HA 189T Upsilon in Czech Republic Recombines with 188T Tau SubClade

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Updated
2011-06-09

On 2011-06-06, the National Institute of Medical Research of the UK published 56 pH1N1 sequences at GISAID sampled in a time period spanning late 2010 to early 2011 with the geographic majority from Europe.  A subclade bearing HA 189T that is 230I-permissive gains 3 members with this deposit, but more importantly the level of polymorphic subclade jumping has accelerated as previously discussed.  The 3' end of a well-defined 188T-bearing subclade from fatal and severe cases in the UK has recombined onto the rare Upsilon subclade (53 sequences, 5.8% CFR). 

The 3 additions to pH1N1_υ are detailed, with the recombinant CzechRepublic32_xM_2011_01_18 shown first.  Though 189T has been found upon 188T backgrounds in several pandemic geographies, this 189T Czech sequence marks the first fully defined, contiguous range, triple polymorphism recombination of 188T background markers onto the 189T Upsilon subclade.

Trailing the polymorphism lists of the 3 Upsilon additions, we also detail two of the several instances of the single polymorphism HA 189T arriving on a 188T background. 

A deposit made 2011-06-05 at GenBank from Fondazione IRCCS Policlinico San Matteo in Pavia, Italy demonstrates another particular instance of subclade elasticity.  A similar crossing of the Czech pH1N1 Tau and Upsilon subclades is found in reverse on a Palermo HA segment sampled via a deep lung wash from a patient suffering Acute Respiratory Distress Syndrome (ARDS).  This 188T Tau subclade sequence, ItalyPalermo02_2011_01_31_severe, takes an 189T from Upsilon and then adds a 208K from an emerging tertiary subclade, resulting in a single 225G-bearing Italian HA segment holding data from three dominant subclades. 

These developments suggest the merit of sampling and directly sequencing a wider variety of sources and tissue types.  The investigators from Pavia have now established a working benchmark for accurately surfacing the actual causative strain sequences from severely ill patients.

On 2011-05-19, the Cantacuzino Institute of Bucharest, Romania deposited 52 sequences at GenBank, representing partial segments (several with potential 3' end recombination from non-pH1N1 primer-matching strains).  A similar adoption of HA 189T onto a known circulating 188T background occurred on RomaniaBihor51551_54F_2011_01_31 with the unusual HA 296R unique to this Romanian deposit and a single 2009 Malaysian HA.  Recall that the polymorphism HA 296H was correlated to numerous fatalities during the early pandemic in Brasil.

Co-location of these transferable components within zoonotic reservoirs provides ample opportunity for exchange.  Expectations should be reset for future pH1N1 antigenic variation as these three dominant subclades continue to demonstrate active cooperation in developing viable Vaccine Escape polymorphisms and then sharing them when perfected.

Upsilon

. . . . CzechRepublic32_xM_2011_01_18 (
. . . . . . . . GISAID HA EPI319447
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 218T [Texas03_M1C2_38M_2010_06_01],
. . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

. . . . AlgeriaG388_1F_2010_12_21 (
. . . . . . . . GISAID HA EPI319430
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn118E (GAa),
. . . . . . . . syn158G (GGg),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc))

. . . . Estonia55236_30M_2011_03_02 (
. . . . . . . . GISAID HA EPI319464
. . . . . . . . 13 Polymorphisms (5 Amino and 8 Silent)
. . . . . . . . 34D,
. . . . . . . . 42W,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc),
. . . . . . . . syn469E (GAg))

Italy

. . . . ItalyPalermo02_2011_01_31_severe (
. . . . . . . . GenBank HA JN017179
. . . . . . . . BronchoAlveolar Lavage
. . . . . . . . 12 Polymorphisms (7 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . syn116R (AGa),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . 208K,
. . . . . . . . 225G,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn428L (tTG),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)

Romania

. . . . RomaniaBihor51551_54F_2011_01_31 (
. . . . . . . . GenBank HA CY090796
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 296R [GISAID Rare 11 – Romania (10) & 2009 Malaysia],
. . . . . . . . HA Truncated after aa296)

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Sweden Demonstrates Extensive Winter 2011 Diversity with 5 pH1N1 SubClades Represented on 11 Deposited Sequences

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Updated
2011-06-03

Across 2011-05-30 and 05-31, the Swedish Institute for Infectious Disease Control published 11 pH1N1 sequences at GISAID sampled in a time period spanning January to April 2011 with the majority in February (6).  The two deposits merit discussion due to the wide variety of backgrounds demonstrated across such a small population of sequences. 

