dothedd
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Post by dothedd on Jan 27, 2012 12:56:49 GMT -5
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dothedd
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Post by dothedd on Feb 22, 2012 0:56:05 GMT -5
Absence of Poultry Contact For H5N1 Tangerang Fatality (02/21/12 19:30)
Absence of Poultry Contact For H5N1 Bali Indonesia Fatality (02/21/12 18:00)
Another H5N1 Bali Indonesia Fatality (02/21/12 16:00)
All 40 H5N1 Exposed Ferrets Died (02/21/12 15:00)
H5N1 Wake Up Call (02/19/12/14:30)
Suspect H5N1 Cluster In East Java Indonesia (02/17/12 14:30)
Vietnam H3N2v Case Raise Transparency Concerns (02/15/12 13:15)
Vietnam H3N2v Case Raises Pandemic Concerns (02/15/12 11:00)
H3N2v Swine Flu Case Confirmed In Long An Vietnam (02/15/12 09:15)
Fatal 2012 Guizhou H5 Similar To Kawaoka Reassortant (02/11/12 18:15)
Focus On H5N1 Transmission Changes (02/10/12 19:00)
More Swine H3N2v Match Failures (02/09/12 23:15)
Novel Swine H3 Human Cluster In Vietnam NOT (02/09/12 16:45)
Suspect H5N1 Cluster In Soc Trang Vietnam (02/04/12 06:00)
2012 Guizhou H5N1 Recombination and RBD Changes (02/02/12 21:45)NSABB Comments On H5N1
Transmission Censorship (01/31/12 23:00)
H3N2v Matched In Iowa Swine (01/31/12 16:45)www.recombinomics.com/whats_new.html
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dothedd
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Post by dothedd on Feb 24, 2012 0:02:02 GMT -5
Detail On Fouchier H5N1 Transmission Paper Recombinomics Commentary 17:30 February 22, 2012
Ron Fouchier and colleagues at the Erasmus Medical Centre in Rotterdam, the Netherlands, created transmissible H5N1 by putting two mutations into the HA surface protein of an H5N1 virus, and one into its polymerase enzyme, before exposing ferrets to it. It spontaneously acquired two more significant mutations, and remained lethal.
The above comments strongly suggest that the H5N1 that transmitted in ferrets began with two receptor binding domain changes, Q226L and G228S, as well as PB2 E627K. Passage in ferrets selected two more changes with S227N and Q196R at the top of the list of likely acquisitions, based on a CDC publication in Virology, "In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity"..
The CDC paper looked at quasi-species in A/Vietnam/1203/2004, which had a number of receptor binding domain changes, including S227N and Q196R which synergized with each other. However, Q196R, when combined with two receptor binding domain changes seen in prior pandemics, Q225L and G228S, produced a dramatic change in receptor binding, favoring 2,6 receptors which are present at high levels in human (and other mammal) upper respiratory tracts. This combination led to detectable H5N1 in the upper respiratory tract of ferrets. However, to achieve efficient transmission, the above construct was placed on a clade 2.2 H5 background, A/egret/Egypt/1162/2006, and 6 H5N1 genes from A/Vietnam/1203/2004, which contained PB2 E627K (which was also in the clade 2.2 isolate from Egypt, and the N1 was replaced with an N2 from seasonal H3N2 (A/Brisbane/10/2007). This construct transmitted in ferrets.
Thus, the Fouchier result demonstrated that the requirement for a clade 2.2 genetic background, as well as a seasonal N2 could be eliminated by two changes on H5 when clade 2.1 from Indonesia was used, indicating the creation of a transmitting H5N1 was easier than changes noted in the CDC paper.
Similarly, the Kawaoka paper showed that H1N1pdm09 genes could substitute for the human N2 and the PB1 E627K.
The results confirm that H5N1 transmission requires a minimal number of changes, and reproduction of the results described in the Science and Nature papers can be easily achieved with the public information described above.
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dothedd
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Post by dothedd on Feb 24, 2012 0:03:39 GMT -5
H5N1 Transmission Bioterrorism 101 Recombinomics Commentary 23:00 February 22, 2012
Paul S. Keim, PhD, chair of the National Science Advisory Board for Biosecurity (NSABB), said he was pleased that the international group favored extending a current moratorium on research on lab-generated H5N1 viruses, but he was disappointed that it opposed publishing the papers in redacted form in the near future.
The above comments re-iterate the NSABB position, and raise serious concerns about the competency of the board, which should resign in mass and be replaced with board members who have some familiarity with influenza evolution and associated scientific literature.
Recent reports have indicated that the two receptor binding domain (RBD) changes added to the Fouchier Indonesia clade 2.1 isolate were among the three changes used by the CDC in their recently published study. The two changes, which have always been discussed as a pair, are Q226L and G228S, which have been the subject of discussion and research since H5N1 was reported in humans in the 1997 outbreak in Hong Kong. These are the two changes cited by WHO when they offer assurances that H5N1 has not acquired a “mammalian” RBD.
Similarly, the change in the second gene is almost certainly PB2 E627K, which also has been under discussion and experimentation since the 1997 outbreak. It was present in a sub-set of human cases in 1997, and was also present in the only fatality in the 2003 H7N7 outbreak in the Netherlands, and has been actively researched by the Kawaoka lab. It is also in both H5N1 isolates used in the CDC study.
Thus, the “secret” changes used by Fouchier are the three most well known H5N1 changes. The “news” in the embargoed Science paper is the fact that these three changes, when augmented by two additional changes selected by passage 10 times in ferrets, lead to efficient transmission which maintains lethality in ferrets.
Passage of influenza in animals to select for a more virulent influenza has been cited in publications from the 1930’s and 1940’s. The first human influenza virus was named WS/33 because it was identified in the Wilson Smith lab in 1933. Influenza was ciculating in London, and experimental ferrets (used in distemper studies) developed flu symptoms. One ferret sneezed in the face of a lab technician, Christopher Mathewes, who then developed symptoms. A filtrate from Mathewes was used to infect healthy ferrets, who then developed the flu. WS/33 was subsequently passaged in mouse brain, to create a neurotropic and more virulent influenza, which was name WSN/33 and is currently in use in influenza labs worldwide.
Thus, the “recipe” for a transmitting H5N1 is to start with clade 2.1 from Indonesia, add the three most widely described changes in H5N1 research, and passage the virus 10 X in ferrets.
However, as noted in the CDC paper, as well as the embargoed Nature paper, similar transmissions can be generated by clade 2.2 H5 from Egypt, or clade 2.3.4.2 H5 from Vietnam, when supplemented by clade 1 internal genes and a human N2 or 7 H1N1pdm09 genes, respectively.
The recipes are considered a “state secret” by the US NSABB, and the request for redacted publications should be rejected out of hand.
The current NSABB board is hazardous to the world’s health, and should be replaced.
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dothedd
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Post by dothedd on Feb 24, 2012 0:07:45 GMT -5
Similarities In CDC and Fouchier H5N1 Transmission Papers Recombinomics Commentary 12:00 February 23, 2012
A reverse genetics virus with HA of EG06-196R/226L/228S, the N2 neuraminidase from a human seasonal H3N2 virus, A/Brisbane/10/2007, and 6 internal genes from a clade 1 H5N1 virus, VN04, known to replicate efficiently in ferrets (Maines et al., 2011), was generated and evaluated in the ferret transmission model. As shown in Table 2, both direct contact ferrets that were housed in the same cage with inoculated ferrets became infected, as evidenced by virus shedding and seroconversion results. In addition, viral shedding was also detected in one of two ferrets housed in adjacent cages and exposed only via respiratory droplets.
The above comments are from the CDC paper, “In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity", published online on November 5, 2011 in the journal Virology. As noted above, the three receptor binding domain changes included the two most noted changes in H5N1 transmission discussions, Q226L and G228S, along with Q196R which was present in H5N1 clusters in Iraq and described in previous studies by Kawaoa. These changes were placed on a clade 2.2 H5 (A/egret/Egypt/1162/2006) which was pl aced on a genetic background using human N2 (A/Brisbane/10/2007) 6 H5N1 clade 1 genes (A/Vietnam/1203/2004), which includes PB2 E627K. This combination led to H5N1 transmission in ferrets via respiratory droplets as stated above.
