Swine H1N1 Explosion in United States

[HenryN]

Originally Posted by gsgs

the same holds for the Qinghai-strain
(even more, since swine don't fly, usually)
yet you call it Qinghai-strain.

The Qinghai strain is an easy call. Most who seriously study the evolution of infleunza viruses use phylogenetic analysis to trace origins. The Qinghai strain is clade 2.2 and it burst onto the scene at Qinghai Lake in May, 2005. The clade 2.2 subsequently spread to more than 50 countries west of China. None of these countries had previously reported Asian H5N1, and ALL isoaltes in poultry, wild birds, and humans were clade 2.2 (Qinghai strain).
'
The outbreak at Qinhai Lake was massive and involved long range migratory birds, which then transported and transmitted the virus. The Qinghai strain, like the Fujian strain (clade 2.3) was a VERY easy call and the strain was named after the isolates from BIRDS. The first reported human cases involving Qinghai 2.2 were in Turkey. The H5N1 wasn't called the Turkey strain, it was called the Qinghai strain (or clade 2.2).

The swine H1N1 circling the globe originated in SWINE. All 8 gene segements had been seen in swine previously, but the most closely swine sequences were easily those identified in Alberta, Canada. However, it is likely that even closer sequences are in swine elesewhere, which is why no one is calling this the Mexican strain, other than those who don't understand its origins.

The swine elsewhere are most likely in the Americas, but there are NO public sequences linking the strain to Mexica swine.

[gsgs]

the reason why it isn't called M**flu is the intervention of Mexico,
not the scientific evidence.
Qinghai lake unlikely is the origin of the strain since there are 4 markers at Qinghai lake which are not seen elsewhere.

We have no outbreak in swine in M**flu (except Alberty months later
with many mutations) so we should name it after the first outbreak in humans,
which was in Mexico. You won't want to name 1918 flu after the (unknown) location of
the first outbreak of that strain in birds.


let's put this discussion to
http://www.flutrackers.com/forum/sho...d.php?t=101180

[HenryN]

Originally Posted by gsgs

the reason why it isn't called M**flu is the intervention of Mexico,
not the scientific evidence.
Qinghai lake unlikely is the origin of the strain since there are 4 markers at Qinghai lake which are not seen elsewhere.

We have no outbreak in swine in M**flu (except Alberty months later
with many mutations) so we should name it after the first outbreak in humans,
which was in Mexico. You won't want to name 1918 flu after the (unknown) location of
the first outbreak of that strain in birds.


let's put this discussion to
http://www.flutrackers.com/forum/sho...d.php?t=101180

Phylogenetic analysis is used to name strains. The swine origin has yet to be identified.

[HenryN]

Originally Posted by gsgs

the reason why it isn't called M**flu is the intervention of Mexico,
not the scientific evidence.
Qinghai lake unlikely is the origin of the strain since there are 4 markers at Qinghai lake which are not seen elsewhere.

We have no outbreak in swine in M**flu (except Alberty months later
with many mutations) so we should name it after the first outbreak in humans,
which was in Mexico. You won't want to name 1918 flu after the (unknown) location of
the first outbreak of that strain in birds.


let's put this discussion to
http://www.flutrackers.com/forum/sho...d.php?t=101180

The science is quite straightforward.

At the influenza meeting in Toronto, a numerical system was announced. Thus, for H5N1 the main sub-clades of interest are clade 1, 2.1, 2.2, and 2.3 - and more recently clade 7). For H1N1 seasonal flu there were clades 2A, 2B, and 2C that were of recent interest.

Since representative isolates are used for vaccnes, the name of the virus is used, like Brisbane/59 for H1N1 and Brsibane/10 for H3N2.

For the swine H1N1, the target has been selected, and it is decidedly California:

(A/resassortant/IVR-153(A/California/07/2009 x IVR-6)(H1N1))

[mixin]

Originally Posted by niman

... but there are NO public sequences linking the strain to Mexica swine.

And how much of a surprise is that?

Smithfield is only the world's largest pork producer and their hog productions in Mexico crank out close to 1.5 million pigs each year. It would absolutely be in their best interest to have NO sequences linking the outbreak to their facilities.

Results would have been much more believable if their testing and the inspections had been done by teams with no monetary interest in the outcomes.

