RECOMBINOMICS

[dothedd]

Delays In trH3N2 Testing and Reports
Recombinomics Commentary 16:45
September 13, 2011


The recent cluster of trH3N2 cases in Pennsylvania and identity with the cases in Indiana raises concerns that more such cases will be reported in the near term. Multiple public sites allow for monitoring of developments, although delays in report can be significant, even for important samples. Human infections with a novel influenza, like trH3N2 are reportable in the US and worldwide in accordance with International Health Regulations signed by all member nations of the UN.

Consequently, these cases appear in the CDC’s weekly MMWR on the reportable diseases page. Although this page should be an early indicator, delays due to testing issues can be significant.
These delays include two important trH3N2 cases. One, A/Pennsylvania/40/2010 was from a case (36M) who developed symptoms on Sept 6, 2010. However, the sample initially tested as seasonal H3N2. More advanced testing, such as an antigen characterization test or sequencing usually involves isolation of the virus, and technical problems led to a five month reporting delay. Consequently, this case was not reported until week 4 in MMWR as well as FluView and the sequence was released April 17, 2011 at GISAID, more than seven months after the infection.

Similar delays were seen for confirmation of the daughter of the index case in Minnesota, A/Minnesota/11/2010. The index case was reported in late 2010 and the sequence was released at GISAID on December 08, 2010. However, in 2010 contacts of the case were under investigation and in the week 21 MMWR influenza update it was announced that the daughter was serologically trH3N2 confirmed and the case was added to the MMWR notifiable disease page on week 30, more than 8 months after the infection.

Thus, prior to the latest cluster, the MMWR notifiable disease table had two trH3N2 cases reported in 2011, but both cases were due to infections in 2010. However, in the week 34 MMWR, the page was updated with the case (2M) in Indiana, A/Indiana/08/2011 (IN/08/11), and index case (2F) for Washington County, A/Pennsylvania/09/2011, bringing the total number reported in 2011 to four. The week 35 MMWR did not include the two later cases (both 9F), who were initially reported by the Pennsylvania Department of Health on September 5, 2011, followed by a CDC “have you heard” on September 6.

Public data on this cluster however, began with the release of the full sequence for IN/08/11 at GISAID on August 25, 2011. The sequence clearly demonstrated that the isolate was related to the earlier trH3N2 sequences for 5 of the 8 gene segments (PB2, PA, HA, NP, NS), but the other three gene segments were acquired via reassortment. The most striking result was the acquisition of the MP gene segment from pandemic H1N1, since this gene segment was critical for the aerosolization of the virus and efficient transmission to humans. The PB1 was closely related to human isolates from the Huron County fair (A/Ohio/01/2007 and A/Ohio/02/2007) prior to acquisition of E618D by recent trH3N2 isolates, and the NA was closely related to another Pennsylvania case, A/Pennsylvania/14/2010. Thus, IN/08/11 had a unique constellation of gene segments, including the m gene segment from pandemic H1N1.

The acquisition of the M gene from pandemic H1N1 raised concerns that the new reassortant would transmit it humans, which was supported when details of the index case were reported in the Sept 2 MMWR early release, which noted that the Pennsylvania sequence, A/Pennsylvania/09/2011, also had the M gene segment from pandemic H1N1, although the MMWR and FluView noted that the Pennsylvania sequence was slight different than the Indiana sequence. However, further support for human transmission came on Sep 5 when the Pennsylvania announced two additional trH3N2 confirmations which also had the H1N1 M gene acquisitions.

The CDC’s prompt release of Pennsylvania sequences on Sep 7 at GISAID and Sep 8 at Genbank raised additional concerns because all three Pennsylvania isolates had the same constellation of genes as the Indiana case, and the two most recent collections from Pennsylvania (August 25 and 26 from A/Pennsylvania/11/2011 and A/Pennsylvania/10/2011, respectively) generated sequences that were virtually identical to the Indiana sequences, strongly supporting human transmission.

In addition, the CDC updated the underlying data for the subtyping table, showing an unsubtypable for week 33, which was almost certainly PA/09/11 based on the Aug 20 collection, which was followed by an unsubtypable for week 34, which almost certainly was from PA/10/11 or PA/11/11 based on collection dates.

However, the reporting on the cluster remains uneven. The MMWR notifiable diseases page still only lists two of the four trH3N2 confirmed cases for 2011, and the FluView still only list two of the four as unsubtypable. Moreover, the reporting delays for the 2010 cases raise concerns that additional cases are under investigation, including more unsubtypable cases.

Comments on the cases under investigation, including additional unsubtypables, would be useful.

[dothedd]

CDC trH3N2 Mis-Match Myth Creates Confusion
Recombinomics Commentary 10:45
September 14, 2011


These viruses are genetically related, but different enough to suggest there was not a common source of infection.

The viruses are similar, but not identical to each other.

The two viruses are similar but not identical.

The viruses in the two children were similar but not identical

The Indiana case was not linked to the others, and the flu-virus strain was slightly different.

The above quotes are from the CDC’s week 34 FluView, the CDC’s MMWR (early release on Sept 2 and week 35 release on Sept 9) and media reports in the United States and China, as well as a Q&A for all four cases.

The comments in the CDC publications have led to the widespread belief that the trH3N2 isolated from Indiana (A/Indiana/08/2011) is distinct from the trH3N2 at the Washington County fair (although the same constellation of genes, including M from H1N1, is acknowledge for all four isolates).

However, the initial comments by the CDC were in reference to the Indiana isolate and the first isolate linked to the fair, A/Pennsylvania/09/2011, which was from a Schuylkill County resident (2F) who visited the fair on August 16, and is the only recent case with direct swine contact (although the nature of that contact remains unclear since the case was only 2 years of age, there were no events on the fair schedule that day that involved swine, no symptomatic swine from the fair have been identified or tested positive for trH3N2, and the positive sample from the patient was collected 4 days after the fair visit).

The CDC subsequently acknowledged the two additional cases (both 9F) from the fair, and published sequences (at GISAID and Genbank) from samples collected August 25 (A/Pennsylvania/11/2011) and August 26 (A/Pennsylvania/10/2011), well after the end of the fair on August 20. Sequences from these two patients, who had no swine contact, were virtually identical to each other and the Indiana sequence.

Thus, the widely cited “not identical” remarks (and no common source) only pertain to the sequence from the Schuylkill resident (PA/09/11), and the virtual identity between the sequence from Indiana (IN/08/1 and two independent isolates (PA/10/11 and PA/11/11) from Washington County (initially test by the PA Department of Health or the University of Pittsburgh diagnostic lab), signal human transmission because of the identity between the sequences, and the lack of direct swine contact by any of the three infected cases.

Moreover, the four isolates from two states represent four independent introductions, signaling efficient transmission of trH3N2 to humans, including the three of the four with no documented or stated swine contact.

The identity between patients unlinked to each other, in separate states, and in patients with no direct contact with swine, is remarkably similar to the first two pandemic H1N1 cases identified in southern California (in adjacent counties) in 2009, and why the CDC should be testing (by PCR for trH3N2) all influenza A cases at this time, which is a month prior to the start of the 2011/2012 flu season.

[dothedd]

Audio:Jul21 Aug9 Aug18 Sep5 twitter

Commentary

CDC trH3N2 Testing / Reporting Creates Physician Confusion
Recombinomics Commentary 14:30
September 14, 2011


What would be far more helpful to ProMED readers who are clinically practicing are specific recommendations for when to report such cases and how to distinguish them clinically (or epidemiologically) from other cases of influenza.

The above comment was published in ProMED by a physician who was clearly confused by recent CDC reports of trH3N2 cases in Indiana and Pennsylvania. This confusion was largely linked to CDC testing and reporting procedures. The vast majority of the trH3N2 cases is identified in the “off season” and almost always involves cases with a perceived swine connection, because trH3N2 testing is largely limited to such cases, even though the majority of cases subsequently do not have a direct swine contact and the sequence data signals human to human transmission. The widespread human to human transmission is not identified because of testing procedures and prior cross reactivity with seasonal H3N2. The focus on swine linkage is abundantly clear in the CDC’s request for samples from patients with a swine link, even though three of the four recent patients have no reported swine contact and sequences from three of the four patients are virtually identical (even though the patients were unlinked, in two states, and infected independently). The linkage to swine is purely driven by the heavy bias is testing, not the origin of the virus, which is being transmitted human to human.

The human to human transmission began to emerge almost a year ago, when WHO issued a pager altert because two trH3N2 cases had been identified. When recipients of the alert became alarmed, they were assured that the trH3N2 was not transmitting in humans because the two cases (from Pennsylvania and Illinois) were isolated 6 weeks apart and the sequences were similar, but did not come from a common source. However, the alert did not included a second Pennsylvania case, which was from a patient who was symptomatic in September within a week of the Illinois patient (subsequently reported by Wisconsin and designated A/Wisconsin/12/2011), and the sequences between A/Wisconsin/12/2010 (WI/12/10) and those from the second Pennsylvania case, A/Pennsylvania/40/2010 (PA/40/10), were virtually identical, nullifying both reasons for the CDC assurances on lack of transmission.

These assurances were degraded further by another case, identified in November, A/Minnesota/11/2010 (MN/11/10), which was also virtually identical to WI/12/10 and PA/40/10. Moreover, the daughter of the index case was also symptomatic and was subsequently serologically confirmed to have also been trH3N2 infected and she had no direct swine contact. The CDC acknowledged the human transmission (other family members were also symptomatic but lab results were classified as “inconclusive”) and selected MN/11/10 as a pandemic trH3N2 vaccine target (two reassortants on a PR-8 genetic background were created and sequences were released at GISAID).

The latest cases were also identified in the off season, and also had a perceived swine link and the CDC again claimed in the week 34 FluView that the Indian and Pennsylvania sequences were different and did not come from a common source. However, once again subsequent sequences nullified the CDC assurances, but the CDC did not acknowledge the identity between the Indian and Pennsylvania sequences and instead focused on the swine connection in the request to clinicians for samples from patients linked to swine, and emphasized the swine linkage on its latest “have you heard” release.

