Ukraine - 100% of New Sequences with Required HA and NA on Cross-Linked Background; 225G on 6 of 11; 1918 Markers Coalesce

Cross-Linked Silent HA and NA Polymorphisms Correlated with Fatal 225G Cases in the Ukraine and Russia

• HA:syn413K encoded from A1281G, AAa->AAg
• NA:syn407V encoded from T1221C, GTt->GTc

 PF11 Sequences Demonstrating Cross Segment Linkage

• Iraq8529E3  with HA 131L, 160L, 194I, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8529M1 with HA 131L, 160L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8531     with HA 130E, 131L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Australia Victoria2129 with potential H5N2 inclusions and NA 454S 
• Australia Victoria2130 with NA 454S
• Ukraine Kyiv377 with mixture of 225D, 225G, 225N, 225S, 225T and 225A
• Ukraine Lviv673
• Ukraine Lviv682
• Ukraine Cherkasy332
• Ukraine Cherkasy333
• Ukraine Cherkasy346
• Ukraine Chernihiv855L with mixture of wt 225D / 225G and additional 1918 Markers (syn238E & 324I), Fatal outcome *
• Ukraine Chernihiv856 with mixture of wt 225D / 225G , Fatal outcome *
• Ukraine Chernihiv857 with mixture of wt 225D / 225G and additional 1918 Markers (186P, syn238E, 324I & G796A), Fatal outcome *
• Ukraine Chernihiv858, Fatal outcome *
• Ukraine Dnipropetrovsk260
• Ukraine Dnipropetrovsk267
• Ukraine Dnipropetrovsk268
• Ukraine Dnipropetrovsk272
• Ukraine Dnipropetrovsk273 with mixture of wt 225D and 225G
• Ukraine Dnipropetrovsk274
• Ukraine Dnipropetrovsk1124
• Ukraine Dnipropetrovsk1171
• Ukraine LvivN2 with 225G
• Ukraine LvivN6 with 225G
• Ukraine TernopilN10 with 225G
• Ukraine TernopilN11 with 225G
• Ukraine Volin226 with 225G *
• MoldovaG120
• MoldovaG140
• MoldovaG181
• MoldovaG182
• MoldovaG191
• HA and NA Norway2924 with mixture of wt 225D and 225G
• HA and NA Norway3364-2
• HA and NA CatNS7362 TamiFlu Resistant
• HA and NA CatS1096
• HA and NA CatS1162
• HA and NA CatS1179
• HA and NA CatS1181
• HA and NA CatS1267
• HA and NA CatS1268
• HA and NA CatS1402
• HA and NA CatS1501
• HA and NA CatS1687
• HA and NA CatS1748
• HA and NA CatS1751
• HA and NA CatS1761
• HA and NA CatS1827
• HA and NA CatS1935
• HA and NA CatS2120 with multiple swine markers
• HA and NA CatS2151 with swine markers and 165N (TamiFlu Resistant CatNS7632 and Russian 225G Salekhard01)
• HA and NA Guangdong02
• HA and NA Guangdong05
• HA and NA SingaporeON1156
• HA and NA Stockholm31
• Sweden Gothenburg2 with 146G, 324I (1918) and markers found extensively in Moldova and Russia 
• HA and NA Russia4 with syn238E and 324I (1918)
• HA and NA Russia12 with 324I (1918)
• HA and NA Russia14
• HA and NA Russia19 with 324I (1918)
• HA and NA Russia74
• HA and NA Russia149
• HA and NA Russia165
• HA and NA Russia171 with 165N
• HA and NA Russia178
• HA and NA Russia180 with 165N, syn239P and 264G
• HA and NA Russia190
• HA and NA Russia191
• HA and NA Kurgan01 with HA 214E (MoldovaG168, G176, G188) and NA mixture at 407 (Fatal 225G Abakan02) 
• HA and NA Omsk02 
• HA and NA Tver2969 with 225G, Fatal outcome
• HA and NA Salekhard01 with 165N and 225G, presumptive Fatal outcome
• HA and NA Orenburg2974 with 225N, potential Fatal outcome
• HA and NA Perm01 with 131P, 225G and 324I, presumptive Fatal outcome
• HA and NA NY3702
• HA and NA NY3715
• HA and NA NY3828
• United States NewYork96
• HA and NA RhodeIsland08
• HA and NA Texas42102708
• HA and NA Texas45072128
• HA and NA Texas45122886
• United States Kentucky19 from an 18 year old subject with HA 298V
• United States Indiana20 from a 10M subject with 5 Avian H5N1 markers *
• US Private Sequence TamiFlu Resistant  
• United States NorthCarolina37 from a 24F subject with HA 298V
• United States NorthCarolina44 from a 50M subject with 6 Avian H5N1 markers *
• United States NorthCarolina46_C2     from a 39F subject with HA 298V
• United States NorthCarolina46_C2C1 from a 39F subject with HA 298V
• HA and NA swine/NC/34752 with 298V 

91 sequences have encircled the globe as of 2010-01-31 * with high fidelity carrying a cross-segment paired set of background markers matching and contributing to fatal cases in the Ukraine and Russia.  225G appears in 14 on this background; 225N once and 225E precisely zero.