[sharon sanders]

Gsgs - We are not calling the Novel H1N1 strain M*** flu. Stop it. You are deliberately provoking a confrontation.

I am not asking again.

[HenryN]

Originally Posted by mixin

And how much of a surprise is that?

Smithfield is only the world's largest pork producer and their hog productions in Mexico crank out close to 1.5 million pigs each year. It would absolutely be in their best interest to have NO sequences linking the outbreak to their facilities.

Results would have been much more believable if their testing and the inspections had been done by teams with no monetary interest in the outcomes.

It is unlikely that the swine H1N1 is limited to one location. The sequences in Alberta were very close, but far enough away to make infection of swine by a worker returning from Mexico unlikely (especially when the worker tested negative).

[gsgs]

Originally Posted by Florida1

Gsgs - We are not calling the Novel H1N1 strain M*** flu. Stop it. You are deliberately provoking a confrontation.

I am not asking again.

so, how do you want me to call it ?
M**flu is, what Sally said.

> No I am not going to ban you

[The Mountains Voice]

Originally Posted by Florida1

Gsgs - We are not calling the Novel H1N1 strain M*** flu. Stop it. You are deliberately provoking a confrontation.

I am not asking again.

I've got to agree with F1 on this one... Not only is it an irrelevant argument as to where this started - it's ultimately an impossibility to prove for the history books. Flu mutates/recombines/evolves, or whatever you want to call it. Todays flu will pick up markers as it travels.

What happens when it grabs something out of an Egyptian pig coinfected with H5N1? We going to call it the Egypto-Mexicali Flying Pig Flu?

Actually - that's not bad. When Swine Flue H1N1 merges with Bird Flu H5N1 - we can call it the Flying Pig Flu

Actually I don't care what it is called - but FT is probably THE most comprehensive source for information on this subject In The World. And we're publicly available to the common Joe. For simplicty & credibility sake we probably should stick to a simple scientific, and universally recognized term. What's it hurt to simply call it Swine Novel H1N1? You and Niman can still argue theory - and we all get to be awed by both of your genetic knowledge And everybody is happy

[tyto]

It will be interesting to see how things play out when a beloved hollywood star or media personality dies of this H1N1 flu.

When a full fledged severe pandemic finally hits this is what will be on the news all the time. The who's who of the dead.

[prepdeb]

Great points Mountains Voice.
Wouldn't we all be relieved if flu viruses were static?
If what may or may not have escaped from a specific spot would remain as it was then, the threat of this novel virus would continue to be mild.

[Thornton]

Additonal reporting and confirmation of the observations by Dr. Niman

Swine Flu Cases DRAMATIC INCREASE in few days as U. S. citizens drop their guard.

http://www.emergencyemail.org/newsem...asp?a=390&z=29

[HenryN]

Swine Flu Cases DRAMATIC INCREASE in few days as U. S. citizens drop their guard.

Swine Flu Cases show dramatic increase in just a few days. New Jersey, Connecticut, Florida North Carolina California and Washington DC show largest increases. Infections on the rise as public awareness drops. State Jun 3rd Jun 5th Jun 5th Jun 3rd Case Cases Cases Deaths Deaths Increase Alabama 94 94 0 0 0% Alaska 1 3 0 0 200% Arkansas 9 9 0 0 0% Arizona 547 547 4 4 0% California 804 973 0 0 21% Colorado 68 75 0 0 10% Connecticut 196 395 1 0 102% Delaware 135 142 0 0 5% Florida 194 247 0 0 27% Georgia 32 33 0 0 3% Hawaii 94 115 0 0 22% Idaho 16 16 0 0 0% Illinois 1151 1357 5 3 18% Indiana 146 173 0 0 18% Iowa 92 92 0 0 0% Kansas 87 92 0 0 6% Kentucky 90 96 0 0 7% Louisiana 122 134 0 0 10% Maine 12 17 0 0 42% Maryland 63 89 0 0 41% Massachusetts 566 787 0 0 39% Michigan 287 298 1 0 4% Minnesota 66 82 0 0 24% Mississippi 34 40 0 0 18% Missouri 41 46 1 1 12% Montana 15 15 0 0 0% Nebraska 43 60 0 0 40% Nevada 113 128 0 0 13% New Hampshire 50 64 0 0 28% New Jersey 74 148 0 0 100% New Mexico 108 108 0 0 0% New York 646 858 8 4 33% North Carolina 21 30 0 0 43% North Dakota 18 23 0 0 28% Ohio 29 35 0 0 21% Oklahoma 87 93 0 0 7% Oregon 159 167 0 0 5% Pennsylvania 226 299 0 0 32% Rhode Island 16 18 0 0 13% South Carolina 49 60 0 0 22% South Dakota 9 10 0 0 11% Tennessee 103 104 0 0 1% Texas 1403 1670 3 3 19% Utah 369 461 2 1 25% Vermont 7 9 0 0 29% Virginia 36 55 1 0 53% Washington 574 577 1 1 1% Washington, D.C. 20 24 0 0 20% West Virginia 3 6 0 0 100% Wisconsin 1905 2217 0 0 16% Wyoming 18 25 0 0 39% Territories Puerto Rico 1 6 0 500% TOTAL*(52) 11054 13217 55)">27 17 20% * Numbers reported by U. S. Federal Government CDC

