HEALTH 12/7-12/14/09 Weekly Bird&Other Flus Thread: D225G and D225N In Utah Patient

Link to last weeks thread:

11/27-12/5/09 Weekly Bird&Other Flus Thread:Worldwide Transmission of D225G

http://www.timebomb2000.com/vb/showthread.php?t=349252

Please See:

Confirmed cases of Swine Flu and maps
http://www.timebomb2000.com/vb/showthread.php?t=330689

Comprehensive Flu Thread, Latest reports, States, Countries, Closings.

http://www.timebomb2000.com/vb/showthread.php?t=330395

Useful Links:

Avian Influenza (Bird Flu)
http://www.cdc.gov/flu/avian/gen-info/facts.htm

Johns Hopkins on influenza:
http://www.iom.edu/Object.File/Master/33/450/Rashid Chotani.pdf

National Avian Influenza Surveillance Information:
http://wildlifedisease.nbii.gov/ai/

CDC
http://www.cdc.gov/flu/avian/index.htm

WHO
http://www.who.int/csr/disease/avian_influenza/en/index.html

CIDRAP
http://www.cidrap.umn.edu/

Official U.S. Government Web site
http://www.pandemicflu.gov/

FAO
http://www.fao.org/ag/againfo/subjects/en/health/diseases-cards/special_avian.html

Public Health Agency of Canada
http://www.phac-aspc.gc.ca/influenza/avian_qa_e.html

European Union
http://ec.europa.eu/dgs/health_consumer/dyna/influenza/country_en.htm

The World Bank
http://web.worldbank.org/WBSITE/EXT...68427~piPK:64168435~theSitePK:1793593,00.html

D225G and D225N In Utah Patient Raises Pandemic Concerns
​

http://www.recombinomics.com/News/12060901/D225G_D225N_Utah.html

The CDC has put HA sequences, A/Utah/42/2009, from a Utah patient (28F) on deposit at Genbank, which has D225G and D225N. Moreover, the sequence from the original sample gives mixed signals at tandem positions, revealing significant heterogeneity that the codon. A clone for the original sample has D225G. D225N and D225G have been identified in necropsy lung samples from Brazil (A Sao Paulo/53845/2009 and A/Sao Paulo/53838/2009 have D225N while A/Sao Paulo/53225/2009 and A/Sao Paulo/53206/2009 have D225G) raising concerns that these polymorphisms are associated with more severe disease.

The severity may be linked to viral load, because D225G and D225N were present as mixtures in early cases in the US in California and Texas. In fact the vaccine target, A/California/7/2009 was a mixture for D225G, as were several other isolates isolated at about the same time in Texas and California. Other isolates in the same areas, as well as New York, did not give mixed signals, but D225G was found in milder cases.

More recently, these changes were found in more severe cases. All four fatal cases in Ukraine had D225G, while the first fatal cases in Norway had D225G and D225E SNPs. The Utah case above however is the first sample with D225G and D225N. In the United States, the two isolates in New York with D225N had an additional polymorphism which was also in A/Ternopil/N11/2009, a fatal case from Ukraine, suggesting additional relationships which are not well represented in the existing database. These relationships may be obscure because of tissue specific expression, and mixtures which are impacted by cloning procedures.

However, the recent findings sequences encoding D225N and D225G, as well as wild type, in the same sample raises concerns that this diversity has paved the way for rapid and varied responses to immunological pressures which has already cause concerns due to the low reactor status of D225G when tested against anti-sera directed against the target of the killed vaccine.

WHO in Denial on Tamiflu Resistance and RBD Changes
​

http://www.recombinomics.com/News/12050902/H274Y_D225G_Denial.html

In the USA outbreak, which involved four severely immuno-compromised patients, cases occurred in a two-week period between mid-October and early November. Three of the four cases were fatal, but the role of H1N1 infection in contributing to these deaths is uncertain.

The above comments are from the WHO update on transmission of H274Y are hospitals in the United States and United Kingdom. As indicated above, the virus was not only was fit enough to transmit human to human, but also lead to fatal infections in the majority of those infected. Although these patients had underlying conditions, the death of three of four demonstrates that the virus is quite virulent.

However, as was seen in comments on the receptor binding domain change in Ukraine which was detected in all four fatal cases, these dramatic developments are discounted in WHO reports. The outbreaks in hospitals are characterized as being somewhat different from the general population. However, although these patients are more likely to develop serious illness, the majority of the human population is naïve for this virus, so initial infection rates would be similar. The immuno-compromised patients are monitored ore closely, so detection in these patients would be increased, but they would be representative of initial infections.

Like the general population, the reports of cases of H274Y have increased dramatically in the past few weeks, how, in contrast to what is implied in the report, is the rate of detection that is alarming. In the US, that rate has increased almost 10 fold in the past few weeks.

Thus, the WHO report is really a denial of the actual resistance situation. The cases in the hospitals are representative of initial infections in the general population and the rate of infection has spike higher leading tyo a large number of new cases, even though a lower number of samples are tested.

