/1977 (the ancestor of Brisbane/2007 after 30 years of evolution).

HA distance USSR/1997 to Brisbane/2007: 9.6%
NA distance USSR/1997 to Brisbane/2007: 12%

HA distance USSR/1997 to California/2009: 19%
NA distance USSR/1997 to California/2009: 17%

HA distance Brisbane/2007 to California/2009: 20%
NA distance Brisbane/2007 to California/2009: 19%

So if you use the yardstick of the changes caused by 30 years of evolution between the 1977 and 2007 viruses, the "swine flu" is roughly 2x that yardstick away from both of them.

 

[lamont]

More useless statistics...

If we take the confirmed fatalities in the US over the confirmed infections, that results in a fatality rate of 0.11%, which should be a high estimate due to infections that were not lab confirmed. If we then divide the 48 lab confirmed fatalities in Mexico by that fatality rate, we get a number of cases of 43,200. It is possible that the fatality rate in Mexico is higher than the fatality rate here due to issues in seeking treatment / poverty / whatever, but we already have an inflated death rate due to under-reporting of cases in the US. So, taking the 43,200 cases we would have expected to see and dividing by the lab confirmed cases in Mexico, there would be 26 unreported cases for every lab confirmed sample.

This site is also reporting 17 cases in Yucatan and 11 cases in Q.Roo. still:

Influenza A H1N1 - Organización Panamericana de la Salud

I think I read that the Mexican government is going to stop reporting statistics like this, though, so this is at least a few days out of date and may not get updated again ("problem solved, nothing to see here, move along, move along....").

 

[lamont]

can you tell i'm bored?

http://portal.salud.gob.mx/opencms/...za/situacion_actual_de_la_epidemia_090509.pdf

there's a PDF from the mexican government on the current numbers, but in acroread on my Macbook I'm only getting '[?]' for all the numbers, so its not too helpful to me.

Here's a backup in case that URL disappears:

http://www.scriptkiddie.org/situacion_actual_de_la_epidemia_090509.pdf

 

[MMM]

So 11 confirmed in Q.Roo. Sask (my home prov) confirmed our first 2 last last week. Both hadjust returned fom vacationing in Cancun area. Today we added 2 more with no Mexico connection.

 

[lamont]

there's a PDF from the mexican government on the current numbers, but in acroread on my Macbook I'm only getting '[?]' for all the numbers, so its not too helpful to me.

Actually it was Preview that it wasn't working with. I installed Adobe Reader and it works fine.

If the cases are truly waning in Mexico, then maybe Mexico needs to close the border to keep the filthy people in the USA from bringing it back in... =)