[Muscade]

Crédits: Siegfried

Swine flu cases jump by 30 percent
By Robert McCoppin | Daily Herald Staff
Contact writer

The number of swine flu cases in Illinois jumped by 35 percent over the weekend - but health officials maintain it's nothing to be alarmed about.
Total cases of the H1N1 virus, probable and confirmed, rose from 1,357 on Friday to 1,828 on Monday, an increase of 471 cases.

While the number of new cases had risen fairly steadily at a pace averaging 217 a week in the previous month, the rate tripled in the past week.

/.../

http://www.dailyherald.com/story/?id=299221

[HenryN]

Commentary

[tropical]

How is amazing, or somebody can say "aligneated", the silence and the public non-awareness to their patients of the GP's and most of the epid/infect. branch horizontal and vertical structure.

Doesn't their role consist also of an awareness of the population to avoid potential wide community infections ...

All remains on the "from above" signals, and such signals, as the one by TV news sources, heavily lacked worldwide now.

Originally Posted by Muscade

Crédits: Siegfried

Swine flu cases jump by 30 percent
By Robert McCoppin | Daily Herald Staff
Contact writer

The number of swine flu cases in Illinois jumped by 35 percent over the weekend - but health officials maintain it's nothing to be alarmed about.
Total cases of the H1N1 virus, probable and confirmed, rose from 1,357 on Friday to 1,828 on Monday, an increase of 471 cases.

While the number of new cases had risen fairly steadily at a pace averaging 217 a week in the previous month, the rate tripled in the past week.

/.../

http://www.dailyherald.com/story/?id=299221

[Muscade]

Same “ordered” declarations on the Canadian side



Nunavut:

Despite the rising number of swine flu cases, Sobol maintained that the disease is no more serious than before.

http://www.cbc.ca/canada/north/story...u-nunavut.html


Quebec:

For Quebec, “it is thus a first case on more than 500, it is a sad history for the family, but for the general measures with the population, there are no changes”, underlines Dr. Poirier.

http://www.cyberpresse.ca/le-soleil/...s-a-quebec.php

[AlaskaDenise]

Originally Posted by niman

Commentary

Commentary

Swine H1N1 Explosion In The United States

Recombinomics Commentary 15:18
June 9, 2009

During week 21 (May 24 - 30, 2009), influenza activity decreased in the United States, however, there are still higher levels of influenza-like illness than is normal for this time of year.

Two thousand seventy-four (31.1%) specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories and reported to CDC/Influenza Division were positive for influenza.

The above comments, from the week 21 CDC report cite a decrease of flu activity in the United States, but measurement of activity is compromised by the announcements of states throughout the country of plans to limit testing to severe cases and clusters. Moreover, even for clusters, the number of samples tested is very small, so even when dozens or hundreds of students are swine H1N1 infected, the official tally for the outbreak is usually just one or two.

However, the ratios within the report indicate activity is high and increasing. For week 21, the flu detected is almost exclusively swine H1N1. Seasonal flu H1N1 was identified in just 4 samples, and only 36 tested positive for H3N2. In contrast there were 1558 confirmed swine H1N1 samples, as well as 148 unsubtypable samples which are awaiting swine H1N1 confirmations. Thus, over 95% of influenza A is swine H1N1 and this extends to all influenza infections, because only 17 samples were positive for influenza B.

