Swine H1N1 Explosion in United States

[rikkitikkitavi]

Re: Swine H1N1 Explosion in United States

The CDC weekly flu report has two separate categories for influenza without subtypes: A (unsubtyped) 311 (15.1%), and A (could not be subtyped) 148 (7.2%). They note that the majority of the cases that could not be subtyped are novel H1N1. Does anyone know more about the unsubtyped category? Why are these samples not subtyped? How many of these are likely to be novel H1N1?

What's truly remarkable is that only 2.8% of the samples have been typed as seasonal A or B. The rest are either novel H1N1 (75.7%), unsubtypable (7.2%, most of which are novel N1N1), and unsubtyped (15.1%). That's why I'm so curious about that last category.

PS: Hi everyone! I'm new here, but have been enjoying the posts here for some time.

 

[Sally Furniss]

Re: Swine H1N1 Explosion in United States

Welcome rikitikitavi!

 

[HenryN]

Re: Swine H1N1 Explosion in United States

The CDC weekly flu report has two separate categories for influenza without subtypes: A (unsubtyped) 311 (15.1%), and A (could not be subtyped) 148 (7.2%). They note that the majority of the cases that could not be subtyped are novel H1N1. Does anyone know more about the unsubtyped category? Why are these samples not subtyped? How many of these are likely to be novel H1N1?

What's truly remarkable is that only 2.8% of the samples have been typed as seasonal A or B. The rest are either novel H1N1 (75.7%), unsubtypable (7.2%, most of which are novel N1N1), and unsubtyped (15.1%). That's why I'm so curious about that last category.

PS: Hi everyone! I'm new here, but have been enjoying the posts here for some time.

Welcome rikkitikkitavi,

The flu data comes from many sources. Some labs just do an infleunza A / B test, so data from those labs is in the unsubtyped category. However, these samples represent a small percentage at this time, because the real question is whether they are swine or human.

The ratio of unsubtyped should approximate the data for the influenza A samples that are subtyped (at this time the vast majority of the unsubtyped infleunza A will also be swine H1N1).

 

[rikkitikkitavi]

Re: Swine H1N1 Explosion in United States

The ratio of unsubtyped should approximate the data for the influenza A samples that are subtyped (at this time the vast majority of the unsubtyped infleunza A will also be swine H1N1).

Yeah, that's what I was afraid it might be. So, really, the probability that anyone with influenza right now has H1N1 swine flu is over 96%. Anne Schuchat of the CDC wasn't kidding when she said a few days ago that "virtually all" of the flu going around was the swine flu.

I'm really surprised that this point has not been more widely disseminated. Most people seem to think that there's a lot of seasonal flu going around still, and that the swine H1N1 is a very small, even negligible, part of what's around. They're shocked when I tell them it's the predominant strain right now.

 

[HenryN]

Re: Swine H1N1 Explosion in United States

Yeah, that's what I was afraid it might be. So, really, the probability that anyone with influenza right now has H1N1 swine flu is over 96%. Anne Schuchat of the CDC wasn't kidding when she said a few days ago that "virtually all" of the flu going around was the swine flu.

I'm really surprised that this point has not been more widely disseminated. Most people seem to think that there's a lot of seasonal flu going around still, and that the swine H1N1 is a very small, even negligible, part of what's around. They're shocked when I tell them it's the predominant strain right now.

That is due in part because reporters think that the probable cases (influenza A positive) are seasonal flu, when they really are swine that haven't been fully confirmed.

 

[HenryN]

Re: Swine H1N1 Explosion in United States

Wow, hard to believe that was written just a few weeks ago, considering where we are now.

Here are swine H1N1 sequences isolated form humans in 2005 and 2007 (click on accession number on left to see detail, which shows that the sequences from 2005 and 2007 were withheld until last month, when they were deposited at Genbank).

gb|FJ986621.1| Influenza A virus (A/Ohio/02/2007(H1N1)) segme... 34.2 2.8
gb|FJ986620.1| Influenza A virus (A/Ohio/01/2007(H1N1)) segme... 34.2 2.8
gb|FJ986619.1| Influenza A virus (A/Wisconsin/87/2005(H1N1)) ... 34.2 2.8

 

[gsgs]

Re: Swine H1N1 Explosion in United States

deaths are going down:

http://www.cdc.gov/flu/weekly/weeklyarchives2008-2009/images/picurve21.gif

 

[HenryN]

Re: Swine H1N1 Explosion in United States

deaths are going down:

http://www.cdc.gov/flu/weekly/weeklyarchives2008-2009/images/picurve21.gif

Please. There were 7 US deaths announced on Wednesday (3 NY, MI, IL, CT, VA), 6 on Thursday (WI, CA, IL, UT, PA, AZ), and 3 yesterday (WA, TX, NY).