Thus, the physicians reading the CDC reports in FluView, MMWR, or “Have You Heard” are operating under the misconception of a swine linkage as well as a relative rare event, when in fact the swine linkage is due to largely limiting testing to cases with a swine link as well as serious delays in routine surveillance that requires virus isolation (antigen characterization test and sequencing) instead of widespread PCR testing for trH3N2, which was used to identify recent cases 9which was subsequently confirmed with sequence data.

However, these testing issues may become moot, because two of the recent isolates have been characterized as unsubtypable because the human H3 sequences from the 1990’s has now evolved away from human in swine, and the sub-typing reagents either fail to recognize the trH3N2 or the CDC has raised the cut-off leading to an unsubtypable result, which more easily identifies the trH3N2 cases.

However, the current focus on swine linkage will limit the number of samples tested by PCR, and significantly undercount the number of trH3N2 cases and spread.

The continued CDC focus on a swine connection in testing and reporting will continue to create unnecessary confusion and delays in the reporting of the true extent of the trH3N2 pandemic.

[dothedd]

CDC Denies Sustained trH3N2 Transmission
Recombinomics Commentary 17:45
September 14, 2011


Likely transmission of swine-origin influenza virus from close contact with an infected person has been observed in investigations of human infections with swine-origin influenza A virus, but has not resulted in sustained human-to-human transmission.

The above comment is from the updated CDC webpage entitled “Reported Human Infections with Swine-Origin Influenza Viruses (SOIVs) in the United States since 2005”, and is an improvement over the early 2011 update which claimed that no human transmission had been laboratory confirmed. In the week 21 MMWR the CDC acknowledged that the daughter of the index case of the trH3N2 cluster in Minnesota had been serologically confirmed to have been trH3N2 infected and the daughter had no reported contact with swine and in the week 30 MMWR that case was added to the number of trH3N2 cases reported in 2011 (although the infection was in 2010).

However, the above claim of no sustained human-to-human transmission is contradicted by the sequence data of 2010 isolates (from Wisconsin, Pennsylvania, and Minnesota) as well as the four 2011 isolates from Indiana and Pennsylvania. The H3 of all of the above are closely related, and the four 2011 isolates have the same constellation of genes, including the M gene from pandemic H1N1 which is critical for sustained human transmission. Moreover, the sequences of three of the four isolates are virtually identical, and no swine contact has been claimed for any of those cases.

The CDC claim of no sustained transmission is solely based on negative data, which is highly suspect since no positive data has been presented for the source of these infections. The only real connection between these cases is the fact that they have been trH3N2 tested and trH3N2 has been confirmed.

The most detail made public this far is for the Indiana case (2M), who had no swine contact, but did have contact with a caretaker who had contact with swine. However, neither the caretaker nor the swine had flu symptoms, and no trH3N2 has been identified, other than the case. Thus, the inability of the CDC to identify a source of the trH3N2 for a case with no swine contact invalidates any claim of no sustained transmission, which also applies to the two Washington County residents who have no known contact with swine and no trH3N2 has been linked to the fair, other than the three tested and confirmed cases.

Thus, the CDC has not provided any scientific basis for its claim of no sustained transmission, which is strongly supported by the identities of the trH3N2 isolated from the Indiana and Pennsylvania cases with no known swine contact.


The CDC should modify its claim of no sustained trH3N2 transmission, which has no scientific or factual basis.

[dothedd]

CDC trH3N2 Transmission Denial Raises Concerns
Recombinomics Commentary 21:30
September 14, 2011


Likely transmission of swine-origin influenza virus from close contact with an infected person has been observed in investigations of human infections with swine-origin influenza A virus, but has not resulted in sustained human-to-human transmission.

The above denial by the CDC of sustained trH3N2 transmission raises serious concerns about pandemic surveillance. Previously, the CDC has offered assurances that the trH3N2 cases did not have a common source and did not represent human transmission. However, as was noted previously, these assurances were negated by additional sequences.

One of the more telling examples was the collection in Pennsylvania, A/Pennsylvania/40/2010, that initially tested as seasonal H3N2. It was determined to be trH3N2 based on subsequent testing which included sequencing. However, the vast majority of seasonal H3N2 samples is not subjected to such additional screening and therefore would be incorrectly designated as seasonal H3N2. Most samples that are PCR tested are samples from patients linked to swine, heavily biasing the association.

The recent cases however provides the most compelling data for human transmission because the three cases from Washington County were not epidemiologically linked, but all three had the same constellation of genes including two that matched each other and an earlier isolate from Indiana. Moreover, all three sequences that were virtually identical were from cases without known contact to swine or each other.

Two of these samples have been designated as unsubtypable, which is likely linked to further evolution away from human sequences or the changing of the cutoff for designation of seasonal H3. These unsubtypable should lead to a dramatic increase in the number of trH3N2 cases reflecting sustained human-to-human transmission.

However, the identification of this transmission is blunted by the CDC’s request for samples linked to swine instead of a request for influenza A`positive samples from young patients collected in the off season, as was the case for the four recent confirmed cases, all of which were under 10 years of age.

The focus on swine linked cases and the reliance on a heavily biased surveillance system that has failed to identify the sources for the recent cases, raises concerns that the CDC is not committed to serious testing unrelated to the unsupported position that trH3N2 is not transmitting in a sustained manner.

[dothedd]

Influenza A Confirmed In Erie Pennsylvania
Recombinomics Commentary 10:30
September 15, 2011


An adult with Type A influenza was reported to the Erie County Department of Health on Monday, said Charlotte Berringer, R.N., the department's director of community health.

"It's the earliest case I have seen in my nine years of following flu," Berringer said. "Other than the year we had H1N1 (2009), when flu cases never stopped."

The above comments raise concerns of additional trH3N2 cases in Pennsylvania. The latest influenza update from the Pennsylvania Department of Health reports no activity for the first two weeks of September, but does note the trH3N2 cases.

Influenza A cases should be sub-typed. Two of the four trH3n2 cases have been reported as unsubtypable, but as reported above, many cases are not tested beyond an influenza A test.

Sub-typing of influenza A cases, especially in western Pennsylvania at this time of year, is critical for determining the spread of trH3N2.

The CDC emphasis on cases with swine links continues tio raise pandemic concerns.

[dothedd]

Week 36 MMWR Has Two Pennsylvania trH3N2 Cases
Recombinomics Commentary 12:15
September 15, 2011


Novel influenza A infection virus ***
2
6
0
4
43,774
2
4
NN
PA (2 )



The above data is from tomorrow’s MMWR (week 36 ending September 10) with two more trH3N2 cases listed for Pennsylvania. Although listed in the current week (Sep 4 – Sep 10), it is likely that these two cases are A/Pennsylvania/11/2011 and A/Pennsylvania/10/2011 from collections on August 25 and August 26 respectively. The two listed cases bring the total reported in 2011 to six, which would include two 2010 cases (A/Pennsylvania/40/2010 which was initially sub-typed as seasonal H3N2 and added to the week 4 MMWR, and the daughter of the Minnesota index case, who was added to the week 30 MMWR after the serological confirmation of trH3N2 was announced in the week 21 MMWR).

The other two cases were reported in the week 34 MMWR and were the cases from Indiana (A/Indiana/08/2011) and the Schuylkill County case who attended the Washington County fair (A/Pennsylvania/09/2011).

Tomorrow’s update makes the MMWR notifiable disease page current for public trH3N2 cases, and any new additions would represent cases not reported to date.

[dothedd]

trH1N1 Transmission In South Dakota Prior to 2009 Pandemic
Recombinomics Commentary 14:11
September 16, 2011



Of 99 event pig-exposed students, 72 (73%) participated in the investigation, and 42 (42%) provided serum samples, of whom 17 (40%) were seropositive and 5 (12%) met case criteria. Of 9 students exposed to other pigs, 2 (22%) were seropositive. Of 8 index case-exposed persons and 10 without exposures, none were seropositive. Pig-exposed persons were more likely to be seropositive than persons without pig exposure (37% vs 0%, P < .01).

The results above are from a recent 2011 paper entitled, “A Pre-Pandemic Outbreak of Triple-Reassortant Swine Influenza Virus Infection Among University Students, South Dakota, 2008”, which demonstrate the ease of transmission of a trH1N1 in late 2008 (40% of tested samples from students with swine exposure had trH1N1 antibodies), prior to the 2009 H1N1 pandemic. These results were similar to the data from the Huron County Fair in Ohio in 2007 where trH1N1 was isolated (A/Ohio/02/2007 and A/Ohio/01/2007) from a presenter (10F) and her father (36M), respectively, and two dozen fair attendees had flu-like symptoms. These events signal efficient transmission of trH1N1 to humans.

Sequences from the H1N1 isolate, A/South Dakota/03/2008, from the student (19M) have been released at GISAID and GenBank and these sequences create a clustering with other human cases identified prior to the 2009, including several isolates from Iowa (most closely related HA sequence, , A/Iowa/05/2007, was from a 2M, who lived on a farm and was in close proximity to swine. The clustering signaled evolution toward human transmission.

Remarkably, the M gene from this case was related to clustering trH3N2 sequences from 2010, highlighting the importance of the M gene in transmission to humans, raising concerns that the acquisition of the M gene from the 2009 H1N1 signals the significant acceleration of the trH3N2 pandemic.

[dothedd]

CDC Update On trH3N2 Cases Increases Pandemic Concerns
Recombinomics Commentary 16:11
September 16, 2011


As a result of intensive surveillance after the identification of two cases of human infection with a novel influenza A virus, one in Indiana and one in Pennsylvania, reported in August MMWR, two additional human infections with novel influenza A virus were identified in Pennsylvania. Both patients were infected with swine-origin influenza A (H3N2) viruses, with illness onset dates of August 18 and August 21, 2011. One patient was hospitalized, but was discharged home and both patients have fully recovered. All three Pennsylvania patients reported contact with pigs at the same agricultural fair in the week preceding symptom onset and enhanced surveillance for human illness continues. Although these additional cases have been detected, exposure to pigs was reported in both cases and no evidence of ongoing transmission of this virus in the community has been identified.

