Thursday, July 30, 2009

Musings on the gradual development of a highly lelthal strain and simultaneous emergence in multiple locations.

This is related to my observations below about more countries seeming to be listing their first deaths. It is taken from a discussion on flutrackers.com in a member's area so I can't link into it. I'll edit it a little bit to remove references to the discussion it was part of.

One thing I am noticing, qualitatively, not quantitatively, is that deaths worldwide seem to be on the increase. Now there's certainly many reasons why this might be, and a large part of it could simply be due to an increase in the number cases, more cases will necessarily be more deaths. But is that all there is to it? Has much of the rest of the world reached whatever "critical point" in number of infections is necessary to start seeing an increase in the number of deaths? Or is there something else going on?

Apparently the CDC still thinks there is no change in the virus versus the vaccine consensus, but as we have now seen, as long ago as a month an apparently poorly understood but potentially very important change was discovered in Brazil. If this change was fit then we have no way of knowing how far it spread since then, and apparently we are not seeing sequences released in a timely manner anywhere, hence we really don't know what we are looking at now.

The lethal second wave struck three ports on the Atlantic Coast of three continents on or about August 22nd (Boston, MA, Brest, France, and Freetown, Sierra Leone). Shipping traffic can't have delivered the lethal strain to them all simultaneously, there is a fair chance that whatever ship(s) involved would have had a significant portion of their crew killed if they carried the lethal strain. But here is a different view.

Twentieth century pandemics (and possibly the Russian Flu of 1889) had a mild first wave that saw the virus get seeded around the world. In the case of 1918, the much more lethal second wave seems to have hit multiple places at roughly the same time. Perhaps this is what happened. As it spread around the world, the 1918 pandemic virus would have encountered other flu viruses and had chances to acquire various traits. As troops and war materiel moved around the world, these different strains would have spread back to other places, meeting up with different strains of the pandemic virus, or still other flu viruses, picking up additional traits. One of these, still not terribly lethal, but almost there, then got spread to these port cities. Three different ships from a single source could have done it, and perhaps it could have been South America, that being one location where the travel time would have been close to equal for all three destinations. With perhaps only one or two relatively small changes left, normal evolutionary pressures could have produced the more lethal strain simultaneously in different locations, and the new strain was much more fit, allowing it to spread.

So is Brazil pointing us that way? Perhaps they are the source of the new infections in Southern Mexico and Central America. Perhaps the "Sao Paulo strain" isn't the "final" more lethal version, but it could be one more step on the way thee. But with airline travel, the final version could easily crop up in multiple locations at the same time. We are looking for an immediate source, to areas where H5N1 is widespread, for instance. But whatever offspring H1N1 and H5N1 might produce will, perhaps, not be distinguishable from the current pandemic strain until a few more key changes crop up, and then it may already be worldwide.

The above was purely speculation, and I may be totally off-base.

Wednesday, July 1, 2009

HIPAA And disclosure of underlying conditions

I recently posted this on flutrackers.com:

Most announcements of deaths in the US have been light on discussion of what constitutes an "underlying condition." Generally, privacy laws are cited. In the US this is predominantly HIPAA (Health Insurance Portability and Accountability Act of 1996). But what exactly does HIPAA protect and it is really being used to hide some unsavoury facts. I am citing Wikipedia in this discussion, but what I see in the cited article more or less matches my understanding as a hospital employee in a non-direct patient care area; I am trained in this yearly for regulatory reasons. Other who work in health care can hopefully add to this discussion. First, HIPAA itself:

http://en.wikipedia.org/wiki/Hipaa

Quote:
The Health Insurance Portability and Accountability Act (HIPAA) was enacted by the U.S. Congress in 1996. According to the Centers for Medicare and Medicaid Services (CMS) website, Title I of HIPAA protects health insurance coverage for workers and their families when they change or lose their jobs. Title II of HIPAA, known as the Administrative Simplification (AS) provisions, requires the establishment of national standards for electronic health care transactions and national identifiers for providers, health insurance plans, and employers. It helps people keep their information private.
The Administration Simplification provisions also address the security and privacy of health data. The standards are meant to improve the efficiency and effectiveness of the nation's health care system by encouraging the widespread use of electronic data interchange in the U.S. health care system.
Quote:
Privacy Rule
The Privacy Rule took effect on April 14, 2003, with a one-year extension for certain "small plans". The HIPAA Privacy Rule regulates the use and disclosure of certain information held by "covered entities" (generally, health care clearinghouses, employer sponsored health plans, health insurers, and medical service providers that engage in certain transactions.) It establishes regulations for the use and disclosure of Protected Health Information (PHI). PHI is any information held by a covered entity which concerns health status, provision of health care, or payment for health care that can be linked to an individual.[10] This is interpreted rather broadly and includes any part of an individual's medical record or payment history.
Covered entities must disclose PHI to the individual within 30 days upon request.[11] They also must disclose PHI when required to do so by law, such as reporting suspected child abuse to state child welfare agencies.[12]
A covered entity may disclose PHI to facilitate treatment, payment, or health care operations,[13] or if the covered entity has obtained authorization from the individual.[14] However, when a covered entity discloses any PHI, it must make a reasonable effort to disclose only the minimum necessary information required to achieve its purpose.[15]
The Privacy Rule gives individuals the right to request that a covered entity correct any inaccurate PHI.[16] It also requires covered entities to take reasonable steps to ensure the confidentiality of communications with individuals.[17] For example, an individual can ask to be called at his or her work number, instead of home or cell phone number.
The Privacy Rule requires covered entities to notify individuals of uses of their PHI. Covered entities must also keep track of disclosures of PHI and document privacy policies and procedures.[18] They must appoint a Privacy Official and a contact person[19] responsible for receiving complaints and train all members of their workforce in procedures regarding PHI.[20]
An individual who believes that the Privacy Rule is not being upheld can file a complaint with the Department of Health and Human Services Office for Civil Rights (OCR).[21][22] However, according to the Wall Street Journal, the OCR has a long backlog and ignores most complaints. "Complaints of privacy violations have been piling up at the Department of Health and Human Services. Between April 2003 and Nov. 30, the agency fielded 23,896 complaints related to medical-privacy rules, but it has not yet taken any enforcement actions against hospitals, doctors, insurers or anyone else for rule violations. A spokesman for the agency says it has closed three-quarters of the complaints, typically because it found no violation or after it provided informal guidance to the parties involved."[23]
Now, there is a segment in there that describes protection of PHI (Protected Health Information). This would be the key part we are concerned with here. Using broad strokes, PHI is any of the data necessary to tie information back to an individual, either medical record information (such as name, dates of treatment) or payment history.

An expansion of PHI:

http://en.wikipedia.org/wiki/Protected_health_information

Quote:
Protected health information (PHI), under the US Health Insurance Portability and Accountability Act (HIPAA), is any information about health status, provision of health care, or payment for health care that can be linked to an individual. This is interpreted rather broadly and includes any part of a patient’s medical record or payment history.
List of 18 Identifiers according to HIPAA 1996:
1. Names;
2. All geographical subdivisions smaller than a State, including street address, city, county, precinct, zip code, and their equivalent geocodes, except for the initial three digits of a zip code, if according to the current publicly available data from the Bureau of the Census: (1) The geographic unit formed by combining all zip codes with the same three initial digits contains more than 20,000 people; and (2) The initial three digits of a zip code for all such geographic units containing 20,000 or fewer people is changed to 000.
3. dates (except year) for dates directly related to an individual, including birth date, admission date, discharge date, date of death; and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older;
4. Phone numbers;
5. Fax numbers;
6. Electronic mail addresses;
7. Social Security numbers(SSN);
8. Medical record numbers;
9. Health plan beneficiary numbers;
10. Account numbers;
11. Certificate/license numbers;
12. Vehicle identifiers and serial numbers, including license plate numbers;
13. Device identifiers and serial numbers;
14. Web Universal Resource Locators (URLs);
15. Internet Protocol (IP) address numbers;
16. Biometric identifiers, including finger, retinal and voice prints;
17. Full face photographic images and any comparable images; and
18. Any other unique identifying number, characteristic, or code (note this does not mean the unique code assigned by the investigator to code the data)
Here is where it gets interesting. Note number 2 in the list. If HIPAA is what is really being used to "protect" the data then all announcements we have are in violation of it since we have more information than state or the other narrow exceptions listed. For all of these deaths we have city and/or county, both of which are protected.

