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USA : Sequence Analysis of H5N1 Bird Flu in Michigan

Sequence Analysis of H5N1 Bird Flu in Michigan
      
      
      The additional testing that we're doing would include sequencing the genetic material. What is the sequence of the genes, and is that consistent with a North American strain or an Asian strain? The fact that this was compatible with our North American virus and not compatible with the Asian high path avian influenza virus that we are able to say that this is not the incursion of that Asian high path H5N1 virus.
      
      
      There's also another test to determine pathogenicity or really two ways to determine pathogenicity. One is, looking at that sequence, that gene sequence. It's through that gene sequence testing that we're able to say that from a genetic standpoint this looks like a low pathogenic virus.
      
The above comments indicate that the H5N1 detected in two of twenty mute swans on Lake Erie in southern Michigan were LPAI (low pathogenic avian influenza.  It is likely that the full sequence will be similar top the recently releases HA sequence of H5N1 detected on British Columbia,A/mallard/BC317/2005(H5N2), almost exactly one year ago. However, the exact sequence can provide valuable clues about the presence of avian HPAI version of H5N1.  In wild birds, that version is most commonly the Qinghai strain.
      
The Qinghai strain was first identified in May of 2005 at Qinghai Lake.  It migrated into southern Siberia for the summer and caused outbreaks in Russia, Kazakhstan, and Siberia.  The strain then migrated to Europe, the Middle East, and Africa, as well as China.  Sequences of the H5N1 from mute swans in Astrakhan have North American sequences suggesting H5N1 may have already migrated to Canada last year. However, HPAI H5N1 has not been reported in Canada.
      
Last year young ducks were tested as part of an expanded banding program across southern Canada.  Four H5 sero-types (H5N1, H5N2, H5N3, H5N9) were identified.  H5N1 was in Manitoba, while H5N2 and H5N9 were in British Columbia.  In Manitoba, an alarmingly 24% were H5 positive.  In the testing in southern Michigan, 2 of the 20 tested birds were H5N1 positive, so the percentage in certain regions of the United States may also be alarmingly high.
      
The high frequency6 of H5 in wild birds is a concern because H5 can become highly pathogenic, and can acquire mammalian polymorphism. Moreover, it can most easily recombine with H5N1 from Asia because of regions of genetic identity.
      
There is already evidence for both processes.  Although a large number of H5 virus was identified last year, only one sequence has been made public.  However, that sequence has polymorphisms shared by swine in Canada as well as H5N1 in Russia.
      
The tandem polymorphism from H1N1 Canadian swine were describe earlier.  Today 2006 HA sequences Russia were released.  A new polymorphism found in three recent isolates from Russia, A/cat/Dagestan/87/06(H5N1),       A/chickem/Krasnodar/199/06(H5N1), A/chicken/Adygea/203/06(H5N1), was also present in the H5 in British Columbia.
      
Analysis of the H5N1 sequence from Michigan can be used to determine of the evolution in the 2006 isolate and can be used to evaluate new polymorphism present in new Qinghai isolates.
      
Full sequences of the Michigan swans should be made public as soon as possible.
Source: Recombimonics

Pandemic fears as bird flu kills seven of this man's close family

JONED GINTING watched his family die one by one. Now he lies desperately ill in hospital with bird flu.
Seven members of his family, including his ten-year-old son, have died within three weeks in what health experts fear is the first case of human-to-human transmission of the disease.

For Mr Ginting, it is a personal tragedy. For the world, it raises the alarming prospect that the H5N1 virus may be passed from one human being to another. Source : Times

CDC : H5N1 Sequence Analysis of North Sumatra Cluster

The CDC head said the genetic sequencing of viruses from the cluster so far has yielded four main findings:

The isolates are all "virtually identical," implying a single source.

They are susceptible to the antiviral drug Tamiflu (oseltamivir).

"There is no evidence of motif changes in the particular areas of the genes that are responsible for how the virus binds to the respiratory tract of people."

The isolates are very similar to viruses previously collected from poultry in the region.

The above comments from the CDC are similar to comments from Hong Kong.  Both groups receive human samples from Indonesia as indicated in the WHO update.  However, as with the earlier WHO updates, more information is available from what is not said in the reports.  Since only part of human sequence has been made public (HA and NA from the first confirmed case in July of 2005), more sequence interpretations come from short and well parsed comments, such as those above.

The first two confirmed cases in Indonesia were associated with short descriptions which contained subtle differences.  The released sequence from the first case in 2005 has a novel cleavage site (RESRRKKR), which is why it was not called “virtually identical” but was said to have ”high homology” with poultry sequences, which have the more common cleavage site (RERRRKKR).  The second sequence in 2005 was called “essentially the same” as poultry (as opposed to essentially the same as the first human sequence), indicating it had the RERRRKKR cleavage site.  Thus, there were two sequences in human cases in the Jakarta area.   Source : RFecombinomicsCDC :

Indonesian cluster of bird flu triggers pandemic fears

he World Health Organization said today that limited human-to-human transmission of bird flu might have occurred in an Indonesian family of which six members died of bird flu. Health experts are trying to trace anyone who might have come into close contact with the family.