A minimum of 5 Pandemic H1N1 subclades are represented in these 11 Swedish sequences.  More than one represented subclade carries revisions that have been associated with laboratory-determined “Low Reactor” status or with illness in previously vaccinated subjects.  None of the 11 Swedish sequences fall onto the Pandemic H1N1 Upsilon subclade (pH1N1_υ), but several, including one Swedish fatality of a 10 year old male, have crossover polymorphisms previously described in the pH1N1_υ superset.

130 polymorphisms (67 amino and 63 silent) are found on these 11 HA segments with 69 distinct HA changes.  The 11 NA segments demonstrate 77 polymorphisms (41 amino and 36 silent) with 38 distinct NA changes.  207 total polymorphisms on 11 Swedish sequences (HA + NA) averages to 18.8 changes per sequence.  A minimum of 5 subclades with 18 changes per sequence, many at known epitopes (antigenic sites), factors as a significantly difficult target to match with a “single-strain per serotype” vaccine strategy. 

Measurable potential for Vaccine Escape increases with circulating diversity as found on these moving targets in Scandinavia and with the clinical and experimental indications of vaccine failure, e.g. HA 128D, HA 158E, et al.

Four of the 11 HA sequences demonstrate 188T of the first pH1N1 emergent nucleotide coding and 2 of those Swedish 188T sequences additionally carry HA 158E in a mixture with wild type.  Another 4 of the 11 HA sequences demonstrate 186P with one additionally carrying HA 158E in a mixture with wild type on a background with avian influenza polymorphisms.  A concentration of 3 HA 158E revisions in 11 samples mimics the high levels found previously in other Asian and European geographies.  The penetration of HA revisions between aa156 and aa159 in Scandinavia is crossing backgrounds and appears to be accelerating.

The fatal case, SwedenMalmoe5_10M_2011_04_21_f, carries 12 HA changes including revision at aa144 (positional to pH1N1_υ 144E & 144T) and equality to the pH1N1_υ superset at syn287G & 377K.  Eight NA changes on the fatal sequence bring the polymorphic total to 20.  That total suggests that aggressive viral revision is correlated to fatal and severe cases.  These recent high incidences of polymorphism jumping between human subclades appear to follow the dictates of co-location on zoonotic avian sequences.

HA

. . . . SwedenMalmoe5_10M_2011_04_21_f (
. . . . . . . . GISAID EPI318269
. . . . . . . . 12 Polymorphisms (6 Amino and 6 Silent)
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . syn474C (TGt),
. . . . . . . . 482I)

. . . . SwedenUppsala6_67F_2011_03_11 (
. . . . . . . . GISAID EPI318263
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . syn474C (TGt),
. . . . . . . . syn480E (GAg),
. . . . . . . . 482I)

. . . . SwedenLinkoping7_19F_2011_03_09 (
. . . . . . . . GISAID EPI318260
. . . . . . . . 15 Polymorphisms (7 Amino and 8 Silent)
. . . . . . . . syn42G (GGa),
. . . . . . . . syn47L (CTg),
. . . . . . . . syn58C (TGc),
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc),
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn307P (CCc),
. . . . . . . . 359A,
. . . . . . . . 377K,
. . . . . . . . syn446K (AAa))

. . . . SwedenStockholm14_32M_2011_02_15 (
. . . . . . . . GISAID EPI318257
. . . . . . . . 18 Polymorphisms (9 Amino and 9 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn33V (GTc),
. . . . . . . . syn34N (AAt),
. . . . . . . . syn99I (ATt),
. . . . . . . . 132S,
. . . . . . . . syn139C (TGc),
. . . . . . . . 145R,
. . . . . . . . 146G,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn456L (TTg),
. . . . . . . . syn465N (AAt),
. . . . . . . . 496S,
. . . . . . . . syn538F (TTt))