This thread is on SWINE flu. The seasonal flu season is OVER. Most deaths worldwide (including the US) are in the 20-65 age range.

 

[gsgs]

Re: Swine H1N1 Explosion in United States

revere about New York, one of the hotspots in USA:

emergency room visits are down from their peak of a week ago
Attendance rates in school were still below average although also up from last week.
All but 4 of the 50 schools that were closed are now open

 

[HenryN]

Re: Swine H1N1 Explosion in United States

revere about New York, one of the hotspots in USA:

emergency room visits are down from their peak of a week ago
Attendance rates in school were still below average although also up from last week.
All but 4 of the 50 schools that were closed are now open

Please. NYC is up to 590 confirmed cases (goes up each day its reported) and upstate NY is filling up fast.

 

[HenryN]

Re: Swine H1N1 Explosion in United States

revere about New York, one of the hotspots in USA:

emergency room visits are down from their peak of a week ago
Attendance rates in school were still below average although also up from last week.
All but 4 of the 50 schools that were closed are now open

Here's the map of NY

http://www.health.state.ny.us/disea...enza/h1n1/docs/state_h1n1_cases_by_county.pdf

Counties reporting confirmed cases for the first time in the past few DAYS are Livingston, Putnum, Ulster, Madison, Ontario, Rensselaer, Steuben (and NY reported 3 deaths on Wednesday and another yesterday).

Cases in the northeast are exploding (ask him about Boston).

http://flutracker.rhizalabs.com/flu...41.21998578493921&lon=-72.718505859375&zoom=7

 

[HenryN]

Re: Swine H1N1 Explosion in United States

revere about New York, one of the hotspots in USA:

emergency room visits are down from their peak of a week ago
Attendance rates in school were still below average although also up from last week.
All but 4 of the 50 schools that were closed are now open

Last week he was saying to close schools in Boston:

Boston blasted for delay closing flu schools
Swine positives in ?medically fragile? environment
<!--//Byline box//-->
By Richard Weir | Saturday, May 30, 2009 | http://www.bostonherald.com | Local Coverage
<!--//Byline box end//--><!--//article Image//-->

Photo by John Wilcox


<!--//article Image//--><!--//article//-->Parents and faculty at adjacent Allston schools, including one that serves ?medically fragile? students, blasted city health officials yesterday for dragging their feet in closing down the building a week after two students tested positive for swine flu.
?These are children we?re talking about. It blows my mind that their health needs are being ignored. I?m disgusted,? said one staffer at Jackson/Mann Elementary School.
The Boston Public Health Commission yesterday ordered Jackson/Mann and the adjacent Horace Mann School for the Deaf , along with the Eliot Elementary School in the North End, shut down for one week, effective Monday.
The state notified the city on May 23 that two Jackson/Mann students had confirmed cases of swine flu. As word got out, absenteeism among the school?s 705 students skyrocketed from 19 percent on Wednesday to 25 percent yesterday.
Jackson/Mann and Horace Mann are located in the same building and their students share a cafeteria, bathrooms, buses and sometimes classrooms. Horace Mann, however, is ?labeled a medically fragile school,? explained an official, noting that many of its 135 students have severe medical conditions such as sickle cell anemia, spina bifida, gastrointestinal feeding tubes and tracheotomy tubes.
?If there is a large population of at-risk children in the same facility, I think they should be more careful there,? said Dr. David Ozonoff, an epidemiologist at the Boston University School of Public Health. ?It sounds like they should have acted sooner.?
But Barbara Ferrer, head of the Boston Public Health Commission, defended the delay, saying there has been little transmission of the flu between Jackson/Mann and Horace Mann students. ?The principal (at Horace Mann) has reported there are very few students out with flulike symptoms, and we have no confirmed cases,? she said.
That is not the case at nearby Jackson/Mann, where the number of absent students rose steadily from 66 on Tuesday to 175 yesterday. Concerned faculty said they made repeated calls to the city all week about the growing problem.
Ferrer said closing a school is ?not the kind of decision you come to lightly? because of the hardship it causes teachers, parents and their kids.
Berta Morales, who kept her fourth-grade daughter home from Jackson/Mann all week out of fear she could contract swine flu, said it was ?ridiculous? that the city took so long to act.
?Who knows how many kids could have been infected in that time? Schools in other cities close down immediately.?

