2009-10-30

Matching Pair of Human-Fit NA Novelty Emerges Independently in Two Distinct Locales during August 2009

The University of Padova deposited 23 Neuraminidase segments at GenBank yesterday. One particularly merits discussion. We were keyed to the sequence by the rare 106I and 248N human pairing, but even more human fitness acquisition was at work upon review.  The NA of A/Italy/180, sampled in August 2009 from a 47M, brings another unique face into ΣPF11.  

NA Amino Acid Codings to 1 Novel Polymorphism and 2 Independent Co-Emergent Signals

  •    45K
  •  386D
  •  426L (synonymous C1276T)
45K is novel to ΣPF11 and is rare to the sub-type being found in only 3 previous H1N1 human sequences. 386D and the C1276T SNP coding for a synonymous 426L are found twice in ΣPF11 and emerged paired and coincident with the Italy180 sequence in the secondary and distinct locale of Catalonia, Spain on a different background during the same time period. The 386D and syn426L polymorphisms appear to be human-fit as they are represented in all recent human H1N1 Seasons (2005-2009).

Neuraminidase Triple Combination
106I, 248N, 286S

Only 25 sequences currently match the 146 amino acids from 106I to 248N, including the Italy134 sequence recently profiled demonstrating the NA Triple Combination herald for Pandemic 2.0.

This new Italian sequence is a marvel in itself, but the argument against random mutation gains strength upon a similar and apparently independent co-emergence. Two perfectly novel introductions paired onto two divergent backgrounds in two different geographies suggest a randomness redundancy. 

A/Catalonia/S1276, sampled 2009-08-19 from a 13F, also demonstrates two of the three novel introductions, but onto a separate NA background.  CatS1276 is a perfect nucleotide match to Italy180 except at 742G generating 248D (1216 of 1217 aligned residues).  Like many of the Catalonia sequences, the initial 47 amino acids of CatS1276 are absent or we might find the 45K there as well.  Even without the full sequence, CatS1276 is unique and stand-alone within ΣPF11 due to the swine 248D conjoined with 386D and C1276T.

45K
Novel to ΣPF11.
Progenitors may include:
A/Washington/03/2009 H1N1 with HA 230I & NA 386D, syn426L
A/New Jersey/30/2008 H1N1 with HA 230I & NA 386D, syn426L
A/Thailand/271/2005    H1N1 with HA 225G, 261N, 263D, 270T & NA:45K, syn346V

386D
CatS1276 is the singular ΣPF11 peer.
Progenitors may include:
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Consensus)
Avian H1N1

syn426L
CatS1276 is the singular ΣPF11 peer.
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Extensive)
Swine H1N1 1990-1999
WSN33

Paired genetic introductions onto disparate backgrounds are not a spline for randomness.  Perhaps a less random examination of the database at hand would provide additional observational evidence for a new school of logic?  Without question, human-fit genetics from previous Seasonal H1N1 and H3N2 are being gained by the Hydra pandemic strains.  In this case, the sub-segment acquisitions are precise and clear.


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2009-10-28

PB2 Changes in Multiple Japanese Sequences downstream of known Virulence Factor

Japanese PB2 sequences deposited today at GenBank carry novel introductions to ΣPF11 and to human H1N1.  A concern comes into play when the PF11 PB2 segment, of avian origin, acquires genetic material from human-fit Seasonal Influenza.

A/Niigata/690, sampled 2009-06-15, carries 702R, unique to ΣPF11 and found previously in 1918, LabVir PuertoRico8, Seasonal H1N1 and Seasonal H3N2.

A/Hiroshima/220, sampled 2009-07-03, carries 704H, unique to ΣPF11, to human H1N1 and to human H3N2.  Progenitor unknown.

These two PB2 polymorphisms are adjacent to a known Virulence Factor.  Note that the 701N discussed in the Palese study is found on Seasonal H1N1, Seasonal H3N2 and on human H5N1.  Apparently H3N2 may be playing a significant role as a recombination donor to PF11.

As you will see from the following listing, PB2 is active at this area in ΣPF11.

