RECOMBINOMICS

[dothedd]

H1N1 First Responder Death In Western Pennsylvania
Recombinomics Commentary 17:40
February 22, 2011


David Sechrist's battle with H1N1 began with mild cold symptoms, according to his father. Within just 36 hours, David Sechrist was so ill he was placed in intensive care in a Pittsburgh hospital.

As a paramedic and dispatcher with a Fayette County ambulance service, David P. Sechrist dedicated his life to helping others.

The 30-year-old Vanderbilt man died Saturday of complications from the H1N1 flu, according to his family.

"H1N1 is a big misconception at this point. Even at the hospital, they said they hadn't seen H1N1 in months."

Flu activity is statewide, but the department noted "significant increases were reported in the southwestern regions."

The above comments note the fatal infection of an EMS worker (30M) in southwestern Pennsylvania (Fayette County which is just southeast of Allegheny County and metropolitan Pittsburgh. A close reading of the Pennsylvania Department of Health weekly report shows a spike in H1N1 in Allegheny County, but since only a small fraction of the influenza A samples are sero-typed, the reported 46 cases (week 6) is small relative to the 373 influenza A cases. However, the number of H1N1 cases is markedly higher than the 6 cases reported two weeks ago (week 4), signaling a recent sharp jump in H1N1 cases in Allegheny county. Fayette county only show 1 H1N1 cases, which is likely due to a lack of sero-typing, since Fayette is reporting 113 influenza A cases.

Monitoring these events is difficult because the Pennsylvania website does not have an archive, and the active link only shows the most recent week. In addition to not having the data for prior weeks, the website has not updated hospitalized cases since week 2. Thus, the true extent of H1N1 cases in the state in general and western Pennsylvania in particular is difficult to appreciate because of access and testing limitations.

As noted above, even first responders who are constantly exposed to pathogens circulating in the community are unaware of the extent of H1N1, as are hospital workers, even though H1N1 levels are exploding in the area, and the Pneumonia and Influenza deaths in the United States (8.9%) are approaching a five year high (9.1%).

Agency efforts to “manage” influenza hospitalizations and deaths remain hazardous to the world’s health. The EMS co-workers are now getting vaccinated because of the recent death. However, the current vaccine has limited efficacy against the H1N1 currently circulating in western Pennsylvania and throughout the northern hemisphere.

[dothedd]

H1N1 Vaccine Breakthrough Sequences
Recombinomics Commentary 21:15
February 23, 2011


The United States DoD-GEIS Flu Program at Brooks Air Force base released a series of partial HA sequences largely from samples collected in December, 2010 or January, 2011 from DoD beneficiary populations. 17 of the sequences were from vaccinated patients and therefore represented vaccine breakthroughs (see list below). 11 of the 17 were the sub-clade with S188T, including one sample, A/Korea/AF21790/2011, which also had S186P. These sequences also had A200T. Four additional sequences were from the S186P sub-clade, while the two sequences without S188T or S186P had A189T. Thus, all 17 sequences had at least one change at positions 186, 188, or 189 and those with S188T also had A200T.

These sequences from vaccine breakthrough patients provide additional data indicating the current vaccine no longer offers significant protection from the H1N1 currently in circulation. The S188T sub-clade is the dominant clade in the northern hemisphere represented by 11 of the 17 breakthrough sequences, signaling widespread vaccine failure.

This failure is largely missed by the antigen chacterization assay, which has failed to identify these sequences as low reactors (only the sequence from India with S188T and S186P was designated a low reactor). The assay has been used to claim that these common sequences were antigenically indistinguishable from the current H1N1 vaccine target, A/California/7/2009, which was used to justify the decision to keep the vaccine target unchanged.

The vaccine breakthrough sequences are consistent with the UK data which showed that the H1N1 vaccine only protected 50% of recipients in the first half of the 2011/2012 season. This rate is probably low because the S188T sub-clade is becoming increasingly dominant throughout the northern hemisphere.

These data and sequences demonstrate the fatal flaw in the current antigen characterization assay and the recommendation to leave the target unchanged.

The vaccine target recommendation should be re-evaluated by an independent scientific committee, and the current WHO influenza consultants, who comprise latest committee, should be removed.

S188T
A/Korea/AF21778/2010
A/Korea/AF21780/2010
A/Korea/AF21783/2010
A/Japane/AF21777/2011
A/Korea/AF21784/2011
A/Korea/AF21785/2011
A/Korea/AF21786/2011
A/Korea/AF21787/2011
A/Korea/AF21788/2011
A/Korea/AF21789/2011
A/Korea/AF21790/2011

S186P
A/Korea/AF21779/2010
A/Korea/AF21781/2010
A/Korea/AF21782/2010
A/North Carolina/AF21797/2011

A189T
A/Arizona/AF21768/2011
A/New Jersey/AF21791/2011

[dothedd]

H3N2 Vaccine Breakthrough In Queensland Australia
Recombinomics Commentary 14:50
February 25, 2011


The WHO regional center in Australia has released a series of HA H3N2 sequences from November / December, 2010 isolates from northeastern Queensland (at GISAID) designated as low reactors (see list below) when tested against ferret anti-sera directed against A/Perth/16/2009. Several of the isolates were also characterized as originating from clusters, and several of the patients had been vaccinated in 2010.

These isolates represent significant vaccine breakthrough. The sequences are from the sub-clade that emerged in early 2010. The first public sequence was A/Pennsylvania/02/2010, but this sub-clade has become dominant in the northern hemisphere and has been occasionally designated as a low reactor by various labs, including the CDC. A series of related sequences was also just released by the Air Force, which were also collected from vaccinated hosts.

However, only three H3N2 isolates from the United States (1%) have been designated as low reactors by the CDC. Moreover, a second isolate from the Australia series, A/Townsville/87/2010, was not designated as a low reactor even though the HA sequence was identical to the subsequent sequence that was designated as a low reactor.

Moreover, the recent recommendation to WHO was to leave the H3N2 target, A/Perth/16/2009 unchanged for the 2011/2012 flu season in the northern hemisphere, which is largely based upon the inconsistent and unreliable antigen characterization test.

The data reveal fatal flaws in the vaccine selection procedure used by WHO and the CDC, wqhich continues to put the world’s population at risk.

A/TOWNSVILLE/106/2010 Mossman
A/TOWNSVILLE/105/2010 Thursday Island
A/TOWNSVILLE/104/2010 Thursday Island
A/TOWNSVILLE/102/2010 Horn Island
A/TOWNSVILLE/100/2010 Wujal Wujal vaccinated
A/TOWNSVILLE/98/2010 Hopevale
A/TOWNSVILLE/97/2010 Thursday Island vaccinated
A/TOWNSVILLE/93/2010 Bamaga
A/TOWNSVILLE/92/2010 Thursday Island Vaccinated
A/TOWNSVILLE/87/2010 Naprunum vaccinated
A/TOWNSVILLE/86/2010 Cairns

[dothedd]

H3N2 Vaccine Breakthrough Sequences
Recombinomics Commentary 17:40
February 25, 2011


The DoD-GEIS Flu Program at Brooks Air Force Base released a series of partial H3N2 recently collected from DoD dependents. Like the recently released H1N1 sequences, many of the H3N2 samples were from previously vaccinated patients, signaling vaccine failure against the Perth/16/2009, which has been again recommended for the 2011/2012 vaccine target for the northern hemisphere.

