Pandemic News/Awareness - Thread 3

promed to report suspect cases from indonesia

http://afludiary.blogspot.com/2008/08/promed-to-report-suspect-cases-from.html

kudos to promed for responding and taking this stance.

a week ago promed mail, the global electronic reporting system for the

international society for infectious diseases, announced that due to the

inability to confirm h5n1 case reports coming out of indonesia, they would

no longer carry reports of `suspected cases'.

following a week of public comment, most of which urged that promed

continue to report on suspect cases... promed has reversed their decision

with this announcement today.

promed-mail has now decided to report all suspected human

cases of h5n1 from indonesia because the usual flow of information

-- first suspect and then confirmation -- is disrupted there because of their

public health policy.

http://www.recombinomics.com/news/08180801/h5n1_promed_resumes.html

the length of the reporting delays is unclear, as is the reason for the failure

of who to report lab confirmed h5n1 cases.

...neither indonesia nor who has commented on the three fatal cases

in north sumatra. associated poultry has tested positive for h5n1, but

recent deaths in the area have been attributed to dengue hemorrhagic

fever, which has symptoms that approximate bird flu.

clearly it is time for more transparency in indonesia, official indonesian

reports notwithstanding.

who has the authority to investigate suspect h5n1 cases and they have

an obligation to report the results of such investigations. it is time for who

to follow the promed lead and increase transparency in indonesia, by

releases human h5n1 sequences generated since the indonesian blackout

from the beginning of 2007, and provide timely situation updates on lab

confirmed cases, including those from july of this year and the three fatal

suspect cases this month.

with permission from effect measure:

antibodies from survivors of 1918 era pandemic

antibodies to the 1918 virus still present in elderly folks after 90

years. wow! who knew?

news reports that nonagenarians had robust antibodies against the

1918 flu strain were intriguing on several levels but i wasn't sure how

many doors were still open to these being antibodies that developed

in the years after 1918. after all, the 1918 subtype was h1n1 which

circulated freely until the 1950s when it was displaced by the next

pandemic strain, h2n2. h2n2 in turn was pushed aside by h3n2 in

1968. then h1n1 returned in 1977 (some say it escaped from a

russian laboratory) and since then h3n2 and h1n1 have been co-

circulating. some years are predominantly h1n1, some predominantly

h3n2, with h3n2 years tending to be more severe flu seasons. how do

we know the people studied in the new paper didn't get their antibodies

well after 1918? so i took a look at the paper, just published in nature,

and it answered my questions and then some. it is fascinating work on

many levels. what's it about?

the authors identified people still alive from the 1918 period and looked

to see if they had antibodies in their blood to the flu variant of the 1918

pandemic:

we identified a panel of 32 subjects aged 91-101 years (that is, aged

from 2 to 12 in 1918), many of whom recalled a sick family member

in the household during the pandemic, which suggested direct exposure

to the virus. of the subjects tested, 100% had serum-neutralizing activity

against the 1918 virus (mean titre 1:562), and 94% had serologic

reactivity to the 1918 ha (as indicated by haemagglutination inhibition

assay (hai) titres of 1:40 or greater; mean titre 1:396), even though

these samples were obtained nearly 90 years after the pandemic. in

contrast, subjects born after the pandemic had markedly lower rates of

positive serum-neutralizing tests against the 1918 virus (9 out of 10

subjects born 1926-35 had titres

1936-45 had titres 1:40, 9 out of 10 subjects born 1946-55 had titres

1:40). (yu et al., nature)

here's what this means. the authors tested the blood of these aged

survivors and found that they had antibodies in their blood that could

prevent infection (neutralization) or reacted with a specific surface

protein (hemagglutinin inhibition) of the 1918 virus. when they looked

in the blood of people born and living at various times removed from

1918 they found lower and lower rates of anti-1918 activity (measured

various ways). but they did more than that.