The above comments from the week 36 FluView provide additional detail on the two most recent trH3N2 from Washington County. Both patients (9F) report swine contact, but the disease onset dates, difference in the sequences from the Schuylkill patient (2F), and comments on a lack of any epidemiological linkages between the three confirmed cases, indicates the infections associated with the fair were due to independent events, as was the Indiana case (2M). However, sequences from the two cases described above (A/Pennsylvania/10/2011 and A/Pennsylvania/11/2011) are virtually identical to the Indiana case (A/Indiana/08/2011) and these three isolates have the same constellation of genes as the patient from Schuylkill County (A/Pennsylvania/09/2011), which cludes the M gene segment, which is critical for efficient human transmission..

These four independent events, including the Indiana case who has no known swine contact, represent relatively severe cases. Both of the earlier cases presented at a hospital Emergency Department, and one was hospitalized. The above data indicates one of the more recent cases was also hospitalized, and the FluView is silent on the fourth case. Therefore, at least 3 of the 4 cases either presented at an Emergency Department, was hospitalized, or both. Thus, although all four cases have now recovered, they represent more severe cases and suggest dozens or hundreds of people have been trH3N2 infected, yet the vast majority of influenza A positive cases reported in weeks 35 and 36 have not been sub-typed. Two cases have been designated as unsubtypable and it is unclear if this is leading to sub-type designations.


The severity of these cases, coupled with limited sub-typing, continues to raise trH3N2 pandemic concerns.

[dothedd]

Absence of Influenza A Subtyping Increases Pandemic Concerns
Recombinomics Commentary 19:11
September 16, 2011


The figure below is from the CDC’s week 36 FluView and the data for week 36 is similar to week 35. The detection of influenza positive samples remains low, and all positives are influenza A. In week 36 both sero-typed samples were listed as seasonal H3N2, but 7 of the 9 samples were not sub-type, as was seen in week 35 when 8 of the 10 samples were not sub-typed.

NOTE CHART LINK BELOW!

The recent detection of 4 trH3N2 cases has increased interest in the sub-type of influenza A positive samples because 2 or the 4 trH3N2 samples are list as unsubtypable as seen at the top of the bars representing week 33 and week 34. The absence of the other two cases from the graph is curious, since the H3 sequences from the four cases are virtually identical, and all four should have given an “unsubtypable” result. However, earlier trH3N2 had been classified as seasonal H3n2, raising concerns that the number of trH3N2 cases in the graph below is higher than the two designated for weeks 33 and 34.

The lack of sub-typing, as well as the absence of two of the four trH3N2 cases from the unsubtypable category raises concerns that the number of trH3N2 samples represented in the table below is markedly higher than the two unsubtypables or the four confirmed cases.

A recent paper on a trH1N1 from South Dakota described trH1N1 antibody detection in 40% of serum samples from students with swine contact. The M gene in the above isolate was closely related to the recent 2010 trH3N2 isolates, incluidng both from Pennsylvania (A/Pennsylvania/14 and A/Pennsylvania/40/2010). The recent trH3N2 isolates have swapped out the above M gene and replaced it with the M gene in pandemic H1N1 increasing tarnsmission efficiencies more. Thus, the four 2011 trH3N2 cases likely represent 100's or 1000's of human trH3N2 infections, raising serious surveillance concerns

The concerns are not reduced by the CDC sequences released for patients infected over the summer. There are only sequences from five patients and A/Maryland/17/2011 is the only patient which is not trH3N2.

An explanation for the lack of sub-typing as well as the two recent trH3N2 cases that are not listed as unsubtypable would be useful.


CHART LINK:

www.recombinomics.com/News/09161103/Wk36_Subtypes_NOT.html

[dothedd]

trH3N2 M Gene Acquistions Raise Pandemic Concerns
Recombinomics Commentary 19:11
September 19, 2011


Of 99 event pig-exposed students, 72 (73%) participated in the investigation, and 42 (42%) provided serum samples, of whom 17 (40%) were seropositive

The above comments are from a recent paper highlighting the efficient transmission of trH1N1 from swine to students at a livestock even in late 2008 in South Dakota. A full set of sequences, A/South Dakota/03/2008, from the index case (19M) have been made public, and these sequences highlight the role of the M gene in transmission.

trH3N2 cases in 2010 led to a pager alert issued by WHO involving two patients from who full sequences were released (A/Wisconsin/12/2010 and A/Pennsylvania/14/2010). Although these isolates could be distinguished (in HA and NA) the M gene in both cases were closely related to each other as well as the South Dakota isolate above. Moreover, two subsequent sets of sequences (A/Pennsylvania/40/2010 and A/Minnesota/11/2010) also had a M gene that matched (see list here).

Three of the 2010 trH3N2 isolates were closely related to each in the HA and NA genes, again indicating these human isolates were dominant in late 2010. Moreover, the other internal genes were closely related to sequences from an outbreak at the Huron County fair in 2007, where trH1N1 was isolated (A/Ohio/02/2007 and A/Ohio/01/2007) from a presenter (10F) and her father (36M), respectively, and two dozen fair attendees had flu-like symptoms. Thus, the human isolates in 2010 had acquired genes from isolates that had been linked to efficient transmission to humans.

The role of the M gene in efficient transmission to humans was highlighted in another paper which generated various reassortanst using genes from the H1N1 pandemic virus and concluded that the M gene was critical for efficient transmission to humans (as determined in a guinea pig model).

The recent isolates from Indiana (A/Indiana/08/2011) and Washington County in Pennsylvania (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011) all have the same constellation of genes with five matching the three closely related sequences from 2010, an NA matching the other isolate from 2010 (PA/14/10), and a M gene segment from pandemic H1N1.

The efficient transmission of trH1N1 in South Dakota and Ohio indicate human infections by swine are not rare. The recent human cases demonstrate a clustering of gene segments which link back to the high transmission events, and the acquisition of pandemic H1N1 suggests that the number of trH3N2 cases is orders of magnitude higher than the four recently confirmed cases.

[dothedd]

CDC trH3N2 Testing Limits and Delays Raise Pandemic Concerns
Recombinomics Commentary 04:40
September 21, 2011


As a result of intensive surveillance after the identification of two cases of human infection with a novel influenza A virus, one in Indiana and one in Pennsylvania, reported in August MMWR, two additional human infections with novel influenza A virus were identified in Pennsylvania. Both patients were infected with swine-origin influenza A (H3N2) viruses, with illness onset dates of August 18 and August 21, 2011. One patient was hospitalized, but was discharged home and both patients have fully recovered. All three Pennsylvania patients reported contact with pigs at the same agricultural fair in the week preceding symptom onset and enhanced surveillance for human illness continues. Although these additional cases have been detected, exposure to pigs was reported in both cases and no evidence of ongoing transmission of this virus in the community has been identified.

The above comments from the CDC’s week 36 FluView describe the two most recent trH3N2 confirmed cases, which update the reported contact with swine (the early report in “have you heard” indicated this cases were in the area of swine). However, this “intensive surveillance” has failed to identify swine with SIV symptoms, swine with an SIV infection, swine with a trH3N2 infection, swine with a constellation of genes matching the three Pennsylvania cases and the case in Indiana, swine with trH3N2 sequences matching the four 2011 cases.

Similar failures have been reported for the Indiana case, which was due to an infection 2 months ago. The samples were collected in week 30 on July 24 and July 27, and the caretaker of the case was linked to swine, but now flu-like symptoms have been reported for the caretaker and no SIV symptoms of lab confirmations have been reported for the swine contacted by the caretaker.

In spite of these failures to connect the four cases with infected swine, the CDC request for additional samples targeted patients with a swine link. Although these samples may be useful, flu season does not officially begin until week 40, so the number of such cases may be limited.
As seen in the graph below, flu confirmations are low, and the expanded view of recent weeks demonstrates an alarming lack of sub-typing in the small number of lab confirmed cases (only 2 of 10 positives in week 35 and 2 of 9 positives in week 36 have been sub-type). This delay in sub-typing is cause for concern, because the sub-typing is the most widespread approach for the identification of 2011 trH3N2 cases, since only the CDC can directly test (PCR) for trH3N2.



State labs can flag potential cases via sub-type (cases would be influenza A positive and H1/H3 negative). However, the absence of sub-typing for the majority of recent cases eliminates or delays these red flags. Moreover, the absence of two of the four lab confirmed cases in the graph below (as well as underlying data, which has not been updated since last week) raises additional concerns that even know trH3N2 may not yield the “unsubtypable” red flag, or be reported promptly. The samples from the Indiana case were collected in week 30, but the graph below lists 1 influenza B and two influenza A samples that have not been sub-typed).

In addition the issues associated with the lack of sub-typing or reporting of confirmed trH3N2 cases, the absence of trH3N2 PCR testing at state labs forces reliance on a notorious “rapid test” which lacks sensitivity and frequently yield false negatives. trH3N2 cases that are negative for influenza A will fall through the testing cracks because these samples will also be negative on H1 and H3 tests because the PCR test for H1 does not recognize H3, and seasonal H3 tests have failed to detect at least two of the recent trH3N2 cases, as seen by the blue caps on week 33 and 34 bars.

Thus, the failure to laboratory confirm linkage between the human trH3N2 cases and infected swine, the focus on cases with swine linkage, the delays in showing all four recent trH3N2 cases as unsubtypable, and the dismal record of the influenza A rapid test, and the identities between the four recent trH3N2 cases seriously increases trH3N2 pandemic concerns.

[dothedd]

Frequent D225G in 1918 H1N1 Autopsy Lung
Recombinomics Commentary 11:30
September 21, 2011


The recent paper, “Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak” included release of partial HA sequences from 12 fatal cases in the United States (largely military bases), increasing the number of 1918/1919 autopsy lung sequences to 17.

The paper noted that three of the four cases collected prior to the pandemic peak had D225G (Camp Dodge - A/Iowa/1/1918, A/Iowa/2/1918 and Camp Jackson - A/South Carolina/2/1918), while only one of the eight samples collected post peak (Camp Upton - A/New York/3a/1918) had D225G. However, the five previously released sequences were collected post peak, and two (A/New York/1/18 and A/London/1/1919) had D225G. Thus, although 75% of the four pre-peak samples is higher than the initial frequency of 40% for the five post peak samples or the 23% for the new total of 13 samples collected post peak, the significance of these differences is far from clear.

