Comments on: Swine influenza A/Mexico/2009 (H1N1) update

By: Alan Dove » Blog Archive » The Other White Meat

Alan Dove » Blog Archive » The Other White Meat — Mon, 23 Aug 2010 14:24:14 +0000

[...] that the viral sequences are being released to the public, though, virologists see no trace of avian or human flu genes in them. It’s a virus reassortant of entirely swine [...]

By: Swine Flu Pandemic: FACT vs FICTION | LushCanopy

Swine Flu Pandemic: FACT vs FICTION | LushCanopy — Thu, 20 Aug 2009 01:56:35 +0000

[...] “Swine influenza A/Mexico/2009 (H1N1) update”. 30 April 2009 [...]

By: kylai23

kylai23 — Wed, 10 Jun 2009 11:28:52 +0000

We are facing the virus of the second wave of H1N1 of 1918. The HA and NS1 gene actually comes from the virus of 1918 which has transmitted to pigs in 1918 and has now resurfaced. If we look at the mortality rate in Mexico, those between 20-60 are very similar to the mortality rate of 1918. The mortality rate in children is much lower probably due to vaccination against Haemophilus Influenza and pneumococcus. Most of the children died not due to the influenza but due to bacterial co-infection which would increase the mortality rate by 10 folds. More women are affacted because the mothers have to take care of the sick children. The low mortality rate in United States is due to vaccination program against pneumococcus and Haemophilus Influenza in the past, better healthcare level, better sanitation and nutritional status. Moreover the death are delayed due to intensive care. If you look at the figures of W.H.O., the mortality rate of U.S.A. is slowly rising to > 0.2 %. The mortality would suddenly jump if the demand for healthcare has outstrip the capacity of the exiting facilities if the mitigation process is inefficient.

By: kylai23

kylai23 — Wed, 10 Jun 2009 04:28:52 +0000

By: Matt Dubuque

Matt Dubuque — Fri, 01 May 2009 12:46:52 +0000

At the end of a recent Science Magazine interview, Dr. Donis of the CDC states that the USA has received 300 samples of this virus from Mexico. That interview is cited favorably by this blog.

It seems to be a conscious and intentional decison not to publish those sequences. And it seems that the Americans are partipating in the decision not to publish.

Why would the CDC fail to publish the sequences of any of the 300 samples Dr. Donis says they have received from Mexico?

Matt Dubuque

By: diana

diana — Fri, 01 May 2009 12:42:13 +0000

Whatever the reason, this strikes me as THE BIG STORY that is not being reported.

By: mdubuque

mdubuque — Thu, 30 Apr 2009 23:46:36 +0000

I did come up with one possible explanation for the protracted delay in obtaining sequencing for Mexican isolates.

I recall that in 2007, there was a big dustup between Indonesia and the WHO over sharing of bird flu isolates because the Indonesians apparently demanded greater quantities of any vaccine developed as a result of Indonesian samples.

Most of the vaccine manufacturing capacity lies in the Northern industrialized world and if this virus comes back with a vengeance this winter there is likely to be extreme competition for the first production units. And third world countries such as Mexico and Indonesia are understandably concerned that any distribution system should not be based strictly on wealth.

Given this recent Indonesian dustup that received far more coverage in the Global South than in the US, Mexico may be playing hardball behind the scenes along the lines of what Indonesia did.

Here is a short recitation of the Indonesian controversy:

http://www.thefreelibrary.com/Indonesia+stands+...

By: birch23

birch23 — Thu, 30 Apr 2009 22:11:40 +0000

Canine influenza emerged a few years ago in Florida in greyhounds, and was found to have come from an equine influenza strain. However, after entering the canine population, the virus is no longer able to infect horses. Perhaps a similar thing is occurring here.

Also, it seems that this H1N1 swine influenza may have actually come from China, based on some information I have from a virology professor at the veterinary school I attend. He has been receiving information from people he knows at the CDC.

By: profvrr

profvrr — Thu, 30 Apr 2009 20:20:27 +0000

I think that Today doesn't read obscure blogs such as this one,
otherwise they would know better. Perhaps I will create a graphic
illustration of the viral genome showing the origin of RNA segments.

By: profvrr

profvrr — Thu, 30 Apr 2009 20:19:29 +0000

The viral RNA is converted to DNA and that is what is sequenced, so
you see thymines. But it's the sequence of the viral RNA, since of
course the viral genome is not DNA.

By: Joe

Joe — Thu, 30 Apr 2009 18:53:57 +0000

This might sound a bit stupid on my part, but why are they described as RNA sequences? When I looked on the site the sequences had thymine in them, and I thought that was replaced by uracil in RNA.

By: Megan

Megan — Thu, 30 Apr 2009 18:26:01 +0000

For some reason the news media are still claiming this swine flu is made up of 4 different segments from human, avian and swine. On the Today show this morning they had blocks that they were using to demonstrate where the different parts of the virus came from and proceeded to “build” a virus made up of the different animal strains. I think this really needs to be cleared up with the public.