Thus, the “recipe” for H5N1 was published in full in a scientific journal which could be accessed by anyone with an internet connection. It provided full detail on the changes, which have been described in detail previously. Moreover, it used well known isolates which had been sequenced and were publicly available at Genbank or GISAID.
Thus, after the details were published describing the US CDC H5N1 transmission results, the US NSABB requested papers submitted to Nature and Science be delayed and censored. Ironically, the CDC paper was more of a recipe for a bioterrorist because it cobbled together a virus that was unlikely to be created in nature because clade 2.2 is now largely limited to Egypt, clade 1 has never been reported outside of southeast Asia, and the assembled virus included a human N2 gene so technically the transmitting H5N1 was really H5N2.
In contrast, the Fouchier paper, which is delayed at Science, started with changes present in the CDC published paper. It had the two most publicized RBD changes, Q226L and G228S, in HA, as well as the most publicized polymerase change, PB2 E627K. The Fouchier paper placed these three well known changes on an Indonesia clade 2.1 genetic background, which also achieved ferret transmission, while maintaining lethality. Passage in ferrets led to the selection of two additional well known changes, and these two changes are of interest to the scientific community, but of little interest to a bioterrorists, since passage in ferrets is a well known technique which would select the two additional changes.
The Kawaoka paper also used a combination that was more likely to be generated via natural selection because he used a clade 2.3.4.2 H5 from Hanoi (almost certainly A/Vietnam/HN31604/2009) which was placed on an H1N1pdm09 genetic background (A/California/04/2009). It is unclear if he also created Q227L and G228L, but it is well known that H1N1pdm09 PB2 can substitute for H5N1 PB2 with E627K to produce efficient human transmission, and H1N1pdm09 is widespread in humans, swine, and turkeys which provide natural opportunities for the creation of an H5 reassortant with a composition that matches the H5N1 used by Kawaoka in his paper in Nature.
Thus, the two delayed papers demonstrate that a subset of the changes used in the published CDC paper, which were on a clade 2.2 H5 from Egypt, could be placed on a clade 2.1 H5 from Indonesia to create droplet transmission in ferrets, which can also be achieved using a clade 2.3.4.2 H5 from Vietnam (on an H1N1pdm09 background).
Therefore, the NSABB request to redact detail in the Fouchier and Kawaoka papers had no scientific basis, and was appropriately rejected by the scientific community familiar with the detail. The papers at Nature and Science should be published immediately, and the NSABB should get a new board that is more knowledgeable about H5N1 evolution and reasons why a transmitting H5N1 would not be a good choice as a weapon of mass destruction.
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dothedd
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Post by dothedd on Feb 24, 2012 0:10:01 GMT -5
Nature Rejects NSABB H5N1 Censorship Request Recombinomics Commentary 15:30 February 23, 2012
“No one should presume to know all the ways in which influenza virus could be misused, and the motivations for doing so, but the consequences could be catastrophic. There are many scenarios to consider, ranging from mad lone scientists, desperate despots and members of millennial doomsday cults to nation states wanting mutually assured destruction options, bioterrorists or a single person's random acts of craziness. These are low-probability events, but they could introduce a new evolutionary H5N1 seed into the environment that seems not to exist in nature. This might not cause a pandemic instantly, but it could start the virus on a new path for pandemic evolution.”
That is the rationale provided by Paul Keim, acting chair of the US National Science Advisory Board for Biosecurity (NSABB), in response to questions posed by Nature (P. S. Keim Nature 482, 156–157; 2012) about the NSABB's recommendation that recent work on the transmissibility in mammals of artificial strains of avian H5N1 influenza virus should not be published in full.The above comments are from the Nature rejection of the NSABB request to publish a redacted Kawaoka paper after the CDC has already published a similar paper that described viruses and methods that produced an H5 that transmitted in ferrets. Like the CDC paper, the Kawaoka uses as H5 from one clade and places it on a background the includes a human NA flu gene. Moreover, the HA and PB1 changes used in the Fouchier paper were also used in the published CDC paper.
Thus, the recipe for a transmitting H5N1 has been published in Virology, and the variations on the theme have been discussed in the media. The fact that H5 from three different sub-clades (clade 2.2 from Egypt, clade 2.1 from Indonesia, and clade 2.3.4.2 from Vietnam) indicates that the detail in the recipe are irrelevant to would-be terrorist.
Thus, the NSABB ignores the science and relies on fears that have nothing to do with full publication of the 2nd and 3rd transmission experiments. The 1st has been published, and the key details for the 2nd and 3rd have been described.
The Keim arguments demonstrate why the NSABB board should be replaced with scientists who have a better understanding of H5N1 evolution and associated risks.
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dothedd
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Post by dothedd on Feb 28, 2012 20:28:46 GMT -5
H5N1 Bioterrorism Media Myth Recombinomics Commentary 12:00 February 24, 2012
The recommendation to publish flies in the face of pleas for self-censorship from a U.S. government watchdog, the National Science Advisory Board for Biosecurity. The board asked researchers to hold back on releasing crucial “how-to” portions of their work for fear the details would fall into the wrong hands and spark germ warfare on a global scale. Anyone who needs the information for legitimate research, the board reasoned, could make a special request for it.
Not good enough, the WHO committee decided. The new knowledge, every last bit of it, should be freely available. From a public-health perspective, the committee wrote in a statement, full disclosure is the best option.
That conclusion is sending shock waves through the global scientific, epidemiological and counter-terror communities.
The above comments grossly misrepresent the true considerations associated with the release of the full manuscripts at Nature and Science because the media myth ignores the CDC paper published in Virology which provided full details for the creation of an H5 that transmits in ferrets via droplets. Thus, any would be bioterrorist would already have a “recipe” prior to the NSABB request. Moreover, the request also came after Ron Fouchier presented his data at a scientific meeting, which has been widely discussed in the media and on scientific forums. Moreover, recent reports indicate the three changes he introduced onto an H5N1 clade 2,1 isolate from Indonesia, HA Q226S and G228L as well as PB2 E627K, were all included in the CDC publication. Thus, the recipe for transmission (add the above three “mutations” to an Indonesian H5N1 and then passage it in ferrets 10X) was public prior to publication, as was the formula for the Yoshi Kawaoka paper, which used a clade 2.3.4.2 isolate from Vietnam as an H5 source, which was placed on an H1N1pdm09 genetic background.
The detail that the NSABB wanted to censor was unnecessary for the creation of a transmitting H5N1. The two labs involved have published extensively previously, so the materials and methods were public and well known, as were the three “mutations” introduced by the CDC in their published studies, as well as the Fouchier delayed study. It is likely that the H5 used by Kawaoka also had some or all of the same changes. The fact that three different labs used different H5 sequences which were supported by a range of associated flu genes, clearly demonstrates that the public information available today allows for the creation of a transmitting H5N1.
The NSABB request did little to thwart bioterrorism. H5N1 is not a bioweapon of choice because it can’t be control. The NSABB request has elevated this poor choice to a level of importance that will increase the likelihood of a terrorist of rogue state will attempt to create a transmitting H5N1. The NASBB request also exposed the glaring lack of expertise on their board, include gross mismanagement leading to absurd requests that made little sense from a scientific or operational point of view.
The request has led to delays in release of critical information necessary for effective surveillance and analysis of a naturally evolving H5N1, as well as a long list of media myths which will significantly impact the much need understanding of the H5N1 threat, which is now greater than ever.
The NSABB would better serve the public by forming a new board that emphasized the need for a serious vaccination campaign, which would significantly decrease the H5N1 threat, regardless of source.