The role of D225G has attracted significant interest in the 2009 H1N1 pandemic because of its linkage to severe and fatal cases, and the current version of pandemic H1N1 also has had D225N and D225E at high frequencies. The finding of D225N in fatal cases in Mexico led to a 2011 pandemic alert, and D225N has also been detected in association with D225G in multiple clusters on multiple genetic backbones (Ukraine, United States, Mexico).

D225G allows for binding to gal 2,3 receptors which are at high levels in human lung, so detection in lung samples is generally higher than samples collected from the upper respiratory tract, and there can be variation in samples collected at different time points. However, the frequent detection of D225G in pre- and post- 1918 pandemic cases indicates it efficiently transmits.

This variation was seen in the fatal cluster at Duke Medical Center in late 2009 when four patients from the same floor died. All four were infected with the same sub-clade, which had H274Y in NA and had the rare HA marker Y233H. Three of the four died within a day of each other, and sequences from each patient were slightly different at position 225. Two samples were collected from the index case. Direct sequencing of the initial sample from the index case was wild type at position 225 (D was detected), but virus isolated from that sample was a mixture of wild type and D225G. Moreover, virus isolated from the second sample yielded a sequence with D225G alone. The sample from a second patient was wild type when sequenced directly, but virus isolated from that sample was a mixture of wild type and D225N. The sequence from the third fatal case was wild type as seen in direct sequencing or sequencing of the isolated virus. Thus, although all isolates had the same characteristic markers (Y233H in HA and H274Y in NA) there was considerable variation at position 225, even in multiple sequences from the same patient or sequential collections.

This type of variation was also seen direct sequencing of autopsy lung samples from Ukraine, which would be more analogous to the 1918 results. In the Ukraine series, the majority of samples had D225G, D225N, or both and phylogenetic analysis identified this heterogeneity in multiple samples on the same branch of phylogenetic trees, signaling the appending of these changes onto identical genetic backbones.
This variation at this position limits the interpretation of the significance of the frequency of D225G in pre and post-pandemic peak samples.

However, it is clear that D225G was common in autopsy lung samples collected in pre- and post- 1918 pandemic peak collections, and the association of D225G with severe and fatal cases in the current outbreak is cause for concern, as is the presence of D225G in all trH3N2 cases.

[dothedd]

CDC Eliminates trH3N2 Unsubtypables (09/27/11 19:30)

CDC Eliminates trH3N2 Unsubtypables
Recombinomics Commentary 19:30
September 27, 2011


The chart below is from the CDC’s week 37 FluView, which continues to show a low level of influenza activity, dominated by influenza A. However, the two unsubtypables reported for weeks 33 and 34, reflecting two of the four reported trH3N2 cases, have been reclassified to seasonal H3N2, raising concerns that these adjustments will “hide” trH3N2 cases and lead to a gross under-representation in FluView reports.

Prior trH3N2 cases were reported as seasonal H3N2 in FluView, although a small number were reported in the notifiable disease pages of MMWR as well as brief descriptions in FluView or summaries in MMWR. About half of the reported trH3N2 cases have been hospitalized and all have had some kind of loose association with swine or swine locations.

The sequences from the2011 Indiana and Pennsylvania trH3N2 cases were virtually identical, and the Indiana case had no swine contact, although his caretaker did have contact with swine. However, no human contacts of swine had flu symptoms and there were no reports of evidence of influenza infections. Similarly, there were no reports of swine symptoms or infections in the Pennsylvania cases, raising concerns of human transmission, that are largely missed because of a lack of testing beyond serotyping that does not distinguish trH3N2 from H3N2.

Moreover, the “adjustment” that led to the removal of the “unsubtypables” may lower the number of positives as reflected in the table and chart. One state, Minnesota, has reported a spike in ILI cases in the past two weeks, which are not reflected in the FluView figures.

Details on why the unsubtypables were classified as seasonal H3N2 would be useful.

[dothedd]

trH3N2 False Negatives Raise IHR Compliance Concerns
Recombinomics Commentary 11:30
September 29, 2011


The elimination of the two subtypables from the CDC week 37 report raises serious questions about the trH3N2 testing and reporting in weekly FluView reports as well as required reporting under International Health Regulations (IHR) mandated for all members of the United Nations. IHR regulations require the reporting of novel influenza infections in humans and the CDC does include trH3N2 cases on its weekly notifiable diseases page of weekly MMWRs, which currently include 6 confirmed trH3N2 cases for 2011 (as in tomorrow's week 38 report).

However, the removal of the two unsubtypables suggests the current assays the CDC uses in routine analysis / reporting fails to identify trH3N2 cases because the week 30 update has no H3N2 cases (and A/Indiana/08/2011 was identified in samples collected during week 30) and the updated table in week 37 has removed the unsubtypable from week 33, when the sample for A/Pennsylvania/09/2011 was collected, and the number of H3N2 cases remained unchanged at five.

Thus, it appears that the 2011 trH3N2 cases are not reclassified as seasonal H3N2 cases, but instead are simply not reported, suggesting the samples fail to meet the CDC requirement for classification as influenza A positive, so instead of being reported as “unsubtypable”, these samples are being falsely reported as “negatives”, even though trH3N2 sequences have been identified in the samples from the Pennsylvania cases, and trH3N2 virus has been isolated from the Indiana case (and the sequence of the trH3N2 isolate matches the direct sequencing of the Indiana and Pennsylvania samples).

Thus, the CDC has reported the recent cases in its MMWR and has noted the cases in text in the CDC FluView, yet is reporting these samples as “negatives” in its updated subtyping table and graph, raising concerns that the vast majority of trH3N2 are being reported as negatives.

These concerns were raised last year when Pennsylvania was reporting unsubtypables in its weekly reports, but these unsubtypables failed to appear in the CDC weekly reports. Pennsylvania leads the nation in the number of trH3N2 isolates from infections in 2010 with two (A/Pennsylvania/14/2010 and A/Pennsylvania/40/2010) and also leads the nation in sequences from 2011 (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, and A/Pennsylvania/11/2010).

One of the 2010 cases, A/Pennsylvania/40/2010, was not reported until 2011 because it was initially reported as seasonal H3N2 and routine testing led to its identification as trH3N2. However, the reporting was delayed because the more advanced testing of antigen characterization and sequencing required viral isolation, which was delayed due to technical issues.

The H3 sequences from the four 2011 trH3N2 cases are closely related to three of the 2010 isolates (A/Pennsylvania/40/2010, A/Wisconsin/12/2010, A/Minnesota/11/2010), but the additional evolution in 2011 has moved these isolates into the unsubtypable category for H3 and apparent also creates influenza A detection issues leading to false negative representations in the CDC FluView.

These detection failures raise concerns that the number of trH3n2 is far greater than the 6 cases reported in 2011. One of those cases was the daughter of the index case in the Minnesota cluster. She was trH3N2 lab confirmed by antibody testing and other family members were “inconclusive” in such test, but had flu symptoms similar tow the two confirmed cases. As noted above, the H3 sequence from the index case, A/Minnesota/11/2010, was virtually identical to the other two 2010 sequences and was a precursor to the four 2011 cases signaling human to human transmission for these isolates.

Moreover, the 2011 sequences include the M gene from pandemic H1N1, which was deemed critical for human to human transmission, and the 2011 Indian case has no history of swine contact. His caretaker has a history of swine contact, but no symptoms or virus has been reported for the caretaker or associated swine, which is also true for the swine at the Washington County fair.

Thus, the failure to identify a source for any of the 2011 cases, coupled with the present of pandemic H1N1 M gene segment, strongly suggests that the number of cases in Indiana and Pennsylvania was far higher than the four reported cases.

This concern is increased by the CDC request for samples from Pennsylvania patients with swine contact, when the CDC assays fail to identify sources for the four known cases in spite of an “intense” investigation. In the week 37 FluView the were only 3 influenza A positive samples for the entire country in spite of increases in ILI reports or Google FluTrend values in multiple cities in recent weeks.

Thus, the CDC “adjustment” in the cut-off for influenza A positive is leading to a large number of false negatives and failure to detect or report trH3N2 cases as mandated under IHR regulations.

An explanation for the elimination of unsubtypables from FluView reports, as well as an analysis of 2010 unsubtypables in Pennsylvania, is long overdue.

[dothedd]

US Pneumonia & Influenza Death Rate Spikes to Epidemic Levels
Recombinomics Commentary 11:30
September 29, 2011


Tomorrow’s week 38 MMWR will report a spike in the Pneumonia and Influenza (P&I) death rate to 6.51%, which is at or above the epidemic threshold, even though only 3 confirmed cases of influenza were reported in the CDC’s week 37 FluView. In week 37 the CDC eliminated the trH3N2 unsubtypables reported in week 33 and week 34 raising serious concerns about the CDC cutoffs for influenza A positive cases.

The CDC had previously reported 4 trH3N2 cases (in Indiana and Pennsylvania) and two of the four had been listed as unsubtypable, which would have been due to registering a influenza A positive, but negative for seasonal H3 or pandemic H1. The week 37 report had eliminated the two unsubtypable, raising concern that these cases were being reported a false negatives and therefore removed from FluView reports. These adjustment were accompanied by a report of just 3 confirmed cases for the entire country, in spite of increase in Google FluTrends for multiple US cities, as well is a spike in ILI cases as a percentage of emergency department visits in Minnesota.

Thus, alternate measures of influenza cases and deaths indicated the 3 cases reported for week 37 in FluView were a gross underestimate of flu activity in the United States, and the increase in the P&I death rate raised additional concern that widespread trH3N2 cases were being falsely reported as influenza A negatives.

[dothedd]

Emergency Influenza-Like Illness Spikes In Minnesota
Recombinomics Commentary 15:00
September 30, 2011


The graph below represents weekly levels of influenza-like illness (ILI) among emergency department visits in Minnesota and depicts a sharp increase in the past two weeks, to levels comparable to those reported during the peak of the flu season in early 2011.


This sharp increase in ILI levels is also supported by increases in influenza in a number of US cites as measured by Google flu trends for Minneapolis, MN; Philadelphia, PA; Miami, FL; Atlanta, GA; Chicago, IL; Dallas and Austin, TX as well as the spike in the Pneumonia and Influenza (P&I) death rate for week 38.. These recent increases are in sharp contrast to the number of lab confirmed flu cases as reported in the CDC’s fluview, which included 3 cases for the entire country in week 37.