the antibodies in our blood are produced by a specific type of immune

cell, called a b-cell. each b-cell produces only one antibody. so we need

a different b-cell for each thing we need an antibody against. the

immune system is a marvelous device that educates b-cells to produce

the right kind of antibodies when it is exposed to an antigen (an antigen

is a protein that can call forth an antibody response). once the antigen is

no longer present (the infection is over with, often with the help of the

antibody), a few of the antibody specific b-cells hang around to act as

long term memory so that if the antigen ever shows up again the body

can react swiftly. it doesn't have to learn to make the antibody again

but merely gives the signal to make many copies of the memory cells.

this is called clonal expansion and it's like having the blueprint on the

shelf so when a new order comes you can start the manufacturing

process right away. no new design needed. no delay. that's how

vaccines work. they induce the body to make memory b-cells so the

next time the tetorifice or polio or anthrax antigen comes along you are

good to go.

it's not a certainty, though, that a particular memory b-cell will last

your whole life (and since my memory is not so good these days, this

is especially plausible to a geezer like me). but this paper seems to

show that for some people, at least, the 1918 memory b-cells are still

around after 90 years. but wait, there's more. the research team

isolated the b-cells from their subjects and found the ones that were

making the antibodies against the virus. they then "immortalized"

these b-cells by fusing them with blood cancer cells to produce clonal

cultures of b-cells that only made one antibody. since different spots

on the virus visible to the immune system might elicit specific antibody

responses (these features are called epitopes), there might be more

than one distinct antibody against any particular virus. indeed the

researchers were successful in producing five distinct monoclonal

antibodies against the 1918 virus. this is very pretty work and there

are a lot of details i haven't gone into with this brief description, but

suffice to say the data convinced me that they really were looking at

the immune response to the 1918 virus and not some subsequent

virus which just cross-reacted with the 1918 virus. there are still a few

alternative possibilities but i think this paper does a good job of making

the case the antibodies are from 1918 memory cells.

we still don't know how typical these people are. after all, they

apparently didn't get sick in 1918 despite being infected and they have

a good enough immune system to last into their nineties. maybe most

of us aren't so lucky and have waning immunity with the years. but this

is some slick work and now that we have the actual antibodies in

sufficient quantity to study we can begin to ask what features of the 1918

virus made it vulnerable. how much of this is transferable to bird flu, the

current pandemic worry, is difficult to say. these antibodies didn't protect

against or react with h5 flu viruses so they aren't a therapy for bird flu.

but understanding the basic science of influenza virus is always a plus.

this is fascinating science. and for a scientist, that's a big deal.

the editors of effect measure are senior public health scientists and

practitioners. paul revere was a member of the first local board of

health in the united states (boston, 1799). the editors sign their posts

"revere" to recognize the public service of a professional forerunner

better known for other things.

Rhode Island

http://www.recombinomics.com/News/08210801/H7N3_RI.html

http://www.flutrackers.com/forum/showpost.php?p=175466&postcount=7

http://www.flutrackers.com/forum/showpost.php?p=175589&postcount=8

Rhode Island, the Ocean State is a tiny jewel of a place that can be crossed

from end to end by car in an hour. Many, many migrant water fowl winter

there, and there is a large resident population of Canadian Geese, and Mute

Swans year round.

The swans are very territorial, and rather cantankerous at times.

They say that getting hit by a swan's beak could break a man's arm,

and I believe it. They are big and powerful birds. Swan populations are

kept at a certain determined level by wardens finding the nests and shaking

the eggs. This is better than killing the swans which the local people would

never tolerate.

Swans are such big birds, much bigger than Canadian Geese. I once

watched a swan in full threat display chase a Canada Goose across a lake

over on the grounds of the Providence Zoo. That goose knew he was in

trouble as the swan was not giving up the chase.

There are swans in many of the lakes, rivers, swamps, and bays throughout

the area. They are beautiful birds. Apparently, the state has chosen them

as sentinels to screen for bird flu. A good choice as these birds are not

migrants, and probably stay in the area.

Speaking of migrants, when I lived in RI, my cottage was only three houses

from the bay. I once sat in my car silently watching hundreds of water fowl

floating in a cove near the shore. I was attracted to the spot because a

young black cat was hiding behind a rock observing them also. He made

the mistake of running out after some small land birds, and his momentum

took him almost to the water's edge. A very large, migrant snow goose

reared up from the water, hissed, almost striking him with a vicious beak.