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dothedd
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Post by dothedd on Feb 28, 2012 20:37:49 GMT -5
All 2011 H5N1 Cases In Egypt Are Clade 2.2.1 G Recombinomics Commentary 22:30 February 24, 2012
The recently released WHO update on pandemic vaccines contained additional information on human H5N1 cases in Egypt. Although Egypt has the second highest number of confirmed H5N1 cases in the world (the 161 is 24 fewer than Indonesia), the most recent sequence, A/Egypt/N04434/2010, is from a March 31, 2010 collection. It was released with 18 additional sequences from 2009 and 2010 (collection dates between June 16, 2009 and March 31, 2010. The sequences were remarkable since all 19 sequences were clade 2.2.1 G (labeled as clade 2.2.1 in WHO updates).
Although this sub-clade, which included a 3 BP deletion (S133del), was first detected in late 2006, it attracted interest because of association with mild cases in the spring of 2007. The interest increased in early 2009 when a large series of mild cases in toddlers was reported, which lowered the case fatality rate for cases in the 2009 calendar year to almost 10% (4/39), in marked contrast to an earlier rate of approximately 40% in Egypt. Moreover, a bioinformatic analysis of H5N1 in Egypt noted similarities between clade 2.2.1 G sequences and seasonal H1N1.
The presence of clade 2.2.1 G in all 19 cases was surprising, because poultry cases had evolved into two major sub-clades (2.2.1 G and 2.2.1 F). Clade 2.2.1 F (labeled as 2.2.1.1 in WHO updates) emerged in late 2007 in vaccinated flocks. However, although the frequency of this sub-clade in chickens has increased, there is only one reported human case, A/Egypt/3300-NARMRU3/2008.
In 2010 and 2011 the H5N1 CFR increased to 40% in Egypt, which generated additional interest in recent cases. The table in the latest WHO report lists 5 new human cases, and all were designated as clade 2.2.1. Four (A/Egypt/N09966/2011, A/Egypt/N10621/2011, A/Egypt/N11126/2011, A/Egypt/N11470/2011) were listed in the phylogenetic tree, and all four mapped with clade 2.2.1 G sequences, including 7 additional isolates listed in the prior WHO report (A/Egypt/N0423/2011, A/Egypt/N0544/2011, A/Egypt/N6322/2011, A/Egypt/N6774/2011, A/Egypt/N6828/2011, A/Egypt/N7562/2011, A/Egypt/N7724/2011). In addition, a prior WHO update also included an additional isolate, A/Egypt/N010360/2011, collected after the samples that yielded the public sequences, which was also clade 2.2.1 G.
The most recent 31 public sequences have all been clade 2.2.1 G, even though clade 2.2.1 F has been detected since late 2007, and only one clade 2.2.1 F case has been reported (in 2008).
The absence of clade 2.2.1 F in any human cases since 2008 raises concerns that clade 2.2.1 G is well adapted to human infections, and the linkage to poultry in the area is more closely related to testing requirements that sourcing of the infection.
Concerns of adaptation are also increased by recently released sequences from Egypt from 2010 poultry isolates, which have PB1 and PB2 recombined sequences with regions from H1N1pdm09 and seasonal H1N1. Moreover, the Kawaoka paper on H5N1 transmisison used H5 on an H1N1pdm09 genetic background.
Sequences from internal genes from human cases in Egypt have been limited to those from 2006. Sequences from internal genes of the human cases should be generated and released immediately.Related links within the text: www.who.int/influenza/vaccines/virus/201202_h5_h9_vaccinevirusupdate.pdfwww.ncbi.nlm.nih.gov/nuccore/CY062486www.biomedcentral.com/1472-6807/9/21www.ncbi.nlm.nih.gov/nuccore/FJ226061
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dothedd
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Post by dothedd on Feb 28, 2012 20:41:44 GMT -5
Egypt H5N1 PB1 Recombination With H1N1pdm09 Recombinomics Commentary 10:30 January 17, 2012
The recently released H5N1 sequences from Egypt have clear examples of recombination in PB1 and PB2 involving seasonal and pandemic acquisitions. These isolates were discussed last year in the PLOS paper “The Epidemiological and Molecular Aspects of Influenza H5N1 Viruses at the Human-Animal Interface in Egypt” which briefly discussed the sequences and provided Genbank accession numbers. However, the sequences were not released until last week.
The paper included a phylogenetic tree for the HA genes, which were similar to other public H5N1 clade F sequences from Egypt, which are vaccine resistant. The paper also discusses human H5N1 in Egypt, which have been clade G (since mid-2009). However, there have been no human H5N1 sequenced from Egypt since March, 2010. At that time most of the cases were mild and in children, which lowered the cases fatality rate in Egypt to less than 10%. The cases with the 3 BP deletion had an bioinformatic profile which has similar to seasonal H1N1 and the 3 BP deletion (133del) was also found in H5N1 sequences in China and Indonesia (see slide 12 from OneHealth workshop; labeled as 133del in clade C).However, more recent cases have been in adults and fatal, raising concerns that the more recent cases involve the vaccine resistant clade F.
The PB1 sequence has clear evidence of recombination. Two of the isolates described in the above paper and displayed on the HA tree were A/chicken/Egypt/Q1011/2010 and A/chicken/Egypt/Q1185/2010 had identical HA sequences, which was also true for the newly released PB1 sequences for Q1011 and Q1185. However, the first 60 nucleotide are identical to H1N1pdm11. The H5N1 sequence for closely related sequences, including the two most closely related sequences in the above paper (A/chicken/Egypt/1/2009 and A/chicken/Egypt/Q1182/2010), have 8 differences, clustered between positions 15 and 53 (T15C, T24C, G26A, G30A, A32T, T37C, T47C, T53C), clearly signal homologous recombination between PB1 H5N1 and H1N1pdm11.
This recombination is also supported by the PB2 sequences, which have additional examples of recombination with H1N1pdm09 sequences as well as seasonal H1N1 and H3N2 sequences, raising concerns of human adaptation.
Moreover, the first 60 nucleotides of A/chicken/Egypt/Q1182/2010 and A/chicken/Egypt/Q1185/2010 exactly match recent H3N2v sequences from Indiana (A/Indiana/08/2011 and A/Indiana/10/2011) and Pennsylvania (A/Pennsylvania/09/2011 and A/Pennsylvania/11/2011).
Therefore, NAMRU-3 and/or the US CDC, who receives samples from NAMRU-3, should immediately release full sequences for human H5N1 cases in Egypt.
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dothedd
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Post by dothedd on Feb 28, 2012 20:44:45 GMT -5
2011 Human H5N1 Sequence Cluster In Egypt Recombinomics Commentary 14:45 February 25, 2012
In 2011 there were 39 H5N1 confirmed cases (15 fatal) in Egypt and 11 are listed in the latest WHO tree. Although the sequences and associated demographic information (age, gender, and location) have been withheld by NARMU-3 / CDC, the samples are numbered sequentially for each calendar year, so time gaps between collections can be approximated by sample number gaps, which are included in the name of the isolates.
One sequence cluster is created by A/Egypt/N0544/2011, A/Egypt/N6774/2011, A/Egypt/N7724/2011, which includes an isolate from the beginning of 2011 as well as two collections from the spring / summer.
These three human sequences are on a branch which includes two poultry sequences, A/chicken/Egypt/11506sf/2011 and A/chicken/Egypt/VIR4453-138/VRLCU/2011. The sequence for the latter is at GISAID and the H5 sequence has two recently acquired non-synonymous changes (R143K and D454N), which are unlikely to significantly affect receptor binding. However, this clustering of sequences from samples collected over a long time frame in 2011 raises concerns that this sub-clade is transmitting human to human.
This concern is increased by 2010 poultry sequences which have recombined PB1 and PB2 which have acquire H1N1pdm09 and seasonal H1N1 sequences. The most recent human H5N1 sequences from Egypt were the 19 released by NARMRU-3 almost 2 years ago. However, only HA and NA sequences were released. The most recent internal gene sequences from cases in Egypt are from 2006.
