bird flu
revere | September 19, 2006[Warning: this post is fairly long and has a reasonable geek factor. It explores the question whether the virulence of H5N1 "must" moderate as the virus evolves.]
The high case fatality ratio of H5N1 (currently around 60%) is a reflection of how virulent this virus appears to be at the moment. Virulence is the ability to cause severe disease. The common cold virus and H5N1 both cause disease (both "pathogenic") but H5N1 is highly virulent, the common cold virus is not. The only thing a virus does is make copies of itself. It doesn't grow, it doesn't eat, it doesn't eliminate waste or move. It…
revere | September 17, 2006Huge industrial style poultry farms, where birds are locked in cages in close quarters, are the perfect environment for disease spread. What about locked up people? Two million of them. Two million.
The US locks up more of its population than any nation on earth. By a long way:
This is not something we've always done in the US. It's shockingly recent, within the lifetimes of virtually everyone who is reading this. It really took off with the Reagan counter-revolution and has continued until today, slowing only because states can no longer afford it:
source: Crooked Timber
Since 1980 the…
revere | September 15, 2006The spin, at least in the headlines, has been that a new study shows treatments for SARS didn't work. Some of the headlines are technically more accurate (e.g., SARS: No evidence that any of the treatments worked), but the impression from media reports remains that researchers found SARS treatments didn't work. In fact, however, that's not what the new study, published in PLoS Medicine, says.
By way of background, SARS is caused by a Corona virus (SARS-CoV). SARS is a frequently serious respiratory disease with prominent risk of acute respiratory distress syndrome (ARDS) and features of an…
revere | September 14, 2006Whenever I hear about the latest H5N1 vaccine fix I have the same reaction. If only we'd started doing this several years ago when the threat of an avian influenza pandemic was plausible, we'd be so much farther ahead, if not "there" by now. But we didn't. CDC chased the bioterrorism phantom, to please King George, and Big Pharma was mainly interested in their obscenely profitable (and sometimes fatal) big items for aches and pains and impotence (oh, excuse, me; I mean erectile dysfunction). Oh, well. We'll take what we can get, now.
The latest is a live virus H5N1 vaccine from MedImmune, the…
revere | September 12, 2006Over the weekend Menno de Jong and his many collaborators published a detailed clinical study of 18 H5N1 patients diagnosed and treated in Vietnam in 2004 - 2005 (Nature Medicine, subscription only). Thirteen of the cases died and five survived. Like many papers that have received media attention, it has important and interesting findings but has also been over interpreted, or at least its findings have been generalized too much. In this case, it is the fault of the authors.
de Jong et al. did virological and immunological studies in 18 bird flu cases and 8 other cases with the more usual…
revere | September 9, 2006It's just early September and already the number of confirmed cases of bird flu in humans has equalled that of all last year. And we are just entering flu season. Since the resurgence of the disease in late 2003 (four cases that year), there has been a steady escalation, with 46 cases in 2004, doubling to 97 in 2005 and as of today already 97 this year And it's only September. WHO now has recorded 244 cases since 2003, with 143 deaths (WHO).
Newspaper editors periodically tire of reporting on bird flu, or run stories that things are looking better, or that a vaccine has been devised. Many…
revere | September 5, 2006CDC's Open Access journal, Emerging Infectious Diseases, has just published an interesting communication from an international team of scientists who surveyed Cambodian villagers in Kampot province immediately after a 28-year old male died of H5N1 infection in March 2005. The team also conducted poultry surveys to estimate the extent to which area birds were infected. The case was said to have handled and eaten sick birds. Medical histories, looking for febrile illness were taken within a week from over 350 villagers. Two months later blood specimens were obtained to see if neutralizing…
revere | September 1, 2006WHO has just issued case definitions for H5N1 infections. Case definitions are criteria that must be satisfied to designate a person as being "a case" of H5N1 infection. Case definitions are not clinical tools but epidemiological ones. Epidemiological measures pertain to populations and require the ability to count cases and at risk populations. For example, a case fatality ratio (sometimes incorrectly called a case fatality rate) is the percentage of people infected with H5N1 that die from the disease. A case definition is necessary to determine the denominator, those infected with H5N1.…
revere | September 1, 2006The Thai newspaper, The Nation, is reporting that Thai researchers will soon report in the CDC journal Emerging Infectious Diseases a case of a dog infected with H5N1 after it was fed infected poultry. The current Indonesian cluster in the hamlet of Ranca Salak in the subdistrict of Cikelet, Garut, West Java involved two male cousins (ages 17 and 20) who fed dead chickens to dogs. There is no information on the dogs in this instance, but we know that cats who eat infected fowl can become infected.
This is not a particular surprise, but it emphasizes again that the mammalian host range for…
revere | August 31, 2006An article in the current issue of Annals of Internal Medicine again raises the issue of passive immunization to treat H5N1 using plasma from recovered cases (Eurealert). The idea is that antibodies against H5N1 in the convalescent blood of a recovered case would be therapeutically effective. This is an old idea and was tried in the 1918 flu pandemic. The current paper is said to be confirmed by a handful of uncontrolled studies published ninety years ago during that catastrophe. The idea certainly has biological plausibility.
