08 October 2006
pogge – at 13:18
Yesterday’s news thread is here.
Leo7 – at 01:21
Article from Fort Wayne Newspaper: Pandemic flu: A guide for families. Read here: http://tinyurl.com/fsy3g
anonymous – at 13:21
Commentary
Mammalian H5N1 Evolution in Indonesia Recombinomics Commentary October 7, 2006 - http://tinyurl.com/mmx3g
The recent announcements of H5N1 bird flu in cats in Indonesia, coupled with results from expanded sequencing of poultry strongly signal the existence of a separate mammalian H5N1 reservoir in Indonesia that is responsible for the vast majority of human cases.
This separate reservoir creates significant problems, because most of the attention has focused on infected poultry, and the mammalian reservoir has been significantly under investigated and under reported.
Therefore, a review of the evolution of this mammalian reservoir is useful. Although Indonesia did not acknowledge H5N1 infections until 2004, the first isolates were from birds in 2003. Sequence analysis of the 2003 and 2004 isolates indicated the H5N1 was Clade 2 and had a number of genetic markers that were specific for Indonesia.
The first human case was reported in July of 2005, and the sequence of the isolate, A/Indonesia/5/2005 had the Indonesia specific markers, but also had a number of unique polymorphisms, including one that created a novel HA cleavage site, RESRRKKR. However, the second human isolate, A/Indonesia/6/2005 had the more common HA cleavage site, RERRRKKR, and was similar to bird isolates. Subsequent human isolates in 2005 had the novel cleavage site, but several had an additional silent change, so although the cleavage site matched the first sequence at the protein level, there were a number of changes at the nucleotide level that divided the sequences with the novel cleavage site into two groups.
However, as the number of sequences increased in early 2006, it became increasingly clear that the human sequences were separating from the poultry sequences, all of which had the common bird cleavage site. The first match of the human sequences was from H5N1 from a throat swab of a cat in Indramayu near a residence were two siblings died from H5N1 infections. The sequence of the cat isolate not only matched the more recent human sequences, but was very close to the sequences of the isolates from the two siblings, A/Indonesia/283H/2006 and A/Indonesia/286H/2006, as well as other human isolates from Indramayu, A/Indonesia/292H/2006 and A/Indonesia/304H/2006. New isolates in 2006 collected from patients in East and West Java were sequenced and all were matches of more recent sequences such as the four human and one cat isolate from Indramayu.
In May of 2006 however, there was a new cluster in the Karo regency in north Sumatra. This outbreak was the largest to date and involve secondary and tertiary transmissions of H5N1. Consequently a meeting was call by WHO and consultants in Jakarta in June. Included in the presentation was a phylogenetic tree that summarized the H5N1 Indonesian isolates as of June 12, 2006.
The tree, which had the human sequences in green and the Karo cluster shaded in pink, clearly showed the match problem. All of the sequences with the novel cleavage site were on the lower portion of the tree and there were no poultry sequences on these two lower branches. Moreover, all of the recent human sequences from Java were on the lowest branch, which was even further from the poultry isolates. Thus, the human isolates were evolving away from the poultry isolates, suggesting the existence of a separate mammalian reservoir.
However, all of the human isolates were from July, 2005 or later, while most of the bird isolates were from earlier dates. Therefore 91 samples were schedule for shipment to Australia for virus isolation and sequencing. The samples were from infections between September, 2005 and March, 2006.
As sequences from these more recent and geographically dispersed isolates began to be published, it was becoming increasingly clear that the vast majority of the human infections on Java were not from domestic poultry. Each human sequence mapped to the lower portion of the tree and which was more distinct from the bird sequences.
The second set of new bird sequences included an isolate with the novel cleavage site. It was from a duck on Indramayu isolated in 2006. However, that isolate match the upper branch of the human sequences, which were composed of six isolates from three patients in 2005. Thus, although every human isolate in 2006 was matching the lower branch, the one duck sequence matched the upper branch.
The third set of poultry sequence had two matched with the lower branch. However, the two matches were from chickens in central Sumatra from 2005. Thus, none of the poultry isolates matched the lower human branch, while all human isolates, as well as the cat isolate, matched the lower human branch.
These data again supported a separate reservoir for the human sequences, and the only matches on Java were from the one cat, and all human isolates. The recent announcement indicates more H5N1 has been detected in cats, but the sequences of those isolates have not been released. Swine H5N1 sequences have been reported, but none match the human sequences.
The match failures pose a major problem because testing of humans is largely limited to patients how have been near dead or dying poultry. However, the poultry association has not been linked to the human infections, so an expanded testing of patients with symptoms is warranted. Similarly, more sequencing of H5N1 from other reservoirs is warranted by the match failures between mammalian and avian sequences.
