H5N1 Polymorphism, Q296H, Arises in Singapore, World’s Busiest Port

A review of HA:296 is in order based on today’s releases.

The polymorphism, Q296H, was found in the 11 year old female death in SaoPaulo43812, is widely conserved in the Northeastern US, is conserved in Italy and is found in Northwestern Europe.

This change has moved into Singapore, a major gateway to the world. Singapore shares the title of Busiest Port in the World with Shanghai in different categories. 296H emerged in Singapore in one of the four sequences sampled on 2009-06-14 and deposited yesterday, A/Singapore/TLL54. No other segments for this sample are on file for review.


  • 2E
  • 35I
  • 66E
  • 296H 
The Glutamate (E) near the beginning matches 1918 and most H5N1. This HA homology additionally occurs with SaoPaulo2233, Italy127 and NY4197, each of which also share 296H with this SingaporeTLL54 specimen under review.

The 296H change is rare on PF11 sequences in Asia with only 2 matches in China (Shanghai143T, Shandong1) and 1 in Japan (Tokushima1).  On the PF11 background, only 31 sequences across the globe now carry 296H.

New York obviously provides a substantial international vector from the airports and seaports.  Shanghai and Singapore vector air and sea extensively.  The Italian port of Ancona provides a significant trans-Adriatic ferry service.

An intra-segment exclusivity exists presently in PF11 between 296H and 206T though donors are proximal in China, Japan, SaoPaulo, Finland and Canada with extensive coverage in New York and Italy.

We suggest tracking for interplay between 296H and the recent RBD changes noted in QC1 and QC2.

Please visit GeneWurx.com for insight into the latest published studies.



Russian Sequences, Omsk01 & Ekaterinburg01, show 2nd unique Quadruple Cross-Segment Combination (QC2)

Two of the sequences released by Russia's Vector lab in the past 7 days demonstrate another unique Cross-Segment Quadruple Combination (QC2) very similar to the combination (QC1) recently noted in the discussion on the Vector released Kazakhstani entry, Almati01.

Please review the sequences from the two samples for validation of this finding.
  • HA / NA : A/Omsk/01/2009
  • HA / NA : A/Ekaterinburg/01/2009
This introduction on the PF11 background carries a quadruple set of amino acids crossing Hemagglutinin and Neuraminidase:

  • HA 206T
  • HA 226R
  • NA 106I
  • NA 248N
Omsk01 also carries NA:127S matching a polymorphic position with TamiFlu resistant Washington28.  Ekaterinburg01 shows NA:259D that appears unique at this time within ΣPF11.  Initial studies indicated that reassortment is impeached as a mechanism for these genetic acquisitions.

The QC2 changes, of course, are not fixed in the geography, as other sequences from the areas demonstrate considerable variation.  Movement within and around the Receptor Binding Domain (RBD) continues to draw our focus.

A University of Wisconsin-Madison study in 2008 found that Glutamine (Q) at 226 mediates the Binding Affinity for SAα2,6Gal (Sialic Acid α2,6) and, in turn, lowers infectivity levels in primary epithelial cells for humans compared to Leucine at that position (226L).  I am not aware of conclusive studies comparing 226Q to 226R in this regard.  Please contact me if you have applicable studies.

226R on PF11 Background (9)
  • Omsk01
  • Irkutsk02
  • Ekater01
  • Finland553 with HA:206T and NA:106I
  • Lishui01
  • ZhejiangDTID-ZJU01
  • Texas17
  • MX4603
  • MXInDRE4487
Mixed signals or absent data for residue 226 appear in 13 ΣPF11 sequences across the US and Mexico.

At any rate, ΣPF11 in Eurasia and the Americas is now varying away from a stable, low infectivity position in the Receptor Binding Domain to an amino acid found in H5N1 at 226 (A/Anhui/2/2005/H5N1).  And I remind you that Anhui2 carries 206T and 296H which we are seeing persistently emerge throughout the world including clustering in Italy and the Northeastern United States.

Scrutiny is required here.

Please visit GeneWurx.com for insight into the latest published studies.



China - Lishui01 PF11 Carries Human-Fit Seasonal Marker at 324

A/Lishui/01/2009 from July 2009 appears to be the first Chinese PF11 sample to carry the robust signal of 324I on HA, a human-fit polymorphism carried on Seasonal H1N1 2008 and 2009 backgrounds as well as 1918 specimens. 

The Lishui HA also shows the rare PF11 226R.  The recent ZhejiangDTID-ZJU01, Ekaterinburg01 and Finland553 carry this polymorphism that profiled early within ΣPF11 in one Texas and two Mexico samples.

Please visit GeneWurx.com for insight into the latest published studies.



United States TamiFlu Resistant NA Triple Combination Analysis

Until today, all ΣPF11 H275Y* cases on file carried 106I on Neuraminidase.

Two TamiFlu resistant sequences from Washington landed with 106V.  Each common amino acid at 106, Isoleucine and Valine, is now represented within ΣPF11 TamiFlu resistant sequences. Additionally, WA28 and WA29 are two of only three TamiFlu resistant strains to carry 248N; Osaka180 is the third. The remaining four GenBank sequences show 248D.