698D - California06
700K - Osaka180 TamiFlu Resistant with NA Pairing of 106I and 248N
701N - Shanghai71T_May with 627K
702T - NJ02
702R - Niigata690
703X - WA29 TamiFlu Resistant
703K - Shanghai71T_May with 627K, Shanghai71T_June
704H - Hiroshima220
714R - Hyogo2
720K - Nebraska02

The previously published segment 4 (HA) of Hiroshima220 shows 130E in a domain that may yield antigenic diversity.  Notice that another human Virulence Factor 225G from the HA RBD has been demonstrated in the locale of Hiroshima.

Further analysis will be conducted as time permits.


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2009-10-23

Potential Catalyst for Pandemic 2.0 Emerges in Italy during July

During the Summer of 2009, an unsuspecting twelve year old boy in Veneto, Italy may have become the host of an influenza strain that is now setting the Pandemic 2.0 stage.

The Northern Italian region of Veneto has a population nearing 5 million and hosts 60 million tourists each year with many passing through the canals of the capital, Venice.  The Laguna Veneta is the largest wetland in the Mediterrean (340mi2 / 550km2) and the delta serves a wide range of migratory bird species. 

The University of Padova lab deposited 24 Neuraminidase (N1) sequences today from Italy sampled during July 2009 (Pandemic 1.5) bringing the total number of Italian NA segments on file to 26.  Antigenic diversity is observed in the Italian sequences, several with novel introductions, but the point variations are not our primary interest in this very important deposit. 

One sequence from the Padova lab signals the first recorded instance of a key transition for this pandemic.  The NA Triple Combination may mark an axis or inflection point for PF11.  A/Italy/134, from a student (12M) in Veneto, demonstrates a match to Seasonal Influenza in a permutation of 3 key markers that we have anticipated as a potential catalyst to Pandemic 2.0

A Balkan emergence had generated the highest probability in our research with the Italian peninsula and bounding northern states ranking as "Very Probable".  Few sequences have been made available to evaluate the Balkan states during this pandemic, so we cannot determine if the recombinations occurred in that area as well as in Italy.  Emergence was expected within a 250 mile radius (400km) of a significant body of water, particularly the Adriatic Sea, the Black Sea or the western boundary of the Caspian Sea.  Of course, we may be searching for our keys under the streetlamp.  So little surveillance is surfaced at this point that rough estimates are the maximum any lab may produce.

In Italy134, this coalescing set of 3 human-fit markers, predicted by our research in mid-May, emerged during the summer, recombined as expected onto the swine N1 background.  As you may observe from the positional study, this sequence may have required two or more in situ polymorphisms from consensus within this geography to gain these genetics.  In the estimation of our research team, random mutation is a less than stellar explanation.  Human-fit Seasonal Influenza and ΣPF11 now have much more in common as ΣPF11 moves into tighter conformation potentially gaining trait enhancements.

Neuraminidase Triple Combination
106I, 248N, 286G : Italy134
106I, 248N, 286G : Seasonal Influenza 2005, 2006, 2007, 2008, 2009
106I, 248N, 286G : H5N1 (Avian, Human), H1N1 (Avian, Swine)
106I, 248N, 286G : 1918 Brevig Mission

This July sequence lays additional groundwork for attractant donations from candidates in previously observed donor serotypes. 

Few Italian points of comparison are available prior to this large NA deposit.  Of the two, NA Italy05 is unremarkable for this study and NA Italy127 is quite remarkable due to temporal and geographic proximity, as you will see in the Italian permutation discussion.  We also note that the Hemagglutinin segments so prolifically available from Italy demonstrate exceptional variance (20 major polymorphisms from 34 Sequences). These Hemagglutinin amino acid revisions include, but are not limited to, 137T, 199N, 200T, 219T, 225E (4), 244I, 261G (2), 277E, 296H (4) and 300S (2).  NA variance is correlated with HA variance in ΣPF11

Antigenic Diversity, even within the sparse 26 Italian NA sequences is observable if only upon reviewing the four permutations of the Neuraminidase Triple Combination.

