masks N95 for the children against the swine flu,H5N1 and the viruses airborne.

Bangladesh slays 117,000 birds on flu fears

DHAKA -- At least 117,000 chickens were destroyed in northern Bangladesh Sunday after avian flu outbreak on one of the country's largest poultry farms, a local official said.

The deadly H5N1 strain of flu was detected on Saturday when 400 chickens died suddenly at the Kazi Farms complex in Thakurgaon town, district livestock chief Mosaddekur Rahman told AFP.

“Tests confirmed presence of the H5N1 bird flu in 15 sheds of the farm and we ordered destruction of all 117,600 layer chickens,” he said.

Kazi Farms is Bangladesh's largest poultry bird and egg producer. General manager of the company Ataur Rahman said another 200,000 eggs had also been destroyed in the single largest outbreak of bird flu in the country.

“Our loss will be more than 400 million taka (six million dollars),” he told AFP.

Bangladesh was hit by bird flu in February 2007, when more than one million birds were slaughtered on thousands of farms across the country.

The last major outbreak was in November 2008 when 10,000 birds were culled over a two-month period, with smaller outbreaks detected in 2009.

Bangladesh's poultry industry is one of the world's largest, producing 220 million chickens and 37 million ducks annually.

The country reported its first confirmed human case of bird flu in May 2008, but the government said the 16-month-old baby who contracted the virus recovered.

Bird flu outbreak reported in five countries

Spike In H1N1 In Texas and Alabama Raises Concerns

Recombinomics.com has the story

Commentary 13:01
March 14, 2010
Doctors have noticed a small rise in the number of flu cases at Texas Children's Hospital in the past few weeks, and health officials are hoping the coming months won't bring a repeat of last spring's rash of swine flu illness.

There were two culture-confirmed cases of Type A influenza in December, three in January and seven in February — all found to be of the swine flu subtype, Demmler-Harrison said.

Five cases of Type A influenza surfaced in the first week of March, but tests are still pending to determine if those are swine flu, she said.

At Andalusia Regional Hospital, positive flu cases are averaging about one per day, said Candie Northey ARH’s director of infection.

“We can’t confirm whether these are H1N1 or typical seasonal flu because the tests we utilize are simple ‘quick tests’ and only reveal positive or negative flu,” Northey said. “We have noted five positive tests through our lab in the last five days, and while this is not a lot, I do feel the need to refresh everyone on how to prevent the spread of flu.”

The same can be said at Opp’s Mizell Memorial Hospital, where Marsha Seppala, MMH’s director of case management and infection prevention, said the first of the year started out relatively slow for positive flu cases.

The above comments describe increases in Type A influenza cases in early March in the Houston area, as well as two cities in southern Alabama.  In the US, seasonal type A flu cases have virtually disappeared.  In 2010 there has only been one confirmed seasonal H1N1 in the entire country, and there has also only been one H3N2 case in the past five weeks.  Therefore, the increase in type A described above is an increase in pandemic H1N1.

This increase is not unexpected.  Although reporters have been requesting a declaration that the 2009/2010 pandemic has ended, each of the past three pandemics had a fall and spring wave.  Moreover, the seasonal flu was crowded out, as has happened with seasonal H1N1 and H3N2.  Therefore, there is no evidence against a spring wave.

In the US the first confirmed swine flu cases were on samples collected March 30 and April1, 2009.  However, the confirmed cases were from clusters involving earlier infections, which would have involved swine H1N1 infections that began almost exactly one year ago.  That outbreak peaked in May, and a similar time frame is expected for 2010.

Pandemic waves begin when a high percentage of the target population has little or no immunity and end when the population does have immunity.  A new wave is driven by a virus that has evolve away from the immunity, as indicated by “low reactor” status, such as those with G158E.  This polymorphism began to expand in the US during the fall wave, and then began to appear in larger numbers in Japan in December. 