Autopsy reports from Ukraine pandemic fatalities continue to demonstrate 225G and cross-segment linkages.  11 Sequences published from the Ukraine on 2010-01-27 covering late October to mid November 2009 show 6 225G sequences.  11 of 11 demonstrate the cross-segment linkage marker of NA syn407V.  6 of the 11 HA sequences are truncated just prior to the syn413K marker, but the 5 that do have the complete HA are a 100% match to the cross-segment marker. 

We would be quite grateful to see the missing portions of the HA segments to validate our model.  Data sparsity is an undesirable parameter when accuracy involves human life.

Incidentally, 6 225G sequences in various mixtures are found in the set of 11 with Chernihiv859 carrying the 'rrt' codon at the amino acid position 225 showing hyper-morphic behaviour like Kyiv377.  4 of those 225G sequences also fall on the cross-segment linkage background.  Chernihiv appears to be on the march to higher virulence using 1918 polymorphisms with additional revisions from the very special bird from Argentina (2008).  Chernihiv355L carries 3 1918 polymorphisms coding for 225G, syn238E and 324I in PF11 with markers from the red-winged tinamou.  Chernihiv357 goes beyond the call of duty by appropriating 5 1918 changes coding for 186P, 225G, syn238E, 324I and 252M in PF11 with markers from the red-winged tinamou.

Recall that 252M was found during July in Brasil, the first country to officially register 1,000 deaths.  Furthermore, this polymorphism was isolated there from post-mortem blood, indicating not only a fatality in the 11 year old girl, but also spread of the viral particles via the bloodstream.  HKswNS1659, a swine sequence frequently matched to PF11 genetic acquisitions, also carries the coding for 252M.

Kyiv377 from early November in the Ukraine demonstrates a level of hyper-morphic behaviour at amino acid 225 that was previously undocumented in ΣPF11, but is the natural progression of the genetic acquisition trend line on this pandemic reservoir.  Two sequences now additionally demonstrate the TamiFlu Resistant 275Y on NA, one from Spain in late November 2009 and one from the US with details stored in a private database. 

Areas covered include Texas (3), the Northeastern United States (5), Kentucky, Indiana, North Carolina (5), China (2), Singapore, Australia (2), the Ukraine (23), Moldova (5), Russia (18), Iraq (3), Norway (2), Sweden (2) and extensive penetration in Spain (17 sequences).

This particular cross linked background pattern may precurse 225G and mixtures of 225D / 225G.  The Orenburg2974 sequence from Russia carries 225N on this background.  Receptor Binding Site (RBS) changes at 225 are associated with fatality, 225G and 225N at a rate higher than 225E.

If LvivN6 is officially confirmed as a vaccine escape event, these cross-segment pairs may be surveilled as potential future effectors of vaccine efficacy failure.

If RBS revisions at Hemagglutinin amino acid 225 are, in fact, instructive of high pathogenicity, then Russia is in the FlightPath for a more virulent winter and the Ukraine has presently built a fog of miasma that appears to be capable of spreading across the globe while leading to an expected 1,000 deaths there in less than 80 days.  
Previous Study on this Topic:

• 2010-01-19 Fatal Ukraine Cross Segment Linkage Extends in the US, Iraq and Australia (HA syn413K and NA syn407V)
• 2010-01-01 HA syn413K and NA syn407V Cross Segment Linkage Increases Range and Penetration
• 2009-12-04 Spain Introduces 2 November Sequences with Cross-Segment Pairing from Fatal Cases in the Ukraine
• 2009-11-28 Ukraine and Spain Cross-Linked HA and NA Silent Changes Circle the Globe
• 2009-11-26 The Ukraine, Norway and Spain Share Paired HA and NA Changes

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

Russia - Ten Samples Yield One 225G, One 225N, One TamiFlu Resistant and Six on the Cross-Linked Background with HA syn413K and NA syn407V

The Institute of Physical-Chemical Medicine of Moscow and Vector introduced sequences today from 10 samples into GenBank with the HA and NA segments.  The 9 samples that are dated were taken in November 2009 and perhaps are representative of ΣPF11 at that stage in Russia.  60% of the deposit today falls onto the cross-linked background with HA syn413K and NA syn407V. 

Tomsk08 from lung tissue is a 225G case, presumably fatal, with 131P and Russia100 carries 225N with 131P.  Russia61 is TamiFlu Resistant in typical fashion with NA 275Y.  None of the three falls on the cross linked background.