106I, 248N, 286G : Italy134 from Veneto, sampled 2009-07
106I, 248N, 286S  : Italy127 from Veneto, sampled 2009-06-17, 256L (H3N2, H5N1 Avian)
106I, 248D, 286S  : 23 Sequences, including Italy05 from May 2009
106V, 248N, 286S : Italy149

Italy134 is most similar at the protein (468/469) and nucleotide (1407/1410) levels to two different groups of sequences: the NA 286G bearing group from Canada (5 of 6 Sequences) and the Asian group (with Louisiana03) carrying the rare PF11 dual combination of 106I and 248N (20 sequences).  The Russian Almati01 and Ekaterinburg01 round out the set with the 106I/248N pairing, but vary at an additional amino acid from Italy134.  Only 24 sequences at GenBank carry the PF11 amino acid homology between 106I and 248N.

Until PF11Ω is achieved, Influenza Flux will continue to vary the virulence and transmute the transmissibility at individual geographies. Future scrutiny of the NA permutations discussed here is merited.  Bear in mind that the current reservoir, even with this instance of tighter human coupling, remains hobbled by transitional genetics.  Fitness determination of this Seasonal NA Triple Combination on the swine N1 background of PF11 remains to be determined at such time as sequences are surfaced.


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2009-10-20

Nagasaki brings Novel HA Introductions into PF11 with 124I and 307S

A Japanese sequence from Nagasaki was published at GenBank today with the antigen Hemagglutinin only.  The sample was collected in July 2009 from a 4 year old female child and represents another unique face to ΣPF11.  

HA Amino Acid Codings to 2 Novel Polymorphisms
  •  124I
  •  307S

124I
Novel to ΣPF11.
Progenitors may include:
A/goose/Hong Kong/8/1976(H1N1)
A/chicken/Hong Kong/14/1976(H1N1)
Movement is common at this residue in human and avian H5N1 and swine H1N1

307S
Novel to ΣPF11.
Progenitors unknown.


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2009-10-19

225G in Receptor Binding Domain Traveled to China without Vaccine Pairing of 206S

The expected Hydra Effect on Hemagglutinin patterns are being validated with the latest sequence deposits.  Multiple antigenic heads continue to arise within single geographic areas while the march from Southern Hemisphere winter strains (May-July 2009) into the Northern Hemisphere ΣPF11 lays distinct markers.

Two sequences today from China carry the Receptor Binding Domain polymorphism coding for 225G similar to the fatal cases during the South American winter.  These sequences represent the first movement of 225G into China and the second into Asia after Hiroshima201, although we have observed 225E in one instance, Changsha78.

This incursion of 225G makes Zhejiang Province one of very few geographic locales to represent both vaccine RBD polymorphisms as 226R was demonstrated mid-summer in A/Zhejiang/DTID-ZJU01/2009.

Let's examine the new Yiwu HA segments for this analysis:
These two Zhejiang province cases were sampled in September making the sequences contemporary for evaluation of the genetic acquisition cycle pertinent to North America today.  Each case continues the recent affinity of 206T with 225G.  Nine of fourteen instances of 225G on record within ΣPF11 are paired with 206T and only one isolated sequence after April has 206S in the pairing. You will note that the live vaccine is based on an early finding in Texas and Mexico (Texas05 pairing of 206S / 225G).  The current sequences continue to demonstrate a directional movement away from those four early Texas and Mexican strains from April. 

The Yiwu11 case, 41F, is specifically noted as having "severe symptoms".  Confidence is increased that these sequences are valid due to independent verification.  The two sequences were managed from separate labs though the hosts were apparently from the same city, Yiwu, and suffered during the same time frame.

Each of the two HA sequences represent a novel introduction into ΣPF11.   Yiwu11's closest GenBank match is 1758 of 1774 nucleotides and ZJU02's closest match is Yiwu11.  The two sequences are an exact nucleotide match (1759/1759) at all alignable positions (sequence truncation at Yiwu11 head and ZJU02 tail), potentially representing perfect transmission in Asia of 225G.  The Catalonia sequences from Spain in early August initiated the first and only previously recorded perfect segment transmission of a 206T / 225G pairing.  The Brasil deaths share amino acid homology, but varied at a silent SNP coding for Lysine at residue 222 (222K). 