However, the appearance of G158E in the most recent public sequences, two Feb 26 isolates from swine in Minnesota is cause for concerns.  These two isolates represent the same sub-clade found in Ukraine, Russia and Norway that had D225G and were linked to fatal cases.  However, the virus is circulating in swine and isolates in Illinois and Minnesota have picked up the same swine polymorphisms.  The detection of the same H1N1 in Minnesota and Illinois indicates the virus is circulating in swine, and the two most recent isolates from Minnesota have added G158E.  Since these isolates are the pandemic H1N1 sub-clade that is widespread in Ukraine, it can jump back into the human population and introduce the swine acquisitions.  Both G158E and D225G are common in swine.  Moreover, 1918 sequence have an equal  mixture of human and swine H1N1polymorphisms acquired via recombination, which would also produce new acquisitions in the Minnesota swine, including G158E.

Thus, the above reports signal the start of a spring wave, and the increases in low reactor polymorphisms like G158E and D225G are likely candidates for increases due to positive selection pressure, which would lead to more severe and fatal cases.

Sequence data on the emerging cass in March would be useful.

Children With Chronic Respiratory Illness Are Vulnerable To Critical H1N1

As critical care professionals develop a better understanding of the progression of H1N1, they are becoming better prepared to treat children with severe cases, according to a new study that will be published in the March issue of Pediatric Critical Care Medicine (PCCM).

Additionally, with careful management, the pediatric critical care system is expected to be able to meet the increased demands of a flu pandemic, according to a resource modeling study published in the same issue of PCCM.

The first H1N1 study focusing exclusively on critically ill children found that children with chronic illness, especially respiratory illness, are more likely to develop H1N1 influenza that requires critical care and that the virus is likely to change course as it attacks the lungs throughout the course of the illness.

"The good news is that all of our patients survived, even though some needed mechanical ventilators and heart medication," said senior author David G. Nichols, MD, professor of anesthesiology/critical care medicine and pediatrics at the Johns Hopkins University School of Medicine.

Compared to seasonal influenza, H1N1 influenza appears to have increased infection rates among children and young adults and varies in severity.

The researchers reviewed cases of 13 critically ill children with H1N1 admitted to the Johns Hopkins Hospital Children's Center pediatric intensive care unit during the spring and summer of 2009. They found that the vast majority (92%) of the children had an underlying chronic disease, usually a lung disease such as asthma, before contracting H1N1 infection.

"Critical H1N1 disease in children has different and rapidly changing manifestations in the patients' lungs," explained Dr. Nichols. "Some children behaved as though they were having an asthma attack, while other children behaved as though they had severe pneumonia. Some children had both or switched from one to the other. These variable and changing manifestations of lung infection made life support with a mechanical ventilator challenging and required us to constantly reassess and readjust treatments."

The researchers also found that children with H1N1 lung disease are at increased risk for developing a second type of pneumonia.

Patients who received treatment with antiviral drugs such as Tamiflu within 48 hours of admission did not have significantly different outcomes than those who received antiviral treatment more than 48 hours following admission.

Study offers positive assessment of PICU surge capacity during pandemic flu

Even during the peak of a pandemic, adequate health care can be provided if patients are managed appropriately. "An influenza pandemic for children can be managed, even allowing emergency care for non-influenza-related acute care children, but only when firm decision-making rules for hospital health care are followed and anti-viral therapy is used to reduce the burden of the disease in the community," said lead author Raoul E. Nap, PhD, directorate of medical affairs, quality, and safety at the University Medical Center Groningen, University of Groningen in the Netherlands.

The researchers modeled pediatric surge capacity of health care facility and pediatric intensive care unit (PICU) requirements over time to assess the adequacy of preparedness planning for an influenza pandemic.

They noted a lack of published and detailed analyses of PICU needs and demands, raising concern that PICU facilities will be a major limiting factor in the provision of care. "We show that PICU surge capacity is likely to be adequate assuming that 'older children' [age > 7-8 years] can be rerouted to an adult ICU environment preserving adequate bed space for 'younger children', that enough adult ICU resources are available and that safe provision of care to children can be guaranteed," said Dr. Nap.

The study's overall assessment that an influenza pandemic can be managed at the level of health care institutions clearly contrasts with other sobering and daunting global analyses presented for ICU capacity, according to Dr. Nap.