Cross Linkage Sequences

Kurgan01   with HA 214E and NA mixture at 407
Russia4      with HA syn238E (1918) and 324I (1918)
Russia12    with HA 324I (1918)
Russia19    with HA 324I (1918)
Russia171  with HA 165N
Russia180  with HA 165N, syn239P and 264G

The silent nucleotide revision coding for a syn238E on Russia4 is notable.  As you can see from the data, genetics found on the 1918 Pandemic strains have been employed from the beginning in the ΣPF11 march.  The G755A, GAg=>GAa, coding for the syn238E is seen on all 1918 sequences and WSN33.  The revision is rare within this pandemic reservoir, demonstrating odd patterning on the 11 instances. 

The silent change is found at the beginning of this pandemic in Germany and the United States in 4 sequences:

Bayern62
Regensburg01
RegensburgD6
Missouri02

And the silent change is found recently after a gap of several months in Belarus, Russia and the United States:

Russia4
Russia14
Russia191
Belarus131
Belarus220
Belarus360
Florida25

Is this re-emergence of the silent change useful to track?  If the change fell silent at the beginning, should it also fail at this moment in time?  Does the syn238E now have a background that allows synergy and conservation?  We remind the scholar this area is only slightly downstream of two major RBD positions that are volatile within this flu reservoir (225 & 226).

This viral reservoir continues to gain genetic information in a pattern trending toward 1918 sequences.  No appearance of stability has yet occurred in this particular geography and neighboring areas.

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

Fatal Ukraine Cross Segment Linkage Extends in the US, Iraq and Australia (HA syn413K and NA syn407V)

Cross-Linked Silent HA and NA Polymorphisms Correlated with Fatal 225G Cases in the Ukraine and Russia

• HA:syn413K encoded from A1281G, AAa->AAg
• NA:syn407V encoded from T1221C, GTt->GTc

 PF11 Sequences Demonstrating Cross Segment Linkage

• Iraq8529E3  with HA 131L, 160L, 194I, 298V and syn419L (Kentucky19 and 225G Utah42) *
• Iraq8529M1 with HA 131L, 160L, 298V and syn419L (Kentucky19 and 225G Utah42) *
• Iraq8531     with HA 130E, 131L, 298V and syn419L (Kentucky19 and 225G Utah42) *
• Australia Victoria2129 with potential H5N2 inclusions and NA 454S *
• Australia Victoria2130 with NA 454S *
• Ukraine Kyiv377 with mixture of 225D, 225G, 225N, 225S, 225T and 225A
• Ukraine Lviv673
• Ukraine Lviv682
• Ukraine Cherkasy332
• Ukraine Cherkasy333
• Ukraine Cherkasy346
• Ukraine Dnipropetrovsk260
• Ukraine Dnipropetrovsk267
• Ukraine Dnipropetrovsk268
• Ukraine Dnipropetrovsk272
• Ukraine Dnipropetrovsk273 with mixture of wt 225D and 225G
• Ukraine Dnipropetrovsk274
• Ukraine Dnipropetrovsk1124
• Ukraine Dnipropetrovsk1171
• Ukraine LvivN2
• Ukraine LvivN6
• Ukraine TernopilN10
• Ukraine TernopilN11
• MoldovaG120
• MoldovaG140
• MoldovaG181
• MoldovaG182
• MoldovaG191
• HA and NA Norway2924 with mixture of wt 225D and 225G
• HA and NA Norway3364-2
• HA and NA CatNS7362 TamiFlu Resistant
• HA and NA CatS1096
• HA and NA CatS1162
• HA and NA CatS1179
• HA and NA CatS1181
• HA and NA CatS1267
• HA and NA CatS1268
• HA and NA CatS1402
• HA and NA CatS1501
• HA and NA CatS1687
• HA and NA CatS1748
• HA and NA CatS1751
• HA and NA CatS1761
• HA and NA CatS1827
• HA and NA CatS1935
• HA and NA CatS2120 with multiple swine markers *
• HA and NA CatS2151 with swine markers and 165N (TamiFlu Resistant CatNS7632 and Russian 225G Salekhard01) *
• HA and NA Guangdong02
• HA and NA Guangdong05
• HA and NA SingaporeON1156
• HA and NA Stockholm31
• Sweden Gothenburg2 with 146G, 324I (1918) and markers found extensively in Moldova and Russia *
• HA and NA Russia4 with syn238E and 324I (1918) *
• HA and NA Russia12 with 324I (1918) *
• HA and NA Russia14
• HA and NA Russia19 with 324I (1918) *
• HA and NA Russia74
• HA and NA Russia149
• HA and NA Russia165
• HA and NA Russia171 with 165N *
• HA and NA Russia178
• HA and NA Russia180 with 165N, syn239P and 264G *
• HA and NA Russia190
• HA and NA Russia191
• HA and NA Kurgan01 with HA 214E (MoldovaG168, G176, G188) and NA mixture at 407 (Fatal 225G Abakan02) * 
• HA and NA Omsk02 
• HA and NA Tver2969 with 225G, Fatal outcome
• HA and NA Salekhard01 with 165N and 225G, presumptive Fatal outcome
• HA and NA Orenburg2974 with 225N, potential Fatal outcome
• HA and NA Perm01 with 131P, 225G and 324I, presumptive Fatal outcome *
• HA and NA NY3702
• HA and NA NY3715
• HA and NA NY3828
• United States NewYork96 *
• HA and NA RhodeIsland08
• HA and NA Texas42102708
• HA and NA Texas45072128
• HA and NA Texas45122886
• United States Kentucky19 from an 18 year old subject with HA 298V *
• US Private Sequence TamiFlu Resistant  
• United States NorthCarolina37 from a 24F subject with HA 298V *
• United States NorthCarolina46_C2     from a 39F subject with HA 298V *
• United States NorthCarolina46_C2C1 from a 39F subject with HA 298V *
• HA and NA swine/NC/34752 with 298V *

