The H5N1 strain of influenza - often referred to as bird flu - is first known to have jumped from chickens to humans in 1997. Since 2004 it has ripped through poultry and wild bird populations across Eurasia, and had a 53% mortality rate in the first 147 people it is known to have infected. Health authorities fear this strain, or its descendent, could cause a lethal new flu pandemic in people with the potential to kill billions.
Flu has been a regular scourge of humanity for thousands of years. Flu viruses each possess a mere 10 genes encoded in RNA. All of the 16 known genetic subgroups originate in water birds, and especially in ducks.The virus is well adapted to their immune systems, and does not usually make them sick. This leaves the animals free to move around and spread the virus - just what it needs to persist.
But sometimes a bird flu virus jumps to an animal whose immune system it is not adapted to.
Highly pathogenic avian influenza A (HPAI) subtype H5N1 has caused family case clusters, mostly in Southeast Asia, that could be due to human-to-human transmission. Should this virus, or another zoonotic influenza virus, gain the ability of sustained human-to-human transmission, an influenza pandemic could result. We used statistical methods to test whether observed clusters of
HPAI (H5N1) illnesses in families in northern Sumatra, Indonesia, and eastern Turkey were due to human-to-human transmission.
Highly pathogenic avian influenza A (HPAI) subtype H5N1 is repeatedly crossing the species barrier to humans. Since December 2003, a total of 291 cases of HPAI (H5N1) have been reported in humans, resulting in 172 deaths (i.e., 59% case-fatality ratio) in 12 countries, mostly in Southeast Asia (1). Among these cases, 31 family clusters have been documented, ranging in size from 2 to 8 family members. How many of these clusters are due to a common avian source and how many are due to human-to-human transmission are important facts to determine. Should one of these HPAI (H5N1) strains gain the capacity for sustained human-to-human transmission, the resulting outbreak, if not contained, would spread worldwide through the global transportation network more rapidly than adequate supplies of vaccine matched to the new variant could be manufactured and distributed (2,3). We analyzed data from 2 of the largest of
the familial clusters to ascertain if human-to-human transmission took place, and if so, how transmissible the strain was.
For the outbreak in Indonesia...human spread did occur...
...even though we determined that human-to-human transmission probably occurred, whether the virus was capable of sustained human-to-human transmission is not clear. This virus may have required very close human contact to be transmitted... the reported prophylactic use of oseltamivir may have played some role in limiting further spread.
We did not find statistical evidence of human-to-human spread for the outbreak in eastern Turkey. This does not mean that no low-level human-to-human spread occurred in this outbreak, only that we lack statistical evidence of such spread.
"It went two generations and then just stopped, but it could have gotten out of control," Mr Longini said.
"The world really may have dodged a bullet with that one, and the next time, we might not be so lucky."
The researchers estimated the secondary-attack rate, which is the risk that one person will infect another, was 20 per cent. This is similar to what is seen for regular, seasonal influenza A in the United States.
Was it the Tamiflu blanket that stopped it or something else, one wonders?
UNICEF Video on the index case and the first diagnosed patient to die of H5N1 in Bali. This is so very sad. So often, the victims are just part of the statistics, names on a growing list of young people. Viewing this, you can not help but feel what a tragedy has occurred in this family. They are heart broken.
Here is the kind of information that you would be more familiar with if you were researching H5N1 cases. This is the current list of Egyptian viral sequences generated by NAMRU 3, the US Naval Lab in Cairo giving the victims name, age, location.
Statistics...
Look at their ages, they are all young. Not all of these cases are deceased. The Case Fatality Rate in Egypt
they have finally released some of the h5n1 sequences from north america that have been hidden away in data banks for these past two years, annoyingly while these scientists were getting this paper published. the sequences tell the story of how h5n1 has traveled, where it has been, and how it has changed. the need to understand this story is critical to determine the risk to this continent. the sequences should never have been sequestered.
the recently released paper, “characterization of low pathogenicity h5n1 avian influenza viruses from north america”, provides detail on the h5n1 isolates from the united states and canada. although these isolates are low path h5n1 with polymorphisms commonly found in north america...
the ha sequences of two isolates, a/mallard/mb/458/05(h5n1) and a/mallard/on/499/05(h5n1) were released at genbank yesterday. polymorphism tracing of newly acquired polymorphisms identified multiple polymorphisms that are in high path h5n1 in asia and clade 2.2. clade 2.2 is the qinghai strain...
of interest was a pair of polymorphisms, c85t and t97c, which were present in most high path h5n1 isolates. an expanded region of identity was found almost exclusively in indonesian isolates (see list).
the region of identity between h5n1 in canada and hpai h5n1 in indonesia is cause for concern. movement of h5n1 polymorphisms have focused on clade 2.2 because all h5n1 west of china is clade 2.2 and has been found in dozens of wild bird species. however, recent sequences from waterfowl in indonesia suggest they are also a key vector in h5n1 movement of clade 2.1 (found exclusively in indonesia).
