New flu virus (novel, non-pandemic) attacks three Saskatchewan hog barn workers

[HenryN]

Originally Posted by pflu

Yes...


Genetic and antigenic characterization — The pandemic that began in March 2009 was caused by an H1N1 influenza A virus that had not been recognized previously in pigs or humans, although six of its eight gene segments were similar to ones previously detected in triple reassortant swine influenza viruses in pigs in North America [16]. This strain represents a quadruple reassortment of two swine strains, one human strain, and one avian strain of influenza

http://www.utdol.com/home/content/to...pulm_inf/18836

No. The quadruple comes from two different swine (North American and Eurasian). There is ONE human gene (H3N2 PB1). The composition of the virus is well known and based on phylogentic analysis.

[HenryN]

Originally Posted by pflu

Pandemic Swine 1 Includes...

The largest proportion of genes comes from swine influenza viruses (30.6 percent from North American swine influenza strains, 17.5 percent from Eurasian swine influenza strains), followed by North American avian influenza strains (34.4 percent) and human influenza strains (17.5 percent)

http://www.uptodate.com/home/content...pulm_inf/18836


Does anybody know what seasonal influenza strains make up that 17.5% (presumably it's H1N1)?

No. The human part is just PB1 (from H3N2). H1 is North American swine. N1 is Eurasian swine.

[pflu]

Originally Posted by niman

No. The quadruple comes from two different swine (North American and Eurasian). There is ONE human gene (H3N2 PB1). The composition of the virus is well known and based on phylogentic analysis.

So you are saying the people who wrote the article I quoted are wrong...

http://www.utdol.com/home/content/to...pulm_inf/18836


Here are the credentials...

Author

Anna R Thorner, MD
Deputy Editor — Infectious Diseases
Instructor in Medicine
Harvard Medical School
Section Editor

Martin S Hirsch, MD
Editor-in-Chief — Infectious Diseases
Editor — Viral Infections
Professor of Medicine
Harvard Medical School
Deputy Editor

Barbara H McGovern, MD
Deputy Editor — Infectious Diseases
Associate Professor of Medicine
Tufts University School of Medicine

[HenryN]

Originally Posted by pflu

So you are saying the people who wrote the article I quoted are wrong...

http://www.utdol.com/home/content/to...pulm_inf/18836


Here are the credentials...

Author

Anna R Thorner, MD
Deputy Editor — Infectious Diseases
Instructor in Medicine
Harvard Medical School
Section Editor

Martin S Hirsch, MD
Editor-in-Chief — Infectious Diseases
Editor — Viral Infections
Professor of Medicine
Harvard Medical School
Deputy Editor

Barbara H McGovern, MD
Deputy Editor — Infectious Diseases
Associate Professor of Medicine
Tufts University School of Medicine

No. I am saying you can't interpret what they said.

[pflu]

Originally Posted by niman

No. I am saying you can't interpret what they said.

"Genetic and antigenic characterization — The pandemic that began in March 2009 was caused by an H1N1 influenza A virus that had not been recognized previously in pigs or humans, although six of its eight gene segments were similar to ones previously detected in triple reassortant swine influenza viruses in pigs in North America [16]. This strain represents a quadruple reassortment of two swine strains, one human strain, and one avian strain of influenza"


So pandemic H1N1 is not Quadruple reassortment, I interpreted the above incorrectly?

[HenryN]

Originally Posted by pflu

"Genetic and antigenic characterization — The pandemic that began in March 2009 was caused by an H1N1 influenza A virus that had not been recognized previously in pigs or humans, although six of its eight gene segments were similar to ones previously detected in triple reassortant swine influenza viruses in pigs in North America [16]. This strain represents a quadruple reassortment of two swine strains, one human strain, and one avian strain of influenza"


So pandemic H1N1 is not Quadruple reassortment, I interpreted the above incorrectly?