Note the reversal of amino acids in ΣPF11 at residue 248 on the pairings (248 and 275) from Seasonal H1N1. Seasonal H1N1 from 2008 into 2009 is predominately 248N on TamiFlu resistant strains with only three 248D sequences. Conversely, the largest percentage of PF11 TamiFlu resistant strains carry 248D (57%). Does the 248N from WA28, WA29 and Osaka represent the logical emergence of a second viable branching with 275Y on the PF11 background?

Surveillance is incomplete. No conclusions may be drawn at this point.

Human-fit Seasonal H1N1 from 2008 and 2009 typically demonstrates the H275Y TamiFlu Resistance marker and a NA Triple Combination at 106, 248 and 286:

106I, 248N, 275Y, 286G

Outside of the TamiFlu marker at residue 275, the remaining three aspects of the Seasonal H1N1 NA Triple Combination showing 106I, 248N and 286G are now represented in several dual permutations on the PF11 background. The variation through individual acquistion is trackable and continues in the past 12 weeks to increase geographically, suggesting a progression to a potential fixing of the entire human-fit, NA Triple Combination on PF11 templates.

At this time, 17 PF11 specimens carry 2 of the 3 NA Triple factors. 13 of those 17 cases are concentrated in a tourist area of southwestern Europe that also has PF11 specimens circulating in geographic proximity with the third seasonal marker, 286G, required to complete the NA Triple. These markers in the NA Triple Combination may herald as precursors for ease of TamiFlu resistance acquisition or may simply mark a more human-fit Neuraminidase.

With those prerequisites concerning the base of PF11 in place, now we return to examine the currently published PF11 TamiFlu resistant sequences against these NA Triple Combination markers. The following permutations are now represented on the seven PF11 anti-viral resistant sequences:

106V, 248N, 275Y, 286S = WA28, WA29
106I, 248N, 275Y, 286S = Osaka180
106I, 248D, 275Y, 286S = HK2369, Yamaguchi22, Denmark528, Hunan SWL3

Can we ascribe this set of unusual permuations to typical Pig=>Human Influenza Flux? As 248N continues to spread widely on PF11 backgrounds, will the pairing of 248N and 275Y become dominant or will we see a future Hydra Effect with two fit branches?

* N1 numbering equal to H274Y TamiFlu resistance in H5N1

Please visit GeneWurx.com for insight into the latest published studies.



Poland303 19M similar to Sapporo1, NJ01, Almati01 and Changsha78

The National Influenza Center in Warsaw deposited two NA sequences today. The second deposit, A/Poland/303/2009, is exceptional. Poland303 from a 19 year old male sampled on 2009-07-10 varies significantly with the first deposit from a 71 year old female sampled in the same week.  Mixed peaks or dropouts may be involved in each sequence at multiple locations.

Further study is required due to several potential anomalies. However, the preliminary inspection shows that Poland303 is most similar to Sapporo1, NewJersey01, Almati01 and Changsha78. The nucleotide similarity is 99% (>1401 of 1407), but the few dissimilarities are curious.

Poland303 demonstrates 8 NA SNPs and is inconclusive at residues 79, 166 and 216 with additional distinguishable amino acid polymorphisms:


The KW at 200:201 appears to be unique within ΣPF11 during our initial enquiries.

Poland282 demonstrates 12 NA SNPs and is inconclusive at 79, 190, 195, 205, 220, 322 and 335 with the following distinguishable polymorphisms:

191L synonymous

The variability between these two sequences and secondly among this group and the others in their geography may signal the presence of a genetic acquisition stimulator or, the more likely explanation, a lab contamination.

Outside of a multi-stage lab contamination (unlikely after reviewing the full set of Poland sequences), these two specimens follow a trend indicative of SNP recombinations with Avian H1N1 from Europe AND Swine H3N2 from Europe.  That capitalised word in the previous sentence is an "AND".  Until we find intermediate forms bearing Neuraminidase hybridisations of European swine H3N2, European avian H1N1 and PF11, the estimation presented here is my most logical explanation for a very unlikely set of sequences.

Please visit GeneWurx.com for insight into the latest published studies.



Almaty, Kazakhstan - Unique Cross-Segment Quadruple Combination (QC1)

A sequence from Kazakhstan's largest city, the capital Almaty, was deposited at GenBank on 2009-08-18 by the Russian Vector lab using the nomenklatura's nomenclature of A/Almati/01/2009 with no collection date. Elevation and population density of the host geography raised our interest in this particular specimen and the signal was correlated upon inspection.

At the amino acid level, Almati01 matches the HA of NewJersey01 and Sapporo1, the NA of Amagasaki1, Amagasaki2 and Hyogo1.  Bear in mind that NewJersey01 is closely related to the Tamiflu-resistant HongKong2369 specimen.