If a cluster is in effect with these two sequences, then we may be observing a foundational, well-passaged, human-fit strain in the Northern Hemisphere heralding Pandemic 2.0 Influenza.    Only time will tell.

A correlation is also emerging in consideration of geography and population ethnicity with nine of the fourteen 225G cases in areas with a substantial Hispanic population. The ethnic profiles of the individual cases are not identified. Yiwu is a burgeoning commodities trading area with a substantial immigrant population including import/export workers from South America.  If we note that NY and Georgia have Hispanic populations, then only Hiroshima remains as a potential non-Hispanic area.  At any rate, the correlation of 225G to areas with Hispanic human genotypes bears scrutiny for pathogen-host interaction at the genetic level. 

Recall that other human-fit genetic advances are recorded in the Zhejiang Province recently.  Of minor note, the Neuraminidase segments of Yiwu11 and ZJU02 are also novel to the reservoir though the amino acid levels match widely.  A third base SNP that merits attention has now spanned from the original introduction in A/Netherlands/602 to ZJU02, A408G coding at residue 136 for a synonymous Glutamine (136Q).  Movement at this amino acid position is implicated in Relenza resistence (136K), though the synonymous change from the Netherlands and Zhejiang is not accorded trait enhancement in the literature.

This advancing Antigenic Diversity and movement of 225G separated from the 206S into a highly populated country prior to winter should generate a call for wider surveillance and more rapid deposition of sequences.


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2009-10-16

Iran deposits Sequences with H5N1 Fingerprints

The first PF11 sequences from Iran were published at GenBank on 2009-10-13.  The three Neuraminidase segments were sampled between 2009-07-27 and 2009-07-30.  Each of the three brings a unique face into ΣPF11.  

Though these sequences all share a starting polymorphism, each develops one or more additional novel antigenic revisions.  The build pattern is suggestive that surveillance efforts are lacking.  The database contains no intermediate forms that would allow us to observe the individual genetic acquisitions from the birds, pigs and humans as they occurred to build this minimum  two step magnetism from H5N1 and H5N2 onto the Iran H1N1 background.


NA Amino Acid Codings to 5 Novel Polymorphisms and 1 Singular Signal

  •     4K
  •   74L
  •   81G
  • 346V (synonymous A1038G)
  • 452S
  • 454S

4K
Novel to ΣPF11.
100% of the Iranian sequences carry Lysine at the fourth amino acid position (4K), a novel finding in the pandemic reservoir that appears to be only recorded in two earlier sequences.
Progenitors may include:
A/duck/Eastern China/06/2000 (H5N2)
A/Fort Warren/1/1950 (H1N1)

74L
Bogota0466N is the singular ΣPF11 instance.
Lorestan1599
Progenitors may include:
red-winged tinamou/Argentina/MP1/2008 H1N1
     with HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G

81G
Novel to ΣPF11.
Lorestan1599
Progenitor unknown.

syn346V
Novel to ΣPF11.
Ghom1550
Progenitors may include:
A/Thailand/271/2005 (H1N1) with NA 45K & HA 225G, 261N, 263D, 264P and 270T, also manages to carry the silent NA:A1038G coding for a synonymous Valine at residue 346 on the Neuramindase (346V) of Ghom1550.  This silent change is found across many serotypes and primarily spans Avian and Swine species.  Influenza Flux may be at work.

452S
Novel to ΣPF11.
Khorasan1583
Progenitor unknown.

454S
Novel to ΣPF11.
Khorasan1583
Progenitors may include:
H5N1 2009 Human Toddler passage Egypt
H5N1 2009 Avian Worldwide
H1N1 2005 Human Iowa swine worker (IA/CEID23/2005)
H1N1 NC swine 36883, HK swine NS1659

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


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HA 263D Observed in Russia, Thailand and Japan

A/Tomsk/01, deposited in late July 2009, introduced the pandemic to 263D on Segment 4 (HA).