The H3N2 from vaccinated patients fell into two sub-clades. The largest was related to A/Pennsylvania/02/2010, the dominant H3N2 circulating in the northern hemisphere. These sequences are closely related to the sequences from Australia, which were classified as low reactors. Several of those patients had also been vaccinated in 2010. The other sub-clade was small and all vaccinated patients were from South Korea.

These data again indicate vaccine failure for H3N2 is widespread. The antigenic differences are not well represented by the antigen characterization test, which is used to select new vaccine targets. The CDC has only identified 5 low reactors (1%) related to Perth/16, although most H3N2 sequences in the United States are related to the low reactors in Australia and the sequences from vaccinated patients in the United States (see list below).

The vaccine failures for H3N2 are in addition to the failures for H1N1, which is consistent with the Pneumonia and Influenza death rate, which is at 8.25% for week 7, which marks the fourth week in a row that the rate has been above the epidemic threshold. Historically, these elevated death rates are linked to vaccine failure. In 2008, when similar levels were seen, all three vaccine target were changed for the following year.

This season, none of the target have been changed, due to reliance of the vaccine committee on the unreliable and insensitive antigen characterization test, which continues to be hazardous to the world’s health.

PA/02/2010-related sub-clade
A/Massachusetts/AF2713/2011
A/Colorado/AF2702/2011
A/California/AF2699/2011
A/Texas/AF2727/2010
A/Arizona/AF2696/2010
A/Alabama/AF2692/2010
A/South Carolina/AF2724/2011

Novel sub-clade
A/Korea/AF2686/2010
A/Korea/AF2707/2011
A/Korea/AF2708/2011
A/Korea/AF2711/2011

[dothedd]

US Pediatric Influenza Deaths Spike Higher In Week 8 Report
Recombinomics Commentary 14:40
March 4, 2011


NJ (2 ), PA (2 ), OH (1 ), IL (1 ), MI (1 ), MN (1 ), KY (1 ), TX (3 ), NV (1 ), HI (1 )

The above numbers and locations represent the pediatric influenza deaths reported in week 8 as indicated in today's MMWR. The 14 deaths represent a dramatic jump from the 6 deaths reported last week, and likely reflect the increases in H1N1 activity in multiple states. The pediatric deaths are a trailing indicator and the above deaths were likely from prior weeks, as seen in last week’s graph below. It is likely that the 15 deaths listed for week 5 will increase and represent the highest number of weekly cases since the spike increases in the fall of 2009.


Later today the CDC report will be released detailing the distribution of the newly reported cases as well as detail on the number of cases linked to H1N1. These increases highlight the immunological escape of the H1N1 circulating in the US, which is dominated by the sub-clade with S188T. These increased levels have also created shortages in liquid Tamiflu, recommended for children.

Thus, the decline in H3N2 and influenza B, coupled with the increase in H1N1, will likely lead to additional weekly reports with high levels of pediatric deaths, which are under-represented because of a lack of testing coupled with a lack of sensitivity for H1N1 cases.

The failure to change the vaccine target for next season will once again create unnecessary pediatric deaths in the US and worldwide next season.

[dothedd]

Novel Swine H1N2 In England With Pandemic H1N1 Genes
Recombinomics Commentary 23:00
March 7, 2011


Weybridge has released sequences from all 8 gene segments from a novel H1N2, A/swine/England/1382/2010, which has internal genes from pandemic H1N1 and an H1 from human H1N1 circulating in the late 70's, early 80's (see list here) and N2 from human H3N2 circulating in the early 1970’s (see list here). Thus, the new reassortant has swapped out six swine genes for the six pH1N1 internal genes (human PB1, avian PB2 and PA, and swine origin NP, MP, NS), which are linked to human H and N external genes.

This combination is similar to the reassortants in Argentina, which had human H1 and N1 or H1 and N2 with six internal gens from pH1N1. This new constellation is consistent with recent H1N2 isolates from South Dakota which have human H1 and N2, with MP from pH1N1 (sequences from the other 5 genes were not released).

Similarly, sequences from North Carolina were just released which had human H1 and N2 and the polymerase complex from North American triple reassortants, which swapped out the remaining three swine genes for the three genes from pandemic H1N1.

Thus, all of these reassortants have human H and N genes with internal genes that have been found in human hosts, raising concerns that these new reassortants can also jump from swine to human and introduce human H and N genes from the 1970’s, 80’s, and 90’s that have been evolving in swine for 3-4 decades.

[dothedd]

Novel Swine H1N2 In North Carolina With Pandemic H1N1 Genes
Recombinomics Commentary 23:50
March 7, 2011


St Jude as released three full sets of novel H1N2 from North Carolina (A/swine/North Carolina/226124/2010, A/swine/North Carolina/226125/2010, A/swine/North Carolina/226126/2010) collected in September 8, 2010. The isolates had a triple reassortant polymerase complex found in North American swine (human PB1 and avian PA andPB2), but had pandemic H1N1 for the other three internal genes (NP, MP, NS). The H1 was from seasonal H1N1 circa 2003, while the N2 was seasonal H3N2 circa 1996.

Thus, the novel H1N2 was a North American H1N2 triple reassortant that had replaced swine NP, MP, and NS with pandemic NP, MP, and NS. This new constellation of genes has much in common with reassortants from Argentina, England, and South Dakota. All have human H and N genes which have been circulating in local swine for 1-3 decades and all have replaced the three swine genes with three pandemic genes, which is matched with a polymerase complex with human PB1 and avian PA and PB2.

Thus, all 8 gene segments have a recent history of circulation in human hosts and therefore have the potential of jumping back to humans from swine. However, each of these jumps would introduce human flu genes that have been evolving in swine for decades.

These newly describe reassortants raise concerns that these flu genes will continue to evolve via recombination involving older human genes with newer swine genes leading to accelerated evolution.

In addition to the above reassortants, Hong Kong has released sequences from hundreds of Hong Kong isolates with receptor binding domain changes, including D225G, D225N, and D225E, in addition to S186P and S188N, as well as changes at position 156-159 including G158E. The circulation of these donor sequences in swine as well as the widespread reports of pandemic H1N1 in swine, continue to increase pandemic concerns.

[dothedd]

Novel Swine H1N2 In Indiana With Pandemic H1N1 Genes
Recombinomics Commentary 21:20

March 8, 2011


St Jude has released a full set of sequences for an H1N2 isolate from Indiana, A/swine/Indiana/240218/2010, collected on Feb 12, 2010. It has a pandemic H1N1 genetic background with a human N2 from 1996 H3N2 and swine H1N1 and NP genes. This isolate is part of a growing trend of reassortment between pandemic H1N1 and various swine triple reassortants worldwide.

Moreover, the recent sequences involve H1N2, which is likely linked to the polymerase complex with human PB1 and avian PB2 / PA, which was initially found in H3N2 swine isolates from the 1990’s. Thus, the jump of pandemic H1N1 from humans back to swine may have selected for swine reassortants that included human N2, which was present in all of the H1N2 swine isolates.

