But wit may not be fashioned in all occasions. Russian honesty this month provided us with a glancing blow. You know the type of impact . . . the one that brings an instant of reflection, a moment of dread and then the pause where clarity imbues the many loose associations and suddenly a fabric is woven? If we've done our job of transforming the raw data into information, you'll be able to see the pattern after reviewing this study a few times.
Therefore, today, we dispense with wit. Brevity will likely leave us as well. If brevity must be excused from this discussion, then a replacement must be located.
Let’s consider density for a moment. For this exercise, we think that density must suffice. As density increases, particles arrive at closer proximity to each other. Critical mass may be achieved. In the infectious disease world, proximity drives multiplicity of exposure and variation occurs. The ΣPF11 reservoir (pH1N1) has already shown expertise as a master of improvisation with revision at 100% of the residues in one critical HA area.
In this matter, particles are most certainly compressing and coalescing as you will see in the data deposited on 2010-06-01 from Russia. 77 sequences were produced, but only 27 were investigational candidates, offering the HA and NA gene segments in sufficient depth to conduct a full-scale analysis concerning the correlation between our predicted cross-linkage background and negative clinical outcomes.
The cross-linkage of the silent HA 413K and the silent NA 407V polymorphisms appears to be a strong predictor of fatality. Cross-Linking may also be indicative of avian inroads onto the human sequence, driving Influenza Flux and the Hydra Effect. In November 2009, the pH1N1 sequence database at GenBank showed that less than one-half of one percent was cross-linked. As predicted and documented, the cross-linked background has been increasing in density around the world since the spark was initially categorised during October and November in the Ukraine.
In developed areas of the world with a significant devotion to observational science, data surveillance allows factual insight for ΣPF11 moving more deeply into bird flu territory. Three countries have provided useful data to this point: Germany, the Netherlands and Russia.
The recent percentages indicate a significant sub-clading involving cross-linkage. German cases demonstrated a 23% cross-linkage rate in a 2010-04-15 deposit of 99 sequences. The Netherlands showed a 53% rate through a 2010-06-29 deposit. Russia, however, confirmed and re-leveled the concept with strong numbers and substantial allied clinical data. Great appreciation must be expressed to the labs in Russia who conduct such dutiful and comprehensive surveillance. The world benefits from data transparency.
A proper dataset was derived by examining the 20 Russian cases from the month of November that provided the required HA and NA sections for cross-segment analysis. The data is reasonably varied on several axes. The sequences were sampled in a range from November 2 to November 30, span 12 distinct geographies and include cases from locales with previous deposits (useful in comparative delta studies). 15 of the 20 sequences demonstrate cross-linking. With Russia calculating to 75% cross-linking, a new threshold is established.
Cross-Linkage Percentage
- 23% Germany . . . . . 2010-04-15
- 53% Netherlands . . . 2010-06-29
- 75% Russia . . . . . 2010-06-01
An increase from 0.5% to 75% draws the eye for further analysis and the sequences tell the truth. 14 of the cross-linked sequences from November in this Russian deposit are confirmed fatalities. 93% of the humans carrying these two "silent" genetic markers died of pandemic influenza. Only 9 of those cases showed a change at amino acid position 225, suggesting that revision at position 225 is not required for expiration, though the combination with cross-linkage suggests increased virulence. The synonymous pairing of HA 413K and NA 407V represents a strong correlation at this point to fatal human cases of pH1N1.
Bear in mind that the United States may lead the world in cross-linkages cases. The count of examined cases is clearly equal to Russia, but more importantly, the partial sequences on file show a strong pattern that cannot be validated or denied due to baffling truncations of data. Western Europe is at significant risk as Spain is currently inundated with these markers and may have been an early donation source to the Ukraine. Other European countries on the wild bird migration FlightPath (Italy and Greece) also pattern the truncations of data that disallow proper validation.
The greater portion of revisions found on these fatal Russian cross-linked sequences share homology with known zoonotic Influenza reservoirs. Most of the cross-linked sequences are hyper-morphic. 95 polymorphisms among only 15 November sequences solve for an average 6.33 changes per cross-linked HA. Three of the HA sequences have 8 revisions and only one has less than 5 polymorphisms. Ulyanovsk_KLA_2009_11_13_xL_f with only 3 changes (all “silent”) was, nonetheless, fatal to the person infected.
Phylogenentic analysis demonstrates significant genetic diversity within this set of cross-linked sequences. The unrooted tree of all 19 xL cases in this deposit (Figure A including pre- and post-November) provides leafing evidence of wide variation. This wide variation suggests an ease of syn413K recombination across multiple disparate pathways or, in a logic reversal, that HA syn413K / NA syn407V may act as a catalyst for increased and varied genetic acquisitions.
Figure A: Tree of Russian Cross-Linked Sequences from 2010-06-01 Deposit
The PF11 background is primed for zoonotic inclusions due to the present wild type homology with recognised avian sources at 138A, 194L, 226Q and 228G. Perhaps the syn413K completes some odd biological circuit with these recognised Avian markers in PF11, allowing a surge of acquisitions. The ongoing presence of the Avian 225G throughout the world signals five of the six Avian differentiation polymorphic locations are habitually found in this human pandemic reservoir. 190E, the sixth and final Avian revision area from the 2000-06 joint study on early pandemic RBD alterations has been predicted for PF11, but not yet publicly documented due to data sparsity and lab procedures that bias sequence output.