Since that novel introduction, four additional specimens have been deposited matching the Tomsk01 nucleotide sequence coding for 263D, spreading the geographical and time range.

A/Thailand/271/2005 (H1N1) is a potential progenitor for this SNP and other recent pandemic acquisitions.

These sequences carry additional HA polymorphisms including 244I on ThaiCU-H9 matching Ancona02 and 405T on ThaiCU-H276 matching TorontoT5362.

You've noticed from our discussions that this HA domain has activity occurring in many parts of the world.  Residue 263 continues to rank as a primary watch position within ΣPF11 for our team.


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Taiwan526 demonstrates HA and NA Nucleotide Diversity while coding for Amino Acid Homology

A/Taiwan/526, sampled in July 2009, Segment 4 (HA) and Segment 6 (NA), provides a working demonstration of silent polymorphisms within each primary antigen.  The amino acid codings of the HA and NA are unremarkable; however, when we examine at the nucleotide level, each segment appears unique within ΣPF11.

The closest HA match is 1741 of 1744 residues while the nearest NA is 1437 of 1441.  Of interest is the HA A781C (ATa to ATc) coding for a synonymous Isoleucine at residue 243 (243I).

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


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2009-10-15

TamiFlu Resistance #12 from Canada, A/Quebec/147365, may drive Unique HA Polymorphism

The twelfth TamiFlu Resistant specimen with a publicly available sequence, A/Quebec/147365, was deposited today at GenBank with all 8 segments.  We shall examine the primary antigens today, Segment 4 (HA) and Segment 6 (NA).

The antigen Hemagglutinin is of interest on this specimen due to the 259S introduction into ΣPF11. Antigens expressing novelty in areas that may affect Human Receptor Binding bear scrutiny.  A second Quebec specimen today is an exact nucleotide match to the HA, A/Quebec/147023 HA.  More important than the novelty and the prospect that the 259S change has spread is the fact that 98 other sequences in the reservoir are a 1700/1701 nucleotide match (99+%) with these two, offering a wide geography for future recombination:


Geography


Sequence Count



New York



59


US (other)


09


Canada


04


Japan


11


Taiwan


01


Moscow


03


Italy


03


France


01


Europe (other)


04


South America


03


You will recall that we've observed significant movement in the domain surrounding residue 259, including the boarding school cases with 259V in Jiangyin, 261V in Singapore, 263D in Tomsk, 264X in Jiangyin, 264S in TamiFlu Resistant WA29 and 264T in NY and Spain. 

259S appears to be found only on Swine H1 from 2003 in two North Carolina samples (NCsw35279, NCsw36681) and does not feature on other previously banked H1N1 (human, avian), H3N2 (human, swine) or H5N1 (human, swine, avian). We may be looking at a series of in-situ, cross-segment Hemagglutinin genetic selections due to TamiFlu pressure, in addition to the H275Y on the Neuraminidase. We would suggest a careful examination of the samples at the Chinese boarding schools for sub-clonal minor populations carrying H275Y on the NA.

The NA of Quebec147365 is an exact amino acid match (469/469) with Denmark528, HK2369, Yamaguchi22, Hunan SWL3, Singapore57, Tokushima2 and Iwate3.  Quebec147365 is also an exact nucleotide level match to Denmark528 and Iwate3.

On Quebec147365 TamiFlu Resistance is indicated in typical PF11 fashion via a Single Nucleotide Polymorphism coding for 275Y on the Neuraminidase. The sequence displays the following NA Quadruple Combination:

106I, 248D, 275Y, 286S

The following permutations are now represented on the twelve PF11 anti-viral resistant sequences:

106V, 248N, 275Y, 286S = WA28, WA29, TX47
106I, 248N, 275Y, 286S = Osaka180
106I, 248D, 275Y, 286S = HK2369, Yamaguchi22, Denmark528, Hunan SWL3, Singapore57, Tokushima2, Iwate3, Quebec147365

Until the 2009-08-21 deposit of the two Washington sequences, all 275Y TamiFlu-Resistant specimens on PF11 backgrounds were paired with 106I.  We continue to see only 3 of the 11 with 106V.