http://www.bostonherald.com/news/regional/view.bg?articleid=1175679&format=text

 

[thebes]

Re: Swine H1N1 Explosion in United States

You have taken what the Reveres wrote out of context. This is the entire quote from their post:

While emergency room visits are down from their peak of a week ago, a time when doctor visits for flu were also increased 15 times over what was expected for this time of year, it was clear that flu was still spreading in the city, with visits still higher than normal. Attendance rates in school were still below average although also up from last week. All but 4 of the 50 schools that were closed are now open. In other words, there may be just as much flu out there now as last week, but people are adjusting to it.

The point of the Reveres' post wasn't to say that the amount of flu in New York was decreasing, the point was to say that no one really knows how much flu there is in the city. They mention that the NYC Health Department is presently doing a phone survey to determine how many people have had the flu, but after pointing out the lack of reliability in such a survey in the age of cell phones, the post concludes:

All this goes to show how epidemiology in the real world can be much more difficult, uncertain and complicated than the simple questions it is trying to answer -- like how much flu is there in New York City? -- would seem.

http://scienceblogs.com/effectmeasure/2009/06/swine_flu_new_york_city.php#more

 

[Dianna]

Re: Swine H1N1 Explosion in United States

Perhaps this would be better placed under venting room..
Why would so many assume the virus is dying down for now? Well I have seen articles from Canada that state just that in the Month of May.
To many arguments over opinions on a novel virus, which I find insane.

We all know things are not turning out geographically correct according to WHO or CDC graphs as this new virus spreads we are in a time that allows us to gather information a pioneering if you will with a new virus.

There are 1450 schools in New York City alone with average 1.1mil children. So a few schools open is just that to me at this point and it may be that way for some time.
Asthma in New York is high and after 9/11 dust exposure I am surprised more adults are not sick.

I hear to many depending on the virus to die down for the summer. I find that even more frustrating. To many factors in my mind I will not depend on the idea summer will give a reprieve to the new virus.
I am only a concerned citizen of this planet. I do care what happens. I also care how things are reported.

http://schools.nyc.gov/default.htm


http://news.xinhuanet.com/english/20...t_11498852.htm

HOUSTON, June 5 (Xinhua) -- Massachusetts health authorities on Friday reported 69 newly confirmed cases of A/H1N1 flu, bringing the total to 854 in the northeastern U.S. state.

The total number is much higher than the figure of 787 released by the Centers for Disease Control and Prevention (CDC) on the same day.

CDC officials said there is always a time gap between the local report and the CDC publication on its website.

Suffolk and Middlesex are the two hardest hit counties which have confirmed altogether more than 600 of the total cases.

Also on Friday, two more schools in the state were closed following the continuous spread of the flu.

Superintendent Richard Silverman announced that Donovan Elementary in Randolph will be closed for a week, as 65 students in the school were absent on Friday.

Meanwhile, Blackstone Elementary in Boston will also be closed, as about 20 percent of the school's 600 students were absent on Friday.

 

[Siegfried X]

Damned if they do, damned if they don't

Damned if they do, damned if they don't

Parents and faculty at adjacent Allston schools, including one that serves ?medically fragile? students, blasted city health officials yesterday for dragging their feet in closing down the building

Health officials have also been blasted for closing schools. Damned if they do, damned if they don't.

If schools are closed and no one becomes seriously ill, we are told it was a mistake to close them. If schools are not closed and someone dies or goes in intensive care from the flu, we are told it was a mistake not to close.

In many cases the government in effect lets parents and students decide. They close the school if lots of students stay home, and leave it open if they don't.

This epidemic has shown that, except in a few rare short-term situations, closing schools won't work in our society. Child care is not available in many cases. Shutting the schools every time a single student was suspected of having the flu would mean that schools would be closed until a vaccine is widely available, whether that took 6 or 12 or more months.