Of a more compelling interest is the first deposited emergence of a particular Cross-Segment Quadruple Combination (QC1) that may prepare the virus for additional human-fitness acquisitions. This Almati01 sequence appears to be the singular ΣPF11 sequence on file that carries the quadruple set of amino acids:

  • HA 206T
  • HA 225E
  • NA 106I
  • NA 248N
The introduction appears to be NA 248N, but the collection date is absent on Almati01 so conclusions may not be drawn. Comparison data is sparse because the neuraminidase segment is unavailable or unpublished on many of the 13 candidate ΣPF11 dual HA combinations of 206T and 225E. Plainly stated, the database coverage to investigate this quadruple combination is far from broad. However, in this case, scarcity breeds clarity, sharpening a focus for future monitoring in anticipation of a more robust dataset. 

Movement within and around the Receptor Binding Domain (RBD) always draws focus on a new specimen.  The genetic acquisition path of ΣPF11, including this profiled specimen, suggests a non-random pattern of polymorphisms.

Please visit GeneWurx.com for insight into the latest published studies.



Introduction to PF11

PF11: Pandemic InFLUenza H1N1

Genetic Acquisition Analysis

A managed campaign of political and laboratory messages in the media continues to state that no changes are found in Pandemic Influenza H1N1. The underlying genetics database, however, demonstrates many acquisitions and a consistent trend of fitness-inducing polymorphisms. As samples have been added each week around the world, a pattern has emerged.

The pattern indicates a persistent hyper-morphic state on the PF11 background at certain positions within particular species. Of certain note is the directional movement on the Hemagglutinin (variously termed HA and H1) and Neuraminidase (variously termed NA and N1) segments. Though all Influenza consistently recombines with existing genetic material from proximal non-self strains, PF11 has demonstrated a march toward human-fit acquisition that is remarkable in speed and geographic spread.

The purpose of these point by point studies is to indicate and discuss several of those key polymorphisms and examine the potential next steps in humans. As you have seen finally released in the media, PF11 in the human-form has now been sequence-confirmed in birds and in swine, allowing hundreds of species as additional “mixing vessels” or recombination reservoirs. This predicted species jump, more importantly, provides flight-based transportation vectors that will easily number in the millions of infected birds with a potential pool of billions in various seasons.

Recall the CDC reports that 70% of all emerging diseases are zoonotic (originate in animals). The asymptomatic flight-based animals transport the disease from their land-based counterparts, the swine, who are playing their normal role as ideal mixing reservoirs for recombination due to their robust tolerance to many strains of Influenza. Pig=>Duck=>Human=>Chicken=>Pig and dozens of additional paired vectors of transmission have been confirmed between human, swine and avian species. The genetic transition state between species, the Influenza Flux, is dangerous for humans due to continual creation of novel antigen and species-specific phenotypical traits that strain the human immune system, elevate the potential for vaccine escape and may produce a negative interplay with that nemesis of vaccine scientists, Original Antigenic Sin (OAS). 

OAS, in a few words, describes the physiological phenomenon observed since 1960 that antibody production to a novel virus is mediated and frequently downgraded by the priming epitope or first infection in an individual host from that species of virus (original childhood infection).  Frequent exposure to novel antigens within a virus species (notably Influenza), via vaccine and/or natural infection, tends to create fewer and fewer new antibodies that bind properly to the slightly dissimilar recent virus / antigen.  The documented process counter-intuitively invokes high-specificity memory B cells from the priming epitope (original childhood infection) which then feeds back signals to reduce the activation of naive B cells toward the new antigen.  Studies observe situations where Antibody Secreting Cells (ASC) produce antibodies to earlier infections in a ratio higher than antibodies to the new infection.

In short, PF11 at this time continues to create a Hydra Effect, attacking the human with many different heads or genetic variations.  The Hydra Effect coupled with the observed Interferon-Deranging, Rapid Replicating Viral (IDRRV) property creates a unique and daunting foe.

We will overview our findings on four gene segments with discussion on inter-segment correlations.


Pandemic InFLUenza H1N1.
Triple Reassortment Virus with Avian, Swine and Human Influenza Genetics, 2009 emergence.

Sigma PF11.
In general, the PF11 Reservoir of genetic material.  Accumulation of all specimens trending to the established pandemic backgrounds.

PF11 Beta.
Today.  Current PF11 specimens. These strains have progressed beyond the initial Spring 2009 PF11 infections, yet continue to be only partially human-fit.

PF11 Omega.
A proposed future PF11 momentary state of peak high-transmissibility and high-virulence potentially correlating to the zenith of the High-CFR window for humans.

PF11 Post-Omega.
A proposed future PF11 state occurring at some point after PF11Ω, having a progressively downrated virulence and the potential for establishing a smaller set of dominant strains in the PF11 Reservoir, ΣPF11.

Polymorphic Homology to Zoonotic Reservoirs.
Found in Influenza A from any animal reservoir.

Polymorphic Homology to Zoonotic Avian Reservoirs.
Found in a primarily Avian Influenza Serotype sampled from any species or in an Influenza A reservoir sampled from an Avian species.

Interferon-Deranging, Rapidly Replicating Virus.
Classification system considering viral expression traits.

Interferon-Deranging, Rapidly Replicating, Enhanced Acquisition Virus.
Classification system considering viral expression traits.

Please visit GeneWurx.com for insight into the latest published studies.