The little cat was tiny compared to that bird, and it is easy to forget how big

these birds can be. Seeing the cat moving rapidly backwards was one of

the funniest natural events that I have ever witnessed.

So, here's the point of this post. H7 is another type of bird flu. Found

in some swans probably a while ago since they have already sub typed it,

they have as usual not revealed the viral sequences in any public

data bases as of yet. Rhode Island small as it is, has farms with chickens.

Farmers have been warned especially in the immediate area where the

swans are, about biosecurity requirements, and farmers around the state

are urged to test their flocks even farms away from waterways. Why?

Well, I would guess, it is because of the tremendous population of Canada

Geese always present in the area, swimming in the same waters as

the swans. And, where do they do lunch, but the farm fields of course,

(not to mention all of the local school fields, but that is another story and

another source of concern).

If poultry begin dying, they will cull all of the flocks to prevent a highly

pathogenic virus from mutating from what is probably a low pathogenic

origin. After all, the swans are not dying so this is most likely a low path

virus, but it's present in Rhode Island waterways if the birds have it.

Humans can be infected with H7 viruses, and usually those infections are

mild...

And as always, there is the possibility though at this time perhaps remote,

that birds co-infected with H5N1 as well as H7 viruses will allow H5N1 to

gain the ability to easily infect mammals learned from H7. That is another

reason why bird flu of any type is being tracked in the USA as in other

countries.

WHO: Oseltamivir Resistance In Seasonal Flu Continues To Spread

http://afludiary.blogspot.com/2008/08/who-oseltamivir-resistance-in-seasonal.html

This is not good.

We are talking about antiviral resistance in H1N1, a seasonal flu. It appears

to be resistant now in many countries to our most commonly used drug,

Tamiflu.

Here is the problem with this. H1N1, you can be vaccinated against.

If you get it, you will get very sick, and some, mostly the elderly or the

very young, may die.

For H5N1, there is no immunity and no vaccination, so if a flu victim has

this virus all bets are off. They could die or end up permanently disabled if

they survive. Most countries are stockpiling Tamiflu to treat this virus

in a pandemic event though there is not nearly enough to treat most

of any population.

Now we are seeing Tamiflu resistance in one type of influenza H1N1,

caused by a single nucleotide polymorphism, piece of virus called an SNP

(pronounced snip), H274Y.

There have been a few cases of bird flu, H5N1 that also had H274Y,

and all of those people died despite Tamiflu treatment.

Here is our concern. H274Y is now apparently widespread in H1N1

infections whether or not the hosts were treated with Tamiflu, and most

were not. Is it only a matter of time before a human being will contract

both H5N1 and H1N1 together? We might then see more cases of H5N1

where Tamiflu does not help the victims at all, and that is a very sobering

thought in a disease with an over 60% CFR because this drug is the only

major defence that we have against the spread of bird flu at this time.

This is it, folks, our major weapon. Every other defense we have involves

the layered mitigation strategies of isolation, culling infected animals, and

social distancing of populations, but no other medications or vaccines

because there are none.

...up until very early this year very few instances of resistance to this drug

had been encountered.

On January 25th, 2008 Norwegian authorities notified the WHO (World

Health Organization) of a sudden high rate of resistance to Tamiflu among

12 of 16 samples (75%) collected in late 2007.

Recombination Drives Global Spread of H1N1 Tamiflu Resistance

http://www.recombinomics.com/News/08230801/H274Y_Global_Recombination.html

"What we're seeing is the evolution of the resistance gene and the

distribution of it throughout the world,'' said Lance Jennings, a clinical

virologist with the Canterbury District Health Board in Christchurch, New

Zealand, who is chairman of the Asia-Pacific Advisory Committee on

Influenza.

"We have a lot to learn about the molecular epidemiology of influenza

viruses.''

Reoccurrence of H5N1 in Benin, West Africa

http://www.flutrackers.com/forum/showthread.php?t=77864

http://en.wikipedia.org/wiki/Image:LocationBenin.svg

Discovered in a routine check, bird flu was present in poultry

at a market in Lokossa. An OIE report was filed.