 

[Siegfried X]

CDC is doing a B+ job

CDC is doing a B+ job

I gave the CDC a B+ grade for their communications so far, and hope they keep it up. The reason I give this grade is because all the criticism of the CDC's press releases so far, including mine, has been based on the CDC's own scientific statements. In other words, even if their press releases sometimes are a little too positive, their scientific communications provide a lot of useful information.

Communication could be far, far worse. I hope the CDC never cuts off their detailed scientific documents, or some of the excellent flu experts they've allowed to speak freely at CDC conferences.

As long as the government provides a lot of information we each can form our own conclusions. But if the government gets burned by criticism and cuts off the information flow, we wouldn't have that opportunity.

The government is communicating better than I thought it would at this point. I always imagined that, like in 1918, there would be much more censorship and much more spin.

 

[Laidback Al]

Re: Swine H1N1 Explosion in United States

The government is communicating better than I thought it would at this point. I always imagined that, like in 1918, there would be much more censorship and much more spin.

There is no need for spin. The general public is complacent and unconcerned.

For those of us willing to inspect the numbers, as we are here at FT, we recognize that the pandemic is expanding. Its virulence, however, is yet to be determined.

As the death starts to mount, I think we will begin to see the spin doctors at work.

 

[HenryN]

Re: Swine H1N1 Explosion in United States

There is no need for spin. The general public is complacent and unconcerned.

For those of us willing to inspect the numbers, as we are here at FT, we recognize that the pandemic is expanding. Its virulence, however, is yet to be determined.

As the death starts to mount, I think we will begin to see the spin doctors at work.

I listened to Thursday press conference, and there was plenty of spin. There wasn't much new information, but the confeence seemed to be designed to downplay the vaccine (it was being made for a clinical trial and the decision to vaccinate was still open), which is almost certainly because there will be no vaccine in the fall, and the spread, which was said to be increasing in some areas and decreasing in others (even though much of the decrease was due to limited or no testing, and the curve of the % positive cases looked like a hockey stick).
The spin helped create the complacency, and will now focus on maintaining the complacency.

 

[gsgs]

Re: Swine H1N1 Explosion in United States

> You have taken what the Reveres wrote out of context. This is the entire quote from their post:

I don't see it

> While emergency room visits are down from their peak of a week ago, a time when doctor
> visits for flu were also increased 15 times over what was expected for this time of year,
> it was clear that flu was still spreading in the city, with visits still higher than normal.

OK. Higher than normal, lower than a week ago.

> Attendance rates in school were still below average although also up from last week.
> All but 4 of the 50 schools that were closed are now open. In other words, there may
> be just as much flu out there now as last week, but people are adjusting to it.

"may be" doesn't tell us much. Does it happen with seasonal flu ? People adjusting to it ?
The curve still has usually one peak and then is going down.

> The point of the Reveres' post wasn't to say that the amount of flu in New York was decreasing,

whether it was the point or not, he still said it

> the point was to say that no one really knows how much flu there is in the city.

if the point is "no one really knows" , then why make that point at all ? Or is it a "point" anyway ?

> They mention that the NYC Health Department is presently doing a phone survey to
> determine how many people have had the flu, but after pointing out the lack of reliability
> in such a survey in the age of cell phones, the post concludes:

it's still useful and I'd like to see the results. Unfortunately they don't tell us, where/when the
results can be seen by normal people like me.

>Al this goes to show how epidemiology in the real world can be much more difficult,
> uncertain and complicated than the simple questions it is trying to answer --
> like how much flu is there in New York City? -- would seem.

"can be" . We should still try to estimate it. That is all what science is about.
If we had desperated on the complexity of science earlier, then where were we now ?

 

[gsgs]

Re: Swine H1N1 Explosion in United States

this is no more than a bad seasonal wave in New York, Boston so far, right ?
Is it worse than 2003/2004 seasonal H3N2 ?
(which maybe would have been considered a pandemic epidemiologically,
but it was still the old H3N2)

and apparantly it is going down, at least in New York (revere,05.Jun)
and nationwide (CDC, Schuchat 26.May)

also down in Mexico (Cordoba,02.May)
and ("probably") in Canada (Butler Jones,19.May)