84 sequences have encircled the globe as of 2010-01-26 * with high fidelity carrying a cross-segment paired set of background markers matching and potentially contributing to fatal cases in the Ukraine and Russia. 

Recent sequences published for Australia and for Iraq demonstrate this background for the first time in those geographies.  The state of Kentucky debuts on this list and New York posts another entry for a total of 4.  Sweden increases by one.  Spain adds two from December.   Russia adds seven from November.  A swine from North Carolina in the US sample on 2009-12-14 adds one for the US.  Three human sequences from North Carolina, submitted alongside the Duke cluster, are on this background.  The TamiFlu Resistant 225G sequences from the cluster do not fall on the cross linked background demonstrating that North Carolina has two potential avenues for 225G, the transmissible cluster strain and the cross-linked background as a precursor.

Kyiv377 from early November in the Ukraine demonstrates a level of hyper-morphic behaviour at amino acid 225 that is previously undocumented in ΣPF11, but is the natural progression of the genetic acquisition trend line on this pandemic reservoir.  Two sequences now additionally demonstrate the TamiFlu Resistant 275Y on NA, one from Spain in late November 2009 and one from the US with details stored in a private database. 

Areas covered include Texas (3), the Northeastern United States (5), Kentucky, North Carolina (4), China (2), Singapore, Australia (2), the Ukraine (18), Moldova (5), Russia (18), Iraq (3), Norway (2), Sweden (2) and extensive penetration in Spain (17 sequences).

This particular cross linked background pattern may precurse 225G and mixtures of 225D / 225G.  The Orenburg2974 sequence from Russia carries 225N on this background.  Receptor Binding Site (RBS) changes at 225 are associated with fatality, 225G and 225N at a rate higher than 225E.

If LvivN6 is officially confirmed as a vaccine escape event, these cross-segment pairs may be surveilled as potential future effectors of vaccine efficacy failure.

If RBS revisions at Hemagglutinin amino acid 225 are, in fact, instructive of high pathogenicity, then Russia is in the FlightPath for a more virulent winter and the Ukraine has presently built a fog of miasma that appears to be capable of spreading across the globe while leading to an expected 1,000 deaths there in less than 80 days.

Previous Study on this Topic:

• 2010-01-01 HA syn413K and NA syn407V Cross Segment Linkage Increases Range and Penetration
• 2009-12-04 Spain Introduces 2 November Sequences with Cross-Segment Pairing from Fatal Cases in the Ukraine
• 2009-11-28 Ukraine and Spain Cross-Linked HA and NA Silent Changes Circle the Globe
• 2009-11-26 The Ukraine, Norway and Spain Share Paired HA and NA Changes

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

Hong Kong reports 225G in Fully Recovered 1 Year Old Male from July at Prince of Wales Hospital

225G is not new. 

The public perception of 225G and the media linkage to hemorrhagic pneumonia is new. 

These Hydra Effect viral backgrounds carrying 225G within ΣPF11 are, in fact, very dangerous strains for what they are doing now and, more importantly, for where they are going . . . no question exists about that risk tendency.  The only question is why hasn't the science community driven the clinical linkages to the forefront before this week?  Fatal outcomes have been documented on record since July in multiple cases from Brasil.

Prince of Wales Hospital in Hong Kong, notable for their handling of the SARS epidemic and additional limited waves in the following years, has released data today concerning the very popular polymorphism, 225G.  A one year old male child presented on July 25 and was reported to have exhibited symptoms as early as July 22.  The report indicates a discharge 3 days after admittance with recovery. 

One week of illness.  One important discussion point for those characterising 225G as essentially a high morbidity polymorphism. 

We certainly do not impeach the idea of higher morbidity.  Biasing any induction solely on singular reports like this Hong Kong case is errant logic, but the evidence does suggest that patience and some exertion may be required to accurately surmise the effector mechanisms of PF11 with and without the pairing of 206T and 225G.  Proceeding with a data basis will slowly build the well-supported pyramidal steps required to undertake a capstone solution against this genetically simple, yet clinically complex disease.

We expect to see another half dozen of the major research areas also report 225G, not because the change is new, but because they’ve had the reins lightened, the leash lengthened, on this particular revision and are now encouraged to report this popular news item. This polymorphism, 225G, is seeded around the world.