The addition of Quebec147365 heavily leverages position 248 toward Aspartate (D) with 8 specimens versus 4 with Asparagine (N). No TamiFlu Resistant specimen on file displays 286G as yet.


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2009-10-07

Antigenic Diversity Increases with 7 Novel H1 SNPs from Chengdu and Jiangyin

On 2009-10-06 China deposited 22 Hemagglutinin sequences and 23 matching partial Neuraminidase sequences from the areas of Chengdu and Jiangyin sampled respectively on 2009-07-26 and 2009-08-16. The two sets of sequences are from patients that were students at boarding schools during an outbreak.  The Neuraminidase segments are far too limited in data for evaluation. The HA segments are remarkable due to the fact that 100% of the distinguishable SNPs are, on first inspection, novel introductions to ΣPF11.  These wild type changes directly upstream and downstream of the Receptor Binding Domain may increase the velocity of vaccine escape.

HA Amino Acid Codings to 7 Novel Polymorphisms and 1 Mixed Signal

  •   76T
  • 131P
  • 191R
  • 238K
  • 259V
  • 264X
  • 286N
  • 502K
All 22 HA sequences carry 206T.  As we have discussed previously, the polymorphism from the mixed signal coding for residue 264 will likely match one of the variations in Seasonal H1N1 2006, 2007, 2008 and 2009, in 1918, in WSN33 or the two appearances on the PF11 background, CatS1161 and NY3012.  That domain is among the most active since late May.

76T
Novel to ΣPF11.
All Jiangyin (10 sequences).
Progenitors may include:
Korea swine 2006 H1N2 (2 Entries)
Iowa human swine worker 2005 H1N1 (IA/CEID23/2005)

131P
Novel to ΣPF11.
All Chengdu (12 sequences).
Progenitor unknown.

191R
Novel to ΣPF11.
Chengdu18
Progenitor unknown.
Further inspection required:
Quail/Nanchang/12-340/2000 H1N1
Beijing/262/95 H1N1 (FluMist Vaccine Virus)

With the 3 residue deletion producing E130del (similar to S129del in several human H5N1 sub-clade 2.2.1.2), a conformational proximity may exist at 192R for alignment and / or transposition onto Chengdu18 residue 191.  These two donor candidates also carry M230I, though the Chinese Quail is the only Avian H1N1 sequence on file with this human-fit RBD change.  Chengdu is approximately 1,100 miles west of Lake Poyang (Nanchang) with a series of inland lakes and rivers on the flightpath.


238K
Novel to ΣPF11.
Chengdu04
Progenitors may include:
Seasonal 2008 H1N1 (1 Entry)
Seasonal 2005 H1N1 (2 Entries)
Guangdong swine 2009 H1N1
NC swine 2008 H1N1 (8 Entries)
PR8_34
LabVir_hvPR8_34
H5N1 Sub-clade 2.2

259V
Novel to ΣPF11.
Jiangyin01
Jiangyin15
Jiangyin16
Jiangyin17
Progenitors may include:
Seasonal 2006 H1N1 (South Carolina/2)

264X
Indistinguishable amino acid.
Jiangyin68

286N
Novel to ΣPF11.
Chengdu40
Progenitors may include:
Swine H1N1 2003-2007 (NC, Ohio, Kansas)

502K
Novel to ΣPF11.
Jiangyin34
Progenitors may include:
red-winged tinamou/Argentina/MP1/2008 H1N1
     with HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G
Seasonal 2009 H1N1
Seasonal 2007 H1N1
WSN33


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2009-10-03

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.


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2009-10-02

Spain's Addition to Third Sub-Clade with HA 225E RBD Change

A/Catalonia/S1120, sampled on 2009-07-20, Segment 4 (HA) and Segment 6 (NA), from a 1 year old child falls into a third sub-clade (with earlier Cat378 and Cat387) in this large sequence deposit from Spain that is varied by position 225 in the Receptor Binding Domain.  Sao Paulo, Brasil showed a very similar hyper-morphic pattern at this position (225G & 225N) during the same timeframe though Brasil was in their winter.  Spain is showing polymorphisms coding for 225G and 225E.