It also has the feeling of an act of desperation. The logistics of…
revere | August 29, 2006Here's a particularly worthless article from the AP: Docs say Tamiflu won't affect foetus.
This is clearly an important question. In the event of a pandemic, Tamflu will be used prophylactically in pregnant women, either by choice or because the women don't know they are pregnant. There is currently no reliable information on effects of this drug on a developing fetus, and there may not be before we are faced with the problem. So data points are useful. But this example is utter non-sense.
In Jakarta, Indonesian doctors are giving a 35 year old 2 months pregnant woman Tamiflu after she…
revere | August 28, 2006I have no doubt deciding who should get awards is a difficult business. Too many worthy candidates, only a few awards.
Still.
This week the 2006 Science-in-Society award winners were announced by the National Association of Science Writers (NASW):
NASW holds the independent competition annually to honor outstanding investigative and interpretive reporting about the sciences and their impact on society for good or ill. The 72-year-old organization of science writers recognizes and encourages critical, probing works in five categories: newspaper, magazine, broadcast, Web and book. The award…
revere | August 26, 2006The headline -- U.S. border states preparing for pandemic flu threat -- sounded weird, but this is about some good ideas. The weird part was expecting this was about hardening the borders to keep bird flu out. In fact, however, it is about something much more sensible: the clear understanding that this virus doesn't care about political borders:
California and Arizona, two states bordering Mexico, are working together to address the emerging threat of an influenza pandemic.
California Governor Arnold Schwarzenegger and Arizona Governor Janet Napolitano have co-sponsored a joint declaration at…
revere | August 25, 2006An excellent story from Bloomberg News by John Lauerman brings us up to date on an issue we raised yesterday concerning giving breaks on biologicals (like vaccines) to countries who deposit sequence data in publicly accessible databases like Genbank:
Poorer countries where bird flu is spreading may license virus strains isolated from their residents and poultry as a way to leverage better access to drugs and vaccines that come from studying those strains.
The plan is being advanced by a new program, announced today, that urges participating countries to place genetic information about their…
revere | August 24, 2006A new initiative on sharing avian influenza data has just been announced, called the Global Initiative on Sharing Avian Influenza Data (GISAID). This is the latest in a series of developments that have opened up influenza sequence data to the world scientific community to an unprecedented extent, a dawning recognition that the usual rules of scientific behavior and etiquette about who "owns" data need modification in the face of a potential devastating pandemic, where weeks or months head start on a scientific pathway can make an appreciable difference.
Last month Indonesia gave permission…
revere | August 24, 2006If you confront other people who think bird flu has gone away as a concern or read news articles to that effect, consider this. In April of this year there were 45 countries reporting infections in their bird or poultry populations. Now, four months later, there are 55. The UN's Food and Agriculture Organization (FAO) continues to warn us that the virus is spreading throughout Asia, Africa and Europe.
The number of confirmed human cases now stands at 240, with 141 deaths. The true number is likely larger, although how much we don't know. So far it is still small compared with the SARS…
revere | August 23, 2006Good news from CDC. Yesterday they announced immediate public release of some 650 influenza gene sequences. The new openness is part of a collaboration with the Association of Public Health Laboratories (APHL):
Through the new collaboration, CDC expects to provide genetic information for several hundred influenza viruses per year as a way to encourage more research on influenza. The sequence data will be available in nearly real time through Genbank, a public-access library for virus sequences managed by the National Institutes of Health, and through an influenza database housed at Los Alamos…
revere | August 21, 2006We had hoped to have better information about the possible cluster of bird flu cases in remote West Java, but the situation remains murky and unresolved. Nothing especially reassuring has yet happened to ease the discomfort of health authorities regarding whatever is happening there, at any rate. Reporting by The Jakarta Post is typical:
A young boy with symptoms of bird flu was rushed to Garut hospital in West Java on Saturday, raising the official number of people suspected of having bird flu from Cikelet village to 10 and pushing health authorities to widen an investigation into a…
revere | August 19, 2006WHO has taken note (.pdf) of the increasing genetic diversity of the H5N1 influenza/A viral isolates as the disease spreads geographically. Clades are genetically related viruses with common ancestors. Since 2003, two such clades have appeared (clades 1 and 2), distinct from the original H5N1 viruses from the 1997 Hong Kong outbreak (now called clade 3). Clade 1 viruses have been isolated in southeast asia (Vietnam, Cambodia, Thailand, Laos), sandwiched between clade 2 viruses from southern China and Indonesia and Malaysia.
Until now, the experimental human vaccines have been made with seed…
revere | August 19, 2006Another possible Indonesian cluster in a remote West Java village is being reported by fragmentary news sources.
One report has it that a 35 year old woman has died in Cikelet, a village where a 9 year old girl and and a 17 year old male are confirmed cases. The male's 20 year old cousin died of presumed bird flu but was buried without being tested. The two cousins worked together and were said to have been infected when they fed dead chickens to dogs. The girl may have been a near neighbor. The new case would be fourth, but there is as yet no clear relationship to any of the other cases.…