Reports have been coming out of DR Congo for the past week of people dying of a mysterious disease, everyone that attended the funerals of two chiefs, that is. Now we are hearing about pigs and chickens dying prior to the people, and more ominously, HCW deaths. They have initially pegged it as a hemorraghic fever disease, but there is no mention of anyone bleeding out in any of these accounts.
Three different flu blogs have addressed these reports. I could use newspaper articles also, and I may, but those links have a way of disappearing, while the blogs and/or forums will preserve this information should it prove to be important.
Migrant birds have tested positive for the H7 strain of bird flu... The H7 strain of the bird flu virus has been detected in Egypt for the first time. Nine migrant birds, all of them ducks, tested positive for the virus when 6,432 samples were taken from the approximately one million birds that annually migrate over Al-Manzalah Lake in the Sharqiya governorate from central and eastern Europe....
The H7 strain samples are now being tested at both the Ministry of Health and Population (MOHP) and Naval Medical Research Unit (NAMRU) laboratories in order to determine the N subtype....
Abdel-Rahman Shahin, spokesman at the MOHP, explains that the H5 and H7 viruses are usually introduced to poultry in a low pathogenic form. It is only after several months that they mutate into highly pathogenic strains. The appearance of the H7 strain is therefore a cause for concern. The virus has been known to infect humans but is less virulent than the H5N1 strain. ...
Veterinary experts, though, warn that the presence of both the H7 and H5N1 viruses in Egypt could facilitate further genetic mutations, which can be caused by the combination of the two types of avian influenza virus which are currently present in Egypt. A combination of the genetic patterns of both viruses, says veterinarian Sami Taha, could result in the appearance of a human-to-human mutation....
This is why there is cause for concern. H7 could give H5N1
the ability to become more transmissible human to human:
H7 is efficiently transmitted from human-to-human, as has been seen in multiple recent H7 outbreaks in Europe, including the recent H7N2 outbreak in the UK. H7N3 was in the UK last year and H7N7 was in the Netherlands in 2003. All three outbreaks resulted in reported human infections.
H5N1 Transportation and Transmission By Wild Birds
Recombinomics Commentary
September 3, 2007
The Wildlife Conservation Society Field Veterinary Program Director William Karesh is among those attending the meeting in Bangkok.
"We tested thousands of birds in Africa, in Nigeria, in that area, and we cannot find a wild bird with the disease. [That] Does not mean it cannot occasionally get into them, but it is probably not going to go anywhere. It is a dead end," he said.
The above comments are very similar to the statements made in August, 2005 by the same investor representing the same organization. At that time he was investigating the dead wild birds at Erhel Lake in Mongolia. A few months earlier, the Qinghai strain of H5N1 was found in dead wild birds at Qinghai Lake in central China. The die-off of over 5000 wild waterfowl infected with H5N1 was without precedent, because H5N1 frequently produced mild or no symptoms in waterfowl. Sequence analysis identified a new clade, designated clade 2.2 which had a number of novel polymorphisms, including an HA cleavage site of GERRRKKR as well PB2 E627K, which was reported for the first time in H5N1 from a bird. The strain was lethal in experimental chickens, resulting in death within 24 hours. The strain was also fatal in experimental mice. The finding of the novel strain in long range migratory birds, including bar-headed geese which could fly 1000 miles in 24 hours, was cause for concern.
The outbreak at Erhel demonstrated that the novel Qinghai strain did not burn itself out at Qinghai Lake. Instead, the Qinghai outbreak was followed by infections at Chany Lake in Siberia and adjacent Kazakhstan, as well as outbreaks in remote regions of Mongolia, including Erhel Lake.
Investigators from the Wildlife Conservation Society were helping to collect and test the birds at Erhel Lake. The Qinghai strain of H5N1 was confirmed, but comments from investigators suggested that because of the number of H5N1 positive dead birds was low, and tests of live birds in the area were negative, the infection would dead end.