As has been known since the sequences were released months ago, the pandemic H1N1 is similar to swine isolates seen previously, which have ONE human flu gene segment (PB1). two avian flu genes segemnts (PB2 and PA), and 5 swine segments. Because it had gene segment from three species it was called a triple reassortment The "novel" part was thought to be due to the fact that the SWINE genes had two origins (HA was SWINE from North America and NA from SWINE from Eurasian). However, subsequent analysis showed that the combination was not new. It had been seen in Thailand previously, and a more recent paper has described it in swine in Hong Kong (for MANY years).

Although the current pandemic H1N1 can now pass easily from H2H, it was SWINE H1 and SWINE N1. The ONLY human gene segment is PB1.

You have managed to misinterpret comments by others to mean that there were human flu genes other than PB1 involved (like H1 or N1?), which is WRONG.

No one is saying that H1 or N1 are human except you (and probably some others on the internet who couldn't read a gene sequence if their life depended on it).

[HenryN]

Originally Posted by pflu

Pandemic Swine 1 Includes...

The largest proportion of genes comes from swine influenza viruses (30.6 percent from North American swine influenza strains, 17.5 percent from Eurasian swine influenza strains), followed by North American avian influenza strains (34.4 percent) and human influenza strains (17.5 percent)

http://www.uptodate.com/home/content...pulm_inf/18836


Does anybody know what seasonal influenza strains make up that 17.5% (presumably it's H1N1)?

No PRESUMPTIONS required. Seasonal (H3N2) genes are ONLY in PB1 (from 1993). H1 and N1 are SWINE. There are NO seasonal H1N1 genes in pandemic H1N1.

[HenryN]

Originally Posted by niman

Please. As has been known since the sequences were released months ago, the pandemic H1N1 is similar to swine isolates seen previously, which have ONE human flu gene segment (PB1). two avian flu genes segemnts (PB2 and PA), and 5 swine segments. Because it had gene segment from three species it was called a triple reassortment The "novel" part was thought to be due to the fact that the SWINE genes had two origins (HA was SWINE from North America and NA from SWINE from Eurasian). However, subsequent analysis showed that the combination was not new. It had been seen in Thailand previously, and a more recent paper has described it in swine in Hong Kong (for MANY years).

Although the current pandemic H1N1 can now pass easily from H2H, it was SWINE H1 and SWINE N1. The ONLY human gene segment is PB1.

You have managed to misinterpret comments by others to mean that there were human flu genes other than PB1 involved (like H1 or N1?), which is WRONG.

No one is saying that H1 or N1 are human except you (and probably some others on the internet who couldn't read a gene sequence if their life depended on it).

Just to clarify, pflu asked which "strain" contributed the human genes and assumed it was H1N1. I took that to mean that he thought the H1 and N1 were human, but on a re-read, (s)he didn't specifically say H1 and/or N1 were human.

The bottom line is that there are NO human H1N1 genes in pandemic H1N1. It is H1N1 because the H is swine H1 and the N is swine N1 (but from North American and Eurasian swine respectively). There is only one human gene segment in pandemic. It is seasonal flu PB1 introduced into swine H3N2 reassortants in 1993.

The subject of this thread however is the novel swine isolates in farm workers in Canada, which DO appear to have human H1 and N1 (circa not given) and the other 6 gene segments may match pandemic H1N1 (or may match other triple reassortants, which are distinct from the pandemic sequences, but have the same constellation of genes).

[gsgs]

depends just how you define it.

"triple reassortment" is not just 3 different viruses infecting one
cell and mixing but rather 2 consecutive "normal" reassortments.

If another 3rd reassortment happens 10 years later,
shall we add it to the other 2 and call it "quadruple" ?

interpret quadruple

[HenryN]

Originally Posted by gsgs

depends just how you define it.

"triple reassortment" is not just 3 different viruses infecting one
cell and mixing but rather 2 consecutive "normal" reassortments.