The week 37 report also removed previously reported unsubtypables for week 33 and week 34, which corresponded to collections dates for trH3N2 cases in Pennsylvania, raising concern that the routine influenza A or H3 assays on trH3N2 cases evaluated by the CDC are being reported as negative, leading to the low levels being reported including the absence of newly discovered trH3N2.

The recent trH3N2 cases in Pennsylvania and Indiana were virtually identical to each other, and the H3 sequence was an evolved version of trH3N2 2010 isolates from Pennsylvania, Minnesota, and Wisconsin. The clustering of these sequences in human trH3N2 isolates supports human to human transmission, a does the failure to identify a swine source for the 2011 cases, including the clustering of three confirmed cases at the Washington County fair in Pennsylvania, as well as the Indiana case who did not have contact with swine.

The recent results raise serious questions about the CDC testing of trH3N2 cases, including the removal of the previously reported 2011 unsubtypables, and the unreported unsubtypables reported by Pennsylvania in late 2010 and early 2011.

A detail explanation of these prior CDC results and modifications is long overdue.

[dothedd]

WHO Acknowledges trH3N2 Vaccine Development
Recombinomics Commentary 14:30
October 2, 2011


Antigenic analysis indicated that these viruses were distinct from currently circulating human A(H3N2) viruses but similar to swine A(H3N2) viruses from previous years as well as to A/Minnesota/11/2010 (H3N2) SOIV (Table 7), from which a candidate vaccine virus is under development.

As the viruses continue to evolve new SOIV candidate vaccine viruses will be developed and announced as they become available. Institutions, companies and others who wish to receive these candidate vaccine viruses should contact WHO at [e-mail] or the institutions listed in announcements published on the WHO website.

The above comments are from the WHO update on pandemic vaccines, “Antigenic and genetic characteristics of zoonotic influenza viruses and development of candidate vaccine viruses for pandemic preparedness - September 2011,” which confirms that the sequences deposited at GISAID by the CDC are under pandemic trH3N2 development.

The report provides antigenic cross-reativities, which confirm the lack of protection offered by the seasonal H3N2 or pandemic H1N1 target in the current tri-valent vaccine, which was recently approved for the 2012 southern hemisphere and is identical to the targets approved for the 2010/2011 and 2011/2012 vaccine target for the northern hemisphere.

However, antisera against the trH3N2 vaccine target, MN/11/10, does cross react with the four recent 2011 isolates (IN/08/11, PA/09/11, PA/10/11, PA/11/11), although the description of trH3N2 cases in the United States is misleading.

[dothedd]

Evolution of New Human Contagion trH3N2
Recombinomics Commentary 19:40
October 4, 2011


The latest series of trH3N2 and trH1N2 swine sequences from 2011 (released at Genbank by Iowa State University) provide additional insight into the evolution of the new human contagion, trH3N2. Although the new swine sequences have key components of the 2011 trH3N2 reported in Indiana (A/Indiana/08/2011), and the Washington County fair in western Pennsylvania (A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011), the swine isolates fail to match the constellation of genes fund in all four human cases, providing additional evidence for the emergence of a new human contagion, trH3N2, and another influenza pandemic.

The 2011 trH3N2 human sequences extended the spread of the 2010 human trH3N2 sequences by retaining 5 of the 8 gene segments. The new contagion has swapped out the other three gene segments, PB1, NA, MP for genes found in earlier human triple reassortants (trH1N1, trH3N2, pandemic H1N1), to create a new human contagion, trH3N2, that can efficiently transmit in humans. As has been mentioned by the CDC and WHO, the 2011 human trH3N2 sequences have acquired a pandemic H1N1 M gene segment, which is critical for the efficient transmission of pandemic H1N1 between humans.

However, the human trH3N2 sequences have also acquired the N2 that was in one of the 2010 Pennsylvania cases, A/Pennsylvania/14/2010, as well as a PB1 more closely related to sequences from the Huron County fair (A/Ohio/01/2007 and A/Ohio/02/2007) and this new constellation of genes was in all four 2011 human trH3N2 cases reported to date, and not in any of the reported swine sequences, including the recently released sequences (trH3N2 and trH1N2) from 2010 and 2011.

The recently released 2011 swine sequences had information on HA, NA, and MP, but this limited sub-set failed to match the human trH3N2 constellation. In 2010 there were H1N2 sequences (including A/swine/Minnesota/A01047604/2010 and A/swine/South Dakota/4/2010) with a pandemic H1N1 M gene and an N2 that matched the recent human trH3N2 sequences. However, a more complete analysis of the Minnesota sequence showed that all six internal genes matched pandemic H1N1, and other such sequences (all six pandemic H1n1 internal genes wrapped in H and N from other triple reassortants) have been widely reported in swine, but not in humans. Therefore, it is likely that the recent H1N2 swine sequences (including A/swine/Minnesota/A01049956/2011, A/swine/Iowa/A01049723/2011, A/swine/Iowa/A01049728/2011, A/swine/Indiana/A01049964/2011, A/swine/Illinois/A01049871/2011, A/swine/Illinois/A01049872/2011, A/swine/Iowa/A01049887/2011, A/swine/Iowa/A01049722/2011) have a similar constellation (as well as a different serotype).

Other recent trH3N2 isolates (including A/swine/Texas/A01049555/2011, A/swine/Texas/A01049556/2011, A/swine/Indiana/A01049750/2011, A/swine/Texas/A01049914/2011, A/swine/Texas/A01049915/2011) have a pandemic M gene segment, but different H3 and N2. Similarly, recent isolates have a matching H3 and N2 (including A/swine/Indiana/A01049744/2011, A/swine/Indiana/A01049745/2011, A/swine/North Carolina/A01049436/2011, A/swine/Indiana/A01049653/2011, A/swine/Indiana/A0109091/2010) but have an M gene related to the 2010 trH3N2 isolates.

Thus, even though the surveillance of 2010 and 2011 swine has increased (including one sequence from July, 2011), none of the public sequences match the 2011 human trH3N2 constellation, strongly suggesting that this new pathogen is transmitting in humans.

The number of human cases has been limited, but all four 2011 isolates have the same constellation of genes including a pandemic H1N1 M gene, which is critical for human to human transmission. Moreover, three of the four sequences are virtually identical, but isolated from distinct locations, including the Indiana case with no swine contact. Moreover, none of the four cases were epidemiologically linked, indicating each infection was independent.

The matching of all four human cases, in the absence of any matches with swine isolates signals an adaptation and spread of this trH3N2 contagion with a novel constellation of flu genes.
The limited testing of H3N2 cases, and the focus on patients with links to swine, continues to raise pandemic concerns.

[dothedd]

Anomalous trH3N2 Reporting Raises Pandemic Concerns
Recombinomics Commentary 23:40
October 4, 2011


The CDC’s week 38 FluView remains confusing with regard to trH3N2 activity. Many cities throughout the US have show recent increases in flu activity based on Google FluTrends, or ILI frequency at Emergency departments in multiple states, yet the weekly FluView is reporting activities that are barely detectable. The initial week 37 report had only three confirmed flu cases for the entire country. The latest report increases the number for week 37 to 10, but only one of the 10 influenza A cases has been sub-type (and was H3N2).

For the past 4 weeks, lab confirmed cases have been dominated by influenza A (only two of 43 cases were influenza B). Of the 10 influenza A cases sub-typed, 9 have been H3N2. However, the number of trH3N2 cases in these lab confirmed samples remains unclear.

Sub-typing of trH3N2 cases is difficult because initial swine H3N2 cases in the United States were initially linked to the infection of a swine with seasonal H3N2, giving rise to a double reassortant with human HA, NA, and PB1. Therefore the reassortants can subtype as seasonal H3N2 as reported for A/Pennsylvania/40/2010. Routine surveillance on that samples eventually identified the trH3N2 case, which was reported 5 months after samples collection. These data raise concerns that many trH3N2 cases are classified as seasonal H3N2.

However, two of the recent trH3N2 cases from the Washington County fair were reported as unsubtypable in the week 35 and week 36 FluView reports. However, these two designations were removed in week 37 without comment. The removable of these two cases could have multiple explanations.

Although there have been 9 confirmed trH3N2 cases since September , 2010, the subtype table and graph have no designation for trH3N2. Thus, the confirmation of trH3N2 in these two cases (by PCR or sequencing), could have led to the removal of the two cases since there was no column for trH3N2 cases.

Alternatively, repeated testing of the samples may have yielded a weak signal for seasonal H3N2, which took the samples out of the unsubtypable column. Similarly, the cut-off value for seasonal H3N2 may have been lowered to yield a seasonal H3N2 designation. Alternatively, repeated influenza A testing may have led to a negative result for the samples, or the cut-off for influenza A positive may have been raised, leading to a negative result.

All of the above could lead to a reduction / absence of trH3N2 cases since the assay for influenza A and/or seasonal H3N2 has produced variable results (all four of the recent trH3N2 cases have HA sequences that are virtually identical, so it representations of the other two trH3N2 also remains unclear.

The recent trH3N2 represent a serious health risk. About half of the cases have been hospitalized and most have no direct contact with swine. Moreover, the detection of two cases a year ago lead to a pager alert by WHO, while the first two recent cases led to an early release MMWR, including a request for samples from symptomatic patients. However, the request was for patients with swine contact, even though the Indiana case had no such contact, and the source of trH3N2 for all four recent cases remains unclear. The caretaker for the Indiana case had swine contact, but the caretaker and swine were asymptomatic and no swine influenza has been identified (and trH3N2 matching the constellation of flu genes in the human cases has not been reported anywhere, in spite of increased swine surveillance and testing in 2010 and 2011). Similarly, no symptomatic influenza infections have been reported for any of the swine at the Washington County fair in spite of an “intense” investigation.

The failure of these investigations to identify swine sources for the four independent infections involving identical trH3N2 constellations as well as virtual identity between of the Pennsylvania sequences and the sequence from Indiana strongly support human to human transmission, which is also consistent with the acquisition of the pandemic H1N1 M gene segment, by the 2011 trH3N2 isolates.

Thus, the sequence and epidemiological data support human transmission, yet the vast majority of influenza A positive samples have not been sub-typed, and the number of lab confirmed cases remain far lower than expected by recent reports of ILI activity, deaths, and flu cases throughout the country prior to the official start of the flu season in week 40.