The predictions of dead end infections in Mongolia, China, and Russia had no real rationale basis. The H5N1 was detected in Russia and Mongolia for the first time, and the match with the Qinghai strain demonstrated that the infection did not die out at Qinghai Lake in May, 2005. The return of Qinghai H5N1 infections a year later in Qinghai Province as well as Siberia and Mongolia in 2006 provided confirmation that the Qinghai strain did not die out in those regions.
However, the H5N1 infections in wild birds in Mongolia and Siberia in the summer of 2005 suggested that H5N1 would spread to Europe, the Middle East, and Africa, as well as south Asia and Korea and Japan because of overlapping flyways. In the following months, all of the above locations, involving more than 50 countries, reported H5N1 infections and in all cases, the H5N1 was the Qinghai strain.
Recently, H5N1 in wild birds in the summer was reported in Germany, France, and the Czech Republic, indicating Qinghai H5N1 was now endemic in wild bird populations in Europe.
Although all of the above outbreaks have been confirmed via isolation and sequencing of H5N1, some groups are still maintaining that the H5N1 in wild birds was died out. These statements are based on assays of live wild birds, which have been shown again and again to produce dismal results. H5N1 was widely detected in Europe in early 2006, yet none of the countries reporting H5N1 in dead or dying wild birds could detect H5N1 in live wild birds. The same was true in Africa, with the exception of the healthy teal in Egypt.
The detection of H5N1 in Egypt in a healthy teal provided insight into the repeated negatives in live birds. Although the teal was PCR H5 positive, efforts to isolate the virus were unsuccessful. The RNA levels were low, so repeated extractions of RNA were required to generate a sequence. The sequence was clearly Qinghai, and was closely related to Qinghai isolates from Austria in 2006. The Egyptian sample was collected in December, 2005, when countries in western Europe and all of Africa claimed that there was no H5N1 in wild or domestic birds.
Thus, the repeated negatives provide little information about the frequency of H5N1 in wild birds. The H5N1 in dead and dying wild birds in the same regions highlights the short-comings of the live bird assays. Other investigators, such as those in Russia, have no problem identifying H5 sequences or antibodies in live wild birds.
The focus of the conservation groups on assays that have significant sensitivity issues for the Qinghai strain of H5N1 in live wild birds, and the failure of these groups to use more sensitive assays, such as those that measure H5 antibodies, remain cause for concern.
As noted above, PB2 E627K was reported for the first time in H5N1 in
birds. This is a polymorphism that until that time had only been found in mammals. Finding this in a bird virus that killed an unprecedented number
of water fowl was significant, as well as alarming because it indicated that
this virus could be capable of infecting mammals. PB2 E627K is a
mammalian polymorphism that is now found in all H5N1 west of China.
H5N1 does not exist only in dead birds. No disease exists in a vacuum. If they
are finding it in dead and dying birds, it must also be carried by living birds in
the same regions. To find it in live birds, you need to want to find it, and you need unbiased scientists willing "to use more sensitive assays, such as those that measure H5 antibodies". As Dr. Niman has pointed out, the Russians have no difficulty in identifying H5 sequences and antibodies in live birds.
The debate over the role of wild birds vs. domesticated birds in the spread of avian flu has teetered back and forth for a couple of years now. Every few months we seem to get an announcement declaring one side or the other relatively innocent, or guilty.
Today, the UN apparently is placing the majority of the blame on domesticated birds; poultry mostly, often raised in squalid and unsanitary conditions, and moved surreptitiously across borders.
Russia on Tuesday reported its third outbreak this year of the deadly H5N1 strain of bird flu after 410 birds died on a poultry farm in the country's south.
Another 414 birds were culled and strict quarantine measures were in place at the farm in Krasnodar region, Russia's animal and plant health watchdog, Rosselkhoznadzor, said in a statement.
Russian authorities plan to destroy at least 22,000 chickens at a poultry farm where 500 birds died of bird flu, it was reported.
Prosecutors may seek criminal charges against the operators of the farm in Razdolny, in southern Russia's Krasnodar Territory, RIA Novosti reported Tuesday.
The outbreak of lethal H5N1 virus was reported to authorities Sunday after birds had already died...
JAKARTA: A 33-year-old male plantation worker from Indonesia's Sumatra island died of bird flu on Thursday, bringing the death toll in the world's worst-affected nation to 85, health officials said.
"He died at 2:00 pm," the doctor treating the victim at the state general hospital in the city of Pekanbaru, Azizman Daad, told AFP.
There are also very disturbing reports from an island off of the coast of
Sumatra about a "Tamiflu Blanket" being applied to two entire
villages. Teams of translators on several flu forums have been
working on deciphering this information since yesterday. These
translators are providing an amazing service to all of us, BTW.