The recent H5N1 transmission paper by the CDC used an Egypt H5 (from a 2006 isolate from an egret, A/egret/Egypt/1162/2006). The current human sequences in Egypt have the 3 BP deletion and similarities with seasonal H1N1, and therefore may transmit more easily than the egret sequence. Similarly, the delayed Kawaoka paper uses H5 on a background with H1N1pdm09 genes, raising concerns that PB1 and PB2 sequences which have recombined with H1N1pdm09 and seasonal H1N1 may transmit more efficiently.
Thus, full sequences from human H5N1 cases should be released immediately by NARMU-3 and/or the CDC.www.recombinomics.com/News/02251201/H5N1_Egypt_2011_Seq_Cluster.html
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dothedd
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Post by dothedd on Feb 28, 2012 20:56:26 GMT -5
2011 Human H5N1 Sequence Indentities In Egypt Recombinomics Commentary 16:45 February 25, 2012
Although Egypt has the second highest number of confirmed H5N1 cases in the world (161), as well as the most since 2009 (110), it has been almost two years since any human sequences were released by NAMRU-3. The most recent human sequence is from A/Egypt/N04434/2010, which was from a March 31, 2010 collection. NAMRU-3 release of human H5N1 sequence data has become increasingly less transparent since they became a WHO regional center. Similarly, the US CDC, another WHO regional center, has failed to release H5N1 sequences from cases in Egypt, even though NAMRU-3 routinely sends samples to the CDC.
However, since both agencies are WHO regional centers, the withheld sequences are used to create clade 2.2 phylogenetic trees used in WHO updates of vaccine targets. The latest WHO update includes eleven 2011 isolates from human cases in Egypt. The phylogenetic analysis demonstrates a cluster for three of the 2011 isolates from early 2011.
However, the two most recent isolates on the tree, A/Egypt/11126/2011 and A/Egypt/11470/2011, have sequences which are identical, even though the sample numbers indicate they were collected weeks apart near the end of 2011, supporting human to human transmission.
The above two sequences are a concern because they form a branch with no poultry isolates and the length of the branch stem signals multiple changes, yet the two human sequences are identical.
The WHO tree only has 11 of the 39 confirmed human cases in 2011, so it is unclear if this cluster is larger than the above two cases, or if there are closely related avian sequences, which is why the full set of 2011/2012 sequences should be immediately released by the CDC or NAMRU-3, who clearly have much more data than is indicated on the tree in the WHO update.
This lack of transparency, which follows the NSABB request to censor the latest H5N1 transmission papers, continues to increase pandemic concerns and remain a hazard to the world's health.
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dothedd
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Post by dothedd on Mar 10, 2012 16:55:06 GMT -5
United States H3N2 Low Reactors Explode In Week 8 FluView Recombinomics Commentary 19:00 March 2, 2012
The CDC week 8 FluView reports a dramatic spike in H3N2 low reactors. In week six, 6/263 (2.3%) H3N2 isolates tested as low reactors. In week seven the frequency doubled to 4.8% (14/291) and in today’s report the frequency spiked to 21.6% (88/407). Thus, for the week 8 report there were 116 new H3N2 isolates tested, and 63.8% (74) tested as low reactors.
The CDC has released 22 US H3N2 sequences from 2012 (collected between Jan 1 and Jan 23) and none are listed as low reactors (although most have no test result listed). However, several have acquired H3N2v polymorphisms (via recombination).
The most dramatic example is A/South Carolina/01/2012, which was collected on Jan 4. Most of the newly acquired polymorphisms in the HA and MP sequences trace back to H3N2v, indicating H3N2v is widespread in the United States, although the last reported cases were from the West Virginia cluster in December, 2011.
Release of sequences from the 88 H3N2 low reactors would be useful.
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dothedd
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Post by dothedd on Mar 10, 2012 16:56:30 GMT -5
H3N2v Acquisitions In United States Seasonal H3N2 Recombinomics Commentary 22:15 March 2, 2012
The CDC has recently released 22 sets of 2012 seasonal H3N2 sequences from cases in the United States. Several of the isolates have recenty acquired polymorphisms which are shared with 2011 H3N2v human cases. 12 such cases were from 2011 infections, including clusters in Iowa and West Virginia. However, no cases have been reported in 2012, raising sensitivity concerns for the current PCR test, which relies on cross reactivates with seasonal H3N2 and H1N1pdm09 NP. Although a sub-set of the 12 confirmed cases were H3 and NP positive, most cases were identified via sequence analysis of samples from patients who had exposure to swine or confirmed H3N2v cases.
Sequence analysis of seasonal H3N2 provides an alternative approach for the identification of H3N2v acquisitions, which occur in hosts infected with seasonal H3N2 and H3N2v (via recombination). Several of the seasonal H3N2 cases have such acquisitions, but the profile of a case (40F) from South Carolina (A/South Carolina/01/2012) is striking. The HA sequence had 5 recent acquisitions (G138T, A246G, A335T, T351C, C379T), and 3 (A246G, T351C, C379T) were also in H3N2v isolates (see list here here here). Similarly, the MP sequence had 3 recent acquisitions (A48G, G324A, C857A), and 2 (A48G, G324A) were also in H3N2v isolates (see lists here here).
Thus, there is little doubt that H3N2v is circulating in the United States, in spite of a lack of CDC reports on such cases.
However, today’s week 8 CDC FluView reports a dramatic spike in low reactors (62.8% of the newly reported H3N2 cases were low reactors). In the past H3N2v sequences have been identified in routine surveillance, including a low reactor result in antigen characterization tests (which is expected for H3N2v since the H3 has evolved in swine and has evolved from seasonal H3 circulating in the 1990’s). The current FluView is silent on the sequences associated with the 88 H3N2low reactors cited in the week 8 FluView.
Release of sequences from these low reactors would be useful. None of the 22 2012 H3N2 sequences at GISAID are designated as low reactors (although only 7 have listed antigen characterization data indicated and all are designated as Perth/16-like).
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dothedd
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Post by dothedd on Mar 10, 2012 16:58:31 GMT -5
Full Fouchier Formula for H5N1 FerretTransmission Recombinomics Commentary 09:00 March 3, 2012
Actually, though, it's the wild-type virus that's odd. In general, when you give ferrets most kinds of H5N1 in their noses, said Fouchier, "they don't get sick at all". The strain he used, collected in 2005 in Indonesia, is known for causing unusual brain-related disease when put in ferrets' noses. Perhaps the mutant has lost this: the ferrets who got it in their noses, either by breathing it in or because it was put there, just got flu.
The above comments, as well as additional remarks, indicate the H5N1 used in the Ron Fouchier ferret transmission studies was A/Indonesia/5/2005 from the first confirmed human cases in Indonesia and the WHO clade 2.1 vaccine target. The use of this H5N1 in prior ferret studies was described in a Fouchier 2011 American Journal of Pathology paper, “Pathogenesis of Influenza A/H5N1 Virus Infection in Ferrets Differs between Intranasal and Intratracheal Routes of Inoculation”. That paper described different pathologies linked to various inoculation routes of A/Indonesia/05/2005, which match the descriptions in the recent report.
Thus, the Fouchier clade 2.1 Indonesian H5N1 virus could kill ferrets and cause neurotropic effects, but the transmitting H5N1 did not kill ferrets. These results are similar to another published paper, which used a 2006 clade 2.2 virus from Egypt. That CDC paper gave detailed descriptions for the creation of an H5N1 that also transmits in ferrets. Similarly, the Yoshi Kawaoka paper delayed at Nature uses an H5 from another H5N1 sub-clade (2.3) which was placed on an H1N1pdm09 genetic background (as described in a prior publication) to also transmit in ferrets.
Thus, the full recipe for two of the three transmission studies is now known, as is the general formula for the third study. Fouchier took a 2005 clade 2.1 isolate, A/Indonesia/05/2005, added three (HA Q226L, G228S; PB2 E627K) of the four changes in the CDC paper, and passaged the H5N1 in ferrets 10 times. The CDC took a 2006 clade 2.2 isolate, A/egret/Egypt/1162/2006, added three HA changes, Q196R, Q226L, G228S and placed it on a clade 1 genetic background, A/Vietnam/1203/2004, which had PB2 E627K, and added seasonal N2 gene from A/Brisbane/10/2004. Kawaoka took a 2009 clade 2.3 isolate, A/Vietnam/HN31604/2009, placed it on an H1N1pdm09 background (A/California/04/2009) and probably added the same two HA changes used in the Fouchier and CDC papers (Q226L and G228S).