Pixie – at 13:25
That was me at anonymous – at 13:21.
Comment: Dr. Niman states here that the Indonesian pig sequences do not match the human sequences any more than the bird sequences do. He has also stated previously that the rat/mice sequences are also not similar to those of the humans and cats.
NJ Jeeper – at 13:46
Another Scientist comes out in suport of prepping. See quote near end of article.
Scientist urge to prepare for a bird flu pandemic
08/Oct/2006: ‘Start preparing for the next flu pandemic’, is the message from the organizer of an expedition to unearth samples of the devastating Spanish flu pandemic in 1918 and 1919. Kristy Duncan, a scientist at the University of Toronto, warns that it is just a matter of time before another deadly bird flu pandemic strikes the world.
Building supplies of food, water, medication and other essential items could help us to tide over the bird flu pandemic, if one strikes.
Duncan, who is also the author of the book, ‘Hunting the 1918 Flu: One Scientist’s Search for a Killer Virus’ said that there are strong similarities between how the Spanish Flu virus killed and how today’s H5N1 strain kills, which raises fear of another deadly pandemic. Duncan had led a scientific expedition during the 1990’s, to exhume the bodies of a group of Norwegian miners, who died in the Spanish flu pandemic.
The subtype of the H1N1 strain (responsible for the Spanish flu endemic) and the current H5N1 strain of the Influenza virus, mainly kill the young and healthy, instead of the elderly and the infants.
Many countries have not yet prepared any emergency plans to counter a bird-flu out break. Only 15% of the U.S businesses have a contingency plan in place for a pandemic, even after the U.S president urged all the businesses in U.S to develop an emergency plan to face a pandemic. The case is much worse in Canada, where only 4% of the businesses have a contingency plan for flu pandemic.
An estimate by the U.S Centers for Disease Control, say that the next pandemic to hit a place like Toronto would leave 700,000 people needing medical attention and 40,000 needing hospitalization. Duncan said that a crisis of this proportion could not be managed, if people are not prepared for it.
She added that, to prepare for a pandemic, people should stock pile food and water that could last up to 6 to 8 weeks and store prescription and non-prescription drugs and other medicines that could last for the same period.
The World Health Organization has been warning of another pandemic ever since 1968, when the last of the three pandemics of the 20th century, occurred. Duncan feels that people are lucky this time, as this is the first time in history they have an opportunity to prepare for a pandemic.
For more information click here http://www.vaccine-info.com
KimT – at 15:06
China http://tinyurl.com/e54eq
China warns of bird flu outbreaks (AFP) Updated: 2006–10–08 07:05
BEIJING - China has reportedly asked local authorities to be on guard against a resurgence of bird flu with the onset of the autumn migration season.
“Autumn and winter are the prime period for bird flu outbreaks,” said Yin Chengjie, vice-minister of agriculture, told the official Xinhua news agency, adding that officials “should not underestimate the difficulties in virus control.”
KimT – at 15:10
Avian Flu Pandemic is Likely Much Ado about Something By Patricia-Anne Tom October 10, 2006
“Pandemics happen. What we don’t know is when it’s going to happen and how bad it’s going to be,” according to Rick Casse, former director of business continuity planning for Gap Inc. Speaking to the Golden Gate Chapter of the Risk and Insurance Management Society Inc. (RIMS), Casse said that’s the reason businesses should prepare for a possible avian flu pandemic.
Klatu – at 16:15
Monday, October 09, 2006
Philippines: Agri dep’t signals bird flu alarm
“MIGRATORY birds have started flocking Northern Mindanao’s wetlands, an Agriculture official said, warning the public against hunting fowls that may carry the dreaded highly pathogenic Avian Influenza or “bird flu.”
‘’‘Joel Rodinas, head of the Department of Agriculture in Northern Mindanao, urged the public to avoid contact with migratory birds and to report suspicious animal diseases. “
Among the bird flu hotspots are the swamps located in the Misamis Oriental towns of Opol, Alubijid, Balingasag, the city of Gingoog and Maramag town in Bukidnon and Bonifacio municipality of Misamis Occidental.’‘’
Rodinas said his office routinely collect samples from all identified migratory birds sanctuaries in Region-10 to detect the virulent AI strain among local fowls.
Effective monitoring and early detection of the disease will be further enhanced with the coming of a high-tech machine capable immediately identifying bird flu, he said.
Currently, local samples are sent to the Manila laboratory for re-examination and for final confirmation, he said.
The machine, to be procured from the grant provided by the Japanese government, will arrive before the year ends, he said, adding early detection of the virus was crucial to its immediate containment.
“Once we have the latest equipment, we can then conduct our tests with authority and confirm the same certainty,” he said.
