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.

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