If another 3rd reassortment happens 10 years later,
shall we add it to the other 2 and call it "quadruple" ?

interpret quadruple

It has been defined MANY times. The additional (4th) reassortment is between North American and Euransian swine gene segments (but since H1 and N1 are human in the latest version, the H and N swine combos have been replaced).

The subject of this thread is the new H1N1 (wth human H1 and N1) in Canadian farm workers (and who ever infected them).

[gsgs]

are there swine with normal seasonal human H1N1 ?

I remember, some strains went from humans to swine but don't exactly
remember which and when.

So, the human H1N1 could have been circulating S2S , parallel
to circulating "triple reassortant" and then one swine got both...

Or one swine with triple reassortant got another virus from a human,
by droplet or food or

[HenryN]

Originally Posted by gsgs

are there swine with normal seasonal human H1N1 ?

I remember, some strains went from humans to swine but don't exactly
remember which and when.

So, the human H1N1 could have been circulating S2S , parallel
to circulating "triple reassortant" and then one swine got both...

Or one swine with triple reassortant got another virus from a human,
by droplet or food or

Two of the Canadian swine (from 2003/2004) had human H1 and N1 (circa 2003). A VERY high percentage of recent swine H1N1 have human H1 and N1 (circa 2003 and 2007), so I really don't understand what you are asking? Almost all of the H1 sequences from US swine temporarily released from Los Alamos were human H1.

[HenryN]

New H1N1 Flu Strain From Pig Farm Found in Canada (Update1)


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By Tom Randall
July 7 (Bloomberg) -- A new strain of H1N1 flu sickened at least two workers at a pig farm in Saskatchewan, Canadian health officials said. Tests found the strain is different from the pandemic swine flu circulating the globe.
The two people recovered from mild illness, and a third case is under investigation, according to a government statement. Pigs from the farm tested positive for a common version of swine flu and didn’t carry the new human version found in the workers.
The risk of the virus is considered low, though disease trackers are testing other workers and continuing to monitor herds, the government said. Health officials worldwide are on heightened alert after a human swine flu virus, identified in April, flashed across the globe infecting at least 1 million people in the U.S. alone, according to the U.S. Centers for Disease Control and Prevention.
“Preliminary results indicate the risk to public health is low,” said Leona Aglukkaq, Canada’s health minister, in the statement. “Canadians who have been vaccinated against the regular, seasonal flu should have some immunity to this new flu strain.”
The new Canada strain is made up of genes from human seasonal flu and genes from swine flu viruses, according to the statement from the Public Health Agency of Canada.
To contact the reporter on this story: Tom Randall in New York at trandall6@bloomberg.net.
Last Updated: July 7, 2009 19:17 EDT

http://www.bloomberg.com/apps/news?p...d=aUAzwSOYmR3g

[HenryN]

Originally Posted by niman

New H1N1 Flu Strain From Pig Farm Found in Canada (Update1)


Share | Email | Print | A A A



By Tom Randall
July 7 (Bloomberg) -- . Pigs from the farm tested positive for a common version of swine flu and didn’t carry the new human version found in the workers.

http://www.bloomberg.com/apps/news?p...d=aUAzwSOYmR3g

This is a MAJOR problem.

[DeniseMc]

If the workers got the flu from the swine, then how did the swine not have the same flu? Makes no sense. What are they not telling us. And are they testing the workers' families, contacts?

[Lizw]

Originally Posted by DeniseMc

If the workers got the flu from the swine, then how did the swine not have the same flu? Makes no sense. What are they not telling us. And are they testing the workers' families, contacts?

I think the assumption is that reassortment or recombination occurred in the workers, who were already infected with one strain, and then contracted a different strain from the pigs. As Dr. Niman has pointed out, that's a major concern. I would be astonished if the workers' families and contacts were not being tested.

[HenryN]

Originally Posted by DeniseMc

If the workers got the flu from the swine, then how did the swine not have the same flu? Makes no sense. What are they not telling us. And are they testing the workers' families, contacts?