The denial of the explosion of H274Y as well as the association of D225G in fatal lung infections raises concerns that these events are being portrayed in an overly optimistic light. Although cases are declining in many parts of the world, these genetic changes in transmission and ant-viral resistance raise concerns that the next wave will be markedly more virulent and difficult to treat at a time when the efficiency of anti-virals and the utility of the vaccine target are in a decline.

Fatal Tamiflu Resistant H1N1 Cases In the Netherlands
​

http://www.recombinomics.com/News/12080901/H274Y_Fatal_Netherlands.html

A third person that the resistant variant of the Mexican flu had been deceased. This confirms a spokesman for the National Institute of Public Health and Environment (RIVM) Tuesday.. The victim, a woman, was already seriously ill when the flu struck.

A spokesman for the Public Health Service Heart Brabant reports that in one hospital in the region a woman who is already ill with the deceased Mexican flu. The other two deceased patients with the resistant variant had been seriously ill before they received the Mexican flu. In four others were also resistant forms of the Mexican flu found.

The above translation describes three H274Y fatalities, as well as four additional cases in the Netherlands. These data extend numbers released last week which indicated a Tamiflu resistance tipping point had been crossed. In the past three weeks the rate of reported H274Y cases in the US increased almost 10 fold, and human to human transmission had been reported at Duke University hospital as well as a hospital in Wales. Other geographic clusters had been reported in the Washington, DC area as well as eastern Pennsylvania in the US, and Edinburgh in Scotland. This explosion in Tamiflu/Peramivir resistance led to concerns of H274Y pairing up with receptor binding domain changes at position 225.

This type of pairings had been seen in seasonal flu. H274Y had jumped from one H1N1 background to another (Clade 2C, Clade 1, Clade 2B) in the absence of Tamiflu treatment. Although H274Y had jumped from background to background within each sub-clade, the movement in Clade 2B was most extensive and when compared with a receptor binding domain change, A193T, the resistance was fixed in H1N1 season flu.

Similar events were seen in H3N2 seasonal flu and the fixing of S31N, Those events centered on two receptor binding domain changes, S193F and D225N.

Consequently, when the first pandemic H1N1 with H274Y and no linkage to Tamiflu treatment was on an HA with D225E there was concerned that the receptor binding domain change would be linked to a more fit swine H1N1 that would transmit in the absence of Tamiflu. These concerns were increased when another isolate in Tennessee had H274Y and D225E.

However, of even greater concern was the linkage of H274Y with D225G because of the associated receptor binding domain change that drove virus to the lower lung and showed resistance to the swine flu vaccine, as seen for one of the Ukraine isolates with H225G.

These concerns were realized with reports out of France which described two fatalities with D225G and one also had H274Y. H274Y in fatal cases is a significant concern, and three of the four cases at Duke died.

The current case in the Netherlands extends the number of fatal cases with H274Y and raises more concerns on linkage between H274Y and D225G.

Ukraine Cases Spike - D225G and D225N Found​

http://www.recombinomics.com/News/12080902/Ukraine_472_D225N.html

2,187,836 Influenza .ARI

132,178 Hospitalized

472 Dead

The above numbers, from the Ukraine Ministry of Health represent a spike in cases yielding a daily increase of 86,578. The jump was widespread, but the biggest jumps were Donetsk increased 12,586 to 160,212 and Dnipropetrovsk which increased 9.813 to 149,358 (see map). This jump may be signaling a move into the real winter season.

Ukraine is under close scrutiny because sequences released by Mill Hill at GISAID had D225G in all four fatal cases and CDC sequences at GISAID identified D225N in new cases, which were also likely fatal, so all HA sequences from fatal cases in Ukraine have had a receptor binding domain change at position 225 (D changing to either G or N). Since the same changes had been seen previously in Sao Paulo, Brazil over the summer, and now cases were being identified in severe and fatal Scandinavian countries,

The finding D225G or D225N in all fatal cases in Ukraine clearly demonstrates that the changes are transmitting, comments from Scandinavian officials notwithstanding. More detail on the new patients and sequences would be useful.

D225N in Ukraine Raises Pandemic Concerns​

http://www.recombinomics.com/News/12090901/D225N_Ukraine.html

New sequences from Ukraine have been placed on deposit at GISAID by the CDC. Although the sequences are partials, the receptor binding domain is covered in all 5 HA sequences. Three of the sequences have numbers and ages of patients which match three of the surviving patients tested by Mill Hill and these three sequences have a wild type receptor binding domain. However, the other two, A/Ukraine/01/2009 and A/Ukraine/02/2009 do not match ages on Mill Hill samples and are likely samples from two fatal cases. Both of these sequences have a receptor binding domain change at position 225, but both have D225N, while the Mill Hill sequences were D225G. Moreover, one of the D225N sequence is a mixture with the wild type sequence.

All sequences are the same sub-clade and collected within a day of each other. They are likely from six fatal cases, once again highlighting the significance of the receptor binding domain and arguing for transmission, since each change is in at least two samples and a change at position 225 is found in 100% of the fatal samples. Both of these changes had been identified in fatal lung infections in Sao Paulo, further linking recent changes (D225G and D225N) to severe and fatal cases.