Recent comments by some of the NSABB board members clearly demonstrates a profound lack of understanding of the published data, which is why the papers should be published in full immediately, and the NSABB board should be replaced with scientists more familiar with the scientific literature on H5N1 transmission.
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Post by dothedd on Mar 10, 2012 17:00:43 GMT -5
Three Recent H5N1 Cases In Dhaka Bengladesh Recombinomics Commentary 19:00 March 5, 2012
Detection of three new human infections with the deadly H5NI strain of bird flu in a week has set alarm bells ringing as scientists have found evidence of the virus in the live-bird market in crowded Dhaka.
The above comments describe three confirmed H5N1 cases in wet market workers in Dhaka, Bangladesh. The first case has been WHO confirmed and has recovered, but the three 2012 cases has doubled the number of H5N1 confirmed cases in Bangladesh. This significant up tick is almost certainly due to clade 2.3.2.1 which has now expanded its geographic spread and was confirmed in crows in India earlier this season. New sub-clade migrate into India and Bangladesh each season, which are closely related to each other.
The first human clade 2.3.2 was described in media reports in the spring of 2008 when a culler (soldier) developed symptoms and was H5 PCR confirmed. However, South Korea denied the culler was infected with clade 2.3.2 because prior human infections in China were clade 2.3.4. Moreover, South Korea used the failure to isolate the H5 virus as an excuse for not filing a report. However, the sequence had V223I and M230I, which were in the Gharbya cluster and fatal clade 2.3.2.1 cases were subsequently reported in China, including the recent case from Shenzhen who had no reported poultry contact (but had wild bird exposure).
The appearance of clade 2.3.2 in south Asia raised concerns of additional human cases, and the three confirmed cases in Bangladesh are likely confirmation of the realization of such concerns.
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Post by dothedd on Mar 10, 2012 17:05:07 GMT -5
Flu-like Death Cluster In Calvert County Maryland Recombinomics Commentary 17:30 March 6, 2012
The first patient, an 83-year-old woman, became sick on Feb. 23. Three of her children, a son and two daughters all in their 50s, arrived on Feb. 28 to take care of her.
The mother died on March 1. One daughter, 56, and her son, 58, both died on Monday while a third daughter, 51, remains at Wash Hospital Center in critical condition.
The above comments describe a death cluster in Calvert County, Maryland. Anecdotal reports also describe a fifth victim, the funeral director who had contact with the bodies. These reports also indicate fatal cases were coughing up blood and the funeral director was hospitalized with breathing difficulties.
More information on testing would be useful.
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Post by dothedd on Mar 10, 2012 17:10:04 GMT -5
Flu-like Death Cluster In Calvert County Maryland Grows Recombinomics Commentary 18:30 March 6, 2012
These people that died apparently went downhill fast and started coughing up blood and then their organs were shutting down. From my understanding it all happened in a matter of 2 days from onset of symptoms. The 5th person is a funeral director that was in contact with the bodies, but I haven’t heard anymore on his condition but after he was in contact with the bodies he soon had a tightness in his chest and trouble breathing
The above comments are anecdotal and posted in response to one of several media reports which have cited 4-5 people who were hospitalized including 3-4 who have died with flu-like symptoms, including pneumonia. The cases are under investigation by health and criminal agencies. The fatality rate in the family appears to be in the 75-100% range, raising serious concerns.
Calvert County is adjacent to the Delmarva peninsula, which has a high poultry population, while the Chesapeake Bay region attracts wild birds. In Asia, clade 2.3.2.1 has expanded is geographical range via infections in wild birds, and this clade has been linked to fatal H5N1 infections, although not in a cluster as large as the one reported for Calvert County.
Similarly, the CDC reported a spike in H3N2 low reactors, but the relationship between these low reactors and seasonal or variant (H3N2v) isolates remains unclear. However, neither has been linked previous with a death cluster of this size. Recent discussions of H5N1 transmission have invoked bioterrorism, which may be the cause of the criminal investigation of a death cluster near Washington, DC.
More detail on the above anecdotal report, as well as symptoms and testing on the fatal cases, would be useful.
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dothedd
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Post by dothedd on Mar 10, 2012 17:18:32 GMT -5
Maryland Flu Death Cluster Coughing Blood At Admission Recombinomics Commentary 01:30 March 7, 2012
Tests confirmed the siblings who died had a type of flu virus known as influenza A, and each also acquired a serious staph infection, Orlowski said. She said it was unlikely the infection was acquired in the hospitals because the siblings arrived coughing blood, adding: “It’s likely they came to the hospital with the infection, which is what caused the cough and fever."
The above comments confirm that the death cluster in Calvert County, Maryland were due to influenza A and the siblings arrived at the hospital coughing blood, as indicated in the earlier anecdotal report, which also claimed that the funeral director was hospitalized.
The initial Clavert County announcement described five cases, including four from one family. The reasons for the downgrade to four remain unclear. However, the attack rate for the affected family is 100% and the case fatality rate is at least 75%.
These high rates and the coughing of blood raise concerns that the infection is due to H5N1 or a virulent H3N2v, both of which have D225G (as does H1N1pdm09 in severe and fatal cases), which is associated with lung infections followed by organ failure (which was also described in the anecdotal report)
Detail on the serotype of the cluster followed by sequence data would be useful.
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dothedd
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Post by dothedd on Mar 10, 2012 17:20:54 GMT -5
High CFR In Maryland Cluster Raises H5N1 Concerns Recombinomics Commentary 11:00 March 7, 2012
Dr. Gio Baracco, associate professor of infectious diseases at the University of Miami’s Miller School of Medicine, speculated, based on the very limited amount of information available, that the cause is non-infectious and could be something environmental.
“The reason is that for most infections, transmission rate is not 100 percent and the fatality rate is not 100 percent,” he said. If the woman’s hospitalized daughter dies, the case fatality rate will be 100 percent, he explained.
The above comments note the high case fatality rate (CFR) in the flu cluster in Calvert County, Maryland and suggest the deaths were not due to an infectious agent. However, most or all of the symptomatic family members have tested positive for influenza A which has raised H5N1 concerns due to the high CFR and the reports of cases coughing up blood upon admission. Human H5N1 cases have a high CFR in part because of D225G and recent transmission studies have demonstrated the ability of H5N1 to transmit in a ferret model using three different H5s (clade 2.2 from Egypt, clade 2.1 from Indonesia, clade 2.3 from Vietnam), all of which have D225G.
Moreover, clade 2.3 has moved into migratory birds and expanded its geographical reach to south Asia and Europe, raising concerns of expansion into North America. The index case for the Maryland cluster was in a rural region adjacent to the Chesapeake Bay, which is home to a large migratory bird population at this time of year. Similarly, the adjacent Delmarva peninsula has a high density of poultry farms, although no H5N1 has been reported in poultry in the Americas.
However, D225G has also been reported in severe and fatal H1N1pdm09 cases, including those in Ukraine in 2009 as well as the Duke Medical Center death cluster. However, most fatal H1N1pdm09 cases are in patients under the age of 65, and the index case in Maryland was 81, decreasing the liklihood pf H1N1pdm09 involvement.
A more likely possibility would be H3N2v which also has D225G. Although only 20 confirmed cases have been reported in the United States, there is no widely available direct test for H3N2v. Although it can be detected in various influenza A tests, additional PCR testing depends on cross-reactivity with seasonal H3 or H1N1pdm09 NP targets, and levels are likely markedly higher than those reported. Moreover, there have been widespread reports of pneumonia throughout the United States, including Maryland, raising concerns that a more virulent H3N2v may appear in human populations.