The following two annotated phylogenetic trees suggest that the xL background is magnetized for changes at 225. For simplicity of illustration, the first annotated tree (Figure B) reviews a set of three triples. Each triple set has one xL sequence with wild type 225 and two Russian sequences related by homology, one each with 225G and 225N. Revision at 225 occurs with great facility on this background.
Figure B: Tree of 3 Selected xL sequences & related Russian cases
The second annotated tree (Figure C) expands an early branch of Figure B, demonstrating the diversity and penetration of the syn177L, 324I, syn413K, syn542S grouping. The manifestation of three additional 225G strains (Ivanovo_AIV, Ivanovo_BOV, MoscowOb_OAM) at this early branch does not appear random, but is indicative that parallel patterns of accumulation are occurring across backgrounds with the silent HA 413K polymorphism.
Figure C: Tree of 3 Selected xL sequences & related Russian cases, expanded
Furthermore, these polymorphisms that have accumulated onto the sequences in Russia align with non-human Influenza reservoirs such as wild birds, domestic food poultry (chickens and turkeys), domestic pets (cats and dogs) and in equines used for racing (horse) and agriculture (donkey).
H5N1, H3N8, H7N7 and H9N2 feature prominently.
The sequence details provide case location, date of sample, indication of cross-linkage (_xL), indication of fatality (_f) and a color coding marking the samples bearing HA 225G. None of these November xL sequences carry the more virulent HA 225N, though 3 homology-related fatal 225N sequences are found in the larger Russia 2010-06-01 deposit. Polymorphisms followed by brackets demonstrate the listing of non-human Influenza serotypes that carry instances of the particular change.
Sometimes density is required for understanding. The truth is in the sequences.
Ivanovo_AMV_2009_11_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . 225G mix,
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Kaluga_INV_2009_11_xL _f (
. . . . 225G mix,
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . 491E [H11],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
MoscowOb_DEI_2009_11_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . 225G,
. . . . syn310V [H3N8, H5N1 (E/A/H), H6, H7N7, H11],
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
MoscowOb_OAM_2009_11_02_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . syn205G [H6, H7N7],
. . . . 225G,
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Lipetsk_BVV_2009_11_10_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . 225G mix,
. . . . syn238E [H2, H4],
. . . . syn240G [H3N8, H6, H9N2, H11],
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Ulyanovsk_KLA_2009_11_13_xL_f (
. . . . syn372Q [H2, H3N8, H4, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Stavropol_BLV_2009_11_18_xL (
. . . . syn6L [H3N8],
. . . . 19I [H3N8],
. . . . syn177L [H3N8, H6, H7N7],
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Moscow_CHSN_2009_11_23_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . 225G,
. . . . 324I,
. . . . syn376D [H2, H3N8, H4, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11]),
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
MoscowOb_KMA_2009_11_23_xL_f (
. . . . 38G [H3N8],
. . . . 225G mix,
. . . . 264T,
. . . . 324I,
. . . . 491E [H11],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Astrakhan_CHRM_2009_11_24_xL_f (
. . . . syn71E [H6N1],
. . . . syn109S [H2, H3N8, H9N2, H11],
. . . . syn177L [H3N8, H6, H7N7],
. . . . syn214K [H9N2],
. . . . 324I,
. . . . syn355H [H2, H5N1, H6N1],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Ivanovo_RNA_2009_11_24_xL_f (
. . . . 0I,
. . . . syn168Y [H9N2],
. . . . 225G/225N/225D wt,
. . . . 269V [H9N2, H11],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn426A [H2, H4, H5, H6, H7N7, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
MoscowOb_ZNF_2009_11_24_xL_f (
. . . . syn71E [H6N1],
. . . . syn109S [H2, H3N8, H9N2, H11],
. . . . syn177L [H3N8, H6, H7N7],
. . . . 324I,
. . . . syn331G [H3N8, H4, H6, H7N3, H7N7, H11]
. . . . syn355H [H2, H5N1, H6N1],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Arkhangelsk_GNY_2009_11_25_xL_f (
. . . . syn134G [H2, H3N8, H4, H5N1 (E/A/H), H6, H9N2, H11],
. . . . syn177L [H3N8, H6, H7N7],
. . . . syn238E [H2, H4],
. . . . syn240G [H3N8, H6, H9N2, H11],
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . 437N,
. . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11])
HA and NA
Ivanovo_KOE_2009_11_25_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . syn310V [H3N8, H5N1 (E/A/H), H6, H7N7, H11],
. . . . 324I,
. . . . syn359E [H5, H7N7, H11],
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
Tambov_LLA_2009_11_30_xL_f (
. . . . syn177L [H3N8, H6, H7N7],
. . . . 225G/225N/225D wt,
. . . . syn310V [H3N8, H5N1 (E/A/H), H6, H7N7, H11],
. . . . 324I,
. . . . syn413K [H2, H5N1, H9N2],
. . . . syn542S [H2, H5N1, H9N2])
HA and NA
