A/H1N1 has mutated to something more deadly - 1918 RBD D225G in Lung Cases in Ukraine and Norway

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1918 RBD D225G in Lung Cases in Ukraine and Norway
Recombinomics Commentary 11:29
November 21, 2009

For the two 1918 HA variants, the South Carolina (SC) HA (with Asp190, Asp225) bound exclusively alpha2-6 receptors, while the New York (NY) variant, which differed only by one residue (Gly225), had mixed alpha2-6/alpha2-3 specificity, especially for sulfated oligosaccharides.

The above description is from a paper analyzing receptor binding domain differences in sequences from the 1918 pandemic. The New York variant had D225G, the same change found in lung tissues from fatal swine H1N1 sequences in Brazil, Ukraine, and Norway. The above result clearly demonstrated a change in receptor specificity for D225G, which was present in A/New York/1/1918 and A/London/1/1919, demonstrating the same change I 1918 that has been described in 2009. Although WHO stated that this change was "not significant" in the Ukraine samples, it was associated with the fatal cases and is cause for concern. The concern was increased by the announcement from Norway indicating the same change was found in fatal H1N1 lung infections there also.

Although there have been comments that this change was "spontaneous" and did not spread, the finding of the same change in all four deceased patients in Ukraine from two distinct locations, indicates it did spread, as did the finding of the same change in multiple cases in Brazil and Norway. Although the concept of "random mutation" has been used to explain away the sudden appearance of the same polymorphism on multiple backgrounds, the appearance via recombination is a much stronger argument for the same change to appear at multiple locations at the same time.

The spontaneous mutation theory, which is the foundation of WHO policy and statements on significance of changes relies heavily on a "selection" component, arguing that the same change keeps appearing on different backgrounds because of string selection pressure. However, this same phenomenon was described for a silent mutation on H5N1, which offers no clear selection pressure. Similarly, a silent change was also found in seasonal H1N1 in sequences that had acquired the Tamiflu resistance marker, H274Y. Thus, these silent (synonymous) changes string argue against a coincidental spontaneous mutation, and instead argue that this acquisition is concurrently acquired because of a widespread common donor.

The concept of acquisition via recombination has serious implications for the current pandemic. It was used to predict the D225G change, in part because the change was "in play" and appearing in July/August sequences at increasing frequency, even though the H1N1 sequences represented different genetic backgrounds. Similarly the clusters of Tamiflu resistance in Wales and North Carolina are also driven by recombination, as happened when the identical change was acquired in H1N1 seasonal flu in patients who were not taking Tamiflu (oseltamivir).

Thus, the concept of recombination predicts that the D225G receptor binding domain change, and the H274Y Tamiflu resistance change, which continue to spread via recombination

Ukraine Dead Increase to 239 - 1,253,558 ill with Influenza/ARI

Ukraine Dead Increase to 239 - Still No Sequences
Recombinomics Commentary 20:26
November 12, 2009
1,253,558 Influenza/ARI

65.615 Hospitalizations

239 Deaths

The above numbers are from the latest update from the Ukraine Ministry of Health. The number of deaths increased 26 to 239, so 50 new deaths have been reported in the past 2 days. Although the virus continues to spread (only 5 of the 27 reporting areas have not topped the epidemic threshold) many of the deaths are still being reported from the hard hit areas in western Ukraine(see map). However, the biggest jump in cases was 6.096 in Kiev to 89,339.

The steady increase in the high level of deaths continues to raise concerns about genetic changes in the H1N1. In this morning's press conference the WHO discussed the need for prompt treatment with Tamiflu, but did not address genetic changes in Ukraine. Only general statements on the stability of the H1N1 were made in response to questions on genetic changes in Ukraine. Today's conference is a week after the last comments on the Ukraine H1N1 sequences which indicated that there were no large changes, but an update would be forthcoming in a "few days". It has now been over a week and no updates on genetic changes have been forthcoming.

The release of the sequences from Ukraine is long overdue.

Withheld Ukraine Sequences Raise Pandemic Concerns

Withheld Ukraine Sequences Raise Pandemic Concerns
Recombinomics Commentary 02:30
November 7, 2009
Right now we know that many clinical specimens and viruses have been sent to one of the WHO collaborating centres for further study. We don't know the results of those studies, and it will probably take a couple of days for the full analysis of those viruses to be available. But in the meantime, what we do not have is any evidence of viruses there or anywhere else as showing any big mutations. I raise this point because I have seen in some media reports that there are reports that WHO or other groups are saying that there are mutations and I want to point out that these are rumours and factually, untrue.