All of these constellations were from 2010 isolates in Argentina, England, South Korea, and multiple locations in the United States (South Dakota, North Carolina, and Indiana).

On a related note, all reported trH3N2 infections in humans in the United States involved infections after the spread of pandemic H1N1, and all 2010 sequences have PB1 E618D, which may also represent a linkage between human adaptation and isolates with N2. There have been 5 reported cases in 2010, including two recent cases in Pennsylvania. The Pennsylvania situation remains unclear because of the large number of unsubtypable isolates, and recent weekly reports, which repeat warnings to physicians to be cognizant of the trH3N2 cases in Pennsylvania.

[dothedd]

#devi l#

Suspect Fujian H5N1 Case In Israel
Recombinomics Commentary 22:10
March 8, 2011


Concern that a poultry farmer from Kibbutz Rosh Tzurim in Gush Etzion contracted bird flu. The man was hospitalized a few days at Shaare Zedek Hospital in Jerusalem. The deadly virus was discovered yesterday in one of his kibbutz runs. Blood tests of laboratory testing verbalist transferred, and results are expected tonight.

The above translation describes a suspect H5N1 case associated with an outbreak on a turkey farm, which led to the culling of 40,000 birds. This outbreak follows reports of H5N1 in poultry in Palestine.

Although H5N1 has been reported previously in Israel and Palestine, the latest outbreak likely involves the Fujian strain (clade 2.3.2), which has been associated with recent wild bird and poultry outbreaks in South Korea and Japan, as well as earlier wild bird outbreaks. The recent outbreaks in Japan included the receptor binding domain change, S227R (in addition to M230I). Tthe first reported human case west of China involved the Qinghai train with the receptor binding domain change S227N, which was predicted.

These earlier reports strongly suggested that the Fujian strain would subsequently be reported in wild birds, poultry, and humans in Europe, the Middle East, and Africa.

If confirmed, this would be the first reported case in Israel, and if clade 2.3.2 is confirmed, this would be the first reported human case west of China. All prior human cases (in Turkey, Iraq, Azerbaijan, and Egypt) have been the Qinghai strain (clade 2.2).

[dothedd]

Novel trH3N2 Swine In Minnesota With Pandemic H1N1 Genes

Recombinomics Commentary 14:35
March 9, 2011


St Jude released a series of sequences from swine isolates from 2009 and 2010 which were triple reassortants which had acquired pandemic H1N1 gene segments. One of the examples was an trH3N2 isolate, A/swine/Minnesota/239105/2009, which had acquired pandemic H1N1 sequences, which replaced PA, NP, and MP segments.

Other sequences from H1N1 and H1N2 isolates from swine in Minnesota also had pandemic H1N1 genes, which are also true for H1N2 swine isolates from Argentina, England, South Korea, and multiple locations in the United States including South Dakota, North Carolina (including 2 distincy constellations), and Indiana.

These recent sequences highlight the ability of pandemic H1N1 virus to exchange genes with other triple reassortants (trH3N2, trH1N1, trH1N2), which are widespread in swine worldwide. The swapping is likely facilitated by the fact the pandemic H1N1 is also a triple reassortant and the polymerase complexes are composed of one human (PB1), and two avian (PB2 and PA) flu gene segments. However, these gene segments have significant sequences, especially those that have been evolving in swine for decades. Many of the triple reassortants also have human flu derived H and N genes, raising concerns that these new combinations will move these novel viruses into the human population.

[dothedd]

H5N1 Confirmed In Bangladesh Toddler
Recombinomics Commentary 22:35
March 14, 2011


A 13-month-old girl was detected with bird flu virus in the capital yesterday.

The girl, however, is not having any serious breathing problem, which is normally the case.

The symptom is so mild that it has been detected because of the extensive surveillance, Mahmudur said, adding that proper treatment of the girl has been ensured.

"She is fine now and will recover soon."

The above comments describe a mild H5N1 case in Dhaka, Bangladesh. This case follows the first confirmed case in Bangladesh (also in Dhaka), who had symptoms in January, 2008, but was not reported until May, 2008.

Like this year’s case, a link to birds was not described, and treatment with an antiviral was not stated. These two cases strongly suggested that H5n1 infections in Bangladesh and India are far more widespread than the two confirmed cases in Bangladesh (and no confirmed cases in India).

Recently Israel also reported a suspect case with mild symptoms that was not lab confirmed. However, the frequent reports of human cases in Egypt strongly suggest that the lack of confirmed cases in Israel is surveillance / reporting related, which is also the case for India.

Testing for H5N1 in humans remains abysmal. Many countries with high levels of H5N1 in poultry, like Egypt or Indonesia, rarely test symptomatic cases that do not have a poultry link. Milder cases, such as the above case, would rarely seek medical attention, and most who did would rarely be tested for H5N1.

The recent receptor binding domain change (S227R) reported in H5N1 in Japan continues to increase concerns that H5N1 in humans is widespread in patients who are not tested.

[dothedd]

H5N1 Confirmed In Another Bangladesh Toddler

Recombinomics Commentary 16:35
March 16, 2011


Another human case of avian influenza has been detected in the Kamalapur area of the capital, two days after a 13-month-old girl was found carrying the H5N1 virus in the same locality.


IEDCR director Prof Mahmudur Rahman told bdnews24.com that a 31-month-old boy had been detected carrying the virus in their lab.


They tested nasal as well as throat swab and blood to confirm the case. The boy showed up with mild symptoms including fever and cough at the IEDCR and ICDDR,B joint surveillance site at Kamalapur, the director said.


Prof Rahman, however, said that the boy was not related to the earlier case.


The above comments on a second confirmed H5N1case (2M) in the same region of Dhaka, Bangladesh (Kamalapur area) raise pandemic concerns. Both cases were mild and not linked, suggesting the number of H5N1 infections is markedly higher than the two confirmed cases.


This epidemiology is similar to the initial H1N1 cases in southern California in the spring of 2009, where the absence of linkage or swine contact indicated the number of unreported cases was large.


Both cases were detected via surveillance and involved swabs from the upper respiratory tract, which would increase the potential for human to human transmission. Neither report mentioned contact with birds, increasing concerns that H5N1 is transmitting in humans in Bangladesh.


Recently released H5N1 sequences from wild birds in Japan (Hokkaido and Fukushima) have receptor binding domain change S227R, in addition to V223I and M230I, has raised concerns of human transmission.


More detail on symptomatic contacts and sequences from the confirmed cases in Bangladesh would be useful.

[dothedd]

S227R In H5N1 In Fukushima Japan
Recombinomics Commentary 18:10
March 16, 2011


Hokkaido University released the H5N1 sequence from a duck in Fukushima, A/duck/Fukushima/2/2011, which was collected in January, 2011. Like the sequence from the whooper swan in Hokkaido, A/whooper swan/Hokkaido/4/2011, it had S227R (in addition to V223I and M230I). A third sequence from Tochigi, A/peregrine falcon/Tochigi/15/2011, had the earlier changes (V223I and M230I), but did not have S227R.

The duck sequence was closely related to the whooper swan protein sequence (the duck also had E362D), raising concerns that the receptor binding domain changes (V223I, S227R, M230I) are widespread in H5N1 clade 2.3.2 in northern Japan, includ ing the region most affected by the earthquake and tsunami.