A detailed explanation for the low number of influenza cases reported in FluView, the lack of sub-typing, the removal of unsubtypables, and the criteria used to classify samples as influenza A positive, H3N2 positive, and disposition of future unsubtypables is overdue.

[dothedd]

trH3N2 Unsubtypable Reporting Raises Pandemic Concerns
Recombinomics Commentary 19:00
October 7, 2011


Today’s week 39 FluView adds to the confusion regarding the CDC reporting of trH3N2 cases. Four recent cases have been described in the CDC’s MMWR as well as their “have you heard” page. However, the reporting of these cases in the subtyping graph in weekly FluView reports has been confusing and inconsistent.



The CDC has released full or partial sequences from the four recent cases (A/Indiana/08/2011, A/Pennsylvania/09/2011, A/Pennsylvania/10/2011, A/Pennsylvania/11/2011) at GISAID and Genbank and the sequences clearly indicate that all four isolates have the same constellation of genes including the acquisition on the M gene segment from pandemic H1N1. This acquisition is a concern because it was deemed “critical” for the jump of pandemic H1N1 from swine to humans, and raises concerns for efficient human transmission of H3N2. These concerns were increased by the identities between the four recent isolates from two distinct locations involving four independent infections, including the Indiana case (2M) who had no swine contact.

Detection of the trH3N2 cases is complicated by the H3 origin, which is human. Thus, an earlier trH3N2 case, A/Pennsylvania/40/2010 was initially reported as seasonal H3N2, but further analysis led to the determination that the infection was due to trH3N2, and the H3 sequence was closely related to other trH3N2 cases in 2010 (A/Wisconsin/12/2010 and A/Minnesota/11/2010) and presumably related to the trH3N2 that infected the daughter of the above Minnesota index case.

However, the 2011 trH3N2 sequences have evolved from the 2010 sequences and the underlying data for week 33 included an unsubtypable shortly after the early release of MMWR was made public. The underlying data from week 35 and 36 included unsubtypables, suggesting the additional H3 evolution led to a negative result for human H3 typing reagents. However, the underlying data (and accompanying figure) for week 37 and 38 removed the two unsubtypables, suggesting the cut-offs had been adjusted to classify the trH3N2 cases as seasonal H3N2 or to report such cases as negative (which might explain why only 2 of the 4 trH3N2 cases were reported as unsubtypables.

However, this week’s FluView increased the confusion because the underlying data again lists an unsubtypable for week 33 (which would correspond to the collection date for A/Pennsylvania/09/2011) and week 34 (which would correspond to collection dates for A/Pennsylvania/10/2011 or A/Pennsylvania/11/2011), but the figure (below) representing the underlying data only displays an unsubtypable for week 33.

Thus, the absence of A/Indiana/08/2011 (samples collected in week 30), as well as one of the most recent confirmed cases from Pennsylvania (samples collected in week 34), and the inconsistencies for the reporting of unsubtypables in week 33 and 34 continue to raise concerns that the number of trH3N2 in the United States is markedly higher than those reported in the sub-typing table and figure reported in weekly FluView reports.

An explanation for these inconsistencies is overdue.

[dothedd]

Bizzare trH3N2 Unsubtypable CDC Reporting In FluView
Recombinomics Commentary 16:00
October 16, 2011


Four human infections with novel influenza A viruses were detected in children from two states (Indiana (1) and Pennsylvania (3)). All four children were infected with swine-origin influenza A (H3N2) viruses; two were hospitalized; all four have since recovered from their illness. The case in Indiana did not report exposure to pigs prior to illness onset, although an epidemiologic investigation concluded human to human transmission was likely as a close contact reported direct contact with pigs prior to the child’s illness onset. The three cases in Pennsylvania were associated with attendance at a local fair where swine were exhibited.


The above comments from the first CDC FluView (week 40) for the 2011/2012 season note indirect linkage of the four trH3N2 cases with swine, but acknowledge that there is no direct linkage for the Indiana case, and is silent on direct contact for the three Pennsylvania cases. Although the three cases in Pennsylvania represent the largest number of confirmed human trH3N2 from a single location, and the flu gene constellation matches the Indiana case, the reporting of these cases in the sub-typing figure and underlying data has been inconsistent and confusing, raising serious questions about the status and reporting of other trH3N2 cases.
The inconsistencies in the 2011 trH3N2 cases follow delays in reporting 2010 cases. The clustering of 2010 cases began a year ago and these clusters were announced in a WHO pager alert for two cases, represented by A/Wisconsin/12/2010 and A/Pennsylvania/14/2010 (PA/14/10). However, at the time of the alert there was a second Pennsylvania case, A/Pennsylvania/40/2010 (PA/40/10) under review, who was infected less than a week prior to the Wisconsin case. However, PA/40/10 was initially reported as seasonal H3N2, and the report of this case as trH3N2 was delayed 5 months and reported in week 4 of 2011. Similarly, an Minnesota case (represented by A/Minnesota/11/2010, was reported shortly after the pager alert, and the index case was linked to additional symptomatic family members. The daughter of the index case subsequently serologically lab confirmed to have been trH3N2, presumably by her father or other family members since she had no reported linkage or contact with swine. However, reporting of this case was delayed 6 months, and testing of symptomatic family members was reported as inconclusive. Moreover, the CDC has used the isolate from the index case to develop a pandemic trH3N2 vaccine.

Concern due to the clustering of the 2010 trH3N2 cases was increased by the clustering of the 2011 trH3N2 cases. All four of the 2011 cases had the same constellation of flu genes. 5 of these genes were closely related to the dominant trH3N2 sequences. The PB1 was related to a prior triple reassortant outbreak at the Huron County fair and represented by two human isolates, A/Ohio/01/2007 and A/Ohio/02/2007. The NA gene in the 2011 isolates was closely related to the gene found in PA/14/10, while the MP gene matched the sequences in pandemic H1N1. The acquisition of the pandemic H1N1 MP gene increased concerns because the MP gene was deemed critical for the jump of pandemic H1N1 from swine to humans.

The presence of this rare constellation of flu genes in all four human 2011 isolates, and absence of this constellation in any swine isolates, strongly suggested that the 2011 trH3N2 was evolving and transmitting in humans. The CDC claim of no sustained transmission was blunted by the failure to identify a source for any of the four confirmed cases. The Indian case had no contact with swine, and although his caretaker did have contact, neither the caretaker no the associated swine had flu symptoms, and no evidence of swine influenza infections have been presented. Similarly, the three Washington County attended the same agricultural fair where swine was exhibited, but no symptoms have been reported for the swine at the fair and the sequences of the cases indicates the isolate from the Schuylkill resident, A/Pennsylvania/09/2011, were distinct from the other two cases, signaling two source linked to the fair, but the sequences from the two latter cases (A/Pennsylvania/10/2011 and A/Pennsylvania/11/2011) were virtually identical to the Indiana case, A/Indiana/08/2011.

The sequence data strongly suggests that the number of trH3N2 cases at the fair was markedly higher than the three confirmed cases, but detection of these cases is problematic because the H3 gene traces back to a seasonal H3N2 infection of North American swine in the 1990’s. This origin led to the delay in reporting the trH3N2 case, PA/40/10, which was initially reported as sesasonal H3N2. However, the 2011 H3 sequences have evolved further, and the initial Washington County fair cases were reported as unsubtypable, indicating this additional evolution had reduced the sensitivity of the human H3 sub-typing reagents for the 2011 trH3N2 cases. Thus, samples identified as influenza A positive, H3 negative would be likely trH3N2, which could be confirmed by the CDC with a PCR test specific for trH3N2. This scenario is similar to initial testing of pandemic H1n1, which were influenza A positive but H1 and H3 negative, which were then sent to the CDC for further testing because the states did not have the reagents for PCR testing for trH1N1. When the volume of samples to the CDC overwhelmed the testing, PCR kits for trH1N1 were then distributed to the states.

Currently, the PCR tests for trH3N2 have not been distributed and detection is dependent on states sending suspect cases to the CDC for further analysis. However, the recent reports in FluView have raised serious question about the state or CDC testing. The reports for PA/09/11 have been inconsistent. All sequences from this case have been made public at GISAID and Genbank, and the case was reported in the early release MMWR as well as the associated text in week 34 FluView, the unsubtypable categorization first appeared in the weekend following publication in these two source in the table of underlying data for the sub-typing figure. The week 33 collection was then reported in the table and figure in week 35 and week 36 reports, but was then absent in the week 37 and week 38 reports. It reappeared in the week 39 report, but as seen in the figure below, it again disappeared in the week 40 report, which had data for the first week of the 2011/2012 seasonal as well as the data for weeks 21-39, which included the collection dates for all four 2011 samples positive for trH3N2.

The reporting of PA/10/11 was even more bizarre and inconsistent. The unsubtypable (sample collected in week 34) was first reported in the week 35 report and was again displayed in the week 36 report. However, it disappeared from the figure and table in week 37 and week 38 reports, and then reappeared in the week 39 table, but not in the week 39 figure, which is based on the week 39 table.
Moreover, the other two 2011 trH3N2 cases, from samples collected in week 30 and week 34, have not been represented in any of the tables or figures (the week 30 data has no reported unsubtypables or H3N2 cases).

The inconsistent and bizarre reporting of the unsubtypables raises concerns that these patterns are linked to the detection of additional trH3N2 cases or suspect cases, and associate changes in criteria for the representation of these cases in the sub-typing figures and tables in FluView.

These changes have been made without explanation, and a clear definition of criteria for reporting of unsubtypable / trH3N2 in the sub-typing figure and table is long overdue.