The term, "Tamiflu Blanket" refers to the public health practice
of giving a population of at risk or exposed individuals the antiviral
drug, Tamiflu prophylactically to prevent H5N1 infection. Any time
a human case occurs, it increases the risk of H5N1 developing the
ability to become more adapted to humans, and this is the biggest reason
for initiating such a hugh undertaking as treating entire villages as is
occurring there now.
Reports are that chickens began dying in large numbers on the island,
but, strangely, there are no recent confirmed human cases. We are
hearing about typhus or typhoid cases instead, but chickens do not die
from these diseases. No confirmed cases + Tamiflu Blanket is most
unusual. None of of us have ever heard of this happening before. But,
there is a precedent of initially diagnosing cases as typhoid and then
announcing H5N1 later.
Obviously, we do not have a clear picture of what is happening there.
At the separate site Tanggamus Iman Sumarjo health agency head has distributed Tamiflu medicine (bird flu medicine deterrent) for free to all the residents in two villages especially those neighborhoods with dead chickens, the administration has continued to do so that every resident gets 10 tablets point Tamiflu medicine, said Faith.
The above translation describes the implementation of a Tamiflu (oseltamivir) blanket for residents of two villages on the island of Palua Tabuan off the coast of southern Sumatra. Thousands of chickens have died with bird flu symptoms and over 100 villagers have been hospitalized with a mysterious illness. Although the illness has been official diagnosed as typhoid fever, the chicken deaths and implementation of a Tamiflu blanket raise serious questions about the true diagnosis for the hospitalized and treated patients.
Further reports seem to indicate that the Tamiflu Blanket is going to cover the entire island of Tanggamus which as noted in the post above is off of the coast of Sumatra.
The above translation indicates the Tamiflu blanket covers the entire island, which is located in the Taggamus regency in Lampung at the southern tip of Sumatra. Although the poultry has not been reported as H5N1 positive, the birds displayed classical H5N1 symptoms, which included a blue comb, throat and nasal secretions, and sudden death. The poultry deaths exceeded 1000 and patients symptoms coincided with the poultry deaths, which began about a month ago.
The current outbreak is linked to four deaths in children, but the majority of patients have recovered and have been diagnosed as having typhoid fever. Media reports do not mention H5N1 testing of poultry or patients.
However, the throwing of a Tamiflu (oseltamivir) blanket over the entire small island signals concerns of H5N1 spread in humans on the island in the Tanggamus regency, Lampung Province, in southern Sumatra
More commentary from Scott McPherson's blog on Indonesia and Democractic
This is a government document. I am printing it in its entirety except for the references which you can get from the link:
Council of State and Territorial Epidemiologists Position Statement
07-ID-01
Committee: Infectious
Title: National reporting for initial detections of novel influenza A viruses
Statement of the Problem:
Human infections with novel influenza A viruses that can be transmitted from person to person may signal the beginning of an influenza pandemic. Rapid detection and reporting of human infections with novel influenza A viruses - viruses against which there is little to no pre-existing immunity - will facilitate prompt detection and characterization of influenza A viruses with pandemic potential and accelerate the implementation of effective public health responses.
Statement of the desired action(s) to be taken:
Add detection of infections and illnesses with novel influenza A viruses to the list of nationally notifiable infectious diseases reportable to the National Notifiable Diseases Surveillance System (NNDSS).
Goals of Surveillance:
1) Rapidly identify and report infections and illnesses among humans with novel influenza A viruses to the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO); 2) ensure prompt confirmation of human novel influenza A virus infections; and 3) facilitate early initiation of appropriate public health responses
This position statement does not address the goals and methods of surveillance that will be needed during an influenza pandemic.
When a state or territory determines that the transmission of a novel strain of influenza inthe general population has become efficient and sustained, this new pandemic influenza strain will no longer be considered novel for the purposes of surveillance. Based on experience with seasonal influenza surveillance, notification of individual influenza cases is unlikely to be either practical or the best use of surveillance resources during this phase of a pandemic (e.g.,
during World Health Organization Phase 6)).
Once widespread community transmission has been established, it is anticipated that other approaches will be used to track the pandemic and guide the public health response (e.g. reporting of aggregate numbers of influenza-related hospitalizations, tracking of rates of influenza-like illness, and tracking of pneumonia and influenza mortality).
Methods for Surveillance:
Case finding is conducted through standard clinician reporting and laboratory testing and reporting methods in use at public health laboratories.