225G is not as wide or as deeply penetrating as 225E.  Our team expected and predicted this Hydra Effect with multiple, human-fit strains on diverse genetic backgrounds that would co-circulate in an emerging pandemic due to Influenza Flux during the pre-PF11_Ω phases.  An enterprising question might be, “How many Hydra strains will co-circulate in each phase?” 

Numerous sub-species are spreading according to the genetic databases, including TamiFlu Resistant and epitope variant strains.  The lead US public health agency reports again this week an instance of a low reactor against the antisera.  Additionally, silent spread may be expected due to the wide geography of consistent SNP genetics.  The present stock explanation of spontaneous random "mutation" will soon be replaced with more rigourous descriptions based on patterns found in factual data.

The epidemiology of this virus did not suddenly change, just the perception.  The only thing that has changed in the last few days is that the leading public health agencies have allowed public reporting of the 225G revision.  This particular popular 225G with commensurate background of 206T has been in active circulation since May after emerging in April, vectored from both New York and Georgia, and is on record with documented fatal cases since July. 

Nothing new there.

Why are the offical public health agencies raising awareness only now?  While we do applaud the release of information and the present focus on matching clinicals to the sequences, we also caution against obverse speculation.  A primary topic of concern is Cytokinic Dysregulation.  Reliance on inspecific terms like "Cytokine Storm" in the media will only continue to misinform the public on a process that is far less understood than the lead investigators would like to admit.

All of which returns us to the basic categories:

• What we do know?
• What we don't know?

What we do know?

Now that matched clinical data is available, however limited, a potential correlation is being drawn on lung tropism. The standing bench studies, including the Palese and JKT team collaboration in 2006, detailing variant tropism based on differential HA reception at α2-3 and α2-6-linked sialic acids evaluated correlative to residue 225 lend evidence to the concept of deep lung involvement though the experiments were conducted by varying permutations of residues 190 and 225 on 1918 variants.  Whereas, we stand in 2009 with quite different genetics that require cross-validation prior to citation with applicability to PF11.

Tissue type targets are compelling studies and this particular superarray protocol may prove even more useful on PF11 than 1918 samples.  We note that though 1918 and PF11 now share 190D and 225G, that all 1918 public sequences show 206S.  206T continues to emerge and conserve regionally in PF11.  All 225G bearing strains after April show 206T, except the July CatNS1706 and the undated Vladivostok01.

Reproducing the glycan microarray procedure with the contemporary and ideal dataset including Brasil and Catalonia may bring a tigher focus onto today's issues.  We couldn't ask for a more balanced set of control factors with Catalonia offering sequences less than one week apart demonstrating both important pairings: 206S/225G and 206T/225G . . . a bench review made to order.

We also do know that a proper immune response, that is a timely and regulated innate immune response, is not occurring in certain of these patients. When the n +1 generations of the virus progeny begin to lyse the host cells, that failure of innate immune function to have responded early leads to an undetected and massive viral load due to the rapid replication trait of PF11. The cell detritus and the density of moving viral particles elicit a host-driven, limited “self-destruct” series of events because the multiple levels of early detection parameters have been bypassed leaving the core essentially defenseless.

What we don’t know?

Much of what we need to know today about Cytokinic Regulation is yet to be studied. 

The systems of feedback loops are extensive with individual effectors often having multiple functions, in some cases, opposing functions.  So please bear in mind that we are looking into an instantaneously self-modifying system that not only self-revises the systemic parameters, but recruits and removes players in the middle of the game and then encourages them to change sides without even changing jerseys.  And to top the difficulties, Heisenberg applies.  Tighten down the screws to look at one molecule and his best friend will no longer stand anywhere near him, though they were conversing with verve before we attempted to measure.

That disclaimer in place, you may still note important aspects of proper cell-to-cell signaling systems from the following discussion as you keep in mind that the presentation is highly compressed for educational purposes.

Though Cytokinic Dysregulation is occurring in most cases at some level of interchange, the 225G and 225E strains may potentially interfere at a more profound level with the early innate response by amplifying the PF11 conserved effect of the NS1 paired Glutamates at residues 96 & 97 that suppresses the IFN synthesis instantiation cycle by binding TRIM25, an early catalyst to RIG-I ubiquination.  Influenza bench researchers don’t know exactly where the failure is occurring or at which combination of cell-to-cell signalers in PF11 or the PF11 225G strains.  Until those identification studies are designed, undertaken and reproduced, discussion at this point is stark hypothesis based frequently on the speaker’s sheer lack of present research content mastery. Apparently, saying “I don’t know?” and then returning to the bench to design and gather a proper foundation of data is a skill rarely encouraged in our “Science for Hire” era.

Our team is unimpressed that the wider science community, with such broad analytical skills and exceptional equipment, relies on pseudo-explanation, this cloud of diversion, by invoking the “Cytokine Storm” phrase.  More than 20 well-characterised and 100 identified distinct molecular signal functions are at work in the early immune response, including cytokines, but not limited to that class of communicators.  Tagging a term for PR purposes is much simpler than tagging a molecule for tracking, but you received your instruments because you can think, not for your ability to improvise inventive talk.