More detail on the status of these patients and sample source would be useful, as would sequence data from multiple sites in the same patient.

However, it is increasingly clear that the receptor binding domain changes are transmitting and are associated with severe and fatal infections.

NIH Bulletin says New York swine
flu victim autopsies show lung damage similar to 1918 Spanish flu ​

http://www.examiner.com/x-29228-LA-...show-lung-damage-similar--to-1918-Spanish-flu

Results from 34 swine flu victims in New York were released by the National Institutes of Health (NIH) in a December 7 bulletin. The swine flu symptoms and effects on the lungs of the victims were similar to the effects of the 1918 Spanish flu, which had an extremely high mortality rate around the world. Other reports of H1N1 infections deep in the lungs have been reported around the world, including Ukraine, China, Brazil, Norway, and the United States, in Iowa and Utah. These infections have been linked to a change in the receptor binding domain of the virus.

Swine flu symptoms and the Spanish flu of 1918

Swine flu symptoms are generally the same as other influenza infections, but a mutation causing the virus to lodge in the lungs instead of the upper respiratory tract causes different symptoms. The 1918 Spanish flu caused bleeding in the lungs, and killed between 20 million and 40 million people worldwide. Bleeding in the lungs has been associated with a change in the receptor binding domain of the virus.

Receptor Binding Domain (RBD) Change in Pandemic A 2009 H1N1 influenza virus

The D225G change in the receptor binding domain for the Novel A H1N1 influenza has been associated with both bleeding in the lungs and a low reaction to the swine flu vaccine.

National Institute of Health Report on swine flu

The NIH reviewed autopsy results from 34 patients that died from the swine flu in New York between May and July. According to Dr. Taubenberger, one of the doctors reviewing the records,

"This pattern of pathology in the airway tissues is similar to that reported in autopsy findings of victims of both the 1918 and 1957 influenza pandemics.”

The pandemic of 1957 was Avian flu, which resulted in approximately 2 million deaths around the world.

Fatal Tamiflu Resistance in Delaware​

http://www.recombinomics.com/News/12090902/H274Y_DE.html

A 52-year-old Kent County man who died Nov. 7 of complications from swine flu had a virus that was resistant to the drugs used to treat it.

The above comments describe another fatal case of H1N1 swine flu in the United States. The Delaware case follows reports of clusters at the Duke Medical Center in North Carolina, a Virginia/Maryland cluster involving at least two patients at Johns Hopkins, and two cases in eastern Pennsylvania. These individual geographic clusters create one large cluster in the east coast since all states involved are contiguous.

Recent reports of resistance signaled the crossing of a tipping point. Human to human transmission was noted at Duke and Wales and WHO warned of a recent spike in cases. Similarly, the report rate by the CDC in the past three weeks is almost 10 fold higher than the prior weeks in the current season.

However, this explosion of cases has also been associated with fatalities, raising concerns that not only was the H1N1 with H274Y efficiently transmitted, but that it was lethal. At Duke the epidemiology supported human to human transmission and three of the four cases died, raising concerns that the H1N1 was more lethal. The Delaware case raises the number of fatal outcomes for the 10 recent cases to four. Similarly, the Netherlands has just reports its their fatality in six recent cases with H274Y, and France has indicated that one of the two fatal cases with D225G was also resistant.

The association of H274Y with a receptor binding domain change at position 225 was been reported previously. The first case of H274Y with associated Tamiflu treatment had D225E and a second cases with H274Y and D225E has recently been seen in Tennessee.

Thus, concerns that the transmission of H274Y has passed a tipping has been increased by the association of receptor binding domain changes with resistance as well as a trend toward fatal outcomes in these cases.

High Attack Rate in Tamiflu Resistant Cluster in Vietnam​

http://www.recombinomics.com/News/12100901/H274Y_Viet_Attack.html

In July 2009, during a 42-hour journey, 10 students socialized together in the same train carriage. None of the students knew each other before the journey, none had contact with a person with suspected influenza in the week before the trip, none were symptomatic during the journey, and none were previously or currently receiving oseltamivir. Fever developed in four of the students within 12 hours after arrival and in two more students within 48 hours after arrival (Fig. 1 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). An additional case was identified in a traveler in a different carriage (Patient G). Nasal swabs, throat swabs, or both from all seven persons were positive for 2009 H1N1 RNA when tested with reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assays, and viruses were successfully cultured from specimens obtained from three of the persons. The H275Y substitution was detected retrospectively in diagnostic specimens obtained from all seven subjects before any oseltamivir treatment

The above description of efficient transmission of H274Y in pandemic H1N1 is from today's New England Journal of Medicine, which confirms the presence of fit virus with H274Y. The attack rate was high. At least seven of ten students were infected, and all had H274Y. Although all recovered, one patient continued to shed virus for 9 days. This cluster was in Vietnam in July and highlights the ease of transmission of H274Y.

Recent clusters of human to human transmission have been described in hospital settings in North Carolina and Wales and in North Carolina, 3 of 4 patients died, raising additional concerns that the H274Y currently transmitting is not only fit, but also lethal.