Pandemic
Cagayan de Oro, which is sandwiched between the region’s wetlands frequented by migratory birds, has already passed an ordinance banning the hunting of migratory birds and creating a bird flu task force.
The Misamis Oriental provincial government has done the same.
Rodinas underscored the local government’s preparedness in containing bird flu, saying local initiatives have helped the country to avoid the dreaded disease, and will minimize the impact in case a bird flu pandemic occurs.
The Philippines is the only remaining bird flu-free region in South East Asia.
Last month, Health Secretary Francisco Duque said the department has standby funds that could accommodate 66,000 patients in case flu pandemic happens.” -excerpt
http://www.sunstar.com.ph/static/cag/2006/10/09/news/agri.dep.t.signals.bird.flu.alarm.html
- Mindanao the southern most island closest to Indonesia and Malaysia…connect the dots.
Klatu – at 17:04
Scientist urge to prepare for a bird flu pandemic
“ that people are lucky this time”
08/Oct/2006: ‘Start preparing for the next flu pandemic’, is the message from the organizer of an expedition to unearth samples of the devastating Spanish flu pandemic in 1918 and 1919. Kristy Duncan, a scientist at the University of Toronto, warns that it is just a matter of time before another deadly bird flu pandemic strikes the world.
Building supplies of food, water, medication and other essential items could help us to tide over the bird flu pandemic, if one strikes.
Duncan, who is also the author of the book, ‘Hunting the 1918 Flu: One Scientist’s Search for a Killer Virus’ said that there are strong similarities between how the Spanish Flu virus killed and how today’s H5N1 strain kills, which raises fear of another deadly pandemic. Duncan had led a scientific expedition during the 1990’s, to exhume the bodies of a group of Norwegian miners, who died in the Spanish flu pandemic.
The subtype of the H1N1 strain (responsible for the Spanish flu endemic) and the current H5N1 strain of the Influenza virus, mainly kill the young and healthy, instead of the elderly and the infants.
Only 15% of the U.S businesses have a contingency plan in place for a pandemic, even after the U.S president urged all the businesses in U.S to develop an emergency plan to face a pandemic. The case is much worse in Canada, where only 4% of the businesses have a contingency plan for flu pandemic.
An estimate by the U.S Centers for Disease Control, say that the next pandemic to hit a place like Toronto would leave 700,000 people needing medical attention and 40,000 needing hospitalization. Duncan said that a crisis of this proportion could not be managed, if people are not prepared for it.
She added that, to prepare for a pandemic, people should stock pile food and water that could last up to 6 to 8 weeks and store prescription and non-prescription drugs and other medicines that could last for the same period.
‘’‘The World Health Organization has been warning of another pandemic ever since 1968, when the last of the three pandemics of the 20th century, occurred. Duncan feels that people are lucky this time, as this is the first time in history they have an opportunity to prepare for a pandemic.” - exerpt
LEG – at 17:21
I can not find any news ref India…am I missing where it might be posted?
Klatu – at 17:52
Kenya Bans Import of poultry banned after bird flu outbreak in Juba, Sudan
The NATION
Publication Date: 10/9/2006
“Importation of poultry and its products using the Lokichoggio Airstrip and roads linking Kenya to southern Sudan has been banned after cases of bird flu were reported in Juba.
Turkana district veterinary officer George Omari yesterday alerted Lokichoggio, Kakuma, Oropoi and Kalokol residents of the new measure.
The World Health Organisation also confirmed the report. The agency’s officials operating in Juba, Southern Sudan, said four birds had died of the flu at a local farm.
However, no human cases were reported.
Dr Omari cautioned hotel owners to observe high standards of hygienic when handling poultry products saying domestic birds were at risk of contracting the disease and spreading it.
He also asked residents to report suspected cases of dead birds to the veterinary department.
The department has started collecting blood samples from birds in the area for testing at the Kenya Medical Research Institute (Kemri), said the officer.
“If some local birds will test positive, the department will kill all birds in the area and pay the owners,” he said.
Dr Omari noted that the International Rescue Committee (IRC), a humanitarian health organisation operating at a refugee camp in Sudan, had started educating people about the disease.” - excerpt
http://www.nationmedia.com/dailynation/nmgcontententry.asp?category_id=1&newsid=83026
Klatu – at 17:53
Map of Sudan, Juba:
witness – at 18:00
Leg at 17:21 The new india thread has some good links to get started.
LEG – at 18:05
thanks witness.
Klatu – at 18:13
The following might come in handy during the next few weeks.
LEG – at 18:26
incredibly helpful Klatu, thanks.