. . . . SwedenStockholm12_2011_02_13 (
. . . . . . . . GISAID EPI318241
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn431L (tTA),
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . SwedenStockholm13_2011_02_09_sH1N1 (
. . . . . . . . GISAID EPI318247
. . . . . . . . 12 Polymorphisms (5 Amino and 7 Silent)
. . . . . . . . syn41N (AAt),
. . . . . . . . 50I,
. . . . . . . . syn154L (tTA) [swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . . . . . . . . with syn69E, 100N, syn154L (CTg),
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, syn215P, 298V,
. . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . syn448L (cTA), syn474C, 482I],
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . 259T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn388K (AAa),
. . . . . . . . 415E mix wt,
. . . . . . . . 454N,
. . . . . . . . syn527L (TTa))

. . . . SwedenStockholm10_2011_02_06 (
. . . . . . . . GISAID EPI318238
. . . . . . . . 11 Polymorphisms (7 Amino and 4 Silent)
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa) [swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . . . . . . . . with syn69E, 100N, syn154L (CTg),
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, syn215P, 298V,
. . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . syn448L (cTA), syn474C, 482I],
. . . . . . . . 100N,
. . . . . . . . 166I [Novel to pH1N1 188T SubClades],
. . . . . . . . 188T,
. . . . . . . . syn215P (CCa) [Vladivistok7_2010_12_03 with 188T],
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 414I [swThailandCU_RA75_2010_01 with 188T],
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . SwedenStockholm11_2011_02_05 (
. . . . . . . . GISAID EPI318235
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg) [swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . . . . . . . . with syn69E, 100N, syn154L (CTg),
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, syn215P, 298V,
. . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . syn448L (cTA), syn474C, 482I],
. . . . . . . . 454N)

. . . . SwedenMalmoe4_2011_02_13 (
. . . . . . . . GISAID EPI318254
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . 128D,
. . . . . . . . syn218A (GCg),
. . . . . . . . syn273T (ACg),
. . . . . . . . 286E,
. . . . . . . . 377K,
. . . . . . . . syn469E (GAg))

. . . . SwedenUmea1_35x_2011_01_28 (
. . . . . . . . GISAID EPI318266
. . . . . . . . 14 Polymorphisms (7 Amino and 7 Silent)
. . . . . . . . syn98F (TTt),
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V,
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . 397D mix wt,
. . . . . . . . syn474C (TGt),
. . . . . . . . 482I)

. . . . SwedenGothenburg1_2011_01_16 (
. . . . . . . . GISAID EPI318244
. . . . . . . . 14 Polymorphisms (6 Amino and 8 Silent)
. . . . . . . . 137T,
. . . . . . . . 144S,
. . . . . . . . 158E mix wt,
. . . . . . . . syn163K (AAa),
. . . . . . . . 186P,
. . . . . . . . syn251L (CTg),
. . . . . . . . syn287G (GGg),
. . . . . . . . syn293L (CTt),
. . . . . . . . 298V [swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . . . . . . . . with syn69E, 100N, syn154L (CTg),
. . . . . . . . . . . . . . . . . . . . . . . . . 189T, syn215P, 298V,
. . . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . syn448L (cTA), syn474C, 482I],
. . . . . . . . syn346G (GGa),
. . . . . . . . syn363G (GGg),
. . . . . . . . 377K,
. . . . . . . . syn474C (TGt),
. . . . . . . . 482I)

NA

. . . . SwedenMalmoe5_10M_2011_04_21_f (
. . . . . . . . GISAID EPI318270
. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)
. . . . . . . . 46T,
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . syn336G (GGc),
. . . . . . . . syn370G (GGc),
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . SwedenUppsala6_67F_2011_03_11 (
. . . . . . . . GISAID EPI318264
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 46T,
. . . . . . . . syn47E (GAg),
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . SwedenLinkoping7_19F_2011_03_09 (
. . . . . . . . GISAID EPI318261
. . . . . . . . 6 Polymorphisms (1 Amino and 5 Silent)
. . . . . . . . syn89S (TCt),
. . . . . . . . syn126P (CCt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn236G (GGc),
. . . . . . . . syn241V (GTg),
. . . . . . . . 299A)