Furthermore, statistical information is reported to, for instance, the CDC and they publish it publicly, and this includes various "underlying conditions." Statistical information is not, apparently, protected, and that is really what we are after here. Some statistical information is available, but parts are being withheld, and I am having an increasingly difficult time reconciling that to the (real) need to protect privacy. There are so many cases where information that really is protected has been released (patient names and/or hospitals), so the decision not to release relevant information is extremely puzzling.

Tuesday, June 23, 2009

Tracking US Deaths versus Deaths in the Healthy

Much is made in official pronouncements as well as in the media about how much increased risk of severe illness and death there is from people who have pre-existing medical conditions if they also contract swine flu. That might be true with seasonal human influenzaviruses. Problem is, this is not a human influenzavirus.

In the US, seasonal influenza is said to kill 36,000 people every year (need source), of which roughly 90% are elderly. It is already borne out by the CDC and the WHO that deaths from swine flu are much higher in the young category than is typical in flu season.

Data from the US also show an increase in deaths from the healthy. I have put together a Google spreadsheet tracking US deaths over time as well as the percentage of total deaths that are in people who do not have underlying medical conditions.

There are some problems with this. I used as the source for my data a different spreadsheet mentioned in a thread on flutrackers.com. (link to original needed) It seems rather complete. The issue is that firm death dates are not given. When no death date was given I tried to use the lag time from other reports from that state to determine where to set a death date. If I couldn't make a determination, I made an assumption of 3-4 days lag. So other people might come up with slightly different graphs, but the trend and final number should be a good match.

To determine if a person was healthy I looked at the remarks. A null comment is assumed to be healthy. If an underlying condition is marked disputed I assumed a healthy individual. Given the risks of pregnancy in this pandemic I assumed pregnancy to be a valid underlying condition.

Here is my spreadsheet:


And here is a chart showing the increase in the death rate in healthy individuals:



There is clearly an upward trend, and we may soon break 50% of all US deaths being from healthy individuals. It is probably true that an elderly person (who is most at risk from seasonal flu) has one or more underlying conditions, so the deaths that made up that graph are probably in young and middle aged people.

Wednesday, June 17, 2009

Rapid onset of symptoms and Death

There was recently a discussion on the Rhizalabs Flutracker message board about the recent (as of mid-June) spate of rapid deaths in young, healthy people. I posted an explanation of why viral pneumonia from influenza seems to cause rapid onset of illness and death (often less than 24 hours) versus more "normal" bacterial pneumonia triggered deaths. This was apparently a well-received explanation as it was requested I repost it periodically. I am posting it here so I can have easy access to it. Note there may be some finer technical details that are off, but I believe this is largely good enough for the layman.

From various things I have read it seems the immune system treats a viral infection of the lungs much differently than it does a bacterial infection. Normally, your immune system has to fight off bacteria by having certain types of immune cells eat (phagocytose?) the organism. This can be done without the the extremely lethal parts of the immune system.

But a virus enters the cell and hijacks the internal mechanisms in order to make more virions. The body must kill parts of itself, either by triggering the infected cell to die (apoptosis?) or outright killing it. Whena virus infects the lungs the body has to mount an attack with essentially its full arsenal. This leads to a cascade that can result in, as I understand it, the spongy material of the lungs being transformed into scar tissue.

The progression is viral pneumonia -> cytokine storm -> ARDS -> (multiple organ failure?) The cytokine storm is a result of the viral pneumonia and ARDS and multiple organ failure are the consequences of the cytokine storm. This all happens very quickly.

Bacterial pneumonia takes advantage of the weakness in the body generated by the viral infection, and typically takes longer to develop. This is the cycle of being sick, getting better, then taking a turn for the worse.

Friday, June 12, 2009

Are we reliving 1918?

I am a member of FluTrackers where my name is wotan. Several weeks ago I started this thread:

I have been reading John Barry's The Great Influenza, and have been struck by a few things. First, I was aware that the first wave in the spring of 1918 was considered mild, but I did not realize the following:

The first wave (assuming it started in Haskell County, KS, which Barry says is more or less impossible to determine) appeared to be slightly more severe in the very beginning, but it was a slightly less severe variant that got out. Compare with Mexico, although I am not entirely convinced that the increased mortality in Mexico was due to anything more than not knowing to use Tamiflu in the early days of the outbreak.

Symptoms from the first wave were so light (apparently less than seasonal flu) that the disease could be mistaken for something else entirely. We have seen anecdotal evidence of swine flu being mistaken for any number of other conditions.