By: diana

diana — Thu, 30 Apr 2009 17:48:31 +0000

It's taken me a while to digest the fact that the Mexican flu viruses haven't been sequences. Shouldn't this be bigger news? Why is it confined to a relatively obscure blog? (No offense, Dr. Racaniello.)

By: mdubuque

mdubuque — Thu, 30 Apr 2009 16:24:52 +0000

Mexico's chief epidemiologist insists this virus did not begin in a Mexican pig farm.

Excerpted from:

http://www.reuters.com/article/lifestyleMolt/id...

"Miguel Angel Lezana, Mexico's chief epidemiologist, told reporters.... the presence of Eurasian swine flu genes in the H1N1 virus makes it unlikely that the disease originated in a Mexican pig farm."

By: Quasidomo

Quasidomo — Thu, 30 Apr 2009 15:13:33 +0000

Yes. What I was trying to say is that the sequenced strain outside Mexico is less virulent and may have been around without anyone really noticing (at least for a few weeks). Once Mexicans starting dying from their different strain, we incorrectly concluded that the less virulent strain was the same strain as the deadly Mexican strain. This is just a hypothesis – but one that can't be falsified until we get sequences from Mexican patients.

By: Hugo Montaldo

Hugo Montaldo — Thu, 30 Apr 2009 14:15:08 +0000

Hugo vet from Mexico (actually animal geneticist), very interesting information. Thanks for the posts.

By: Matt Dubuque

Matt Dubuque — Thu, 30 Apr 2009 14:01:46 +0000

I do not understand why you are morally certain that the German and New York isolates arose from Mexico.

What factual basis is there to form a positive, irrevocable conclusion that there were not two separate outbreaks?

I think it is exceedingly premature to conclude that; we only have anecdotes to support it.

Also, the critical phrase "reasonable nucleotide substitution rate" remains undefined and I'm not certain all (or even a majority) of virologists would agree on what that term means. Precisely what quantitative assumptions describe that phrase?

By: diana

diana — Thu, 30 Apr 2009 13:56:45 +0000

Why have the only fatalities been Mexican? "Are the Mexican deaths just calling attention to a different (existing) strain that isn't very virulent?"

Wouldn't it be the opposite? If only Mexicans have died, would this not be evidence that their strains are MORE virulent?

Also, the biggest cluster of infection outside of Mexico is New York City. Why is this?

By: Matt Dubuque

Matt Dubuque — Thu, 30 Apr 2009 13:53:47 +0000

How do we account for the April 24 comments of Dr. Marie Gramer below, who has perhaps the largest library of swine flu virus isolates in the nation the day after Schuchat's comments?

http://cottontopssandbox.wordpress.com/2009/04/...

Excerpted here for your convenience:

"There have been no reports of this virus in pigs, said Dr. Marie Gramer, a swine flu expert with the University of Minnesota’s college of veterinary medicine. “It doesn’t seem to be very similar to anything that is currently circulating, from what I have,” said Gramer, who has an extensive library of swine flu virus isolates. Continued:

http://www.medicinehatnews.com/content/view/938... "

Where are the isolates that she examined that caused her to make these comments physically located right now?

By: Matt Dubuque

Matt Dubuque — Thu, 30 Apr 2009 13:35:56 +0000

Why has there been no clarification of Anne Schuchat's comments? They were extraordinarily specific and it was clear at the time that she had a high confidence level that her remarks were accurate.

Specifically, can we have access to those same isolates that caused her to make that conclusion? Surely that bold assertion was based on an isolate she possessed.

Where is that isolate now?

Don't we have a right to know?

By: Quasidomo

Quasidomo — Thu, 30 Apr 2009 12:41:53 +0000

I don't understand why we don't have sequence data from the Mexico cases where individuals have died. Is it not possible that there are two strains out there and that the more virulent strain is still mostly contained in Mexico? The cases in San Diego were reported before we even knew about the Mexico outbreak. Are the Mexican deaths just calling attention to a different (existing) strain that isn't very virulent?

By: Steven

Steven — Thu, 30 Apr 2009 11:38:58 +0000

Does vaccination to seasonal flu confer any resistance to the mutated H1N1 version?

By: Technocrat

Technocrat — Thu, 30 Apr 2009 10:56:07 +0000

But you still agree that this virus appears to contain genetic pieces from from four virus sources, correct? (one avian influenza viruses, one human influenza viruses, and two swine influenza viruses).

By: Michael_Day

Michael_Day — Thu, 30 Apr 2009 10:28:38 +0000

Regarding Dr. Schuchat's statement, could it be that if you trace the lineage of certain viral genome segments that their origin could be avian, for example? i.e., perhaps the A/swine/Indiana/P12439/00 isolate was/is a reassortant originally containing some segments of avian origin? Just a thought, I have not personally looked closely at these sequences…