Think.

Eighty billion dollars in research should arrive at a better answer with higher specificity and actionability than the blanket “Cytokine Storm” tome.  Data and procedure discover Facts.  Anything less is purely Public Relations.

Our team continues to hold an opinion that we first described in 2006 concerning Cytokinic Dysregulation and the NS1 protein of Influenza.  Succinctly, the viral ability to suspend innate immunity for up to two days post-infection, as characterised by Mount Sinai this year, prevents the early and required pro-inflammatory Cytokinic Response to viral detection.  That blunting, taken in conjunction with detailed studies around adaptive immunity, may result not only in failure to clear the virus from some patients in a timely fashion, but also in failure to produce a useful quantity and competence of memory T-cells and Ab.  The early failure to clear a rapidly replicating virus like H5N1 or PF11 results in a frank trauma to the immune system when the first generations of viral progeny lyse their host cells after being undetected and flood the tissues with virii and toxic cell detritus.  That disorderly surge of human and viral proteins en masse activates a late and cascading pro-inflammatory response that frequently fails to down-regulate properly.

This explanation is contrary to "pop" science reports that a normal and robust immune response over-generates cytokines and attacks self indiscriminately.  We hold that, by the time the virus has lysed thousands of cells and released millions of virii, that most adjacent tissue areas are "fair game" for immune response due to toxic cell detritus and viral travel.  That flooding of antigen and waste matter, widespread and instantaneous to the immune system, may further interact with some virally induced derangement of the alternative pathway of complement and generate the intensive up-regulation of signaling, pro-inflammation cascades and the resultant tissue damage described in the clinicals as DIC, DAH and ARDS.

Ergo, the findings of massive tissue damage on necropsy is the result of a failed early innate immune response, not a normal robust response.  A normal, properly up- and down-regulated robust innate response clears infection in more than 90% of various infections (viral, fungal and bacterial) and proceeds to generate Ab in short order via the adaptive arm of immunity.

When viral hosting cells properly detect intrusion, flag themselves for apoptosis (cell death) and are then assisted by cytotoxic T-cells, the injection of fragmentins via perforin "tubes" induces an endogenous apoptotic program literally cutting DNA into 200 base multimers (fragments) and eventually condensing chromatin.  That organised molecular result is far less inflammatory and far more useful for antigen identification than the disorderly outcome of a virally "exploded" cell.  Now you can see why proper genetic expression during each phase of this programmed cell death guarantees a lower pathology than the chaotic and toxic outcome of lytic host cell destruction resulting from viral NS1-induced, delayed genetic expression. 

A confluence of PF11 traits (failed early detection, multi-tropism and rapid replication) against the host-pathogen interface may force a limited "self-destruct" in the host upon eventual detection in an attempt to save the organism.  That limited "self-destruct" is not the desired outcome of a normal and robust immune response, but occurs due to a failure of the immune system to detect and respond early in the process.

Timing matters. 

Individual viral genetics and individual host immune genetic expression are primary effectors that must no longer be discounted under the clouds of some nebulous "Cytokine Storm" or Mysterious Mutation.

May we see the sequences paired with the clinicals?

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

Wisconsin Virus Commits Zoonosis and Fails; Influenza Flux at Work

JCVI / the Medical College of Wisconsin submitted a set of sequences to GenBank on 2009-11-11. The sub-segment genomic variance that occurs when viral diseases commit zoonosis is demonstrated. We’ve discussed the coinage, Influenza Flux, in the past.  One particular Wisconsin sequence provides a useful discussion point for the sub-segment, bidirectional influx / reflux (emergence / reversion) of genetic material between distinct species-adapted, viral reservoirs.

• A/Wisconsin/629-D00117, sampled 2009-05-28, from a 3Y
• A/Wisconsin/629-D01058, sampled 2009-05-04, from a 7Y

WiscD0117 considered alongside WiscD1058 may demonstrate with simplicity an observable situation early in the pandemic where a viral reservoir attempted species-specific (human) adaptation and failed. Documenting the reservoir’s failures to adapt may be as important to future scholars as analysing the path of beneficial adaptation within the zoonosis to humans.

The two Hemagglutinins are homologous, but for a single silent nucleotide variance. WiscD1058 is identical to Canadian sequences (2) to the immediate north and Mexican sequences (2) on the same continent to the distant south.  WiscD0117 from the 3 year old, however, stands alone at the nucleotide level though matching hundreds of PF11 sequences at the amino acid coding.

A silent SNP at the third base codon, A592G, sets this sequence as novel within ΣPF11 even today (5 months later), revising “CTa -> CTg” and coding for a synonymous Leucine at residue 179, (syn179L). The A592G SNP appears at GenBank within A/swine/Hong Kong/1110/2006 of serotype H1N2.

We widened the input series for a geographic match and temporal proximity to enhance the results.

