Comments on: How fast can influenza change? http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/ Meddling with things mankind is not meant to understand. Also, pictures of my kids Thu, 09 Sep 2010 15:33:45 +0000 hourly 1 http://wordpress.org/?v=3.0.1 By: fall flu update: hini-shot news at Dr. Leigh Saint-Louis http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-31637 fall flu update: hini-shot news at Dr. Leigh Saint-Louis Tue, 25 Aug 2009 23:47:44 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-31637 [...] i am on record as being against the flu. i have an attitude problem with segmented RNA genomes (40-50 mutations yearly?!), i’ll admit. i do not like their unpredictability, sudden virulence appearing as if out of [...] [...] i am on record as being against the flu. i have an attitude problem with segmented RNA genomes (40-50 mutations yearly?!), i’ll admit. i do not like their unpredictability, sudden virulence appearing as if out of [...]

]]> By: gsgs http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22842 gsgs Mon, 04 May 2009 18:27:16 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22842 yes, it often evolves faster after species switches, i.e. in 1918, but how much ? I expect 40-50 mutations in the genome per year. Human H3N2 acquires ~35 mutations per year. Sometimes(rarely) we have very few mutations over years in Swine also recombinations, I'm not sure about the reasons. This was i.e. observed in Korean swine, so I'm a bit careful about comparing the Korean sequences with the actual ones yes, it often evolves faster after species switches, i.e. in 1918, but how much ?
I expect 40-50 mutations in the genome
per year.
Human H3N2 acquires ~35 mutations per year.
Sometimes(rarely) we have very few mutations
over years in Swine also recombinations,
I’m not sure about the reasons.
This was i.e. observed in Korean swine, so I’m a bit careful about comparing the Korean sequences with the actual ones

]]> By: iayork http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22832 iayork Mon, 04 May 2009 15:46:43 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22832 Looking at changes and assuming that the new H1N1 is going to drift/adapt at the same rate as previous viruses is not a safe assumption. This virus has clearly jumped species fairly recently. We know that viruses undergo rapid, intense selection when they jump species. So we would expect this new virus to show significant changes from other viruses, that were already adapted to their host and didn't undergo the same selection pressure. We can't tell which changes are recent and adaptive, and which are representative of long-term drift. If you're trying to use sequences to look at time of change, you really need the original swine version of the virus, not a version that's cycled through humans for an unknown period. Unfortunately, for this virus we still don't have any swine-adapted sequences. Looking at changes and assuming that the new H1N1 is going to drift/adapt at the same rate as previous viruses is not a safe assumption. This virus has clearly jumped species fairly recently. We know that viruses undergo rapid, intense selection when they jump species. So we would expect this new virus to show significant changes from other viruses, that were already adapted to their host and didn’t undergo the same selection pressure. We can’t tell which changes are recent and adaptive, and which are representative of long-term drift.

If you’re trying to use sequences to look at time of change, you really need the original swine version of the virus, not a version that’s cycled through humans for an unknown period. Unfortunately, for this virus we still don’t have any swine-adapted sequences.

]]> By: gsgs http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22830 gsgs Mon, 04 May 2009 15:40:57 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22830 ahh, well. Sorry. Not 11 years hidden. The best matches are from the 1998 outbreak where this strain first appeared and reassorted, but when recent virus have same distance as one of them to a direct 1998 ancestor, then their estimated most recent common anchestor is only 5.5years back, since the accumulated differences add up in both directions. So, what's the latest calculated most recent common ancestor date ? I get 2002 for A/sw/Korea/CY04/2007(H3N2) in PB1 , still 7 years which is unusual. Other viruses usually have closer relatives in genbank. ahh, well. Sorry. Not 11 years hidden. The best matches are from the 1998 outbreak
where this strain first appeared and reassorted, but when recent virus have same distance
as one of them to a direct 1998 ancestor, then their estimated most recent common anchestor
is only 5.5years back, since the accumulated differences add up in both directions.
So, what’s the latest calculated most recent common ancestor date ?
I get 2002 for A/sw/Korea/CY04/2007(H3N2) in PB1 , still 7 years which is unusual.
Other viruses usually have closer relatives in genbank.

]]> By: iayork http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22713 iayork Sun, 03 May 2009 02:03:18 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22713 <em>11 years because it closely matches a version of swine flu that appears among pigs in 1998 and apparently has become dominant in piggeries in the US ever since.</em> That makes sense, and it's almost certainly where the meme comes from. But I've seen people interpreting this exactly opposite - that the new Mexican H1N1 has been hiding somewhere for 11 years (implying dark secrets held by governments, fill in your conspiracy blank) in its present form but unknown to science. According to your interpretation, the <em>parent</em> virus has been around and studied for 11 years, and we don't know how long the new virus has been around but it's very likely a very short time. That fits with the observations. The conspiracy/incompetence theories don't. 11 years because it closely matches a version of swine flu that appears among pigs in 1998 and apparently has become dominant in piggeries in the US ever since.

That makes sense, and it’s almost certainly where the meme comes from. But I’ve seen people interpreting this exactly opposite – that the new Mexican H1N1 has been hiding somewhere for 11 years (implying dark secrets held by governments, fill in your conspiracy blank) in its present form but unknown to science. According to your interpretation, the parent virus has been around and studied for 11 years, and we don’t know how long the new virus has been around but it’s very likely a very short time. That fits with the observations. The conspiracy/incompetence theories don’t.

]]> By: Bret http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22701 Bret Sun, 03 May 2009 00:35:48 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22701 11 years because it closely matches a version of swine flu that appears among pigs in 1998 and apparently has become dominant in piggeries in the US ever since. Source? God know how many articles off researchblogging.org :) 11 years because it closely matches a version of swine flu that appears among pigs in 1998 and apparently has become dominant in piggeries in the US ever since.

Source? God know how many articles off researchblogging.org

:)

]]> By: Sandra Porter http://www.iayork.com/MysteryRays/2009/05/02/how-fast-can-influenza-change/comment-page-1/#comment-22694 Sandra Porter Sat, 02 May 2009 23:19:06 +0000 http://www.iayork.com/MysteryRays/?p=1047#comment-22694 Cool. We'll have to take a look at the sequences :-) Cool. We’ll have to take a look at the sequences :-)

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