The CatS1120 sequence shows 225E paired with 206T.

Neuraminidase Quadruple Combination
CatS1120 = 106I, 248D, 275H, 286S


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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:
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.


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H5N1 Coding from 2009 Egypt Toddler Cases enters PF11 Reservoir via Japan, NA 450G

A/Shizuoka/793 was deposited yesterday at GenBank with Segment 4 (HA) and Segment 6 (NA) from a sample taken 2009-06-15.

Influenza Flux is at work demonstrating increasing Antigenic Diversity.  The Japanese geography continues to produce genetically diverse PF11 strains with two significantly variant sub-clades represented in the two sequences deposited yesterday from the Shizuoka Prefecture. 

Shizuoka793 is unique within ΣPF11 for several reasons.  Though the Neuraminidase gene segment is identical at 1408 of 1410 residues to most recent geographically proximal Japan sequences and many NY specimens, the two exceptions provide us an exercise in origins:

  • A1028C coding for A343E (Glutamate) 
  • G1348A coding for S450G (Glycine)
Neither of these polymorphisms appear to have precedent within ΣPF11 and, as yet, we have not identified a donor candidate within the H1N1, H3N2, H1N2, H5N1 or H5N2 reservoirs for the NA:343E.  450G, on the other hand, has a lineage that is of interest considering the risk groups that we are seeing at the moment with this pandemic.

450G found on the pandemic Shizuoka793 in mid-June appears in low density among several serotypes of human Influenza specimens worldwide at GenBank and 18 are H5N1 specimens collected and sequenced by the NAMRU-3 team in Egypt between January and June 2009, immediately prior to the Shizuoka infection.  16 of those patients were under the age of 5 and geographically dispersed

Other recent matches are 7 H3N2 Seasonal 2009 cases, 17 H3N2 Seasonal 2008 cases, 5 H1N1 Seasonal 2008 cases, 13 H1N1 Seasonal 2007 cases, 11 H1N1 Seasonal 2006 cases and a swine farm worker from Iowa in 2005.  Though the Glycine at 450 is an uncommon Human Influenza polymorphism, the coding appears to be easily donated, moving between Avian, Swine and Human species on H5N1, H3N2 and H1N1 serotypes.  Clinical data on the Shizuoka case and the H5N1 infected toddlers would allow valuable insight.

The Neuraminidase Quadruple Combination on this sequence is 106I, 248D, 275H, 286S.

The Shizuoka793 Hemagglutinin is a perfect match (1701/1701) to 22 PF11 specimens from geographies including Sao Paulo, Finland, Italy and 18 specimens along the US Eastern Seaboard.  The HA 296H polymorphism deepens in Japan with this deposit being only the second in Japan, the eighth in Asia and the fifty-first in the world.  The sub-clades bearing 296H do not appear to have become dominant in any single geography, but have, nonetheless, continued alongside the dominant strains.  As of this moment, the Intra-Segment Exclusivity between 296H and 206T continues within ΣPF11 though 206T is widely circulating proximally to this specimen.

Cross-segment linking is suggested with all HA:296H specimens sharing the NA combination of 106I, 248D, 275H, 286S (for those 44 with NA on record).  No specimen bearing HA:296H is on record as TamiFlu Resistant or as carrying the NA:286G from Seasonal Influenza (H1N1/H3N2) or H5N1.

This specimen also demonstrates the strong pairing between 296H and the 2E originally found in 1918 sequences and now several PF11 HA segments.

We would be very happy to report that sub-clades are coalescing and stability is occurring within ΣPF11, but the data does not support such a view.  Even casual observation of the sparsely available sequences shows ongoing genetic acquisition leading to Antigenic Diversity and widening sub-clades.  Reversion and flux appear.

Tracking of these non-random linkings would certainly be assisted by a more robust database of recent sequences.