Influenza Flux Dataset
Samples Selected for Evaluation
Samples in purple show 100% Homology

A/Mexico/InDRE13551, sampled 2009-04-28
A/Mexico/InDRE13555, sampled 2009-04-29
A/Wisconsin/629-D01058, sampled 2009-05-04
A/Canada-PQ/RV1758, sampled 2009-05-08
A/Canada-QC/RV1954, sampled 2009-05-17
A/Wisconsin/629-D00117, sampled 2009-05-28
A/Wisconsin/629-D00829, sampled 2009-05-28 (324I)
A/Wisconsin/629-D01026, sampled 2009-05-28
A/Wisconsin/629-D01083, sampled 2009-05-28 (252L)
A/Wisconsin/629-D02144, sampled 2009-05-28 (324I, identical to WiscD0829)
A/Wisconsin/629-D00223, sampled 2009-05-30 (159T)
A/Wisconsin/629-D02013, sampled 2009-05-30 (35I)

Note the reasonable number of data points around the WiscD0117 sequence of interest. Many of these carry independent recombinations, including 35I, 159T, 252L and 324I.  All sequences shown on the list demonstrate the wild type 592A, except WiscD0117, including the two sequences that were sampled AFTER the original A592G SNP. 

Either an attractant signal was very strong to revert the silent SNP in the subsequent Wisconsin samples or the SNP was never transmitted.  In either case, ΣPF11 tried a new identity and then determined that the previous genetic footprint was more suitable.

Wisconsin is an area of interest for our evaluations due to the unusual clinical presentations and outcomes.  Influenza Flux may be more strongly driven in Wisconsin and causality must be determined.  ΣPF11 is on record as attempting new permutations in this geography, fixing them when useful like 324I from 1918 and discarding them like the syn179L when unneeded.

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

Capital of Spain Moving to the Front in the Race for PF11 Antigenic Diversity

The capital area of Spain is generating pandemic strains of particular Antigenic Diversity in Pandemic Influenza H1N1.

Introductions into a pandemic reservoir merit tracking to identify potential vectors of inter-"host species" viral genetic material.  We watch always for something new.  Influenza, as you have read, may be reasonably expected to have a certain level of genetic flux, a certain level . . . but not necessarily the levels we are witnessing within ΣPF11.

Novelty can get very old sometimes, but tempus fugit and so do birds. 

First, Argentina reports genetic novelty corresponding to fatal cases in a sequencing partnership with Columbia University.  Then, Sao Paulo releases 9 sequences splashing across 6 HA backgrounds.  So we studied the data, however sparse.  And we studied closely, under a resigned certainty that the "bad news" was expected, even predicted.  We were confident that ΣPF11's first winter passage in humans would unavoidably derive new sub-clades due to the weather . . . until balmy Spain transparently reported yesterday, somewhat courageously and seemingly with full disclosure. 

Coastal Spain was not in winter during July and August of 2009.  Mallorca's beaches were not covered by tourists bundled against the stark cold.  Yet Spain is demonstrating a very similar rate of genetic acquistion into the pandemic reservoir as nations who were passaging through the cooler weather of their traditional "cold and flu" season.  We would like to say that seeing this rate of change in the summer took us at a complete surprise, but that nagging feeling of knowing gnawing has been persistent every time we discuss tourist areas, the logistics of congregation points, summer camps and the microbiological traits of PF11 (IDRREAV^*).

The first sequence profiled here is certainly not unworthy of mention; however, the pattern shown is also not the most curious of the summer specimens.  The middle of the road may be a good place to plant our feet as this pandemic begins to veer.  So this novel specimen and apparently new sub-clade gets a fresh piece of paper, a clean slate, all to its ungainly self.

A/Catalonia/NS1161, sampled on 2009-07-28, Segment 4 (HA) and Segment 6 (NA).

I only want to discuss the Hemagglutinin in detail today, but you may envelope yourself in the Neuraminidase at your leisure.  I believe you may even find that Segment 7, the Matrix Protein, waits on the rack in your size.

HA Amino Acid Codings to 4 Impractical, but Impressive Polymorphisms

•   48K
• 206A
• 225E
• 264T

None of these changes are prolific within ΣPF11. 

264T occurs on 1 other PF11 background.  225E in the Receptor Binding Domain is rare with a total of 37 occurences worldwide (25 in Catalonia).  206A and 48K are each individually novel to this reservoir.  No permutation of any two of these changes appears to occur together in the sequence record outside of CatS1161.  The probability is calculably low for a series of three independent polymorphisms randomly arising on a single Catalonia background having 225E.  That variability index on the HA would contrast somewhat with the NA.  Did we mention yet that the Neuraminidase gene segment is entirely stable?

48K
Novel to ΣPF11.
Progenitors may include:
1918
WSN33
Seasonal H1N1 1983
Taiwan H1N1 1985
swine Wisconsin H1N1 1997, 1998
swine Hong Kong H1N1 2001

206A
Novel to ΣPF11.
Progenitors may include:
A/South Africa/42/2000(H1N1) - single instance located on GenBank.