The first wave persisted in the northern hemisphere into August. Obviously, we are still in it here at the end of May.

There were isolated incidences of more severe disease during the first wave. There is at least some anecdotal evidence to support this in the current outbreak as well.

I'm still fairly early into the second wave in the book, so I don't know what else I will find.


Sadly, the parallels continue. Consider for a moment the demographics attacked by the 1918 Spanish Flu:

The unusually severe disease killed between 2 and 20% of those infected, as opposed to the more usual flu epidemic mortality rate of 0.1%.[9][12] Another unusual feature of this pandemic was that it mostly killed young adults, with 99% of pandemic influenza deaths occurring in people under 65, and more than half in young adults 20 to 40 years old.[23] This is unusual since influenza is normally most deadly to the very young (under age 2) and the very old (over age 70), and may have been due to partial protection caused by exposure to a previous Russian flu pandemic of 1889.[24]


Source: Wikipedia

Now, consider the demographics for the 2009 pandemic so far:

57% of the cases that we're having reported to us occur in people 5 to 24 years of age, and 41% of the hospitalizations are in that same age group -- the older children and young adults. But I also want to tell you about the rates, the cases per 100,000 population, and let you know that the highest rates of hospitalization are actually in children under 5. And the next highest rates are in those people 5 to 24. So it looks like this is a virus that's disproportionately affecting younger people but there are still lots of infections and hospitalizations in older persons.

Source: Flutracker's post of CDC transcript.


Let's make this clear. Seasonal flu disproportionately attacks the elderly. The 2009 pandemic flu attacks the young! The 1918 pandemic flu attacks the young!

Will the 2009 pandemic grow as severe as 1918? Probably not, but that it might is the scary thought.

Tuesday, May 26, 2009

Is this a Pandemic or not?

The short answer is yes.

The long answer requires an understanding of what a pandemic is.

From the Wikipedia article:

Definition

According to the World Health Organization (WHO), a pandemic can start when three conditions have been met:[1]

* Emergence of a disease new to a population.
* Agents infect humans, causing serious illness.
* Agents spread easily and sustainably among humans.

A disease or condition is not a pandemic merely because it is widespread or kills many people; it must also be infectious. For instance, cancer is responsible for many deaths but is not considered a pandemic, because the disease is not infectious or contagious.


This is a generic pandemic definition, and not specific to influenza.

For the case of an influenza pandemic we will add the following:


Influenza pandemics occur when a new strain of the influenza virus is transmitted to humans from another animal species. Species that are thought to be important in the emergence of new human strains are pigs, chickens and ducks. These novel strains are unaffected by any immunity people may have to older strains of human influenza and can therefore spread extremely rapidly and infect very large numbers of people. Influenza A viruses can occasionally be transmitted from wild birds to other species causing outbreaks in domestic poultry and may give rise to human influenza pandemics.


So, what are we dealing with? The novel influenzavirus A(H1N1) that is currently circulating is, by definition, a new virus in humans (though containing genetic material from previous human strains of influenzavirus type A), it definitely infects humans and can cause serious illness, and is capable of sustained spread between humans. Furthermore, it is a new virus from a different species (pigs). Therefore, despite the WHO's attempts at not declaring a full pandemic, the "classical" conditions are met.

It bears repeating, a pandemic does not have to be highly lethal, it has to infect humans in large portions of the world. The "Swine Flu" is doing just that, and the virus doesn't care what people say about it.

Monday, May 11, 2009

Why the concern

The novel strain of A/H1N1 influenza (swine flu) represents a potential threat to the health and lives of a large segment of the population worldwide. Although many are choosing now to discount this threat, it still remains despite the "mild" nature of the illnesses produced thusfar.

For those who want to look at the number of people officially listed as having become infected and those who died, here is what the World Health Organization says as of 5/11:

Influenza A(H1N1) - update 25

That translates out to around 1.13%. Seasonal influenza kills about 0.001% worldwide (citation needed). Granted, there are real problems with the numbers but out by the WHO, but for those who would point to that as evidence this is nothing bad, you have to look at what else the numbers say.

There is also the concern that the H1N1 and H5N1 (bird flu) viruses could meet in, perhaps, a pig or human, and the resulting virus could be highly transmissable like the novel H1N1 and with the high fatality rate of H5N1 (50-60% of persons infected with H5N1 die) (citation needed).

To be continued....