"We recommend that an adaptable planning model for pediatric surge capacity be an integral part of a preparedness plan for a pandemic flu," Dr. Nap concluded.

"H1N1 has greatly impacted every pediatric critical care medicine program world-wide," said PCCM editor Patrick M. Kochanek, MD, FCCM. "I view the dissemination of new information on this disease as the top priority for our journal. The reports from both Baltimore and the Netherlands in the March issue of Pediatric Critical Care Medicine present, respectively, valuable information on the impact of critical respiratory disease produced by H1N1 in children with underlying chronic conditions, and explores PICU surge capacity."

Source:
Sophie Tosta
Society of Critical Care Medicine

Widespread H1N1 Low Reactor G158E In US Raises Concerns

Recombinomics.com has the story

Commentary 12:01
March 12, 2010
Recently released sequences by the CDC at GISAID have G158E, raising concerns that these low reactor sequences are becoming more widespread.  G158E is in earlier isolates from Germany, A/Bayern/62/2009 and A/Bayern/69/2009.  Although these two isolates have synonymous changes that distinguish the two viruses from each other, the only recent non-synonymous change was G158E.  Mill Hill ran an antigenic Characterization test on both, and declared both “non-reactors”. 

The CDC also tested Bayern/69 and also declared it a low reactor.  However, the recent (October and November) isolates in the US were tested, but not labeled low reactor.  Included in the recent sequences with G158E are three isolates from Washington (A/Washington/60/2009, A/Washington/61/2009/ and A/Washington/65/2009).  Although all three isolates have G158E, they have different combinations of other polymorphisms, placing them in different sub-clades, signaling recombination..

The most recent isolate, Washington/65 also has E377G.  Several other US isolates with G158E have E377K (Texas/65/2009, Idaho/10/2009, Minnesota/18/2009, Arizona/18/2009, Hawaii/29/2009) as well as isolates in Japan (A/Hyogo/1597/2009) and Greece (A/Athens/16606/2009), indicating this sub-clade has spread significantly.

The reason behind the failure of the CDC to classify some of these recent isolates as “low reactors” is unclear.  Prior to last week, only two low reactors were reported by the CDC in the US, and both had a change at the adjacent position N159D.  Both position map to the same antigenic site and a recent paper on the effectiveness of 1918 anti-sera on the 2009 H1N1 noted that escape mutants also mapped to this antigenic site.  However, a recent WHO reported noted that there were differences between labs running antigen characterization tests, and a new universal reference anti-sera had been created using pooled sera from patients, which was available in late 2009.  This new reagent may have produce a negative low reactor result because a pooled sera would have a wider range of antibodies, relative to the traditional tests, which use ferret antibodies from experimental animals immunized with the vaccine target. 

Since there are approximately 5 amino acid differences between California/7/2009 and the consensus H1N1 sequence, the ferret reference sera may be more sensitive than pooled sera, especially if the sera is from patients infected with H1N1 instead of being vaccinated with California/7.  If the sera is from vaccinated patients it is unclear which vaccine was used because there are at least three different sequences in various commercial products.  Even within the US the killed vaccine has Q226R, while the live vaccine has D225G.  In Europe the adjuvented vaccine has both, but as mixtures with wild type.  These differences could affect results, especially for D225G, which Mill Hill designated as a low reactor.  In a recent antigenic characterization of an isolate from Ukraine, which had G158E and D225G, the CDC did not classify it as a low reactor, suggesting that the assay being used by the CDC lacks sensitivity.

These differences involving polymorphisms that had been independent mapped to antigenic sites, and have tested as low reactors in earlier assays raise serious concerns about the validity of the recent negative results by the CDC, especially if pooled anti-sera is being used.

Uniform false negatives remain hazardous to the world’s health.

Egypt has plan to battle Bird flu

CAIRO: The Egyptian health ministry said this week that the country is moving ahead with efforts to stall the spread of the deadly avian influenza, or the H5N1 virus, after a surge in reported cases were reported in recent weeks. The ministry hopes that their efforts can curtail the virus from causing a widespread epidemic in the country, or mutating with the swine flu virus to cause what health have feared would be a super virus.