The high penetration rate in Vietnam suggests H274Y is widespread in mild cases, but is largely undetected because of limited testing. However, media reports in August suggested H274Y was spreading in Vietnam and recent reports suggest 6% of cases in Vietnam may have H274Y.

In the US, the detection of H274Y has recently increased almost 10 fold, signaling a crossing of a tipping point.

H5N1 H1N1 Cluster in Dien Bien Vietnam​

http://www.recombinomics.com/News/12100902/H5N1_H1N1_Dien_Bien.html

More and anxiety on the basis of when Dr. Nguyen Tran Hien, Director of Institute of Hygiene and Epidemiology PRIVATE announce the result of epidemiological investigations deaths due to bird flu recently in Dien Bien. Male patients age 23 in the city of Dien Bien death from respiratory failure due to severe viral pneumonia was confirmed by test results: The patient died from H5N1.

When investigating the epidemiology of close contact with patients, medical experts are concerned when they discovered the children of influenza A/H1N1 infected patients. Meanwhile, the Forum chickens living in the cousin has test results positive for H5N1 virus.

The above translation suggests a family in Dien Bien, Vietnam has tested positive for H5N1 and H1N1. Poultry belonging to the family has also tested positive for H5N1.

Vietnam represents a hot zone where H1N1 and H5N1 are co-circulating. H1N1 is very promiscuous and has been isolated from a variety of mammalian species as well as turkeys. Thus, Vietnam would offer an environment for co-infections in a wide range of host including human.

Swine Flu Accidentally Resurrected From the Dead?​

http://motherjones.com/blue-marble/2009/06/swine-flu-accidentally-resurrected-dead

Amid an unsettling report today of Tamiflu resistance in a Danish A(H1N1) patient, comes a study in The New England Journal of Medicine tracing the swine flu's 90-year evolution.

The current flu strain has genetic roots in an illness that sickened pigs at a swine show in 1918 in Cedar Rapids, Iowa. A near-century of development since then may include this flu's accidental resurrection from an extinct strain.

Here's what likely went down. At the same time the 1918 flu pandemic was spreading among humans, pigs were hit with a similar respiratory illness. Early experiments confirmed the 1918 swine virus and a human strain emerged about the same time.

According to the authors of the new paper, there was a temporary "extinction" of this strain of virus from humans in 1957. But then it reemerged 20 years later in a small 230-person outbreak in 1976 among soldiers in Fort Dix, New Jersey. That outbreak did not extend beyond the military base.

However the next year H1N1 reemerged in people in the Soviet Union, Hong Kong, and northeastern China. The genetic origin of that 1977 strain turns out not to be the 1976 Fort Dix strain. Instead, it was closely related to a 1950 human strain.

Which means that given the genetic similarity of the two strains, reemergence was likely due to an accidental release during laboratory studies of the 1950 strain that had been preserved as a "freezer" virus.

Ouch. Hate it when that happens.

The authors hypothesize that concerns about the Fort Dix outbreak stimulated a flurry of research on H1N1 viruses in 1976, which led to an accidental release and reemergence of the previously extinct virus a year later. The reemerged 1977 H1N1 strain has been circulating in various seasonal influenzas ever since—including today's.


Or maybe it wasn't such an accidental a release? Conspiracists, restart your engines.

Hidden Transmission of H1N1Tamiflu Resistance​

http://www.recombinomics.com/News/12100903/H274Y_Hidden.html

Of these 32 reported cases of oseltamivir-resistant pandemic (H1N1) 2009 influenza virus, 16 were associated with the treatment of influenza, including in 7 immunosuppressed patients; 13 with chemoprophylaxis (usually following known exposure to another infected person); and 3 had no history of oseltamivir treatment or prophylaxis.

The above comment from the WHO Oct 30 Weekly Epidemiology Record appears to be missing the cluster of seven patients who were infected with pandemic H1N1 with H274Y during a train trip in Vietnam. The train trip was in July and the first three cases were confirmed on Sept 9, yet there has been no mention of this large cluster until publication in the current New England Journal of Medicine. However, the WER compilation has no category for cases who were treated with Tamiflu, but had H274Y in samples collected prior to treatment. It is common for samples to be collected prior to treatment, although the resistance is frequently detected long after the patients have been treated and recovered, yet the only grouping of such cases would be in the patients "associated" with Tamiflu treatment.

As seen in the cluster from Vietnam, the "association" of Tamiflu treatment has no relevance because the patients were resistant prior to treatment. However, the reporting by WHO leaves the impression that the association with treatment was relevant, when the vast majority of the time it is not (because the patients are resistant prior to treatment).

This clear slanting of the data is not limited to WHO reports. Weekly reports from the CDC also do not distinguish between patients treated with Tamiflu even though they are already Tamiflu resistant, and those patients who present with resistance during treatment.

In cases where H274Y is detected after treatment has begun, the relationship between the treatment and the generation of resistance is likely to be more related to detection of resistance than creation of resistance. In the first cases in Singapore, the patient initially tested as wild type, but was H274Y positive two days later, suggesting H274Y was already circulating as a minor species.