NOTE THE CHART WITHIN THE TEXT:

www.recombinomics.com/News/10161101/trH3N2_Unsubtypable_Bizarre.html

[dothedd]

Week 42 MMWR Reports Seventh trH3N2 Case In 2011 (10/28/11 12:40)

Is US CDC Playing A Shell Game With trH3N2 Unsubtypables? 10/27/11 23:30)

Maine CDC Requests Influenza A Positive Samples (10/27/11 19:00)

Week 42 MMWR Has Seven Novel Influenza Cases In 2011 (10/27/11 15:30)

Maine trH3N2 Unsubtypable Not Reported In CDC FluView (10/26/11 21:00)

Washington County trH3N2 Cluster Update Fails To Find Source (10/26/11 19:00)

2011 Human trH3N2 Constellation Absent In Swine (10/26/11 14:30)

Most Recent US Adolescent H3N2 Sequences Are trH3N2 (10/25/11 01:20)

CDC Hopes and Dreams On 2011 trH3N2 Swine Link (10/24/11 22:30)

CDC Hopes and Dreams On 2011 trH3N2 Evolution (10/24/11 17:30)

Fuzzy CDC Summary of SOIV / trH3N2 In Humans Needs Update (10/22/11 09:00)

CDC In State of Denial Regarding trH3N2 Human Transmission (10/21/11 23:15)

Maine trH3N2 Sequences Signal Human Transmission (10/21/11 20:40)

ProMED Comments on Swine Exposure By 2011 trH3N2 Cases (10/21/11 18:30)

Maine trH3N2 Inconclusive Sub-typing Raises Concerns (10/20/11 20:30)

Maine Issues trH3N2 Health Advisory (10/20/11 18:30)

Maine trH3N2 Not Reported In Week 41 MMWR (10/20/11 16:00)

Maine trH3N2 Evolution Raises Detection Concerns (10/20/11 13:30)

trH3N2 Case in Maine Matches Indiana and Pennsylvania (10/18/11 17:50)

trH3N2 Case In Maine Raises Pandemic Concerns (10/18/11 01:30)

Four Hospitalized Suspect H5N1 Cases In Lombok Indonesia (10/17/11 13:40)

Fatal H5N1 Cluster In Bali Indonesia Increases To Three (10/17/11 12:20)

Fatal H5N1 Cluster In Bali Indonesia Raises Concerns (10/17/11 02:40)

www.recombinomics.com/whats_new.html

SORRY , BUT I CANNOT POST THESE INDIVIDUALLY NOW, BUT THEY ARE WORTH THE READ!!!

I broke two bones in my lower right arm... and in my wrist, wherein there is a steel plate with pins holding the wrist together, and in place. That is the short version.

I HAVE ALL I CAN DO TO CONQUER MY COMPUTER MOUSE, that also appears to be on PERCOCET. The up side is, I will be ambidextrous in 13 weeks.

[dothedd]

#

www.recombinomics.com/whats_new.html

SORRY , BUT I CANNOT POST THESE INDIVIDUALLY NOW, BUT THEY ARE WORTH THE READ!!![/color]

Indiana DoH Denies Novel trH3N2 Circulation In Humans (11/03/11 23:30)

Indiana DoH Reports Second trH3N2 Case As Inconclusive (11/03/11 22:15)

Indiana DoH Confirms Second trH3N2 Case (11/03/11 20:00)

Recent Indiana and Maine trH3N2 Cases Not In Week 43 MMWR (11/03/11 15:20)

RBD Changes In Fatal 2011 H5N1 Case In Indonesia (11/03/11 12:20)

CDC Charade On trH3N2 Swine Exposure Raises Concerns (11/02/11 19:45)

Absence of Maine trH3N2 Unsubtypable Increases Concerns (11/02/11 12:45)

Maine CDC Confirms Second trH3N2 Case In October (11/01/11 22:15)

Fatal Unsubtypables In the United States Raise Pandemic Concerns (11/01/11 18:15)

Three October trH3N2 Cases In Maine and Indiana Match (11/01/11 16:45)

New Indiana and Maine trH3N2 Cases Raise Pandemic Concerns (11/01/11 12:45)

Emergence of A Human Contagion trH3N2 (10/31/11 12:25)

[dothedd]

SORRY, BUT I CANNOT POST THESE INDIVIDUALLY NOW, BUT THEY ARE WORTH THE READ!!!

www.recombinomics.com/whats_new.html

First Novel Swine trH3N2 Raises Pandemic Concerns (11/20/11 23:45)

USDA Identifies First Novel Swine trH3N2 In New York (11/20/11 13:40)

Maine trH3N2 Sequence Matches Signal Human Transmission (11/19/11 21:00)

Tale of Two CDC trH3N2 Reports Raises Pandemic Concerns (11/19/11 16:00)

trH3N2 Swine Exposure Exposed (11/19/11 14:20)

Swine Exposure Drives trH3N2 Testing (11/17/11 18:15)

Hong Kong Swine trH3N2 Distinct From Human Isolates (11/17/11 13:40)

Indiana DoH Detects trH3N2 With Newly Approved PCR Test (11/17/11 09:00)

Maine CDC Detects trH3N2 With Newly Approved PCR Test (11/16/11 20:00)

Both Maine trH3N2 Cases Linked To Fryeburg Fair (11/16/11 13:00)

Fryeburg Pig Scramble Raises trH3N2 Swine Exposure Issues (11/16/11 04:15)

CDC Have You Heard? Exposure On 2nd Maine trH3N2 Case (11/15/11 12:00)

Cumberland Pig Scramble Raises trH3N2 Swine Exposure Issues (11/15/11 01:30)

Vague trH3N2 CDC Case Reporting Raises Concerns (11/14/11 22:00)

CDC trH3N2 Testing Continues To Be An IHR Reporting Issue (11/14/11 15:40)

More Swine Match Failures With Novel Human trH3N2 (11/14/11 11:30)

US Region 4 Influenza A Cases Raise trH3N2 Concerns (11/13/11 10:00)

IHR Date Error Based On CDC Reports Raise trH3N2 Concerns (11/13/11 02:00)

Lack of Sero-typing of US Flu A Positives Raises trH3N2 Concerns (11/11/11 16:11)

Indiana Veterinarian With trH3N2 In Week 44 MMWR (11/10/11 22:30)

Asymptomatic Swine Linked To Indiana Veterinarian With trH3N2 (11/10/11 19:30)

Taiwan CDC Warns Of Travel To The United States Due To trH3N2 (11/10/11 14:00)

Hospitalized Indiana Veterinarian With trH3N2 (11/10/11 12:30)

70% Of Confirmed Influenza In ME IN PA Are trH3N2 (11/09/11 20:20)

No Thought On trH3N2 Transmission Raises Concerns (11/09/11 16:00)

WHO History Report On trH3N2 Raises Concerns (11/09/11 14:00)

Atypical Pneumonia In Indiana Children Raise trH3N2 Concerns (11/08/11 19:45)

R193M and RBD Changes in H5N1 Fatal Cluster In Bali Indonesia (11/07/11 16:45)

RBD Changes in H5N1 Fatal Cluster in Bali Indonesia (11/07/11 14:30)

trH3N2 Pandemic Vaccine Target Media Myth (11/05/11 20:20)

trH3N2 Pigs To People Media Myth (11/05/11 19:00)

(****Influenza A Deaths in Seals In New England (11/05/11 11:30)

CDC trH3N2 H2H Transmission Qualifiers Speak Volumes (11/04/11 20:00)

CDC Confirms New trH3N2 Cases In Indiana and Maine (11/04/11 18:45)

ProMED Comment on trH3N2 Rumor Raises Concerns (11/04/11 15:30)

[dothedd]

flutracker.rhizalabs.com/

www.recombinomics.com/whats_new.html

Greetings from the one hand typist.

MERRY CHRISTMAS/HAPPY HOLIDAYS[/b]


WHO Issues Pandemic H3N2pdm11 CDC PCR Kit Guidance (12/03/11 02:45)

CDC H3N2pdm11 Name Blame Game (12/02/11 23:45)

Iowa Swine trH3N2 Constellation Matches H3N2pdm11 (12/01/11 19:00)

Kansas Swine trH3N2 With H1N1pdm09 M Gene (12/01/11 14:00)

Curious CIDRAP Comments on Swine H3N2pdm11 Match NOT (11/30/11 21:30)

Curious CIDRAP Comments on Swine H3N2pdm11 Match (11/30/11 07:00)

CDC Calls H3N2pdm11 Human Transmission A Mystery (11/29/11 23:45)

Fatally Flawed ECDC H3N2pdm11 Risk Assessment (11/29/11 22:00)

The 2011 H3N2pdm11 Pandemic Puzzle 11/29/11 20:00)

Iowa H3N2pdm11 Surveillance Raises Pandemic Concerns (11/29/11 7:30)

trH3N2 Swine Close Contact Media Myth (11/28/11 21:00)

CDC Novel trH3N2 Swine Exposure Coupe De Grace (11/28/11 01:00)

Clarify CDC Confusion On Novel trH3N2 In US Swine (11/27/11 16:00)

Retraction of Claim of Novel trH3N2 In US Swine Overdue (11/27/11 13:15)

CDC Novel trH3N2 In United States Swine Scam (11/26/11 23:45)

WHO Prepares for trH3N2 Pandemic (11/26/11 17:30)

CDC Curious Comments on Novel trH3N2 In US Swine (11/26/11 14:20)

Media Myths On trH3N2 Emergence and Significance (11/25/11 21:20)

Media Myths On trH3N2 Evolution and Significance (11/25/11 20:20)

CDC Claim of Widespread Novel trH3N2 In Swine Is False (11/25/11 18:40)

CDC Again Cites Swine Exposure In Request For trH3N2 Samples (11/24/11 18:15)

Iowa trH3N2 Cluster Of Five Forces WHO Alert (11/24/11 17:00)

Transmission In Iowa trH3N2 Cluster of Five Raises Concerns (11/24/11 15:30)

75% of US Sequenced Influenza A+ Under 10 Cases Are trH3N2 (11/23/11 22:45)

CDC Releases trH3N2 Sequences from Iowa Cluster (11/23/11 15:20)

Silent Spread of trH3N2 Across the United States (11/23/11 14:00)

Media Myth On Seasonal H3N2 Vaccine Utility Against trH3N2 (11/23/11 12:30)

CDC In Denial Of Sustained trH3N2 Human Transmission (11/23/11 11:45)

CIDRAP Maintains Media Myth On trH3N2 Swine Exposure (11/23/11 06:45)

Most United States Adolescent Influenza A Is trH3N2 (11/23/11 05:30)

CDC Have You Heard On trH3N2 Cluster In Iowa (11/23/11 03:00)

Three trH3N2 Cases In Iowa Confirm Pandemic (11/22/11 23:45)