The sale of poultry between any of Egypt’s 29 governorates is to be banned, and a major Health Ministry-led awareness campaign will alert the public to the dangers of raising birds at home, Sabir Galal, deputy chief of the Veterinary Medicine Section at the Health Ministry, told local newspapers.

“Bird flu has become endemic in this country … the fear now is that the virus can assume more dangerous forms in the days to come,” he said.

The ministry also said it would stop inoculating birds after vaccines had proved incapable of stopping the virus from spreading.

With 105 infections to date and 30 deaths, Egypt is the world’s third most affected country by avian influenza, according to the World Health Organization. The reason for Egypt’s large number of cases is due to its proximity to three continents and is a regular stopover for migratory birds from Asia, Africa and Europe.

Low Reactor G158E In 2010 Swine Pandemic H1N1

Recombinomics Commentary 12:50
March 11, 2010
Recently released sequences by the US National Veterinary Labs in Ames, IA included two sequences from MN swine, A/swine/MN/8762-1/2010 and A/swine/MN/8762-2/2010, which have G158E.

Both sequences have a collection date of February 26, 2010, which represents the most current public 2010 pandemic H1N1 sequence and the first examples of G158E in swine pandemci H1N1.  This polymorphism has been linked to a “low reactor” designation by Mill Hill and the CDC.  It is also in the antigenic site associated with immunological escape from neutralizing monoclonal antibodies which react with 1918 and 2009 pandemic H1N1.  The number of reported sequences with G158E is on the rise in Asia and Europe.  Examples have also been reported in the United States although CDC has reported these as examples as California/7 like, raising questions about recent antigenic characterizations.  WHO has acknowledge inter-lab differences and has proposed a new standard using pooled human antibodies, which may produce uniform test results with lowered sensitivity.

The detection of G158E in February swine H1N1 isolates provides additional signals that the rate of H1N1 evolution is increasing.  These sequences have D1381G, which is widely detected in human sequences including those in Ukraine and Norwat with D225G (see list here).  However, the Minnesota swine isolates have a number of non-synonymous changes which are largely limited to swine isolates See list here here here here).  These may be present in human 2010 sequences, but release of such sequences is significantly delayed, and only a handful of human 2010 sequences have been released. The largest number were just released by Greece, and 3/9 had D225G, which is another polymorphism being reported at increasing frequencies.

The latest sequence from declineChina, A/Beijing/22811/2009, was also just released.  The December, 2009 isolate has 9 recently acquired non-synonymous changes in HA, once again signaling increased H1N1 evolution.

As H1N1 evolution is increasing, antigenic characterization tests are increasingly suspect.  Similarly, the number of samples being collected and the release of data is on a , while the start of a new wave is being signal.

The current degrading H1N1 surveillance is becoming increasingly hazardous to the world’s health.

H1N1 Greek and Russian D225G Sequences Identical

Recombinomics Commentary 18:50
March 10, 2010
Recent sequences from the National Influenza Centre for northern          Greece include 9 sequences from 2010, of which 3 had D225G.  Three more November isolates had D225G, including A/Thessaloniki/2812/2009.  Three of the isolates had D225G as the only recent change, but the other three has polymorphisms found in three different sub-clades.  The above sequence was an exact match (see list here here here here) with A/Bryansk/IIV2971/2009, which had been collected 11 days earlier from a lung sample, suggesting the Russian sequence was from a fatal case.  Clinical information from the Greek isolate was not included, but the samples were from a study of severe and fatal cases in Greece, suggesting the D225G positive samples were from such cases.

The identity between the samples collected in Russia and Greece  11 days apart provides compelling evidence that the H1N1 is transmitting with D225G and is not due to spontaneous mutations, which is the WHO working hypothesis.  Transmission is also supported by sequences from autopsy lung in Ukraine, where 27/37 samples had D225G, D225N, or both.  The same association of these changes with fatal cases was seen in the Duke death cluster where 3 of 4 samples from the first three patients, who were on the same ward, had D225G or D225N.