Benin is bounded on the N by Niger, on the E by Nigeria, on the S by

the Gulf of Guinea (Atlantic Ocean), on the W by Togo, and on the

NW by Burkina Faso.

Affected population

Live chickens purchased at the market in Lokossa as part of the

routine surveillance and of the training of managers and other

laboratory officials on biomolecular techniques at the Veterinary

Laboratory of Parakou.

H1N1 flu viruses growing more resistant to Tamiflu

http://www.cidrap.umn.edu/cidrap/content/influenza/panflu/news/aug2508tamiflu.html

With influenza season well under way in the southern hemisphere, one

of the three kinds of seasonal influenza virus is becoming increasingly

resistant to the antiviral drug oseltamivir (Tamiflu), the World Health

Organization (WHO) reported last week.

Thirty-one percent (242 of 788) of influenza A/H1N1 isolates from 16

countries that were tested in recent months carried a mutation

associated with oseltamivir resistance, the WHO said. In South Africa, all

of the 107 isolates tested had this mutation, known as H274Y, the agency

reported.

Other countries and areas that tested 10 or more isolates and found

resistance included Australia, 100% (10 of 10 isolates); Ghana, 20%

(2 of 10) Hong Kong, 17% (97 of 583); and Chile, 13% (4 of 32 isolates).

The findings strengthen a trend that that was first observed last January

in Norway and subsequently in many other countries.

... the WHO said in June that no link between "oseltamivir exposure and

resistance at the individual patient level was noted."

The increasing oseltamivir resistance in H1N1 viruses has puzzled experts.

In an editorial published by Eurosurveillance in January, authorities said

resistant viruses with the H274Y mutation had been seen in previous flu

seasons but were rare and did not spread easily. But the more recent

H1N1 isolates with the mutation were "fitter" and were spreading in the

community, they wrote.

Southern Sudan?

There are unconfirmed reports of the appearance of H5N1 in

Southern Sudan possibly putting Kenya at risk.

http://crofsblogs.typepad.com/h5n1/2008/08/kenya-on-bird-f.html

No way to know for sure as of yet, and here is a translation denying

the presence of bird flu in Sudan.

http://www.flutrackers.com/forum/showpost.php?p=177373&postcount=2

Togo, West Africa

http://www.recombinomics.com/News/09100802/H5N1_Togo_Uvs.html

An outbreak of bird flu has been confirmed in the West African nation of

Togo for the first time since last year, the Health Ministry said Tuesday.

The virus was detected at a poultry farm housing more than 4,500 birds

in the village of Agbata outside the capital, Lome, said a ministry statement

read over state television. It was not known how many birds died, but more

than 80 per cent of those infected by the flu were fatalities, the ministry said.

What's Going On in Pakistan?

http://afludiary.blogspot.com/2008/09/pakistan-bird-flu-jitters.html

For some unreported reason, the Pakistani govt is issuing an alert.

I don't suppose that they would go to all the trouble of doing this for

nothing.

Chairing a meeting at his office, the minister said that the executive

district officers (EDOs) of coastal areas especially Karachi, Hyderabad,

Badin, Thatta and Sanghar have been instructed to remain alert about

the possibility of bird flu. He instructed the general public that if they find

dead birds, chickens from Siberia at any place, they should inform the

district bird flu committee, EDO agriculture and wildlife office in order to

ascertain its causes and take precautionary steps.

He also asked the people to get their domestic animals vaccinated, adding

he said all the poultry farm owners should ensure proper vaccination of

birds in order to protect them from bird flu.

He asked the people to avoid swimming in coastal areas, lakes and other

spots where birds are found and not to touch any dead bird.

The Philippines, Too Close to Bird Flu Infested Countries for Comfort

http://www.flutrackers.com/forum/showpost.php?p=179180&postcount=1

The Sangguniang Panlungsod (SP) said it will deliberate on a proposed

ordinance that seeks to prevent and control the possible entry or

outbreak of Avian Influenza (AI) in this city.