These dramatic differences are due in part to declines in seasonal flu. Normally, there is no week 21 report, because the flu season for the northern hemisphere runs from week 40 to week 20, which is justified by the low levels of seasonal flu at this time.

However, swine H1N1 is a novel flu virus which has just entered the human population, so natural immunity is limited. Moreover, the swine H1N1 has an avian PB2, which has optimal activity at 41C, in contrast to seasonal flu, which is most active at 33 C. Thus, the swine H1N1 is expanding in the warm off season.

This is most easily seen in the detection frequency, which, as noted above was 31.1% for week 21. This level is higher than the 25.1% in week 6, which was the peak week for flu in the 2008/2009 season. Thus, even though testing has been largely scaled back, the detection frequency is at record levels and above the peak week in February, reported at the height of the seasonal flu season.

The effect of the limited testing can be see in a recent Effect Measure blog from the Boston area, where flu activity is increasing (see Maps). All six members of the Revere''s extended family had flu symptoms, and one family member was tested and was influenza A positive. The high incidence of swine H1N1 throughout the country, and the dramatic acceleration in the Boston area, leaves little doubt that the 100% attack rate is due to an aggressive swine H1N1. Similarly, the range of symptoms in the family members also highlights reasons behind the lack of testing, since many members had relatively mild symptoms. Similarly, flu-like symptoms were widespread at the associated pre-school, but there was no indication that the school would close or notify parents of the widespread infections. Similarly, the lack of additional testing on the influenza A positive patients strongly suggests that none of these H1N1 infected cases will be reported. However, the high level of swine H1N1 at this time allows for a close approximation by simply measuring influenza A and tabulating people with influenza-like symptoms.

The lack of reporting has create a false impression of the extent of spread. Similarly, the mild nature of most infections has blunted the impact of the fatal infections of patients between the ages of 20-55. Normally, 90% of flu infections are in patients 65 or older. The swine flu however targets younger patients, and most deaths are in this younger age group.

Moreover, severe cases are on the rise. Manitoba just asked for an additional 15 ventilators to treat patients in Winnipeg. The vast majority of the 26 patients currently on ventilators are in the 20-55 age group, and more than half are from the aboriginal population.

The high frequency of the severe influenza in these patients raises concerns that the accelerating spread of swine H1N1 worldwide will lead to severe cases in selected populations in Asia and Africa, leading to additional concerns.

Thus far, the 2009 pandemic parallels the 1918 pandemic, which was a swine H1N1 that had moved into a human population in the spring of 1918, leading to mild cases. However, the virus turned lethal in the fall, after adapting to its human hosts, which devastating consequences, including the deaths of 20-50imillion people, which were largely in the 25-44 age group.

The increasing parallels between the pandemics of 2009 and 1918 continue to create increasing concerns.

.

[jeanne]

http://www.breakingnews.ie/world/eykfeykfsney/rss2/


Sharp increase in number of swine flu deaths
Print09/06/2009 - 18:52:24
There's been a sharp rise in the number of worldwide deaths blamed on swine flu.

249 people are thought to have died after contracting the H1N1 virus - a rise of 90 in the last 24 hours.

More than 26-thousand people in 73 countries including Ireland have contracted the virus.

The World Health Organization says it's likely to continue spreading.



Related Links:
09/06/2009 WHO: Flu pandemic may be happening
09/06/2009 Sharp increase in number of swine flu deaths
06/06/2009 Fourth case of swine flu confirmed in North
06/06/2009 Number of UK swine flu cases passes 500 mark
02/06/2009 Swine flu outbreak 'getting closer to pandemic'
02/06/2009 Second case of swine flu in North
02/06/2009 Three more cases of swine flu in Ireland
31/05/2009 Fourth Irish case of swine flu in confirmed
30/05/2009 Eleven more swine flu cases confirmed in the UK
28/05/2009 Second swine flu outbreak on cruise ship
27/05/2009 Dept of Health confirms third swine flu case
25/05/2009 Second Irish swine flu case confirmed
23/05/2009 Russia confirms first swine flu case
23/05/2009 Two more cases of swine flu confirmed in UK
22/05/2009 Flu alert lowered in Mexico City
20/05/2009 Swine flu cases top 10,000 mark
19/05/2009 Four new swine flu cases in UK
17/05/2009 UK swine flu cases pass 100 mark
15/05/2009 Third Texan death from swine flu confirmed
15/05/2009 Countries urged to share swine flu samples

http://www.breakingnews.ie/world/eyk...xzz0Hy0VG9BI&D

looks like we're off!