But the world's health agency said that as of now there has been no evidence to indicate that the H5N1 virus has mutated to a form that is easily transmissible between humans. The problem as far as they are concerned is that a definite source of infection in the family has not been identified. This according to WHO regional spokesman Peter Cordingley is very worrying.

"We have seen clusters in the past and we have seen what was almost certainly (maybe) limited human to human transmission in some cases," he said. "But this is significant because it's the mother of all clusters. It's seven people, six of whom have died and possibly an eighth as well who died before samples could be taken so this is the mother of all clusters." Source : Foodconsumer.org

Swine to Human H5N1Transmission in Indonesia?

Among the confirmed deaths on Wednesday was a 38-year-old catering businesswoman from Surabaya who had dealt with live pigs and pork meat before she died last week.
      
The above comments on a confirmed death in Surabaya are cause for concern.  Last year H5N1 infected swine were identified in Surabaya.  Reports indicated that all eight genes had been sequenced in Japan, and the sequence included a polybasic cleavage site. Although the sequence was generated over a year ago, it has not been made public via deposition at the public database at GenBank or Los Alamos. Instead it is almost certainly being withheld in the WHO private database.
      
Only one human H5N1 sequence has been deposited from Indonesia.  That sequences has a novel HA cleavage site of RESRRKKR, which is not found in any sequence at GenBank.  However, a recent report suggested that the novel sequence was in human isolates from Indonesia as well as a cat isolate from Indonesia.
      
Novel sequences are common in swine H5N1, in part because there are a limited number of such sequences.  All public swine H5N1 sequences have come from China, and most have novel HA cleavage site. The common H5N1 sequence is RERRRKKR.  Two of the swine sequences, A/swine/Guangdong/1/2003(H5N1) and A/swine/Shandong/2/03(H5N1), but even in these cases the nucleotide sequence that encodes the cleavage site is relatively rare.  It is unique for the Guangdong sequence and shared with a few wild bird isolates in the Shandong sequence.
      
Several of the swine isolates,  A/swine/Fujian/F1/2001(H5N1), A/swine/Fujian/1/2003(H5N1), A/swine/Guangdong/2/2003(H5N1), A/swine/Guangdong/4/2003(H5N1, A/swine/Guangdong/5/2003(H5N1) have the REIRRKKR sequence which is shared with a small number of waterfowl including Guangxi ducks, and A/swine/Anhui/2004(H5N1), which has REGRRKKR which is also found in a small number of waterfowl.
      
These small number of isolates in these swine H5N1 sequences raise the possibility that the novel sequence in the human isolates in Indonesia also come from swine.  In any event, the human and swine sequences from Indonesia should be released, and the source of the novel HA cleavage site should be determined. Source : recombinomics

Vaccine : not ready...try to evitate the 1976 tragedy from ABC News

For nearly nine years, infectious disease specialists at Rochester University Medical Center in Rochester, N.Y., have been conducting tests as part of a broad national effort to develop a bird flu vaccine.

Beginning in late 1997, the human trials have tested 30 different vaccines, all pegged to the H5N1 virus. The testing is funded by National Institute of Allergy and Infectious Diseases at Rochester and six other centers around the country.

What's happening in Rochester and elsewhere is a reminder of another pandemic scare 30 years ago.

The pandemic never occurred, but the vaccine produced to protect Americans had tragic consequences.

In 1976, three American soldiers at Ft. Dix, N.J., died from swine flu, raising fears of a pandemic. Unlike bird flu, the swine flu virus was transmitted person to person.
The administration of President Gerald R. Ford mounted a national campaign urging Americans to get swine flu shots. In a famous photo opportunity that year, Ford himself rolled up his sleeve and was inoculated. But the vaccine was unsafe.  Thirty-two people died and hundreds of other developed paralysis from Guillain-Barre syndrome... Source : ABC 

 

1st human case of H5N1 bird flu found in Jordan

Egypt has reported 5 people infected, two of whom died now: Jordan reported its first human case of bird flu on Friday in an Egyptian labourer who was believed to have become infected while on a holiday in his home town in Egypt, health officials said. Health Minister Said Darwazeh said the man, a 31-year old labourer, who had lived in Jordan for three years, had been taken to hospital on Thursday after suffering severe breathing problems three days after arriving from his home town in Fayoum where people had been in close contact with infected poultry.
Source : Reuters

Cameroon : New Case of H5N1

The government of Cameroon, the fourth African country affected by the deadly H5N1 virus, has confirmed the presence of a second case of bird flu. Source : Reuters

Experimental Bird Flu Vaccine Falls Short

Only about half of the people who received an experimental bird flu vaccine produced antibodies indicating they were protected, researchers report.

Although the dose needed for even this modest effect was extremely high (about 12 times that of the annual flu vaccine), officials stopped just short of calling the trial a disappointment.

"We had hoped it would be better," acknowledged principal investigator Dr. John Treanor, a professor of medicine and an associate professor of microbiology and immunology at the University of Rochester Medical Center. Source : Forbes

Czechs testing dead bird for H5N1 bird flu strain

The Czech Republic is testing a dead swan for the H5N1 strain of bird flu, the first suspected case in the central European country. Source : Reuters