The presence of H274Y as a minor species also explains the rapid appearance of H274Y on patients being treated prophylactically with Tamiflu (5 or 6 days after the start of treatment).

Moreover, WHO and the CDC have yet to show a single case supporting H274Y emergence via a spontaneous mutation. In the cases of two immune-suppressed patients in Washington, no data was present to exclude detection as early as 5 days after the start of treatment. One patient had wild type at day 4, and had H274Y at day 11, but could have had detectable levels as early as day 5. Similarly a second case had wild type at day 1 and H274Y at day 18, but results from samples collected at day 3 and 6 were not disclosed. Thus, there was no data presented that would exclude the presence of H274Y as a minor species, and since the two Washington patients were infected with the same sub-clade, it is likely that these patients also did not develop H274Y via spontaneous mutation.

Thus, neither WHO, CDC, nor Roche have presented data supporting a spontaneous mutation in seasonal H1N1 or pandemic H1N1, although all frequently cite random mutation as the underlying basis of antigenic drift.

However, all cases of Tamiflu resistance in H1N1 involve H274Y and there are no recent examples of Tamiflu resistance in H3N2, indicating early reports of resistance in Japanese children treated with sub-optimal dosages of Taniflu were an anomaly which has been eliminated by proper dosing.

Thus, the report of seven passengers in Vietnam in July strongly suggest that reports by WHO and the CDC seriously underestimate the frequency of H274Y transmission by combining hospital cases with H274Y prior to treatment with cases where H274Y is detected during treatment.

This slanted reporting and poor surveillance continue to be hazardous to the world's health.

D225G and D225N Diversity In Fatal Utah Case?​

http://www.recombinomics.com/News/12100904/D225G_D225N_Utah_Fatal.html

A Davis County woman died from the H1N1 flu July 24, bringing the total number of flu deaths in the state to 17, according to Utah Department of Health data released Wednesday.

It's the first H1N1-related death to be reported in two weeks.

Health Department spokesman Tom Hudachko said it is unknown whether the woman, who was between the ages of 18 and 39, had any underlying health conditions.

The above report matches the demographic data for a case (28F) from Utah, which has D225G and D225N. The sample collection date also matches the date of death. The initial sequences were released at GISAID, but now the sequences are also available at GenBank. One sequence, A/Utah/42/2009 is from the original sample and has mixed signals for D225G and D225N. This combination could also code for D225S, although no such sequence has been described previously in pandemic H1N1. The second sequence is a clone which gives a clean D225G signal. The presence of sequences which can encode for D225G and D225N has not been reported previously in a single sample, but recently released CDC sequences from two patients in Ukraine had D225N, while four sequences from fatal cases released by Mill Hill had D225G. Both of the changes had been previously found in fatal cases in Sao Paulo Brazil and the recent association of these sequences with fatal or sever cases has raised concerns that the frequency of these changes is increasing, which could lead to more fatalities and severe cases in the next pandemic wave.

These concerns have been increased by a recent report on one of the Ukraine sequences, which was designated as a "low reactor" raising concerns that sequences with D225G (or D225N) could evade current natural immunity as well as immunity generated by the killed vaccine.

Therefore more information on the Utah case would be useful. Many of the fatal cases with D225G have been linked to a rapid decline and lung destruction, so information on the Davis country fatality and relationship to the samples collected on the date of her death would be useful.

Fatal Tamiflu Resistant Cases Spike in the Netherlands​

http://www.recombinomics.com/News/12110901/H274Y_Fatal_Netherlands_Spike.html

Until this week were 11 patients diagnosed in the Netherlands, including 5 this week, with a New Influenza A (H1N1) virus that is resistant to the antiviral agent Tamiflu (oseltamivir) that such patients are treated. Four of these patients are deceased.

The above translation highlights the dramatic jump in H274Y in the Netherlands, which is associated with a high case fatality rate. The number of cases with H274Y has almost doubled in the past week and the case fatality rate for the 11 cases is above 36%. This high rate raises concerns that isolates with H274Y also have receptor binding domain changes, leading to a high CFR. In France, two fatalities with D225G were identified, and one of the two had H274Y. These associations are creating increased concerns.

Release of the sequences with H274Y would help determine if a new sub-clade is emerging with lethal markers like the D225N and D225G identified in Ukraine.

Fixing Fatal Tamiflu Resistance in Pandemic H1N1​

http://www.recombinomics.com/News/12110902/H274Y_Fatal_Fix.html

The recent report of H274Y cases doubling in the Netherlands in the past week, including 4 of 11 fatalities, has raised concerns that Tamiflu resistance has not only jumped to an evolutionarily fit pandemic H1N1 , but a lethal sub-clade. Similar numbers were reported in the United States where 10 new cases of resistance were described and four were fatal.