The three receptor binding domain changes raise concerns that this emerging sub-clade could infect humans. These concerns were increased by the recent reports of two confirmed H5N1 cases in the Kamalapur area of Dhaka, Bangladesh.


Prior H5N1 cases in birds and a child in Bangladesh were associated with clade 2.2. However, clade 2.3.2 has been circulating in wild birds in Japan, Russia, and Mongolia since 2009, and there are concerns that this sub-clade will spread to areas to the southwest, including Bangladesh and India.



Sequence data on the two confirmed cases in Bangladesh would be useful.

[dothedd]

Bangladesh H5N1 Cluster Raises Pandemic Concerns
Recombinomics Commentary 20:45
March 16, 2011



"We are lucky that the strain (clade 2.2) of H5N1, which circulates in Bangladesh, is less virulent, so it causes less infection to humans," he said.

"But we have to be careful as it has the potential to change into another class (2.1), which was highly infectious to human," he added.

The first human case in May 2008, a 15-month-old boy, got the virus when his mother slaughtered a chicken at home and later cuddled him with unwashed hands.

The above comments from a media report on the current H5N1 cluster in a Dhaka slum (Kamalpur), suggests that the infections were due to clade 2.2 (Qinghai strain), which was true for the case confirmed in 2008 (H5N1 sequence was clade 2.2.3), which was also in Kamalpur. However, more recent H5N1 reports have described clade 2.3 (2.3.2) in wild birds, which are the likely origin of the current outbreaks (human and avian) in Kamalpur.

In 2005 the Qinghai strain was identified in bar headed geese at Qinghai Lake in China, and this sub-clade spread to Europe, the Middle East, and Africa, as well as south Asia, including Bangladesh, India, and Pakistan. This sub-clade arrived from locations in southern Russia and northern Mongolia, where clade 2.3 has replaced clade 2.2. Therefore, it is likely that the H5N1 currently circulating in Bangladesh is clade 2.3, not clade 2.2 (or clade 2.1, which has only been reported in Indonesia).

Clade 2.3.2 has generated more concern based on recent sequences from wild birds collected in 2011. Sequences from Hokkaido and Fukushima have S227R, which is a concern because changes at position 227 are known to affect the specificity of receptor binding. In H5N1, S227N was associated with increased affinity for gal 2,6 receptors which is found in human cells located in the upper respiratory tract. It was predicted to appear in human isolates from the Middle East, which was confirmed in the first case in Turkey in early 2006.

The H5N1 detected in nose and throat swabs from the two Kamalpur toddlers, raising concerns that the H5N1 was more efficiently transmitted in humans. This concern was increased by two additional RBD changes, V223I and M230I, which were present in the Gharbya cluster, the largest human cluster reported to date in Egypt. Both of these changes had been reported previously in clade 2.3.2, and M230I is dominant in seasonal H1N1, H3N2, and influenza B.

Moreover, the two recent cases in Bangladesh have much in common with the first two H1N1 cases, reported in southern California in the spring of 2009. Those two cases had no reported contact with swine or each other, indicating a large number of unreported human cases led to the concurrent detection of the first two confirmed cases who were more than 100 miles apart.

Similarly, there has been not reported link between the two H5N1 cases with birds or each other. Moreover, both cases were mild, and detection of mild cases is more difficult because most infections will not lead to doctor or hospital visits, and most such visits will not test for H5N1.

Thus, like the H1N1 index cases in 2009, these two H5N1 cases were identified through routine surveillance. Although these two cases were mild, the presence in two toddlers from the slums of Dhaka, raises concerns for rapid spread and evolution to more virulent versions as the H5N1 adapts to human hosts. Moreover, the recent wild bird isolates with S227R were from northern Japan, where impacts from the recent earthquake and tsunami could be significant.

Release of the sequences from these two cases as well as symptoms and testing associated with contacts would be useful.

[dothedd]

Fukushima Radiation Raises H5N1 Pandemic Concerns
Recombinomics Commentary 13:13
March 17, 2011


The continuous release of radiation from the Fukushiam Daiichi nuclear plant has increased H5N1 pandemic concerns. Recently released H5N1 sequences from a duck in Fukushima, A/duck/Fukushima/2/2011, have receptor binding domain (RBD) change S227R, which was also present in a whooper swan sequence from Hokkaido,A/whooper swan/Hokkaido/4/2011,indicating this change is widespread in northern Japan. These changes are on a clade 2.3.2 genetic background that also has V223I and M230I, changes found in H5N1 from the Gharbiya cluster in Egypt.

The radiation released at the Daiichi plant is forecast to go east to the Aleutian Island, and the back over Russia, China, and Korea, where H5N1 is circulating in wild birds. Exposure of H5N1 to ionizing radiation can lead to rapid genetic change, which may increase the ability of H5N1 to transmit in humans.

Moreover, the earthquake and tsunami have led to overcrowding conditions in displaced persons, which would also favor viral spread. Recent two H5N1 cases in Bangladesh were detected with swabs from the upper respiratory tract, signaling a greater ease of transmission in humans.

Thus, the radiation release demands close monitoring of H5N1 currently circulating in wild birds and poultry in Japan and South Korea, as well as humans in the region with upper respiratory tract infections.

[dothedd]

Fukushima Radiation and H5N1 In Wild Birds In Japan
Recombinomics Commentary 13:13
March 17, 2011


Information received on 16/03/2011 from Dr Toshiro Kawashima, CVO, Animal Health Division, Ministry of Agriculture, Forestry and Fisheries, Tokyo , Japan

Summary

Report type Follow-up report No. 8
Start date 15/12/2010
Date of first confirmation of the event 19/12/2010
Report date 16/03/2011
Date submitted to OIE 16/03/2011
Reason for notification Reoccurrence of a listed disease
Date of previous occurrence 01/04/2009
Manifestation of disease Clinical disease
Causal agent Highly pathogenic avian influenza virus
Serotype H5N1
Nature of diagnosis Clinical, Laboratory (basic), Laboratory (advanced), Necropsy
This event pertains to the whole country
Related reports Immediate notification (20/12/2010)
Follow-up report No. 1 (22/12/2010)
Follow-up report No. 2 (19/01/2011)
Follow-up report No. 3 (23/01/2011)
Follow-up report No. 4 (04/02/2011)
Follow-up report No. 5 (14/02/2011)
Follow-up report No. 6 (24/02/2011)
Follow-up report No. 7 (03/03/2011)
Follow-up report No. 8 (16/03/2011)

The above comments summarize OIE reports on confirmed H5N1 in wild birds identified throughout Japan, including northern Japan. Sequences from three isolates from these outbreaks have been made public at Genbank. Two of the three (in Hokkaido and Fukushima) have S227R. All three sequences are the Fujian strain (clade 2.3.2) which have been circulating in wild birds for several years, including the large outbreaks in Japan, South Korea, and Russia in the spring of 2008. The clade 2.3.2 sequences have two additional receptor binding domain changes (V223I and M230I), which were present in the clade 2.2 sequences from the Gharbiya cluster in Egypt in late 2006. The Gharbiya cluster is the largest H5N1 cluster in Egypt reported to date. All three patients died and the RBD changes raised concerns of increase transmission in human.