Urdar-Norge – at 18:51
I am allredy very thankfull to Duncan. It was the expidition on Svalbard in Norway that made me aware of the pandemic threat. Its good she now warns people :)
Urdar-Norge – at 18:51
I am allredy very thankfull to Duncan. It was the expidition on Svalbard in Norway that made me aware of the pandemic threat. Its good she now warns people :)
Monotreme – at 18:51
Mississippi, USA
Doctor will lecture on pandemic flu issues
A timely topic, “Pandemic Influenza: To Worry or Not to Worry,” is the first Issues + Answers of the 2006–07 Gulf Coast Public Lecture Series.
Sponsored by the University of Southern Mississippi and the Sun Herald, the lecture will be Thursday evening in Gulfport. A question and answer session is also scheduled.
[snip]
What: “Pandemic Influence: To Worry or Not to Worry,” the first in the 2006–07 Gulf Coast Public Lecture Series
When: 7 p.m. Thursday
Where: Auditorium, Memorial Hospital at Gulfport (the former West Elementary School; turn east at hospital parking garage and watch for signs)
Monotreme – at 18:54
California, USA
Avian Flu Pandemic is Likely Much Ado about Something
“Pandemics happen. What we don’t know is when it’s going to happen and how bad it’s going to be,” according to Rick Casse, former director of business continuity planning for Gap Inc. Speaking to the Golden Gate Chapter of the Risk and Insurance Management Society Inc. (RIMS), Casse said that’s the reason businesses should prepare for a possible avian flu pandemic.
According to Casse, the influenza strain H5N1 that currently is a bird flu, has the potential to mutate into a human virus. Previously, he said the virus wasn’t very widespread. However, starting last year, the virus has been spreading rapidly throughout the wild and domestic bird populations, and now is in 10 countries — countries in which Gap does business in. Further emphasizing the concern, the virus is spreading from birds to mammals, which indicates it is evolving, Casse said. “It’s those potential mutations to the virus that make it more easily transmitted among people and create some of the risk of a pandemic,” he said.
[snip]
And in the meantime, Casse recommended businesses create a preparedness plan that takes into account work stoppages for long periods of time and high employee absences.
Monotreme – at 18:56
Michigan, USA
Local officials prepared for flu pandemic
MARQUETTE — The best way to cope with a possible pandemic influenza situation is to be self-reliant, according to local health officials.
The Marquette County Health Department helped put on a pandemic influenza tabletop exercise at Northern Michigan University recently, simulating a scenario in which Marquette County was wracked by the effects of pandemic influenza.
“It’s critically important that people no longer make the assumption that the government will provide all the services that are needed,” said Cal Burdick, the health department’s emergency preparedness coordinator. “It’s really essential that people plan on being as independent as possible.”
[snip]
However, it’s a fine line between wanting to tell people about the enormity of the potential situation but not incite panic, Burdick said.
“The best way to stem panic is to give people the information beforehand so they can anticipate and prepare for the worst,” he said. “It’s a very serious illness that could result in death. However, if people take certain measures to protect themselves it would certainly lessen their chance of contracting something like that.”
DennisC – at 23:15
The Chinese Ministry of Agriculture has striking news- Outbreak of Bird Flu in NW China “ new outbreak of bird flu was detected in a village situated NW China. According to the Chinese officials the H5N1 virus has already killed nearly 1,000 domestic birds. The laboratory test confirmed the fact that the Chinese authorities failed in preventing the outbreak of new bird flue cases. The Ministry of Agriculture has publicly admitted that more should have been done to prevent the outbreak….
Unfortunately this is the second outbreak of bird flu to be reported in China in less than ten days. Health experts confirmed the existence of H5N1 virus in China’s Inner Mongolia Region at the end of September. “
DennisC – at 23:31
not H5N1, but problems “near” the last Thai H5N1 death Sep 26
“More than 138,000 people in 20 flood-hit provinces have suffered from water-borne diseases, the Public Health Ministry said yesterday. The flood situation remains at crisis levels in several areas …
number of people with water-borne diseases has increased sharply. More than 5,000 people sought medical treatment in hospitals and health stations on Saturday alone. Most turned up with symptoms such as fever, rash and athlete’s foot, a skin disease caused by fungus..
and just to keep the Thai situation in perspective from the Thai update site
“Cumulative number of patients under surveillance are 5,177 cases … There are 21 cases under investigate reported, of which waiting for laboratory result”
09 October 2006
On the fence and leaning – at 00:00
Klatu: Thanks for the map. That helped me a ton.
Hey Mods: Klatu’s map is very helpful. Would it be a good idea to put it somewhere on the site where we can find it easily in the future. Easier than combing through past News Posts.
lugon – at 04:57
This is not strictly news, but it’s related to Awareness Week and the distinction between bird flu and pandemic flu. It’s in Spanish - here.