The report this week out of Vietnam left little doubt that H274Y was being efficiently transmitted to previously healthy young adults when seven students were infected during a train ride. Six were among ten students in one car, while a seventh was in another car, suggesting at least two independent transmission events. However, these patients recovered, even though the treatment with Tamiflu had little value since they were Tamiflu resistant prior to treatment. Sequences from these patients have not been released, so the relationship of this cluster to reports of sporadic cases is unclear.

However, sequences from the first Tamiflu resistant case without exposure to Tamiflu have been released and the HA sequence had a receptor binding domain change, D225E. Linkage between H274Y resistance and receptor binding domain changes was of concern because the fixing of H274Y in seasonal flu was linked to receptor binding domain changes. The key change in the fixing of H274Y was A193T, which emerged near the end of the 2007/2008 season and become dominant in the summer of 2008 in the southern hemisphere. This gave rise to an increase in H274Y to almost 100% of seasonal H1N1, with additional changes involving various combinations of polymorphisms at positions 187, 189, and 196,

The linkage between receptor binding domain changes and fixing of anti-viral resistance was also seen in S31N in seasonal H3N2. That change was linked to a change at position 193 (S193F),, as well as a change at position 225 (D225N).

Thus, when the H274Y in pandemic H1N1 was found in an isolate that had D225E, there was concern that the receptor binding domain could facilitate the spread of H274Y via a fit H1N1. These concerns were increased by a recent sequence from Tennessee which had H274Y and D225E.

However, two additional changes at position 225 were reported in pandemic H1N1 (D225G and D225N) and these changes were associated with fatal lung cases in Sao Paulo. The concerns were increased when sequences from Ukraine were released, which identified D225G in four of four fatal cases. Recently released sequences have added to the concern when the two new sequences, which were likely from fatal cases, had D225N. Both of these changes were found in a fatal case from Utah.

Concern that H274Y was pairing up with D225N was increased in a report from France which cited two fatal cases with D225N and one of the two had H274Y. An expansion of this pairing could have dire consequences, because of the recent linkage between severe ad fatal cases with D225N, since Tamiflu remains as a first line defense against more severe cases of H1N1.

These concerns could be more appropriately addressed with the release sequences from the recent cases, including those that were fatal.

The fixing of H274Y In seasonal fu was linked to the jumping of H274Y and key polymorphisms from one genetic background to another via recombination. In pandemic H1N1, both H274Y and D225G have been found on multiple genetic backgrounds raising concerns that H274Y will soon be fixed in pandemic H1N1 and this fixing may be linked to receptor binding domain changes associated with severe and lethal infections.

D225G and D225N Diversity Confirmed in Fatal Utah Case
​

http://www.recombinomics.com/News/12110903/D225G_D225N_Utah_Fatal_Conf.html

A 28-year-old Utah woman who died this summer of H1N1 swine flu had a mutated form of the novel virus.

The state routinely sends samples to the CDC for it to sequence to look for significant mutations -- ones that would be resistant to the vaccine, for example.

That is not the case with the Utah mutation. Even if the mutated virus was passed from this woman to someone else, and there is no evidence it has, "the vaccine would still be protective," Herlihy said.

"Mutations occur very regularly in influenza," she said. "We are monitoring for genetic mutations of significance. We do not believe this is a genetic mutation of clinical significance."

The above comments confirm that A/Utah/42/2009 with D225G and D225N was from a fatal (28F) case. However, the additional comments regarding significance and effect on the vaccine are curious. The two receptor binding domain changes have been noted at increased frequencies since the summer and almost all cases were severe or fatal. In Sao Paulo, D225G was identified in two patients and D225N was in two others and all four were fatal. A case in China recovered after a month in the hospital and was described as the first severe cases in the province. In Ukraine, Mill Hill sequenced H1N1 from four fatal cases, and all four had D225G. The CDC sequenced two more, which were also likely to be from fatal cases, and both had D225N. The Ukraine data was followed by a review of samples in Norway and three patients with D225G were identified. Two were fatal and one severe. France also found two patients with D225G and both were fatal (and one also had H274Y).

The above confirmation extends the changes to the US and again involves a fatal case who was 28 and not said to have an underlying condition.

Although the CDC has placed these sequences on deposit, they have not released an antigenic characterization. Similarly, the two samples from Ukraine were said to be California/7-like based on PCR instead of neutralizing titer generated by ferret reference sera.

Mill Hill tested one of the Ukraine sequences with D225G and classified it as a "low reactor" indicting the titer was at least four fold lower than the positive control, raising vaccine reactivity concerns. Thus, the basis for the statement that the vaccine would "be protective" is unclear.

Similarly, after the WHO called the changes in sequences from fatal cases in Ukraine insignificant, the finding of D225G in dead and severe cases in Norway led to a revision of the "not significant" statement.

In June and July there was a spike in Utah deaths. 10% of the US fatalities in that timeframe were from Utah. The presence of D225G and D225N in the above fatal case suggests that these changes were circulating in the area and may have contributed to the spike in fatalities.

Release of sequence data from samples collected at the site of infection, such as lung, would be useful.