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2009-10-01

TamiFlu Resistance #11 from Japan, A/Iwate/3, Exact Nucleotide Match to Denmark528

The eleventh TamiFlu Resistant specimen with a publicly available sequence, A/Iwate/3, was deposited today at GenBank with only Segment 4 (HA) and Segment 6 (NA).

The NA of Iwate3 is an exact match (469/469) with Denmark528, HK2369, Yamaguchi22, Hunan SWL3, Singapore57 and Tokushima2.  Iwate3 is also an exact nucleotide level match to Denmark528.

On Iwate3 TamiFlu Resistance is indicated in typical PF11 fashion via a Single Nucleotide Polymorphism coding for 275Y on the Neuraminidase. The sequence displays the following NA Quadruple Combination:

106I, 248D, 275Y, 286S

The following permutations are now represented on the eleven PF11 anti-viral resistant sequences:

106V, 248N, 275Y, 286S = WA28, WA29, TX47
106I, 248N, 275Y, 286S = Osaka180
106I, 248D, 275Y, 286S = HK2369, Yamaguchi22, Denmark528, Hunan SWL3, Singapore57, Tokushima2, Iwate3

Until the 2009-08-21 deposit of the two Washington sequences, all 275Y TamiFlu-Resistant specimens on PF11 backgrounds were paired with 106I.  We continue to see only 3 of the 11 with 106V.

The addition of Iwate3 heavily leverages position 248 toward Aspartate (D) with 7 specimens versus 4 with Asparagine (N). No TamiFlu Resistant specimen on file displays 286G as yet.


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TamiFlu Resistance #10 on Novel PF11 Sub-Clade, A/Tokushima/2

The tenth TamiFlu Resistant specimen with a publicly available sequence, A/Tokushima/2, from 2009-07-18 was deposited today at GenBank with only Segment 4 (HA) and Segment 6 (NA).

The NA of Tokushima2 is an exact match (469/469) with Denmark528, HK2369, Yamaguchi22, Hunan SWL3 and Singapore57.  Zoonosis is always at work during an Influenza Flux and this time we seem to be reverting.  A careful look at this Tokushima2 sequence at the nucleotide level appears to demonstrate the emergence of a novel sub-clade within ΣPF11 due to the SNP C435T coding for a synonymous Serine at residue 145 (145S).

This synonymous genetic acquisition does not appear to be found on any available PF11 background at this time, but does appear widely in swine and avian H1N1 across Thailand and Europe including Italy, Spain, the UK, Scotland, Denmark, Belgium, Germany and France between 1980 and 2007.  More strikingly, the SNP appears recently in a 2005 Korean avian H3N8, a 2005 Italian avian H5N1 and a 2006 Italian swine H3N1.  Previous specimens demonstrate that C435T seems to cross serotypes easily, appearing on H4N1, H6N1 and H10N1.

On Tokushima2 TamiFlu Resistance is indicated in typical PF11 fashion via a Single Nucleotide Polymorphism coding for 275Y on the Neuraminidase. The sequence displays the following NA Quadruple Combination:

106I, 248D, 275Y, 286S

The following permutations are now represented on the ten PF11 anti-viral resistant sequences:

106V, 248N, 275Y, 286S = WA28, WA29, TX47
106I, 248N, 275Y, 286S = Osaka180
106I, 248D, 275Y, 286S = HK2369, Yamaguchi22, Denmark528, Hunan SWL3, Singapore57, Tokushima2

Until the 2009-08-21 deposit of the two Washington sequences, all 275Y TamiFlu-Resistant specimens on PF11 backgrounds were paired with 106I. Today we see 3 of 10 with 106V.

The addition of Tokushima2 continues to leverage position 248 toward Aspartate (D) with 6 specimens versus 4 with Asparagine (N). No TamiFlu Resistant specimen on file displays 286G as yet.

The Tokushima2 HA also carries a synonymous SNP coding for 277N that is only found in two sequences within ΣPF11, A/Castro/JXP and A/Stockholm/28.

A more robust database of sequences would be useful.

An n higher than 10 gives us a place to begin.


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