The above comments from Keiji Kukuda offer some general comments on the Ukrainian H1N1 sequences at Mill Hill in London. He specifically says WHO doesn't see any "big" mutations in the samples being sequenced, which would refer to reassortment or Tamiflu resistance. However, the changes seen in Ukraine do not require "big" mutations. Small mutations, such as SNP can have profound effects for a virus like pandemic H1N1.

That virus normally circulates in swine, and has recently jumped to humans. It already has many characteristics with the 1918 pandemic strain. Both are swine H1N1 that jumped to humans. Such species jumpers can increase efficiencies with small changes. One good example is position 627 in the PB2 gene. That position comes in two forms. When there is glutamic acid (E) at that position, the PB2 enzyme copies the viral genetic material most efficiently at 41 C, the body temperature of a bird. However, if that position has a lysine (K), the enzyme is most active at 33 C, the temperature of a human nose in the winter. The swine H1N1 has an E, which may be why it goes well in lung, which is 37 C and closer to the optimal replication temperature of 41C. However, a single change that produced the most efficient replication at 37C would lead to even higher levels in the lungs, which could lead to frequent cytokine storms, like those in 1918, instead of the less frequent level seen in Ukraine.

However, the rapid spread of H1N1 in Ukraine (see map), coupled with the high frequency of hemorrhagic pneumonia raise concerns that a small change is leading to a more virulent virus. Similarly, the rapid spread of the virus could also be affected by a small change in another gene, such as HA, which controls entry of the virus to cells and influences tissue tropism.

Mill Hill has acknowledged that they have at least 15 H1N1 positive samples from Ukraine, which would identify a Ukranian specific change. The delay in the announcement of sequence results raises concerns that such changes have been detected, and such changes are undergoing further analysis.

The number of cases in Ukraine continues to expand. The number of patients with H1N1 symptoms is now approaching 1 million. Cases have been increasing at almost 200,000 per day, so it is likely that tomorrow's report will have over 1 million cases. This rapid spread increases concern that the 15 sequences at Mill Hill contain one or more of these small changes, which has led to a delay in the announcement of sequence results.

More detail on the sequences at Mill Hill is overdue. The rapid spread of H1N1 in Ukraine demands rapid sequence results. Continued delay will only increase concerns.

Vaccine refusal by doctors and nurses increases worldwide

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According to a study published online by the British Medical Journal, more than half of healthcare workers surveyed in Hong Kong said they would refuse to be vaccinated against swine flu because of a fear of side effects and doubts as to efficacy.

Additionally, GP newspaper, a weekly newspaper for UK family doctors, conducted a survey of UK physicians regarding the swine flu vaccine and found that up to 60% of GPs may choose not to be vaccinated against swine flu, with many concerned about the safety of the vaccine.

The Daily Mail reported that a week ago, a poll of nurses showed that a third would turn down the opportunity of being vaccinated against swine flu. The Mail also claimed a poll of doctors for Pulse magazine found that 49 per cent would reject the vaccine with 9 per cent undecided.

Richard Hoey, editor of Pulse, said: 'The medical profession has yet to be convinced by the Government's whole approach to swine flu, with most GPs now feeling that the Department of Health overreacted in its policy on blanket use of Tamiflu. Inevitably, that has coloured feelings about the planned immunisation campaign. The view among many doctors is that the Government hasn't yet made its case for why such a huge vaccination program needs to be rushed in for what seems to be an unusually mild illness."

Health officials in Japan have recommended against prescribing Tamiflu to teenagers over fears it causes a rise in “neuropsychiatric events”. The researchers said that clinical trials had shown that about 20 per cent of adults reported side-effects of either nausea or vomiting after taking Tamiflu.

There are also concerns regarding cases of Guillain Barre Syndrome, which can lead to paralysis and even death. A mass swine flu vaccination programme in the U.S. in 1976 caused far more deaths than the disease it was designed to combat, and Britain's Health Protection Agency watchdog has asked doctors to look out for cases of GBS when the vaccinations begin.

According to Dr. Mercola, who publishes a natural health news letter, "[Tamiflu]...is part of a group of anti-influenza drugs called neuraminidase inhibitors, which work by blocking a viral enzyme that helps the influenza virus to invade cells in your respiratory tract. Serious side effects include convulsions, delirium or delusions, and 14 deaths in children and teens have been reported as a result of neuropsychiatric problems and brain infections. Japan actually banned Tamiflu for children in 2007 because of the steep risks. It was also around this time that the U.S. FDA began reviewing reports of abnormal behavior and other brain effects in more than 1,800 children who had taken Tamiflu.