Dr. Dante Corros, head of the Office of the City Veterinarian, initiated the

move for the city to adopt an ordinance to this effect, considering that

Roxas City has been hosting or lies along the path of migratory birds that

can be carriers of AI.

Although the Philippines remains free of the deadly bird flu virus, the

government has not allowed any let-up in its campaign to maintain the

status since 2004. In contrast, majority of the countries in Southeast Asia

are affected by bird flu.

Australia waits for H5N1

I knew that Australia was in close proximity to Indonesia but

just 3 klicks from New Guinea is way closer than I realized.

It is rather hard to believe that at least some infected birds have

not crossed these straits already. We have seen elsewhere that

finding H5N1 is a combination of being willing to find it, first of all,

and then using the most up to date methods of testing. Testing

should include tracheal samples, and the most accurate primers.

Perhaps they should check with the Russians or the Japanese on

how to most accurately do these tests. Those two countries have

been very transparent about the results of testing when positive

results have occurred. You really have to wonder, given this

particular location, how they could not find any virus by now. I

am thinking that this is just about miraculous.

http://crofsblogs.typepad.com/h5n1/2008/09/australia-waits.html

...given that avian influenza was prevalent in Indonesia, which has the

highest number of reported cases and deaths of any part of the world,

and its proximity to Australia, there was a high likelihood it would

eventually be detected here.

Dr Clarke has been involved in a study of migratory birds moving from

South-East Asia and Papua New Guinea to northern Australia, with the

aim of tracking how disease spreads.

He has made several trips to the Torres Strait to take samples from birds

and study their migration patterns.

He said this was the obvious pathway of any disease like bird flu moving

into Australia because Australian islands are just 3kms from the Papua

New Guinea coastline.

egypt

http://www.recombinomics.com/news/09220801/h5n1_tanta.html

the official said the egyptian health ministry in a statement

today that the directorate of medical affairs western province received

notification from the hospital admitted the arrival of mahala housewife

called huda noah shish share the status of the village of tanta suffer from

very high temperature and bone pain after taking a sample of blood for

analysis labs central show bird flu.

the above translation describes a suspect h5n1 case in egypt. there have

been no confirmed cases this season, but birds in the area have tested

positive for h5n1 and the above translation suggests she has also tested

positive.

h5n1 has been endemic in egypt, in spite of an aggressive vaccine program.

last season a vaccine resistant strain arose, but none of the human

sequences from last season have been released...

southeastern russia

http://www.recombinomics.com/news/09260801/russia_fujian_again.html

with permission from recombinomics:

re-emergence of fujian h5n1 in southeastern russia

recombinomics commentary 14:48

september 26, 2008

the new form of the virus of bird flu is discovered in the

khasan and the [khankayskom] the [proimorya] regions.

probably, to new infection littoral is obliged to vietnam or laos

according to him in the seaside edge for the first time in russia was,

precisely, set reliable barrier to bird flu in april of this year, when the

center of infection was discovered in one of the farmer economies it

was ussuri.

the above translation describes new bird flu outbreaks in southeastern

russia. the translations do not identify the infected birds or provide

direct comments on the identity of the bird flu, but the comparison to

outbreaks in southeast asia and comments on the earlier outbreak in

the spring, strongly suggest the fujian strain of h5n1 has re-emerged

in russia at locations along the coast in areas adjacent to china and

north korea (see satellite map).

full sequences from an isolate from the outbreak in the spring have

been released. the ha is clade 2.3.2, while the remaining seven gene

segments are clade 2.3.4. these sequences are virtually identical to

multiple isolates from northern japan from akita, hokkaido, and aomori.

although south korea has not released sequences, media reports

indicate the h5n1 from the spring korean outbreak are also closely

related to the published sequences.

the spring outbreaks in the whooper swans in japan were linked to

migration to the north. although russia reported excessive poultry

deaths in kamchatka over the summer, h5n1 outbreaks were denied.

the recent report on the re-emergence of h5n1 in the primorie region

in russia suggests unreported h5n1 is also in circulation in china, korea,

and japan.

more detail on the russian outbreaks would be useful.