An increase in H3N2v cases is also supported by the explosion of H3N2 low reactors in the week 8 CDC report. H3N2v has a human H3 that jumped to swine in the 1990’s and therefore would produce a low reactor profile in the CDC’s antigen characterization test as seen in 63.8% of the newly reported case last week. The CDC was silent on the spike in low reactors, and none of the 22 isolates from 2012 were listed as low reactors, although all were collected in January and only 1/3 had antigen results and all were Perth/16-like.
Samples from the Maryland death cluster have been sent to the CDC for analysis. Release of sequences from the current cluster as well as the low reactors listed in the week 8 FluView report would be useful.
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Post by dothedd on Mar 10, 2012 17:22:15 GMT -5
Maryland Denies Additional "Similar Clusters" of Deadly Flu Recombinomics Commentary 14:30 March 7, 2012
As the Calvert County Health Department has reported, DHMH is aware of four cases in adults from a single family with severe respiratory illness; three have died. At this time, no other similar clusters have been reported from Calvert County or elsewhere in the state.
The above comments are from the latest update from the Calvert County Health Department and DHMH. It now notes that no similar clusters have been detected, which leaves open the definition of a “similar” cluster, as well as the status of individual cases. The reported cluster is unusual because the attack rate in the family was 100% and the case fatality rate was 75% with the sole survivor still hospitalized. Thus, it is unclear if clusters with no fatailities or fewer fatalities are considered similar. An earlier anecdotal report indicated the funeral director was hospitalized with symptoms, and the initial press release on the outbreak cited 5 cases (which has since been downsized to 4). The same anecdotal reported indicated cases were coughing up blood and rapidly declined, which has subsequently been confirmed in media reports, which also cited additional cases, including at least one fatality under investigation. The serotype of the influenza A positive samples has yet to be disclosed, which is also true for the number of cases under investigation, regardless of cluster status.
An update on the serotype, as well as the number of suspect cases under investigation would be useful.
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Post by dothedd on Mar 10, 2012 17:23:23 GMT -5
Maryland Death Cluster H3 Confirmed Recombinomics Commentary 16:30 March 7, 2012
Initial testing of two of four family members in Lusby, three of whom have died, suggests that that the serious lung infection suffered by all four was a complication of seasonal flu. A fourth family member remains hospitalized at Washington Hospital Center and is improving.
The above comments from the latest update from the Calvert County Health Department website indicate the Calvert County, Maryland death cluster was linked to seasonal influenza. A call to the health department indicates the state lab obtained an H3 serotype. However, it remains unclear if the H3 is Perth/16-like and recognized by the current H3N2 vaccine or a "low reactor” as described in the week 8 FluView.
Moreover, it remains unclear if this is a Perth/16 variant or an H3N2v which gives and H3 positive on the CDC PCR test. H3N2v has D225G, which is associated with patients coughing up blood.
More detail on the PCR testing and sequences from the CDC would be useful.
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Post by dothedd on Mar 10, 2012 17:24:27 GMT -5
Another Fatal H3 Case In Maryland? Recombinomics Commentary 18:45 March 7, 2012
My 33 year old sister died on Tuesday morning in BWMC (old North Arundel) she got sick over the weekend was coughing up blood by Monday and died 4:30 am Tuesday. Hospital said it was pneumonia. but It happened so fast. sounds just like what these people had.
The above comments represent another anecdotal report on flu-like cases in the Washington DC area. The above fatal case (33F) was said to be at the Baltimore Washington Medical Center, just south of Baltimore, and was in response to comments on the Calvert County cluster, which has been H3 confirmed.
Although these comments are unconfirmed, the earlier description of the Calvert cluster coughing up blood was confirmed by subsequent media reports.
Although an earlier press release denies additional similar clusters, the above description appears to be a single case that was not part of a reported cluster.
More information on suspect cases in the Washington DC area would be useful, as would sequence information and more detail on the H3N2 low reactors described in the week 8 FluView.
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Post by dothedd on Mar 10, 2012 17:26:10 GMT -5
H3 "Strain" In Maryland Death Cluster Remains Unclear Recombinomics Commentary 18:45 March 7, 2012
State health officials say today that lab tests confirm that two of the members of a Calvert County family who died early this week of severe respiratory illness had Influenza H3, a strain of the flu that has been going around this season.
The above comments confirm the Recombinomics commentary published this morning on the H3 sero-type of the HA from the fatal Calvert County, Maryland cluster. However it is unlikely to be the “strain” of flu that has been going around this season.
Recombinomics called the Calvert County Health Department as well as the Maryland Department of Health and Mental Hygiene, and the US CDC to get a clarification on the testing that led to the report that the influenza A was seasonal flu, since the CDC has reported an explosion of H3N2 low reactors in the week 7 and week 8 FluView reports. The antigen characterization data indicated an new H3 had replaced the H3N2 strain that had been circulating earlier this season.
The CDC did not comment on this explosion and therefore it was unclear if the low reactors were a drift variant of the current seasonal H3N2 vaccine target, Perth/16, or were widespread H3N2v, which would also generate a low reactor result.
Moreover, the CDC PCR test distributed to state labs can identify H3N2v under ideal conditions, but most confirmed H3N2v cases gave negative, inconclusive, or seasonal H3 results, and H3N2v was confirmed by CDC sequencing.
The cluster in Maryland was determined to be H3 by the Maryland state lab, which was used for this morning’s announcement by Calvert County. Media at the Maryland state lab suggested I e-mail the specific testing questions, and also noted that the best source of information would be the CDC, who had already been asked via cell phone and e-mail about testing and the relationship between the H3 result generated by the Maryland state lab and the low reactors reported by the CDC, which may be H3N2v.
As of this commentary, neither agency has responded to the e-mailed questions, and the relationship between the H3 in the death cluster, the low reactors reported by the CDC, and H3N2v remains unclear, but the likelihood that the H3 “strain” in the Maryland death cluster matches the seasonal H3N2 dominant in the US in 2011 and early 2012 is extremely small.
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dothedd
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Post by dothedd on Mar 10, 2012 17:27:32 GMT -5
Growing H3 Maryland Death Cluster Raises Concerns Recombinomics Commentary 12:00 March 8, 2012
"We don't yet know what this is about," Orlowski said. "She has a fever and a cough. They were all together at a funeral last week. Individuals could easily have caught the flu–a large gathering of people, hugging, consoling, possibly sharing a meal."
"If the individuals had the flu at that time it is quite likely that others are showing signs of the flu," says Orlowski. 'If I was in that family and felt ill, I would seek medical attention early."
The above comments strongly suggest that the sister of the index case (81F) for the Calvert County, Maryland cluster is also infected by the H3 confirmed in her sister, nieces, and nephew. This case raises serious concerns about the Calvert County announcement of no new cases or clusters, which appears to be dependent on lab confirmation and thus, is ignoring symptomatic contacts, include the above hospitalized case.
Moreover, the above case has fever in cough, in contrast to media reports claiming that the only symptom upon hospitalization was fever.
Moreover, the funeral cited above is almost certainly the March 3 funeral (in Lusby) for a nephew, who was killed while falling a neighbor’s tree, also in Lusby. Thus, the transmission chain appears to be active, and new cases should be developing symptoms this week.
More information on cases under investigation would be useful, as would detail on the H3 testing (which has been withheld), including full sequences for all eight gene segments.
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Post by dothedd on Mar 10, 2012 17:29:01 GMT -5
Withheld Maryland Death Cluster Data Raises H3N2v Concerns Recombinomics Commentary 15:00 March 8, 2012
Testing by the DHMH Laboratories Administration has confirmed that two of the cases had Influenza H3, a strain of Influenza A that has been circulating this season.
The above comment from the DHMH press release updating the Calvert County, Maryland death cluster is carefully worded and does not say that the H3 is seasonal H3N2, and may in fact be H3 from H3N2v. The state labs can only do PCR testing, which can produce a pattern (seasonal H3 and H1N1pdm NP positive) that is suggestive of H3N2v, but confirmation requires sequencing (which is done by the CDC). Although there have not been any reported H3N2v cases in 2012, the second case in Indiana, the two cases in Maine, the three cases in Iowa, and the two cases in West Virginia were all from H3N2v circulating this season (and thus H3N2v has an H3 that has been circulating this season).