The recent acquisition of S227R increased concerns because of the known changes in receptor binding specificity due to S227N, which was predicted and confirmed in 2 of the 4 sequences from Turkey in 2006. The recent reports of two confirmed cases in Kamalpur, a Bangladesh slum have increased concerns that clade 2.3.2 has migrated to Bangladesh and is involved in the two recent cases (as well as symptomatic contacts).

The worsening situation at the Daiichi nuclear power facility in Fukushima, Japan increases concerns that the H5N1 circulating in wild birds and poultry in the region will be impacted by the release of ionizing radiation. This radiation can lead to rapid evolution of clade 2.3.2 H5N1, which may lead to selection of changes that increase transmission in humans in the region. These changes could quickly spread through displaced persons living in crowded conditions that are far from ideal.

Close monitoring of these persons as well as H5N1 sequences from wild birds and poultry, a timely release of such sequences would be useful.

[dothedd]

Lack of Poultry Link In Bangladesh H5N1 Cluster
Recombinomics Commentary 01:45
March 18, 2011

The case is a 16 month old female from Kamalapur, Dhaka. She presented at a influenza sentinel surveillance on 8 March with a history of cough and fever and subsequently recovered.

A detailed epidemiological investigation and contact follow up is being conducted by a team of epidemiologists from IEDCR, ICDDRB and WHO Bangladesh.

[The 2 human cases of avian influenza A/H5N1 virus infection identified recently in the Kamalapur area of Dhaka (only the 2nd and 3rd cases ever recorded in Bangladesh) are unusually in that both are young children with mild symptoms of respiratory infection. Exposure to infected poultry is a common feature, - Mod.CP]

The above WHO comments on the first H5N1 case in Bangladesh in 2011 clear do not cite a link between the confirmed case and poultry. Similarly, the media reports on both cases fail to cite any link between the two H5N1 confirmed cases and poultry.

Both patients presented at a surveillance center in Kamalapur, Dhaka with flu like symptoms, This surveillance center typically takes samples from every fifth patient with flu-like symptoms, which are initially tested for influenza A. Positives are sub-typed and those that are not sub-typable for H3N2 or H1N1 are then tested for H5N1. In both cases, the H5N1 was detected via routine surveillance. The above Promed comment (in brackets) on exposure to infected poultry is not supported by any public documents, and is rather misleading. If ProMed has such evidence it should be cited specifically.

In the absence of such documentation, the two cases in Kamalapur bear a striking resemblance to the first two US H1N1 cases in the spring of 2009. Like the Kamalapur cluster, the clustering was in time and space, but was not associated with contact with each other or an animal source.

As happened in 2009 with H1N1, an epidemiological investigation is currently being conducted by WHO.

Test results on symptomatic contacts would be useful.

[dothedd]

Tamiflu Resistant H1N1 Cluster In Delaware
Recombinomics Commentary 01:45
March 24, 2011


Delaware’s Division of Public Health (DPH) is following up on an antiviral-resistant influenza case identified March 2 in a child from Kent County. The child was not hospitalized and has fully recovered.

The specimen – part of a random sample submitted for routine anti-viral resistance testing – was reported as oseltamivir-resistant the first week of March.

Delaware’s Division of Public Health (DPH) is following-up on three additional antiviral-resistant influenza cases. Lab results provided March 21 found that a 1 month-old girl and a 33 year-old woman from Kent County were infected with influenza strains found to be resistant to oseltamivir.

A 3 year-old Sussex County boy was also identified as having had antiviral resistant influenza.

The above comments describe a cluster of four cases of H274Y in recent H1N1 cases in Delaware, strongly suggesting the resistance is transmitting. The releases do not suggest the samples were collected after Tamiflu treatment. Instead the samples were part of routine surveillance and the index case was not hospitalized, which also argues against treatment.

The finding of three cases in the same week in the small state of Delaware is in marked contrast to the three cases reported for the entire United States for the entire flu season, as indicated in the CDC week 10 report.

This cluster signals transmission of Tamiflu resistant H1N1 that is evolutionarily fit in patients who appear to have been previously healthy and not treated with oseltamivir prior to sample collection. The cluster in previously healthy patients is in contrast to the previously reported Duke Medical center cluster.

[dothedd]

Spike In H3N2 Low Reactors In The United States
Recombinomics Commentary 18:25
March 24, 2011


Four hundred eighty-three (99.0%) of the 488 tested were characterized as A/Perth/16/2009-like, the influenza A (H3N2) component of the 2010-11 influenza vaccine for the Northern Hemisphere. Five viruses (1.0%) of the 488 tested showed reduced titers with antiserum produced against A/Perth/16/2009.

Five hundred thirty-five (96.9%) of the 552 tested were characterized as A/Perth/16/2009-like, the influenza A (H3N2) component of the 2010-11 influenza vaccine for the Northern Hemisphere. Seventeen viruses (3.1%) of the 552 tested showed reduced titers with antiserum produced against A/Perth/16/2009.

The above comments from FluView weeks 9 and 10 respectively reflect the dramatic jump in H3N2 “low reactors” reported in the week 10 CDC FluView. Most of the sequences associated with the low reactor designation were reflected in HA sequences recently released by the CDC at GISAID. 14 of the released HA sequences were designated as low reactors by the CDC (see list here).

Phylogenetic analysis of the HA sequences raised serious questions about the sensitivity and reproducibility of the antigenic characterization test used to identify low reactors. This assay has been used for decades, but the release of sequences from tested isolates continues to raise serious questions about the validity of this assay.

This assay plays a pivotal role in the selection of new vaccine targets, as well as claims of “matches” between the vaccine target and circulating virus. These claims have a checkered and disturbing past, and the use of this assay to justify the use of this year’s targets in next year’s vaccine has raised significant concerns, as multiple reports describe vaccine failures associated with the current targets, and released sequences identify glaring inconsistencies.

The latest set of sequences extends the inconsistencies. Phylogenetic analysis identifies clustering of low reactors such as two isolates from Minnesota (A/Minnesota/17/2010 and A/Minnesota/18/2010) and one from Wyoming (A/Wyoming/09/2010). However, two other isolates from Minnesota (A/Minnesota/12/2010 and A/Minnesota/13/2010) and one from Maine (A/Maine/02/2010) are virtually identical to the three low reactors, but are not designated as low reactors. More dramatic examples were demonstrated by two closely related sequences from New Jersey (A/New Jersey/02/2010 and A/New Jersey/02/2011) which were designated as low reactors, while sequences which were identical to A/New Jersey/02/2011 (A/Alaska/01/2011, A/Delaware/10/2010, A/Nevada/04/2010, A/Pennsylvania/36/2010, A/Vermont/02/2011, A/Washington/04/2011) were not. Similarly, additional sequences closely related to the two New Jersey low reactors (A/Georgia/24/2010, A/Maine/02/2011, A/Louisiana/05/2010, A/Massachusetts/04/2010, A/New Jersey/01/2011, A/North Dakota/02/2011, A/Pennsylvania/41/2010, A/South Carolina/04/2010, A/South Dakota/02/2011), were also not designated as low reactors. The above sequences represent a few of the glaring inconsistencies, which are both common and widespread in the recently released sequences. Low reactors populate multiple additional branches, suggesting the vast majority of the recently released sequences are low reactors. Moreover, virtually all of the isolates were collected prior to the latest meetings of the WHO and US advisory committees on vaccine selection. Both committees recommended unchanged targets for the 2011/2012 influenza season in the northern hemisphere.