State and territorial epidemiologists in conjunction with public health laboratories will report to CDC all human infections with influenza A viruses that are different from currently circulating human influenza H1 and H3 viruses. These viruses include those that are subtyped as non- human in origin and those that are unsubtypable with standard methods and reagents. Core surveillance data will be reported to NNDSS through the National Electronic Telecommunications
System for Surveillance (NETSS) or the National Electronic Disease Surveillance System (NEDSS), as per state protocol. Submission of specimens from health department laboratories to CDC's influenza laboratory for confirmation and full characterization is a parallel component.
Case Definition narrative:
Clinical presentation: Illness compatible with influenza virus infection.
Laboratory evidence: A specimen from a human that is reverse transcriptase polymerase chain reaction (RT-PCR)- or culture-positive for influenza A and tests negative for currently circulating human H1 and H3 subtypes. (For example, any specimen that is RT-PCR-positive for influenza A and H5 in testing performed by a public health laboratory would meet these criteria).
Case Definition tables:
Suggested codes for case ascertainment:
To be developed for this condition, which depends upon laboratory diagnosis by a public health laboratory
Detailed definitions for case classification:
Confirmed case: A case of human infection with a novel influenza A virus detected by a public health laboratory that has been laboratory confirmed by CDC.
Probable case: A case of human infection with a novel influenza A virus detected by a public health laboratory or a case that meets the clinical criteria and is epidemiologically linked to a confirmed case, and for which laboratory confirmation by CDC's influenza laboratory was either not done or was inconclusive.
Suspected case: (1) A case of human infection with a novel influenza A virus detected by a public health laboratory, and for which laboratory confirmation by CDC is pending; or (2) A case that meets the clinical criteria and isepidemiologically linked to a confirmed case, and for which laboratory testing for influenza is pending.
Period of Surveillance:
Ongoing, beginning in January 2007
Background and Justification:
On December 13, 2006, the United States formally accepted the revision of the International Health Regulations, referred to as IHR (2005)
(http://www.hhs.gov/news/press/2006pres/20061213.html). This international legal instrument governs the roles of the WHO and its member countries in identifying and responding to and sharing information about public health emergencies of international concern
The updated rules are designed to prevent and protect against the international spread of diseases, while minimizing interference with world travel and trade. The revised regulations add human infections with new influenza strains to the list of conditions that Member States must immediately report to WHO. An outbreak of infections with a new influenza A virus that demonstrates human-to-human
transmission could signal the beginning of the next pandemic. Robust epidemiologic and laboratory surveillance systems are required for a coordinated public health response to infections with a novel influenza virus subtype. Early detection of an influenza virus with pandemic potential will permit identification of viral characteristics (e.g., genetic sequence, antiviral susceptibility, and virulence) that will affect clinical management and public health response measures. It should also facilitate development of virus-specific vaccine and testing
strategies.
All state public health laboratories have the capacity to test respiratory specimens for influenza viruses with sensitive and specific assays that can detect human and non-human influenza A viruses. They also have the capacity to subtype currently circulating human influenza A H1, H3, and avian H5 (Asian lineage) viruses. The detection or confirmation by a state public health laboratory of an influenza A virus that is unsubtypable with standard methods (e.g., real-
time RT-PCR assays for human influenza A(H3) or (H1) viruses), or a nonhuman influenza virus (e.g., H5) from a human specimen, could be the initial identification of a virus with pandemic potential. Novel strains detected by tests performed by non-public health laboratories using assays not validated by CDC should be immediately reported to the state health department and the state public health laboratory for confirmatory testing. Prompt notification of CDC by a state epidemiologist in conjunction with the public health laboratory will permit rapid confirmation of results and reporting to WHO, and aid prompt viral characterization and the development of virus-specific diagnostic tests. Based on experience with seasonal influenza surveillance, notification of individual influenza cases is unlikely to be practical, useful, or the best use of surveillance resources during the pandemic phase. Once widespread community transmission has been established, it is anticipated that other approaches will be used to track the pandemic and guide the public health response (e.g. reporting of aggregate numbers of influenza-related hospitalizations, tracking of rates of
influenza-like illness, and tracking of pneumonia and influenza mortality).
indigo girl
5,173 Posts
Detecting Human-to-Human Transmission of Avian Influenza A (H5N1)
Yang Y, Halloran ME, Sugimoto J, Longini, Jr IM. Detecting human-to-human transmission of avian
influenza A (H5N1). Emerg Infect Dis. 2007 Sep; [Epub ahead of print]
http://www.cdc.gov/eid/content/13/9/pdfs/07-0111.pdf
(hat tip flutrackers/laidback al)