They are saying the swine did not have the same virus, strongly suggesting the workers were infected elsewhere (with H2H a real possibility - they also are not giving disease onset dates for the 2 or THREE workers - the third worker may have been infected by the first 2).

[HenryN]

Originally Posted by Lizw

I think the assumption is that reassortment or recombination occurred in the workers, who were already infected with one strain, and then contracted a different strain from the pigs. As Dr. Niman has pointed out, that's a major concern. I would be astonished if the workers' families and contacts were not being tested.

I think the main issue on H2H is upstream, not downstream.

[gsgs]

workers with seasonal flu at this time of year is unlikely.
More likely that they didn't find the swine with seasonal human flu
or the new reassortant yet

they should know, if the same HA and NA circulated this season in Canada

[pflu]

gsgs made a very good point earlier that the mutation likely occurred earlier in the year because very little seasonal H1N1 is circulating now.

If this thing has in fact been around for a few months, more cases are going to surface.

[HenryN]

Originally Posted by pflu

gsgs made a very good point earlier that the mutation likely occurred earlier in the year because very little seasonal H1N1 is circulating now.

If this thing has in fact been around for a few months, more cases are going to surface.

The number of known swine H1N1's with human H1 and N1 is VERY large and they have been around for MANY years (including H1 and N1 from 2003 as well as 2007).

[pflu]

The reports says that these guys were sick in the middle of June, 3 weeks ago. They obviously new what this was several weeks ago, what prompted the sudden media release?

I'll bet there is already more to this story that we haven't heard.

[HenryN]

Originally Posted by pflu

The reports says that these guys were sick in the middle of June, 3 weeks ago. They obviously new what this was several weeks ago, what prompted the sudden media release?

I'll bet there is already more to this story that we haven't heard.

The release is linked to the analysis. The reports have already stated that initial data pointed to swine and human, which then led to human with swine genes, which then led to sequencing of many or all genes, which then led to media story on a novel virus.

[pflu]

Originally Posted by niman

The release is linked to the analysis. The reports have already stated that initial data pointed to swine and human, which then led to human with swine genes, which then led to sequencing of many or all genes, which then led to media story on a novel virus.

It was a rhetorical question.

[HenryN]

Originally Posted by pflu

gsgs made a very good point earlier that the mutation likely occurred earlier in the year because very little seasonal H1N1 is circulating now.

If this thing has in fact been around for a few months, more cases are going to surface.

Earlier in the year based on what????

I didn't see anything that said it was a contemporary human H1 and N1. In fact the comments that current vaccines would offer "some" protection suggested it was NOT 2008/2009. Similarly, the lack of any comments on H274Y (Tamiflu resistance) would also suggested it was NOT 2008/2009. Moreover, as mentioned earlier, there are MANY swine H1N1 isolates with human H1 and N1 which are from human seasonal flu from 2007 and 2003.

[pflu]

Originally Posted by niman

Earlier in the year based on what????

I didn't see anything that said it was a contemporary human H1 and N1. In fact the comments that current vaccines would offer "some" protection suggested it was NOT 2008/2009. Similarly, the lack of any comments on H274Y (Tamiflu resistance) would also suggested it was NOT 2008/2009. Moreover, as mentioned earlier, there are MANY swine H1N1 isolates with human H1 and N1 which are from human seasonal flu from 2007 and 2003.

I don't know, just ignore what I said

[HenryN]

New Flu Virus Found In Canadian Pig Farm Workers

Featured Article
Main Category: Swine Flu
Also Included In: Flu / Cold / SARS; Veterinary
Article Date: 08 Jul 2009 - 2:00 PDT



The Canadian authorities have announced that a new strain of influenza A virus has been found in two pig farm workers in the Province of Saskatchewan but it is not a new strain of A(H1N1) pandemic swine flu.

In a press statement released yesterday, 7 July, the Public Health Agency of Canada (PHAC) said they were working closely with the health authority in the Province of Saskatchewan to "assess the public health risk from a new strain of influenza" that had been detected in two workers on a hog farm in the province.