Additional data on vaccine failures in Air Force dependents as well as patients in Europe, including the UK, and Australia also revealed vaccine failures linked to the influenza A targets (A/California/07/2009 and A/Brisbane/16/2009, raising additional concerns over the recommendations to leave the targets unchanged. In addition, the pneumonia and influenza death rate has been at or above the epidemic threshold for the past seven weeks (tomorrow's week 11 report will show a jump to 8.61%), which is historically associated with vaccine mismatches such as this year and 2008, as seen in the graph below.



In 2008 all three vaccine targets were mismatched and changed for the following year, in contrast to this year when all three remained unchanged. Moreover, in 2008 the H1N1 target (A/Solomon Islands/3/2006) was initially called a match by the CDC, but phylogenetic analysis indicated that the target was no longer circulating and had been replaced by A/Brisbane/59/2007 and A/Hong Kong/2652/2006 and both prototype had a large number of HA changes, which were subsequently shown to represent antigenic differences easily identified by an anti-sera directed against the Brisbane target grown in mammalian cells, in marked contrast to the CDC anti-sera produce in chicken eggs which failed to distinguish the the sub-clades. This mismatch was associated with the widespread appearance of oseltamivir resistance (H274Y) in the 2007/2008 season in the northern hemisphere, and the fixing of H274Y during the 2008 season in the southern hemisphere. The switch to the Brisbane target in the 2008/2009 came after Brisbane/59 evolved further, leading to more vaccine failure. This year the vaccine mismatch linked to pandemic H1N1 is associated with the appearance of oseltamivir resistance in Delaware, raising concerns that the cluster signals the re-emergence of H274Y and possible fixing in the upcoming season in the southern hemisphere, where the mismatched vaccine is being distributed.

The continued reliance on the outdated, inconsistent, and insensitive antigenic characterization test by the WHO and US vaccine selection committees continues to be hazardous to the world’s health.




LINK WITH CHART:
www.recombinomics.com/News/03241102/H3N2_LR_US.html

[dothedd]

H1N1 Atypical Pneumonia Death Cluster In Juarez Mexico
Recombinomics Commentary 23:55
March 24, 2011


The transportation officer who died of atypical pneumonia in what is considered the first death of the epidemic of human influenza A (H1N1) that caused the issuance of a general health warning on the state to prevent more people from becoming infected.

It should be noted that four other people are hospitalized and under medical observation following presents a clinical picture of atypical pneumonia.

An Agent road have already died and there are ten more affected.

The above translations from recent stories in Mexico describe a 10-14 cases of atypical pneumonia which are likely H1N1 infections. These cases are clustered in and around Juarez, Mexico and have led to influenza vaccination of 250 transport officers, and a warning for the region.

This warning and associated actions raise concerns that H1N1 circulating in the area is producing more severe illness leading to pneumonia, hospitalizations, and death.

More detail on the condition of these patients, as well as sequence data from the influenza isolated from these patients, would be useful.

[dothedd]

H1N1 Death Clusters Spread Throughout Chihuahua Mexico
Recombinomics Commentary 00:55
March 25, 2011


Duarte Jaquez said that of the 15 cases it is known, eight occurred in Ciudad Juárez - apparently one of which ended in death, "six in the state capital, and another in Cuauhtemoc, thus extending the measures the entire population to prevent the spread of the virus and the loss of human lives. The announcement came in the room balconies at the Government Palace, after they obtained the results of laboratory tests carried out yesterday to five cases in Ciudad Juarez, which has been positive reaction to the influenza A H1N1.

The above translation confirms that the atypical pneumonia in Juarez, Mexico is due to H1N, and the cases have spread throughout the state, of Chihuahua including six cases in the capital, Chihuahua.

The warning, death, and vaccination of 250 traffic co-workers raise concerns that a more severe form of H1N1 is spreading in northern Mexico. Moreover, the recent H1N1 vaccine failures in the northern hemisphere raise additional concerns that the vaccination of co-workers will have limited utility. The current vaccine that is in use in the northern hemisphere has been produced for the southern hemisphere, so no vaccine targeting the current H1N1 sub-clade is available.

The sub-clade with S188T has become dominant in the northern hemisphere, buit a cluster with H274Y has recently been reported in Delaware, and increased severity raises concerns that additional receptor binding domain changes, including D225G/N make cause significant increases in intensive care admissions.

More detail on this more virulent H1N1 sub-clade would be useful.

[dothedd]

Chihuahua Mexico Declares Epidemic Alert On H1N1 Clusters
Recombinomics Commentary 05:55
March 25, 2011


The Chihuahua state government today declared an "epidemic alert" for a flu outbreak that has claimed the life of a policeman and two others infected and has to fifteen people under suspicion.

Duarte said that one of the patients likely originates in the U.S. El Paso (Texas), who is suspected to have been the one who brought the virus to neighboring Ciudad Juárez.

According to information from the Department of Health of El Paso in 2010 were confirmed eight cases of influenza A, while in the first two months of this year were already 29 confirmed cases.

The above translation indicates the recent H1N1 outbreak has raised concerns leading to the declaration of an“epidemic alert” for the entire state of Chihuahua reflecting the spread of cases from Juarez to the capital, Chihuahua.

The above comments suggest the H1N1 originated in El Paso, which led to the rapid spread and death. Although 250 traffic police have been vaccinated, the utility of the vaccine for H1N1 currently in circulation remains questionable. Most recent sequences in the United States, from isolates collected in late 2010, had S188T, which was linked to vaccine failures reported in the UK.

Although the CDC has recently released 2011 H3N2 and influenza B sequences, public sequences for H1N1 have not been updated since early February.

Release of more current H1N1 sequences from the US, as well as sequences from the severe cases in Chihuahua, would be useful.

[dothedd]

H1N1 Death Cluster In Juarez MexicoTraffic Department
Recombinomics Commentary 03:05
March 26, 2011

killed the commander of the Municipal Traffic Department (DGTM), Rosario Isidro Gutiérrez Palma 33. It is recalled that it began as an atypical pneumonia.

With this death, added three people have died after contracting the H1N1 virus that keeps tabs on at least five people in the frontera. El officer was hospitalized this week in the Poliplaza because of atypical pneumonia and was in intensive care because of illness caused by H1N1 influenza virus, as in days past the Transit Department went on alert because of the death of one of its elements and the severity of whom died this morning, so all the corporation was vaccinated and is monitored to prevent further cases inside.

It was last Wednesday when he confirmed the death of an officer named Knight, 26, who was the first victim of the H1N1 virus and reportedly the Health Sector, also a woman had been killed recently because of the same disease.

The above translation describes three H1N1 deaths in Juarez, Mexico. At least two of the deaths involved members of the Transit Department, and one media report suggested the infection was transmitted during a demonstration on the use of a breathalyzer kit. However, regardless of the method of transmission to the two officers, the death of two young adults (26M and 33M) signals an increased virulence in the circulating H1N1. These two infections led to the vaccination of 250-300 members of the force as well as alerts for Juarez, the state of Chihuahua, and all of Mexico as additional cases were identified throughout the country.