The three D225G cases in 2010 is the largest number reported to date from a single country this year and the nine cases from 2010 is also the largest number of sequences from a given country.  D225G has been reported in a 2010 Russian isolate, but thus far there have been few 2010 sequences made public.

However, the finding that D225G is in a Ukraine low reactor raises concerns that the frequency of D225G in 2010 cases will be markedly higher than 2009.

Mum tells how she survived horror swine flu ordeal

A MUM has told how she fought back from the brink of death after catching swine flu.

Victoria Fleming's family feared she would die after she suffered multiple organ failure.

The 40-year-old - who has no underlying health problems - was put into a coma and flown to England for vital life support.

She spent weeks in intensive care and had to use a walking frame after finally being able to get out of bed.

Victoria, from Carluke, Lanarkshire, said: "I am lucky to be alive.

" I was as ill as I could possibly be without dying."

Trade union organiser Victoria, mum to six-year-old Amy, was given Tamiflu after she fell ill at work.

But she became seriously sick within days and was rushed to Wishaw General Hospital with breathing difficulties.

Her vital organs began to fail and doctors took the decision to put her into a coma.

Her terrified parents and husband Frankie were told there was nothing more medics could do to save her.

But hours later doctors secured a place at Glenfield Hospital in Leicester for treatment on a special machine which gives the blood oxygen.

Victoria was flown south where she had 75 hours of treatment.

She was later returned to Wishaw where she was in intensive care for three weeks.

Victoria said: "The treatment in Leicester made all the difference.

"The machine takes your blood through a tube and adds oxygen and removes carbon dioxide before replacing it via another tube. Luckily, I responded really quickly. My dad and husband never thought for a moment that I might not recover, but my mum still gets upset sometimes thinking about the day they were told that my organs were shutting down."

Victoria talked of her ordeal after the Daily Record exclusively revealed that Gayle Cassidy, Scotland's longestsuffering swine flu victim, had lost her battle with the killer virus.

Insurance worker Gayle died at Glasgow's Western Infirmary last month.

Victoria said: "I got so emotional when I read about Gayle Cassidy. Our stories are the same but have a very different ending. I couldn't stop crying."

Victoria has been able to return to work gradually - but it could be up to a year before she recovers fully.

She said: "I can't do any proper exercise because of open sores on my feet.

"My toes and heels went black because of the illness. My fingernails and patches of my hair have fallen out.

"I have scars in my neck from the treatment but I wear them with pride because it's a reminder of the treatment that saved my life."

The swine flu outbreak has killed 69 Scots but cases continue to fall.

H1N1 Low Reactor G158E In Athens Greece

Dr Henry Niman

Recombinomics Commentary 11:13
March 10, 2010
Recently released sequences from Mill Hill at GISAID included a sequence, A/Athens/16606/2009, from Greece collected on December 26, 2009.  The sequence contained G158E, which was found in low reactors designated by Mill Hill and the CDC.  Although only a partial sequence was released, it contained E377K, which was also in the Hyogo/1597/2009 isolate from Japan, indicating G158E was transmitting.  Similarly, four of the G158E sequences from Japan also had A200T including one sample with H274Y.  Another sample in Japan had D225N, while samples in Italy and Russia had D225G.

These various combinations signal movement of G158E from genetic background via recombination, which was also seen for D225G, D225N, and H274Y.  D225G has also been designated a low reactor marker, leading to concerns that these markers will be more common in upcoming waves, including the wave which may be beginning now.

Increases in these markers would lead to more severe and fatal cases as indicated by the association of D2225G/N in Ukraine, Norway, and Greece.  Although current approaches has yielded high frequencies of D225G, the detection of D225G in egg isolates from mild cases raises concerns that low levels of D225G may be widespread, and increases may be missed with current assays which focus on direct sequencing and growth of virus in mammalian cells, which failed to identify D225G in milder cases, which had D225G in egg isolates.  However, this failure may be linked to mixtures in these samples, which may be less common as immune responses reduce the level of wild type receptor binding domains