An investigation by scientists at the National Microbiology Laboratory of the PHAC in Winnipeg, found that the new strain contains genes from human seasonal flu and swine flu viruses. However, it is not a new strain of the pandemic A(H1N1) flu virus that has killed more than 400 people worldwide and contains human, swine and avian flu genes.

Chief Public Health Officer of Canada, Dr David Butler, said:

"As required under the WHO's International Health Regulations, Canada has notified the WHO about the detection of this novel influenza virus."

Since the pandemic alert countries like Canada that have a large pig farming industry have increased animal and human flu surveillance.

The workers were only mildy ill and have since made a full recovery, while a third case is still being investigated, said the PHAC.

According to a Reuters news report, Dr Greg Douglas, chief veterinary officer for Saskatchewan, said that the new virus contained genes from a seasonal H1N1 human flu strain and a flu virus commonly found in pig herds called triple reassortant H3N2.

Health Minister Leona Aglukkaq told the press that the national authorities were working closely with the province of Saskatchewan to find out as much as possible about the new flu virus.

"Preliminary results indicate the risk to public health is low and that Canadians who have been vaccinated against the regular, seasonal flu should have some immunity to this new flu strain," said the Health Minister.

Butler added that:

"The Government of Canada remains vigilant and we will continue to keep Canadians informed of any new developments."

Government investigators have also tested some of the pigs on the farm where the infected workers worked, and found that some were infected with swine influenza A, which is not uncommon among pig herds on farms.

However, the PHAC said there was no evidence that the new strain found in the workers was present in the pigs.

Douglas added that the infected herd did not show unusually high signs of illness. He said pig herds often got the flu and it usually only affects them mildly.

He reminded the press that this was not a food safety issue but a human health issue and that "Saskatchewan pork continues to be safe".

Investigations are continuing, with PHAC scientists working with Saskatchewan public heath officials to monitor workers on the affected farm and in the rest of the province's pig industry.

The Canadian Food Inspection Agency (CFIA) is also advising on how best to keep an eye on the swine herds and carrying out diagnostic tests in support of the preliminary tests carried out at the national labs in Winnipeg.

Source: Public Health of Canada, Reuters.

Written by: Catharine Paddock, PhD
Copyright: Medical News Today
http://www.medicalnewstoday.com/articles/156692.php

[HenryN]

Commentary

[gsgs]

do we have a good short review of genetical diversity of swine H1N1
(and H1N2) since 1998 (in North America)


until 1998 there was just only classical swine-flu (H1N1) in pigs
in North America, right ?



1979 avian virus to swine in Europ, all 8 degments AAAAAAAA
1998 triple reassort in North America AHASSSSS
swine H1N2


I found something about human H1N1 in swine in China


--------edit-----------------
human H1 in American swine:
49 >A/swine/Saskatchewan/18789/02(H1N1)
50 >A/swine/IL/00685/2005(H1N1)
51 >A/swine/North Carolina/63607-39/2008(H1N1)
52 >A/swine/North Carolina/63607-10/2008(H1)
53 >A/swine/NC/00573/2005(H1N1)
54 >A/swine/Ohio/K1130/06(H1N1)
55 >A/swine/Ohio/K1207/06(H1N1)
56 >A/swine/Ontario/48235/04(H1N2)
57 >A/swine/Ontario/55383/04(H1N2)
58 >A/swine/Ontario/52156/03(H1N2)
59 >A/swine/Minnesota/63607-7/2008(H1N1)
60 >A/swine/IL/07003243/2007(H1N2)
61 >A/swine/Minnesota/SG-00239/2007(H1N2)
62 >A/swine/Minnesota/225-10/2008(H1N1)
63 >A/swine/Iowa/63607-34/2008 (H1N1)

[HenryN]

Originally Posted by niman

If it is recent seasonal H1N1, then it is also Tamiflu resistant.

Confirmed.