It is likely that the outbreak in Mexico is linked to the outbreak in Venezuela, as well as recent deaths in the United States near the Mexican border, including the teacher (55F) south of San Antonio, TX.

The timing of this outbreak is almost exactly two years after the pandemic H1N1 began to spread. Like 2009, the frequency of seasonal influenza has begun to decline, allowing for the emergence of variants.

Release of H1N1 sequences from the severe and fatal cases in Mexico, Venezuela, and southwest United States would be useful.

[dothedd]

Juarez Mexico H1N1 Death Cluster Raises Pandemic Concerns
Recombinomics Commentary 01:30
March 28, 2011


The latest victim was Isidrio Gutiérrez Palma, Road Agent Juarez, who was the officer's patrol partner Aaron Rodolfo Caballero, who also died on Tuesday for the same reason.

The PRI in the local Congress legislator confirmed that Liz Aguilar also contracted the H1N1 virus, for which he was subjected to treatment and is stable.

The above translation confirms the relationship between two of the fatal cases in Juarez. Although media reports have cited a breathalyzer interlock device on their shared patrol car, the two agents undoubtedly had many common source for potential infection. The fact that both young adults (33M and 26M) died is of considerable concern, as is the initial diagnosis of atypical pneumonia.

The diagnosis suggests that there was difficulty confirming that the pneumonia was caused by pandemic H1N1 suggesting the virus has continued to evolve, leading to reduced sensitivity in with the reagents widely distributed.

These changes raise concerns that a new sub-clade will emerge that will limit the utility of current vaccines as well as antibodies generated against earlier versions of H1N1. Moreover, the new sub-clade may have additional receptor binding domain changes and/or changes like D225G may be more prevelant. The infection of a local legislator suggests the H1N1 has spread rapidly, and the number of severe and fatal cases may be markedly higher than the number recently reported..

Release of sequences from the severe and fatal cases is critical. The CDC’s release of H1N1 sequences is lagging. Last week the released 2011 H3N2 and influenza B sequences, but the lats release of H1n1 sequences was February 2, 2011 (and the vast majority of those sequences was from 2010.

2011 H1N1 sequences, including recent isolates from Mexico and Venezuela, should be released immediately.

[dothedd]

2011 and 2009 H1N1 Similarities In Mexico Raise Concerns
Recombinomics Commentary 14:50
March 28, 2011


In an updated report on Sunday, the Ministry of Health reported that besides the four deaths from the H1N1 influenza in the state are seven people who are infected the virus, while eight others could also be carriers because of the atypical pneumonia that presented.

The above translation is from a report providing more detail on initial cases in Mexico. All are under 65 years of age and in multiple locations in northern Mexico in the state of Chihuahua. The cases are in addition to the four fatal cases, who were all between the ages of 24-35, which have strinking similarities with the 2009 outbreak in Mexico almost exactly 2 years ago. At the time, seasonal flu levels were declining, and the outbreak of lethal atypical pneumonia in previously healthy young adults created significant concern.

These were H1N1 cases that were positive for influenza A, but negative for seasonal H3 or H1 because the H1N1 was of swine origin which failed to react with sub-typing reagent that targeted human influenza sequences. Consequently, the cases were described as atypical pneumonia. Similar influenza A positive cases were identified in southern Caliifornia in samples collected March 30 or April 1. Sequencing of the cases identified swine triple reassortant viruses in cases that were over 100 miles apart and how no evidence of contact with each other or swine.

In the past 2 years H1N1 has spread worldwide and labs have reagents that can detect the swine H1N1 sequences. However, the recent cases in northern Mexico were initially characterized as atypical pneumonia because of sub-typing difficulties, raising concerns that the H1N1 in the recent cases represents a more evolved sub-clade which is emerging now because of reduced competition from seasonal influenza.

Moreover, at least two of the fatalities were in traffic agents who were partners, indicating the H1N1 in that cluster was particularly virulent, killing two young adults (26M and 33M). The H1N1 has spread rapidly, leading to alerts in Juarez, the state of Chihuahua, and the entire country.

These additional similarities between the 2009 and 2011 outbreaks require a rapid release of sequences from the cases in Mexico, as well as sequences from the United States. The release of 2011 H1N1 sequences by the CDC has been delayed. Last week 2011 H3N2 and influenza B sequences were released, but the last submission of H1N1 sequences was February 2, and the released sequences were largely from December, 2010 collections.

The relationship between the sequences in Mexico and Venezuela, and the in the United States is of interest, as are recent changes. Swine sequences from the US and other countries worldwide include a broad array or reassortants which involve H1N1, H1N2, and H3N2 triple reassortants with segments from the pandemic H1N1 sub-clade.

These newly formed genomes create additional threats since all 8 gene segments have a history of transmission in humans.

[dothedd]

Withheld 2011 H1N1 US Sequences Raise Pandemic Concerns
Recombinomics Commentary 15:30
March 28, 2011

The H1N1 influenza outbreak that affects the state of Chihuahua originated in Texas and New Mexico, said yesterday the governor Cesar Duarte Jaquez.

"It is confirmed that the lady who died recently in capital Chihuahua came from a Texas trip, just as those who are infected in Ciudad Juárez are all related to a trip to the United States, or have had contact with U.S. citizens "he said.

The above translation on relationships between the H1N1 outbreaks in northern Mexico and the United States raise additional concerns about the 2011 sequences in the United States and the delay in release by the CDC. Recently the CDC has been releasing series of H1N1, H3N2, and influenza B sequences almost simultaneously. Last week H3N2 and influenza B sequences from 2011 collections were released, but H1N1 sequences have been withheld. The last CDC release was February 2, 2011 and most released sequences were from December, 2010. The recent evolution of H1N1 in the United States is not public.

These sequences and antigenic characterizations were known prior to the recent decision to leave the 2011/2012 vaccine targets for the northern hemisphere unchanged, even though death rates are at historic highs and multiple reports on vaccine failures have been published.

The sequences from late 2010 were dominated by the sub-clade with S188T, which was also linked to vaccine failures. Similar changes flanking position 190 were also seen in the 2009/2010 northern hemisphere season which led to vaccine failures of seasonal H1N1, which was also associated with the fixing of Tamiflu resistance (H274Y).

The vaccine target selection is heavily dependent on antigen characterization tests with are insensitive and unreliable. These fatal flaws are most striking in seasonal and pandemic H1N1. The lack of sensitive led to a limited number of low reactors last season in US isolates (all were limited to changes at position 159). This low sensitivity is also present in the CDC FluView, which cites only one low reactor in the 2010/2011 season, even though most sequences have S188T which is linked to low reactor status. One isolate, A/Kentucky/09/2010 had three changes linked to low reactor status (G158E, S188T, and D225G) but was not designated as a low reactor by the CDC.

In addition to vaccine target selection, the sequences are important for monitoring H1N1 evolution, including receptor binding domain chnages. Recent swine sequences from the US and elsewhere, including England and South Korea, signal extensive reassortment between triple reassortants (H1N1, H1N2, H3N2), and pandemic H1N1, which is also a triple reassortant. These combinations involve genes with a long history of transmission in humans, raising concerns that H1n1 variants could again jump from swine to humans, which is most likely to happen at the present time, as happened in 2009 when seasonal flu levels decline.