225E
37 instances within ΣPF11: Catalonia (25), Europe, Asia, Russia and United States.
Progenitors may include:
Seasonal H1N1 2007

264T
A/New York/3012 from April 2009 within ΣPF11: single instance early in pandemic.
Progenitors are unknown.

Neuraminidase Quadruple Combination
CatS1161 = 106I, 248D, 275H, 286S

The Neuramindase is an exact match for 460 PF11 sequences on file, and is a 100% match (1243/1243) on 11 of those at the nucleotide level.  Though the HA is highly variant, the NA seems to have been spared, matching precisely to 7 other Catalonia sequences in this deposit, to Stockholm37 and to 3 geographically dispersed specimens carrying 225E (NJ01, Sapporo1, Changsha78).

As we have mentioned that the phylogenic tree for these South American sequences have a very low ratio of leaves to branches, you should realise that this sequence is one of several that are defining.  This specimen has gone out on a limb for you, all alone. But don't be remorseful for this single strand of negative-sense RNA because he's not really alone.  That uniqueness creates a commonality if you pull away from the tree a bit and recognise that it's filled with single leaf branches just like this one.  If he could think, I think he would say to you, "Don’t weep for me. I’ve traveled far and vacationed well. I fed at the buffet and chose the best desserts. Don’t worry about me; I’m going shopping now and I'll be back this way soon wearing a stylish new jacket," and then he'd turn and begin training the other branches for the next replication cycle.  He's really not alone.

This sequence is surrounded by others almost as odd as himself, so you could say that he's in good company . . . that is if you consider a gallery of unmasked rogues as good company.  I can hear them musing now, "Somewhere ages and ages hence I shall be telling this with a sigh. Two rogues converged on a sunny beach and I, I selected the one most traveled by and that has made all the difference."

If a virus were non-random, that is.

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

H5N1 and 1918 Receptor Binding Domain Change, HA 225G, Emerges On Two Sub-Clades in Spain

Spain deposited 239 sequences today at GenBank.

A/Catalonia/NS1706, sampled on 2009-07-29, Segment 4 (HA) and Segment 6 (NA)
A/Catalonia/NS2001, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)
A/Catalonia/NS2008, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)

225G is found on these 3 Spanish Hemagglutinins as in the 2 Sao Paulo cases during the same late July to early August timeframe.  On the CatNS1706 specimen, 206S is paired with the 225G; whereas, the Brasilian deaths were 206T and 225G similar to CatNS2001 and CatNS2008.  During the same timeframe, two cities more than 5,000 miles distant with an ocean between them each have emergence of multiple novel sub-clades for their geography related to the Receptor Binding Domain residue 225.  Consider seasonality and your puzzlement is enhanced.

225G is consensus for H5N1, is carried on NewYork1918 and only appears in 8 other PF11 sequences across the US and Mexico.

SaoPaulo53206
SaoPaulo53225
MX3955
MXInDRE4114
NY04
GA01
TX05
TX11

225X is demonstrated several times in the US proximal to 225G in area and time.

NY11
NY31
TX10
CA13
NE02

CatNS2001 and CatNS2008 also feature HA 298V, a potential reversion to swine sequences or to 2008 Seasonal.  Because 206T is featured in these two sequences and 206T is exclusive of 296H, we may perhaps postulate a secondary acquisition pathway for an unidentified human-fit, trait-enhancing domain (HA296:301). 

Three additional sequences in this deposit carry the pair of 206T and 298V:

• A/Catalonia/S1237, HA, sampled 2009-08-13
• A/Catalonia/S1248, HA, sampled 2009-08-18
• A/Catalonia/S1286, HA, sampled 2009-08-25 

All 5 of these Catalonia 298V specimens carry a 225 polymorphism, either 225E or 225G.

An Intra-Segment Exclusivity exists within the Catalonia specimens between 206S and 225E.  24 of 25 Catalonia 225E specimens carry 206T, all but the unusual CatS1161 with 206A.

Neuraminidase Quadruple Combination

• CatNS1706 = 106V, 248N, 275H, 286G 
• CatNS2001 = 106I, 248D, 275H, 286S
• CatNS2008 = 106I, 248D, 275H, 286S
• CatNS1237 = 106I, 248D, 275H, 286S
• CatNS1248 = 106I, 248D, 275H, 286S
• CatNS1286 = 106I, 248D, 275H, 286S 

NA 286G appears on 30 GenBank specimens within ΣPF11, 24 of them from Catalonia. 

Non-Random Acquisition Acceleration appears to be underway in potential trait-enhancing domains of both Antigen segments.  Influenza Flux is a two way street with clearly defined lanes and many points of ingress.

The Hydra Effect is demonstrated in the phylogenic trees of Brasil and Spain.  When your tree is all branches with only a few leaves at each tip, you aren’t going to get much protection from the sun unless you decided very early to be standing on just the right spot when the perfect light of noon arrives.

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