Goat Flu Epidemic Reported in Netherlands​

http://www.emaxhealth.com/1275/90/34758/goat-flu-epidemic-reported-netherlands.html

Following on the heels of bird flu and swine flu, there are now reports from the Netherlands of an outbreak of goat flu. Online news sources report that up to 2,300 people have been infected by goat flu and that six individuals have died of the disease.

Goat flu, also known as Q fever or Q flu, affects both goats and sheep. It is caused by bacteria called Coxiella burnetii, which are released when pregnant goats or sheep experience a spontaneous abortion. The bacteria spread very easily according to experts.

The Dutch Ministry of Agriculture has confirmed that the virus has been detected at 55 to 350 Dutch farms, with the most affected areas being the cities of Eindhoven and Tilburg. According to the Dutch News, agriculture ministers announced on Wednesday afternoon at a news conference that they will begin culling herds of goats. The unofficial number of animals to be killed is between 15,000 and 20,000, mainly goats, to help prevent further spread of the disease. All infected sheep and goats that have been vaccinated will be slaughtered, as will all pregnant goats and sheep on farms where the disease has been identified.

Symptoms of goat flu include severe headache, chills, perspiration, aching muscles, diarrhea, slow pulse, and general illness. The acute version of the disease lasts for up to 14 days, but individuals who get a chronic type may have the disease for up to two years. In the chronic version, fatigue is the main symptom. The disease can also cause lung and heart problems.

All of the six individuals who died of goat flu had other health problems. At this point, there are no recorded cases of transmission of goat flu infection from person to person. A spokesperson from the public health institute RIVM, Roel Coutinho, told Trouw that the goat flu epidemic may be the result of an aggressive goat farming initiative in the Netherlands. In 1995, there were 7,600 goats in the country, but today there are more than 350,000. Unfortunately, the flu epidemic is about to change those numbers significantly.

Pulmonary Pathologic Findings of Fatal 2009 Pandemic
Influenza A/H1N1 Viral Infections​

http://arpa.allenpress.com/pdf/i1543-2165-134-2-1.pdf

A PDF File, click link to read.

D225G and H274Y in Illinois Case
​

http://www.recombinomics.com/News/12130901/D225G_H274Y_IL.html

Recent reports of increased Tamiflu resistance, coupled with a strong associate of two receptor binding domain changes, D225G and D225N, has raised concerns that the two polymorphisms may be recombining to generate a lethal H1N1 that is Tamiflu resistant. Interest in the two receptor binding domain changes was increased dramatically by results from Ukraine which had one of these changes in six of six fatal cases. The reports on D225G led France to check prior cases and D225G was found in two fatal cases. Of concern was the finding of H274Y in one of those cases.

A review of recently released sequences has found the same combination in sequences deposited by the CDC at GISAID. The isolate, A/Illinois/11/2009, was collected on July 31, which is during the same time frame as the train ride in Vietnam that led to at least seven cases of H274Y. In July/August the receptor binding domain changes were noted in fatal cases in Sao Paulo.

The increases in detection of H274Y have been reported by the WHO and CDC in recent weeks. In the US, four of ten cases were fatal, while in the Netherlands, four of eleven cases were fatal. However most of these sequences as well as those from the Vietnam train in July have not been released.

An increase in surveillance for these markers as well as the prompt release of sequences would be useful.

Tamiflu Resistance Spike in US Raises Transparency Concerns
​

http://www.recombinomics.com/News/12140901/H274Y_CDC_Hide.html

A total of 29 cases of oseltamivir resistant 2009 influenza A (H1N1) viruses have been identified in the United States since April 2009. In specimens collected since September 1, 2009, 19 cases have been identified in the United States, including three newly identified cases since last week. The proportion of oseltamivir-resistant 2009 H1N1 viruses does not represent the prevalence of oseltamivir-resistant 2009 H1N1 in the U.S. Most cases were tested because drug resistance was suspected. All tested viruses retain their sensitivity to the neuraminidase inhibitor zanamivir. Of the 29 total cases identified, 19 patients had documented exposure to oseltamivir through either treatment or chemoprophylaxis, eight patients are under investigation to determine exposure to oseltamivir, and two patients had no documented oseltamivir exposure. Occasional development of oseltamivir resistance during treatment or prophylaxis is not unexpected. Enhanced surveillance and increased availability of testing performed at CDC are expected to detect additional cases of oseltamivir resistant 2009 influenza A (H1N1) viruses, and such cases will be investigated to assess the spread of resistant strains in the community.

The above paragraph from the week's CDC report (week 48) announces three more cases of Tamiflu resistance in the US. This number matches the increases for each of the past 3 weeks and brings the total for the past 4 weeks to 16, which is much higher than previous weeks, which usually had 0 or 1 new cases. This recent spike in cases has also been reported by WHO and raises concerns that H274Y is efficiently transmitting. Moreover, recent deaths of patients with H274Y in the US (four of ten) and the Netherlands (four of eleven) have raised concerns that patients with H274Y also have D225G, which has been associated with fatal cases in the US, Ukraine, Norway, Brazil, and France. Moreover, patients with D225G coupled with H274Y have been reported in France and the United States.