AFP reports a team of researchers led by Paul Chan from the Chinese University of Hong Kong surveyed over 8,500 doctors, nurses, and other health professionals working at 31 hospital departments in Hong Kong. Participants were questioned first in early 2009, when the WHO influenza pandemic alert was at level 3, and again in May, when level had just be raised to 5. Results were virtually the same both times, with only 47 and 48 percent saying they would get vaccinated.

Two reported deaths and hundreds of adverse Tamiflu reactions

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Tamiflu puts 600,000 at greater risk of a stroke

GPs have been put on alert over fears that Tamiflu can put some people at greater risk of suffering a stroke. A Government watchdog is concerned that the anti-swine flu drug can interact with the blood-thinning medication warfarin, which is taken by more than 600,000 people in the UK. The combination can dangerously thin the blood, putting patients at risk of uncontrolled bleeding which can lead to a stroke.

The Medicines and Healthcare products Regulatory Agency has already received reports of such cases and has asked health professionals to watch out for more. Last night an expert warned that the dangers have been increased because people given Tamiflu over the national flu hotline are not being warned properly about the possible warfarin risk.

The MHRA has now received 418 reports of suspected adverse reactions to Tamiflu, including two deaths. Of these reactions,12 were are due to interactions with warfarin. The number may be small, but the MHRA is sufficiently concerned to place all such reports under 'close review'. More...

Tamiflu-resistant swine flu cases multiply

Consider the following excerpt from today's Canadian Press:

TORONTO — Canada has recorded a case of Tamiflu-resistant swine flu virus, in a Quebec man who had been given the drug to prevent infection. Meanwhile, Japan revealed Tuesday it had found a second such case of Tamiflu resistance, in a person who has no ties to the country's earlier reported case. The cases are the fourth and fifth globally since the new H1N1 virus was discovered in April.

Dr. Guy Boivin, Canada Research Chair on emerging viruses and antiviral resistance in Quebec City told CBC news: "he suspects the Quebec father was already infected when he was given a low preventive dose of the antiviral drug Tamiflu. Boivin suspected the father’s virus adapted to the drug at that point, becoming resistant."

If the Quebec father was already infected, who infected the father? Wouldn't they be spreading a resistant strain?

Recombinomics Commentary 04:15
July 22, 2009 - source

"We know the exact, specific mutation, and this is a mutation that has been reported before in human viruses that were resistant to Tamiflu, so it's not totally unexpected," said Boivin.

Boivin said he suspects the Quebec father was already infected when he was given a low preventive dose of the antiviral drug Tamiflu.

The above comments describe another case of oseltamivir resistance in pandemic H1N1 swine flu. The description indicates the resistance is due to H274Y because all reported oseltamivir resistance since 2007 has been H274Y in H1N1. Earlier this month there were three cases described, and two of the three were also on prophylactic oseltamivir. However, since all cases have involved H274Y, the treatment may simply be aiding in the detection of H274Y, rather than selecting for de novo mutations. Sequence data reports consensus sequences, so a low level of H274Y would not be seen unless multiple clones were sequenced or levels increased due to the elimination of wild type H1N1 by oseltamivir treatment.

In addition to the H274Y in Quebec, a sequence released today from Yamaguchi Province in Japan also had H274Y. The characterization sheet provides little detail on the patient, but Yamaguchi Province gives detailed reports on each H1N1 confirmed case, and the reports give no support for the development of H1N1 in contacts under prophylactic treatment. Therefore, it is likely that the Yamguchi isolate is from a sample collected prior to Tamiflu treatment.

The sequence of A/Yamaguchi/22/2009 is distinct for the other two published sequences with H274Y. However, like A/Hong Kong/2369/2009, there are several NA sequences which are exact matches, other than position H274Y. These precursors are widespread, and the earliest isolate is from the United States (Sullivan county in New York), and all subsequent isolates are from other countries (Japan, China, Brazil) once again raising questions about surveillance of mild H1N1 cases in the United States. In Japan there have been no reported pandemic H1N1 deaths and most of the cases in in Yamaguchi province have been mild and patients have recovered without hospitalization.

These two cases of resistance raises the total to five and all involve H274Y, the same polymorphism reported in seasonal H1N1, where the level quickly rose to 100% last season and is reported at 100% in the southern hemisphere this season. The presence of H274Y on seasonal H1N1, which is co-circulating with pandemic H1N1, offers the opportunity of recombination between seasonal and pandemic H1n1 to allow the H274Y to jump from seasonal H1N1 to pandemic H1N1.

The reports of H274Y in five patients this month raises concerns that the frequency will rise in the near term, with recombination and genetic hitchhiking driving the levels to 100%, due in part to widespread use of oseltamivir and in part to the large reservoir of H274Y in seasonal flu.