Thus, the withholding of H1N1 from 2011 isolates in the United States increases pandemic concerns.

Sequences from the United States, Mexico, and Venezuela should be released immediately.

[dothedd]

Absence of 2011 H1N1 Texas Sequences Raise Concerns
Recombinomics Commentary 19:30
March 28, 2011


The H1N1 influenza outbreak that affects the state of Chihuahua originated in Texas and New Mexico, said yesterday the governor Cesar Duarte Jaquez.

"It is confirmed that the lady who died recently in capital Chihuahua came from a Texas trip, just as those who are infected in Ciudad Juárez are all related to a trip to the United States, or have had contact with U.S. citizens "he said.

From January to date in the state of Texas have identified 226 cases of H1N1...

The above translation suggests that the outbreak in Chihuahua in northern Mexico was linked to H1N1 circulating in Texas and New Mexico in 2011. However, the CDC has not released any 2011 H1N1 sequences from either state. The only public sequence from either state, A/Texas/14/2010, was collected on November 30, 2010.

The CDC has access to samples from both states, as well as samples collected by the Air Force as part of a surveillance program based in Brooks AFB in Texas, yet the only public pandemic H1N1 sequences from Air Force program are from the 2009/2010 season.

The absence of sequences from these states raises serious pandemic concerns. Although WHO declared an end to the 2009 pandemic in August, 2010, H1N1 continues to circulate. Recently, H1N1 has begun to evolve at an increased rate. This evolution has been associated with vaccine failures and dominance of sub-clades with receptor binding domain changes, including S188T and S186P.

The absence of swine sequences related to the 2009 pandemic was notable, and demonstrated a clear shortcoming of H1N1 surveillance in swine. The absence of Texas sequences from the 2010/2011 season raises serious surveillance concerns, which is exacerbated by the withholding of 2011.

This lack of transparency, couple with the decision to leave the 2011/2012 H1N1 vaccine target unchanged continues to be hazardous to the world’s health.

[dothedd]

H1N1 Death Toll Mounts In Chihuahua Mexico
Recombinomics Commentary 21:15
March 28, 2011

Last night, a woman of between 20 and 25 years of age died of H1N1 influenza, as there are already 5 deaths from this disease across the state.

The above translation indicates the death toll in Chihuahua is rapidly rising. All five fatalities have been young adults, and bear striking similarities with the 2009 outbreak, which was almost exactly 2 years ago. The spike in severe and fatal cases at a time when seasonal flu is in decline raise concerns that the H1N1 in northern Mexico represents a variant. The concern was increased by descriptions of cases as atypical pneumonia instead of H1N1.

The sharp rise in hospitalized and fatal cases in Venezuela, as well as additional regions of Mexico, provides additional similarities with 2009. Media reports in Mexico suggests the Chichuahua outbreak is linked to H1N1 in the United States in general, and Texas and New Mexico in particular. However, the CDC has not released any 2011 sequences from either state, and only one sequence for the entire 2010/2011 season has been released.

Similarly, the number of 2011 sequences from the entire United States has been limited because the last release was February 2, 2011 and was largely from December, 2010 collections.

Release of recent sequences from severe and fatal cases in the United States, Mexico, and Venezuela is overdue.

The long delay in the release of US 2011 sequences raises signficant transparency issues.

[dothedd]

H1N1 Outbreak In Chihuahua Mexico Imported From Texas
Recombinomics Commentary 21:15
March 28, 2011

The outbreak of H1N1 influenza that is registered in the state came from a person who traveled to Odessa, Texas, arrived in Chihuahua and spread to other people, said Sergio Piña Marshall, Secretary of Health of the State Government.

"A patient came, got serious and died. It was detected by molecular biology that it was H1N1 virus, were made through the analysis and epidemiological fence family were vaccinated and got control, "said the state official.

The above translation provides additional data supporting a United States origin of the H1N1 outbreak in Chihuahua, Mexico. Data from WHO’s FluNet indicates that influenza in Mexico has been dominated by H3N2 (see graphs below). H1N1 is rarely detected and influenza levels have declined markedly in 2011. In contrast, H1N1 levels in the United States are slightly less than H3N2, and like Mexico, influenza levels in general are now declining significantly.

LINK TO CHARTS:

www.recombinomics.com/News/03281106/H1N1_Mexico_Texas.html

CONTINUED:
In contrast to these prior trends, H1N1 cases in Chihuahua have spiked higher in the past week, including 5 deaths. Moreover, media reports have cited imported cases from Texas and New Mexico, suggesting that the sudden spike in H1N1 cases is linked to these visitors.

Imported H1N1 was cited by many countries in the spring of H1N1, when airport monitoring was increased and most cases were linked to the United States. The outbreak in Mexico appears to be following a similar path.

US sequences from late 2010 are dominated with the sub-clade with S188T and are similar to sequences isolates from the late 2010 outbreak in the UK. However, the case fatality rate for the Chihuahua outbreak is alarmingly high, raising concerns that the H1n1 is a more lethal variant.

The CDC has withheld 2011 H1N1 sequences. None have been released from 2011 collections in Texas and New Mexico, and only one sequence has been release for the entire 2010/2011 season.

Release of these sequences is long overdue.

[dothedd]

H1N1 Deaths Extend To Jalisco Mexico
Recombinomics Commentary 13:30
March 29, 2011


In the Old Civil Hospital of Guadalajara killed a 53-year-old resident of Michoacán and sick with influenza A H1N1. Arturo Rangel, head of the Department of Epidemiology of the Ministry of Health Jalisco (SSJ), reported that this death is the first in the state for this cause

The above translation describes an H1N1 death in Jalisco, which is far south of the five deaths reported in Chihuahua. This is the first confirmed death in Jalisco this year and reflects the differences between the United States and Mexico. In Mexico most influenza A in the 2010/2011 season was H3N2 and the cases peaked in late 2010. Currently there was little influenza circulating prior to the recent outbreak, which was first reported in Chihuahua, but has now spread throughout the country.

The reported deaths lag behind infection, which are producing a high rate of severe and fatal cases, almost exactly 2 years after the pandemic H1N1 was reported in Mexico and the United States. The first confirmed H1N1 case in the US was collected March 30, 2009. At the time previously healthy young adults were dying in Mexico due to atypical pneumonia, which was subsequently confirmed to be pandemic H1N1.
Multiple reports indicate that the outbreak in Chihuahua originated in New Mexico and Texas, where H1N1 levels are markedly higher than Mexico and are similar to H3N2 levels. However, sequence data from New Mexico and Texas has been withheld. There are no public 2011 from either state, and only one sequence for the entire 2010/2011 season, collected November 30, 2010, has been made public. That sequence has S188T, which is present in the dominant sub-clade in the United States and was responsible for the outbreak of severe and fatal cases in the United Kingdom at the end of 2010.

However, the difficulty in sub-typing the cases in Mexico raises concerns that this sub-clade has evolved further in 2011, leading to outbreaks in Mexico and Venezuela.

Release of sequences from severe and fatal cases in all three countries is overdue.