However, the CDC report does address those concerns because critical data has been withheld. In week 48 the number of samples tested for H274Y spiked higher, but there is no indication of these are recent samples or an update of surveillance done on samples collected in the spring or summer. Similarly, the location of these cases or outcomes are not given, and there is no indication that patients who developed resistance during treatment are distinguished from patients who were resistant prior to treatment, but fell into the "suspect" category because they failed to respond to Tamiflu.

The Vietnam cluster described in this week's New England Journal of Medicine that would represent such cases. Seven passengers on a train developed H1N1 infections that had H274Y. However, like most patients worldwide, the resistance was not discovered until long after treatment and discharge. The infections were in July, but the first lab confirmations were in September. Although Tamiflu treatment is not effective against H1N1 with H274Y, all patients recovered, but clearly represented infections of a fit and readily transmissible H1N1 with h274Y.

However, using the CDC classification system, these patients would have "documented exposure to Tamiflu" but would not be examples of resistance that developed due to treatment.

Although this is the CDC's largest category, they have yet to show a single example of a case that developed resistance after prolog treatment with Tamiflu. They have described two immuno-compromised patients in Seattle who initially tested as wild type and became H274Y positive during treatment, but one developed resistance between day 4 and 11 of treatment, while the second became positive between days 1 and 18. Results on samples collected on days 3 and 6 were not disclosed, leving open the possibility that resistance was present on day 2 of treatment, supporting the transmission of a significant sub-population, which is easily detected after a few days of Tamiflu treatment. This was seen in the first H274Y patient in Singapore, whi converted to H274Y positive after two days of treatment, as well as prophylactic patients who developed symptoms 5-6 days after the start of treatment.

The failure of the CDC to report any patients who developed H274Y after prolonged treatment, and the efficient transmission of H274Y in Vietnam in July, raise concerns that the weekly reports by the CDC are carefully designed to withhold key information such as the H274Y status prior to treatment, the dates and locations of samples, as well as outcomes of patients who are H274Y positive.

This lack of transparency continues to be hazardous to the world's health.

Receptor Binding Domain Changes in Texas​

http://www.recombinomics.com/News/12140902/RBD_TX.html

JCVI and The Methodist Research Institute deposited 137 complete sets of sequences from Texas at GenBank. Sequences from Houston and Brownsville were collected last spring and it is assumed that the sequences from Harris County, which surrounds Houston, were collected during the same time period. Texas has had a number of fatal cases, especially this fall, so the sequences allowed for analysis of receptor binding domain changes and Tamiflu resistance.

Although H274Y has been detected recently in Texas, and the Texas sequences are the same sub-clade as multiple sequences from the Houston or Harris County area, there were no examples of H274Y in the 137 NA sequences, confirming that requirement of most isolates in the spring of Tamiflu exposure to select for a sub-clade circulating below detection limits.

Similarly, detection of receptor binding domain changes were also rare. In the spring there were examples of isolates with D225G in Texas and California, and in some cases the samples were mixtures, such as the vaccine target, California/7. However, only one of the 137 HA sequences, A/Texas/42291877/2009, had D225G (as a mixed signal). Similarly, only one sequence had D225N. A/Texas/43132503/2009 and three sequences had D225E (A/Texas/45061755/2009, A/Texas/45061670/2009, A/Texas/45034157/2009).

These data support sequences by others which shows that the receptor binding domain changes are rarely detected, even in areas where it was detected shortly after swine H1N1 jumped to humans. However, these detection issues may be related in part to receptor binding specificities and such sequences may be more prevalent in the lower respiratory tract. Similarly the association with fatal cases has been more prevalent in the summer and fall, which may be linked to viral load. In the spring H1N1 was entering the human population, and low levels of virus may have been able to infect the naïve population. Increased immunity would lead to selection of higher levels of virus, which may have contributed to the more frequent detection in fatal cases.

Of recent concern has been the association of D225G with H274Y which has been reported in France and the United States. Increase surveillance, including samples from infected organs in fatal cases, would be useful.
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WHO Reports Death of 57th Bird Flu Victim in Viet Nam ​

http://www.who.int/csr/don/2009_12_11/en/index.html

11 December 2009 -- The Ministry of Health has reported a new confirmed case of human infection with the H5N1 avian influenza virus. The case has been confirmed at the National Institute of Hygiene and Epidemiology (NIHE).

The case is a man from Dien Bien Phu city, Dien Bien Province. He developed symptoms on 18 November, was hospitalized at Dien Bien general hospital and died on 28 November 2009.

The source of exposure is currently under investigation. His family keep some chickens and wild geese in their household.

Of the 112 cases confirmed to date in Viet Nam, 57 have been fatal.

Cumulative Number of Confirmed
Human Cases of Avian Influenza A/(H5N1) Reported to WHO​

Totals at link.

http://www.who.int/csr/disease/avian_influenza/country/cases_table_2009_12_11/en/index.html

Link to next weeks thread:

12/15/-12/22/09 Bird, Other Flu Weekly Thread:Bird flu reappears in N Vietnam

http://www.timebomb2000.com/vb/showthread.php?t=350548