CDC Definition of Swine Exposure For trH3N2 Cases (11/22/11 21:15)

CDC's Curious Chronology of 2010 trH3N2 Cases (11/22/11 14:00)

ProMED trH3N2 Close Contact Comment Concerns (11/21/11 22:30)

Abysmal Maine trH3N2 Testing Raises Concerns (11/21/11 13:00)[b] [/b]

[dothedd]

West Virginia trH3N2 Cluster Confirmed )12/21/11 19:30)

Expected Explosion of Novel Influenza Clusters In United States (12/21/11 14:00)

Expected Explosion Of Novel Influenza Cases In United States (12/20/11 23:00)

WHO Issues Warning On Novel Influenza (12/20/11 13:30)

CDC Recommends Increased Influenza Testing of Children (12/19/11 23:30)

CDC Requests Increased Influenza Testing In All States (12/19/11 22:30)

An Increase In US Influenza A Sequencing Is Overdue (12/19/11 21:00)

WHO Deafening Silence On Novel Flu Cases Raise Concerns (12/19/11 16:30)

West Virginia trH3N2 Cluster Raises Concerns (12/19/11 12:30)

Novel Influenza Limited Human Transmission Myth (12/18/11/11:15)

False WHO Comments On trH1N2 Minnesota Infant (12/17/11 16:15)

West Virginia trH3N2 Cluster? (12/16/11 19:30)

Minnesota trH1N2 Delayed Detection (12/16/11 11:00)

False PAHO Comments on WV trH3N2 and MN trH1N2 In Swine (12/15/11 12:00)

Hong Kong Issues RFI To WHO and CDC On H3N2pdm11 (12/14/11 20:15)

Delays With trH1N2 Minnesota Case(s) Raise Concerns (12/14/11 18:45)

Media Myth On trH1N2 Minnesota Mutation (12/14/11 15:45)

ECDC Cites Serious trH3N2 and trH1N2 Testing Issues (12/14/11 14:15)

ECDC Update On H3N2pdm11 Risk Ignores trH1N2 (12/13/11 23:45)

CDC Updates Comments On H3N2pdm11 In Swine (12/13/11 19:45)

CDC Urban Legend: H3N2pdm11 Not In Big Cities (12/12/11 21:45)

CDC Discovers H3N2pdm11 Pandemic By Accident (12/12/11 15:00)

Human Transmission of Multiple Novel Influenza Constellations (12/12/11 12:00)

78% of US 2011/2012 Adolescent Flu A+ Sequences Are Novel (12/12/11 07:45)

PB1 E618D In Novel trH1N2 In Minnesota Case Raises Concerns (12/11/11 12:30)

Media Myth On Relatedness Between Novel H1N2 and H3N2 (12/09/11 23:00)

Abysmal H3N2pdm11 Surveillance Raises Pandemic Concerns (12/09/11 21:00)

Novel H1N2 Case In Minnesota With H3N2pdm11 Genes (12/09/11 17:00)

Novel H3N2pdm11 Case In West Virginia (12/09/11 16:30)

trH3N2 HA NA MP Matches With Ohio H3N2pdm11 Parent (12/08/11 19:30)

trH1N2 Matches With NA and MP H3N2pdm11 (12/08/11 14:00)

Increasing H1N1pdm09 M Gene In US trH1N2 Swine (12/07/11 22:30)

Ohio trH1N2 Swine Solves H3N2pdm11 Pandemic Puzzle (12/07/11 08:00)

Ohio trH1N2 Swine Is Other Parent For H3N2pdm11 (12/06/11 22:20)H1N1pdm09 M Gene Drives Genetic Instability In American Swine (12/06/11 12:45)[/b]



ttp://flutracker.rhizalabs.com/

www.recombinomics.com/whats_new.html

[dothedd]

Marin County California Issues H3N2v Alert (01/06/12 21:30)

US HHS Contracts for H3N2v Vaccine Clinical Trials (01/06/12 16:00)

West Virginia H3N2v Cluster N2 Recombination (01/05/12 23:55)

MP Identies Confirm West Virginia H3N2v Cluster Transmission (01/05/12 21:30)

Flu-like Illness In 23 Contacts of H3N2v West Virginia Cluster (01/05/12 05:20)

Pediatric H3N2v Case In Napa County California (01/05/12 03:30)

Shenzhen H5N1 P198S Is In Clade 2.2 Escape Mutant (01/04/12 16:30)

HA Changes In Fatal H5N1 Case In Shenzhen Raise Cincerns (01/04/12 12:40)

Q196K and S227R in Fatal H5N1 Case In Shenzhen China (01/04/12 03:40)

Clade 2.3.2.1 in Fatal H5N1 Case In Shenzhen China (01/01/12 21:20)

Critical H5N1 Case In Shenzhen China (12/30/11 22:45)

H1N1v H1N2v H3N2v Testing Bottleneck Expected (12/29/11 12:00)

H1N1v H1N2v H3N2v Cases Dominate US Influenza Sequences (12/28/11 13:30)

Genetic Instability in H1N1v Wisconsin Case (12/28/11 03:30)

Fatal H3N2v With H1N1pdm09 M Gene In Kansas Swine (12/27/11 18:30)

CDC Calls Novel Human Triple Reassortants Variants (12/26/11 15:00)

CDC Requests 24 Hour Notification of H3N2v Suspect Cases (12/26/11 12:00)

PCR Failures Raise Novel Influenza Pandemic Concerns (12/25/11 19:30)

Sustained trH3N2 Transmission In West Virginia (12/25/11 12:30)

Novel Under 10 Flu Cases In the United States Approach 100% (12/25/11 9:30)

More CDC Curious Comments On H3N2pdm11 In US Swine (12/24/11 14:00)

West Virginia Large and Extended trH3N2 Cluster (12/23/11 23:15)

West Virginia Issues trH3N2 Alert (12/23/11 19:15)

trH3N2 Transmission In West Virginia Raises Pandemic Concerns (12/23/11 17:15)

Novel trH1N1 Case In Wisconsin Raises Pandemic Concerns (12/23/11 15:30)

North Dakota Issues trH3N2 Health Advisory (12/23/11 12:15)

Hidden Novel Influenza Pandemic (12/22/11 23:45)

Iowa Novel Influenza Testing Paradox (12/22/11 16:45)

West Virginia trH3N2 Cluster Raises Detection Concerns (12/21/11 21:00)

[dothedd]

H5 Transmission On An H1N1pdm09 Genetic Background (01/25/11 19:30)

Fatal Suspect H5N1 Case In Cengkareng Indonesia (01/25/11 14:15)

Fatal Suspect H5N1 Case In Tangerang Indonesia (01/25/11 12:45)

CDC Selects New H3N2v Pandemic Vaccine Target (01/23/11 21:45)

China Censors News On H5N1 Guizhou Case (01/23/11 16:45)

HA S227N and PB2 E627K In Fatal H5N1 Cambodia Case (01/23/11 11:00)

Absence of Poultry in H5N1 Fatal Case in Guizhou China (01/22/11 14:00)

H5N1 Transmission Experiment Halt - Censorship Continues (01/20/11 19:00)

Indonesia Confirms H5N1 Cluster In North Jakarta (01/20/11 06:45)

WHO Confirms H5N1 Cluster In Fayoum Egypt (01/20/11 05:45)

The Pseudoscience and Pseudonature H5N1 Health Hazard (01/20/12 04:00)

Published H5N1 One Change From Efficient Transmission (01/19/12 22:30)

H5N1 Fatal Cluster In Tanjung Priok North Jakarta Indonesia (01/19/12 16:30)

H5N1 Clade 2.3.2.1 Migrates Into South Asia (01/18/12 23:45)

Egypt H5N1 PB2 H1N1pdm09 and Seasonal H1N1 Recombination (01/17/12 23:45)

Suspect H5N1 Cluster in Fayoum Egypt (01/17/12 17:20)

Egypt H5N1 PB1 Recombination With H1N1pdm09 (01/17/12 10:30)

Egypt H5N1 Recombines With Seasonal H1N1 H3N2 pH1N1 (01/13/12 23:30)

Wisconsin H1N1v Links US H3N2v China H5N1 Swiss H1N1v (01/08/12 20:15)

www.recombinomics.com/whats_new.html

[dothedd]

H1N1pdm09 Recombination In Egypt H5N1 Raises Concerns
Recombinomics Commentary 21:00
January 25, 2012

The recently released H5N1 sequences from Egypt contain H1N1pdm09 sequences in the PB1 and PB2 gene segments. The recent comments by Yoshihiro Kawaoka on the data in the censored Nature paper indicate H5 on an H1N1pdm09 genetic background transmits in ferrets. Although the paper remains censored, the comments suggest H5 was added to 7 gene segments from H1N1pdm11. However, an earlier study suggested that the H1N1pdm09 M gene was critical for the jump from swine to humans, so it is unclear if the other six gene segments are required for transmission.

However, the presence of H1N1pdm09 gene sequences in the H5N1 isolates raise concerns that additional combinations are likely and the status of such combinations are far from clear. The most recent human H5N1 sequence from Egypt are from cases in March 2010. More recently, clusters in Egypt have been confirmed and an increased case fatality rate has been noted, raising concerns that H1N1pdm09 internal genes may be present in human cases in Egypt.

NAMRU-3 typically generates H5 and N1 sequences for human cases in Egypt, while samples are frequently sent to the CDC in Atlanta for further analysis. These sequences should be released immediately. The presence of such sequences may signal and enhanced transmission in humans and may be related to the confirmation of clusters.

Although the H5 transmission in ferrets in the Kawaoka study did not produce a lethal H5N1 in the ferret model, the wide circulation of such sequences in human populations could have significant implications, as has been demonstrated for the H1N1pdm09 M gene in trH3N2 (H3N2v) and trH1N1 (H1N1v) cases in the United States in 2011.

The Kawaoka Nature paper highlights the need for full sequences from cases in Egypt. This need applies to other recent cases, such as the clusters in Indonesia. Only HA and NA sequences were released from the Bali cluster, which also had clear evidence of recombination. Similarly, no sequence data has been released for the cluster in North Jakarta.

The censored papers at Nature and Science highlight the dangers of a transmitting H5N1 and demand more timely and transparent release of H5N1 sequences.