Recombinomics requested (via phone discussions and detailed e-mails sent yesterday morning) a clarification on PCR and/or sequencing result, and neither DHMH nor the CDC has responded at this time.
This failure to respond has increased concerns that the influenza H3 cited above is in fact H3 from H3N2v.
A response to the above written requests, as well as release of sequence data from isolates from the above cluster, would be useful.
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Post by dothedd on Mar 19, 2012 23:41:45 GMT -5
More H5N1 Links Between Indonesia and Egypt
Recombinomics Commentary 19:15
March 14, 2012
Recently, the Indonesian Research Center Institute For Veterinary Science in Bogar, West Java released a series of 2007/2008 H5N1 chicken sequences (A/chicken/West Java/Smi-Sud1/2007, A/chicken/West Java/Smi-Hj18/2007, A/chicken/West Java/Smi-M6/2008, A/chicken/West Java/Smi-M1/2008, A/chicken/West Java/Smi-Biot/2008) which had much in common with earlier public (A/chicken/Indonesia/Timika_10/2006, A/chicken/Indonesia/Tanggerang_10/2007, A/chicken/Indonesia/Sukabumi_10/2007, A/chicken/Indonesia/Sukabumi_3/2007) and private (A/Ck/West Java/M05/2008, A/Ck/West Java/M06/2008, A/Ck/West Java/M07/2008 - see slide 12) clade 2.3.1 sequences from West Java, as well the dominant sub-clade 2.2.1 G circulating in Egypt.
The sequences in Indonesia evolved from a 2006 sub-clade represented by (A/Chicken/West Java/SMI-CSLK-EC/2006, A/chicken/West Java/SMI-CSLK-EB/2006, A/Chicken/West Java/PWT-WIJ/2006, A/Chicken/West Java/SMI-PAT/2006, A/chicken/Jakarta/DKI-Nurs/2007). The more recent sequences acquired a number of changes including a 3 BP deletion (S133del) as well as a non-synonymous change C500T (I151T).
However, both of these acquisitions, as well as a synonymous change, C321T, which was in the earlier sequences from the West Java sub-clade, were appended onto an Egyptian clade 2.2.1 genetic background to create clade 2.2.1.G, which was first reported in Egypt in early 2007 and has become the dominant sub-clade in Egypt. This sub-clade became prominent in human cases in early 2009 where almost all cases in Egypt were in toddlers. These cases were mild and only 4 of the 39 H5N1 confirmed cases in Egypt died (in contrast to the 40% case fatality rate in Egypt before and after the 2009 series). Moreover, since mid-2009, all reported human H5N1 sequences in Egypt have been clade 2.2.1 G.
These new sequences add to the compelling data supporting influenza evolution via recombination, which places the same polymorphisms on multiple genetic backgrounds. This rapid evolution has significance with regard to transmitting H5N1. Rubin Donis from the US CDC published a paper on modifications of a clade 2.2 isolate from Egypt, which included three changes two receptor binding domain changes on HA (Q226L and G228S) as well as PB2 E627K. Ron Fouchier from the Erasmus Medical Centre in the Netherlands placed the same three changes on a clade 2.1 isolate from Indonesia and passaged the construct in ferrets 10 times to select for two additional changes, on of which was likely Q196R, which was also used by the CDC team. Thus, the same set of changes on two different H5N1 backgrounds was linked to efficient transmission in a ferret model.
Although the two receptor binding domain changes at positions 226 and 228 have not been identified in natural H5N1, changes at positions 223 (V223I) and 230 (M230I) were found in a clade 2.2 fatal cluster in Egypt, and these two changes subsequently became fixed on clade 2.3.2 isolates in wild birds and a recent fatal human case in Shenzhen.
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Post by dothedd on Mar 19, 2012 23:45:35 GMT -5
Curious CDC Comments On Maryland Death Cluster
Recombinomics Commentary 22:30
March 19, 2012
Genetic sequencing has confirmed that this is a typical human seasonal H3N2 virus that is more than 99% similar to other H3N2 influenza viruses submitted by the state of Maryland this season. While full antigenic testing is pending, based on genetic sequencing of some of the samples, these viruses are close to the H3N2 component of the 2011-2012 seasonal vaccine such that vaccination should offer protection against these viruses.
The above CDC comments on the H3N2 death cluster in Maryland are curious. The cluster was reported shortly after the CDC week 8 FluView revealed a dramatic spike in H3N2 low reactors. At the time the CDC had released 22 H3N2 sequences from samples collected in 2012, and none were designated as “low reactors”.
However, recently the CDC updated antigenic characterization data on seven of the isolates, which were designated as low reactors, and five of the seven (A/Alabama/02/2012, A/North Carolina/01/2012, A/South Carolina/03/2012, A/Oregon/01/2012, A/South Dakota/02/2012) mapped to the same sub-clade. Moreover, 10 additional isolates (A/Georgia/01/2012, Idaho/02/2012, A/Iowa/01/2012, A/Nebraska/01/2012, A/Nevada/01/2012, A/South Carolina/01/2012, A/Utah/04/2012, A/Vermont/01/2012, A/Virginia/01/2012, A/Washington01/2012 which were not characterized anigenically, phylogenetically mapped into the same sub-clade as the five isolates above indicating the vast majority of 2012 H3N2 isolates in the United States were low reactors.
The CDC has not released the sequences from the Maryland cluster, but it seems likely that these isolates will be low reactors and have the receptor binding domain change V223I, which was present in the sub-clade with most of the recent low reactors (see list here), which includes A/South Carolina/01/2012, which has acquired multiple H3N2v polymorphisms and the new 2012/2013 H3N2 vaccine target A/Victoria/361/2011.
Therefore, release of the sequences would be important for the clarification of the curious comments by the CDC above.
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Post by dothedd on Mar 20, 2012 10:50:19 GMT -5
CDC Identifies 2012 H3N2 Low Reactors In United States
Recombinomics Commentary 12:30
March 20, 2012
A/California/7/2009 (H1N1)pdm09-like virus A/Victoria/361/2011 (H3N2)-like virus B/Wisconsin/1/2010-like virus
The above isolates are the vaccine targets for the 2012/2013 season for the northern hemisphere. The H3N2 target was changed from A/Perth/16/2009 which showed a 16 fold reduction (from 2560 to 160) when tested against A/Victoria/361/2011, as demonstrated in table 2 of the February.2012 WHO vaccine update.
This significant drop in titers is linked to the dramatic increase in low reactors reported by the CDC from week 8. At that time the CDC had released 22 H3N2 sequences from 2012, but none were designated as low reactors (only 1/3 had been tested). The antigen characterization data was recently updated, which include the designation of 7 H3N2 isolates from 2012, and 5 of the 7 represented the same sub-clade, which has a number of non-synonymous changes, including A198S and V223I, both of which are also in A/Victoria/361/2011 (collected in late 2011), the new H3 vaccine target.
In addition to the 5 isolates listed as LOW REACTORS, 10 additional isolates mapped as the same sub-clade. Thus, 15/22 of the January 2012 isolates (collection dates through January 23) were the same dominant sub-clade that is represented by the new target, and was widespread worldwide in January (se list of GISAID sequences with V223I or A198S).
Thus, the dominance in January 2012 in the US suggests that the vast majority of February 2012 H3N2 cases in the United States would be low reactors with the two receptor binding domain changes cited above. However, the CDC update on the Maryland death cluster indicated the sequence data supported recognition by the 2011/2012 vaccine, which used Perth/16 as the H3N2 target, which had a 16 fold reduction in titer when tested against Victoria/361.
Release of the sequences from the Maryland death cluster would be useful.