[Muscade]

51 new cases today for a total of 593. The cases in Quebec doubled in one week.
June 9: 593
June 2: 307

[AlaskaDenise]

Do we know if early (1916 or 1917) 1918 A/H1N1 contained the lethal NS1/92 mutation? If it was acquired in 1918, how much did that add (% of lethal mutations) to it's lethality? I've often wondered where it comes from, given that it isn't in the seasonal human flu. Where does it hide, or is it self-initiating like the polybasic cleavage site? I wonder if in 1918, it was present in a circulating avian flu, just like today.

I tried to look up early sequences in the NCBI database & couldn't find any (even only HA) prior to 1918.

.

[wotan]

To my knowledge the only samples of 1918 H1N1 that have been sequences are post 1st wave. I certainly don't recall having read of any. And right now, that would be some handy information to have.

[AlaskaDenise]

Originally Posted by wotan

To my knowledge the only samples of 1918 H1N1 that have been sequences are post 1st wave. I certainly don't recall having read of any. And right now, that would be some handy information to have.

I was hoping they might be sequestered in a private database.

(added) I just searched for ANY species A/H1N1/HA prior to Dec 1917, and the database came back with zero. !

.

[ironorehopper]

Originally Posted by AlaskaDenise

Do we know if early (1916 or 1917) 1918 A/H1N1 contained the lethal NS1/92 mutation? If it was acquired in 1918, how much did that add (% of lethal mutations) to it's lethality? I've often wondered where it comes from, given that it isn't in the seasonal human flu. Where does it hide, or is it self-initiating like the polybasic cleavage site? I wonder if in 1918, it was present in a circulating avian flu, just like today.

I tried to look up early sequences in the NCBI database & couldn't find any (even only HA) prior to 1918.

.

I think that no entry before 1918 is due to the fact that the only 1918 human pandemic virus samples were result of a laboratory re-construction rather than isolation from samples collected on the field. The research done in frozen soil to exumate corpses of individuals died by spanish flu resulted in the discovery of viral fragments, subsequently re-built, in fact creating hybrids.

...

[AlaskaDenise]

Yes, the first sample was Brevig Mission frozen human.

I thought someone had some very old bird samples, from birders. However, not being well preserved they may have been far less than complete segments.

.

[HenryN]

Originally Posted by ironorehopper

I think that no entry before 1918 is due to the fact that the only 1918 human pandemic virus samples were result of a laboratory re-construction rather than isolation from samples collected on the field. The research done in frozen soil to exumate corpses of individuals died by spanish flu resulted in the discovery of viral fragments, subsequently re-built, in fact creating hybrids.

...

I believe there is a 1902 chicken isolate from Japan. For Breveg Mission, the viral genes were from a frozen victim (which I believe is true for all 1918 sequences).

[Siegfried X]

On the other hand today is the last day of school in my area. I wonder if three months without school will dampen the flu in the USA since most flu victims are under 25 years old.

[wotan]

Where do they spend those 3 months? Daycare? Hanging out with friends at the mall?

[Mamabird]

Originally Posted by AlaskaDenise

Do we know if early (1916 or 1917) 1918 A/H1N1 contained the lethal NS1/92 mutation? If it was acquired in 1918, how much did that add (% of lethal mutations) to it's lethality? I've often wondered where it comes from, given that it isn't in the seasonal human flu. Where does it hide, or is it self-initiating like the polybasic cleavage site? I wonder if in 1918, it was present in a circulating avian flu, just like today.

I tried to look up early sequences in the NCBI database & couldn't find any (even only HA) prior to 1918.

.

The pandemic 1918 virus did not have the "lethal NS1 92 mutation". Only a very few earl H5N1 viruses have had this characteristic. It is rare.

[Siegfried X]

Where do they spend those 3 months?

In front of the television, maybe playing video games.