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dothedd
Senior Member
Joined: Dec 27, 2010 20:43:28 GMT -5
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Post by dothedd on Mar 25, 2012 22:35:04 GMT -5
Additional Swine H3N2v Match Failures Recombinomics Commentary 17:00 March 20, 2012
The latest update of Genbank sequences includes 10 sets of US H3N2v swine sequences, including 6 which have an H1N1pdm09 M gene (A/swine/Minnesota/239105/2009, A/swine/Iowa/A01049036/2010, A/swine/Missouri/A01047968/2010, A/swine/Missouri/A01047969/2010, A/swine/Minnesota/A01047396/2011, A/swine/NE/A01101010/2011). However, none of the 10 sets have an H3 gene that matches the H3 lineage found in all 12 human H3N2v cases from 2011.
Thus, in spite of enhanced surveillance by the USDA since the 2009 pandemic and the detection of H1N1pdm09 M genes in H3N2v isolates from 2009, 2010, and 2011, only two matches of the human lineage have been identified and both isolates (A/swine/NY/A01104005//2011 and A/swine/Iowa/A01202640/2011) were from collections made in September, after the human cases in July and August from Indiana and Pennsylvania.
Although the first 7 cases in 2011 were identified via a CDC program that targets cases with swine exposure, none of the 7 cases have been linked to H3N2v identied in epidemiologically linked swine, and only one case was linked to symptomatic swine, which tested negative for influenza.
The two swine matched were from samples collected through an FDA anonymous testing program and both isolates were from lung samples, signaling severe or fatal swine infections. The only confirmed examples of H3N2v in contacts of index cases have been other humans. In Iowa neither the index case nor the two confirmed contacts had a history of recent swine exposure, which was also true for two symptomatic family members, who were not tested. The same absence of swine exposure was reported for the West Virginia cluster, where H3N2v was confirmed in a daycare center classmate, and 23 contacts had influenza like illness but were not tested. In the Iowa and West Virginia clusters the sequences from the H3N2v positive contacts matched the sequences of the index case.
In contrast, the recently released swine sequence from Nebraska matches swine sequences from Kansas, Iowa, and Texas. Although this lineage is the largest series of confirmed H3N2v swine sequences with an H1N1pdm11 M gene, no corresponding sequence has been found in humans. Instead the human cases in 2011 evolved from the most dominant 2010 human H3N2v sequences for five genes (PB2, PA, HA, NP, NS) while the other three genes in the first 10 human cases was from sequences found in an Ohio H1N2 isolate (A/swine/Ohio/FAH10-1/2010), and the two most recent sequences (from West Virginia) have the same genes except the N2 is from H3N2v circulating in swine.
Thus, the epidemiological and sequence data supports human transmission of H3N2v in 2011 and the two matches from September collections are due to this constellation jumping from humans to swine.
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dothedd
Senior Member
Joined: Dec 27, 2010 20:43:28 GMT -5
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Post by dothedd on Apr 3, 2012 13:48:04 GMT -5
CDC Dual Use of Inconsistent Flu Antigen Characterization Data Recombinomics Commentary 13:50 March 27, 2012
The MDHMH says it was the same strain, and I know of someone who privately asked the CDC if it was a drifted variant, and was told no.
CDC has confirmed that the influenza viruses isolated from the cluster of severe respiratory illness in one family in Maryland are seasonal influenza A H3N2 viruses. Genetic sequencing has confirmed that this is a typical human seasonal H3N2 virus that is more than 99% similar to other H3N2 influenza viruses submitted by the state of Maryland this season. While full antigenic testing is pending, based on genetic sequencing of some of the samples, these viruses are close to the H3N2 component of the 2011-2012 seasonal vaccine such that vaccination should offer protection against these viruses. The above comments represent an Internet rumor (in red) and an official CDC statement (in blue) on the H3N2 sequences from the death cluster in Maryland, suggesting that the sequences represent a Perth/16-like sub-clade and recognized by the current influenza vaccine which uses Perth/16 as the H3N2 target.
However, sequences released by the CDC, including sequences from samples collected in February, strongly suggest that the sequences from Maryland are drift variants with limited reactivity with the current vaccine.
In the week 8 FluView, the CDC reported a large spike in low reactors (isolates producing a 4 fold or greater reduction in titer when compared to the current Perth/16 target). Although the CDC had released 22 H3N2 sequences from 2012, none were classified as low reactors. i.e A/PERTH/16/2009-LIKE (H3N2) LOW GP (although antigen characterization results were listed for 1/3 of the samples). However, shortly thereafter the CDC designated seven 2012 isolates as low reactors with the above designation. Phylogenentic analysis indicated that 5 of the 7 formed a drift variant sub-clade with a number of non-synonymous HA changes, include two that were in or near the receptor binding domain, A198S and V223I. These changes were also present in the newly selected H3N1 vaccine target, A/Victoria/361/2011.
However, the other two low reactors were in another drift variant, which also had a change near the receptor binding domain, S199A, which was in a candidate vaccine target, A/Brisbane/299/2011.
Thus, the seven isolates designated by the CDC as low reactors fell into two distinct sub-clades, and vaccine targets representing each sub-clade had been selected by the CDC, (appropriate constructs had been generated, with sequences released at GISAID). Moreover, the CDC released additional 2012 sequences and virtiually all fell into these two sub-clades, indicating Perth/16-like sequences were no longer circulating in the United States in 2012 (which was alos true for the entire northern hemisphere), and the current H3N2 vaccine component would have limited utility.
The recently released sequences by the CDC increased the number of United States H3 sequences from February, 2012 collections to 11, and the number of January, 2012 H3 sequences to 37. Although none of the 2012 H3 sequences were from Maryland, virtually all fall into the two drift variant sub-clades listed above, with the Victoria/361-like sub-clade dominating, including a February 15 isolate from Delaware, A/Delaware/02/2012. Similarly, the only Maryland H3 sequences from the 2011/2012 season, collected on December 26, A/Maryland/21/2011, also has A198S and V223I and is in the Victoria/361-like sub-clade, although it is characterized as Perth/16 like (A/PERTH/16/2009-LIKE (H3N2) GP), which is also true of a subset of the 2012 sequences which are in the Victoria/361 sub-clade.
This inconsistency is clearly demonstrated within the Victoria/361 sub-clade, as seen in phylogenetic analysis. A/South Carolina/03/2012 (SC/03/12) is designated as a low reactor, yet two isolates which evolved from SC/03/12 (i.e. have all of the synonymous and non-synonymous changes seen in the H3 sequence from SC/03/12), A/South Carolina/01/2012 and A/Delaware/02/2012 are characterized a Perth/16-like. Similarly sequences (A/Minnesota/04/2012), which have evolved from A/South Dakota/02/2012 (designated as a low reactor) are also designated as Perth/16-like. Thus, both February 15 isolates (the most recent public sequences) have evolved directly from sequences designated as low reactors by the CDC, yet are designated as Perth-like, allowing the CDC to use related sequences to justify a new H3 vaccine target, because of a limited cross reactivity with the current target, and also claim that the related sequences are similar to the current target, as indicated in the above CDC statement and internet rumor.
This dual use of antigen characterization data is similar to the data fro H1N1 in the 2007/2008 season, when the vaccine target was Solomon Island/03, which was no longer circulating in the United States. Although Solomon Island/03 had been replaced by Brisbane/59 or Hong Kong/2562, these isolates were called Solomon Island/03-like at the beginning of the 2007/2008 season by the CDC, based on an insensitive antisera used by the CDC. Subsequent antisera developed by Ausatralia demonstrated significant antigenic difference between the three sub-clades, and that assay was used to identify Brisbane/59 isolates, which was the target for the 2008/2009 season. Thus, two different results on Brisbane/59-like sequences were used to claim a vaccine match with Solomon Island/03, as well as justify a change in target from Solomon Island/03 to Brisbane/59.
These internal inconsistencies, which provide evidence for a vaccine match as well as a need to change vaccine targets, are once again used to claim that the Maryland death cluster sequences, which are almost certainly drift variants of Victoria/361 or Brisbane/299 (and likely to be Victoria/361), are not drift variants and likely to react with vaccine against Perth/16, which has been replaced in 2012 in the United States by the two drift variants cited above.
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