. . . . SwedenStockholm14_32M_2011_02_15 (
. . . . . . . . GISAID EPI318258
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . 20T,
. . . . . . . . 44S,
. . . . . . . . 119K mix wt,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn378N (AAt))

. . . . SwedenMalmoe4_2011_02_13 (
. . . . . . . . GISAID EPI318255
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 240I,
. . . . . . . . 264I,
. . . . . . . . syn339S (TCa),
. . . . . . . . syn383T (ACt),
. . . . . . . . 397K,
. . . . . . . . 442I)

. . . . SwedenStockholm12_21F_2011_02_13 (
. . . . . . . . GISAID EPI318242
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . 83M,
. . . . . . . . 173K,
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . SwedenStockholm13_2011_02_09 (
. . . . . . . . GISAID EPI318248
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . 20T,
. . . . . . . . 40I,
. . . . . . . . 46T,
. . . . . . . . syn157T (ACt),
. . . . . . . . syn229S (TCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa))

. . . . SwedenStockholm10_31F_2011_02_06 (
. . . . . . . . GISAID EPI318239
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc))

. . . . SwedenStockholm11_38F_2011_02_05 (
. . . . . . . . GISAID EPI318236
. . . . . . . . 7 Polymorphisms (2 Amino and 5 Silent)
. . . . . . . . syn162P (CCc),
. . . . . . . . syn240T (ACc),
. . . . . . . . 241I,
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn398E (GAa),
. . . . . . . . syn416D (GAc))

. . . . SwedenUmea1_35x_2011_01_28 (
. . . . . . . . GISAID EPI318267
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . 46T,
. . . . . . . . syn187G (GGt),
. . . . . . . . 273T,
. . . . . . . . 313R,
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

. . . . SwedenGothenburg1_22M_2011_01_16 (
. . . . . . . . GISAID EPI318245
. . . . . . . . 7 Polymorphisms (5 Amino and 2 Silent)
. . . . . . . . 46T,
. . . . . . . . 79P,
. . . . . . . . syn187G (GGt),
. . . . . . . . 313R,
. . . . . . . . 394I,
. . . . . . . . syn430R (CGg),
. . . . . . . . 467V)

Supporting Sequences HA

. . . . Milan18_2011_01_11 (
. . . . . . . . GenBank JF801862
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa11,
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . Milan163_2011_01_14 (
. . . . . . . . GenBank JF801878
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa11,
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa327)

. . . . UKEngland334_2010_12_15 (
. . . . . . . . GISAID EPI309641
. . . . . . . . 9 Polymorphisms (6 Amino and 3 Silent)
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 157Q mix wt,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . UKIreland72392_2010_12_07 (
. . . . . . . . GISAID EPI309663
. . . . . . . . 10 Polymorphisms (7 Amino and 3 Silent)
. . . . . . . . 59S,
. . . . . . . . syn69E (GAa),
. . . . . . . . 100N,
. . . . . . . . 158E mix wt,
. . . . . . . . 163T mix wt,
. . . . . . . . 188T,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S (AGc))

. . . . Vladivistok7_2010_12_03 (
. . . . . . . . GISAID EPI306383
. . . . . . . . 12 Polymorphisms (7 Amino and 5 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 85A,
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 236I,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N (AAt),
. . . . . . . . syn538F (TTt))

. . . . JapanTochigi105_2010_11_20 (
. . . . . . . . GISAID EPI305439
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . syn10Y (TAc),
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 166Q mix,
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . 205W mix,
. . . . . . . . syn338G (GGc),
. . . . . . . . HA Truncated after aa347)

. . . . AlabamaAF2073_2010_02_14 (
. . . . . . . . GISAID EPI276240
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . 59S,
. . . . . . . . 269L,
. . . . . . . . 377K,
. . . . . . . . HA Truncated after aa386)

. . . . Hawaii03_2010_02_08 (
. . . . . . . . GISAID EPI278818
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 38G,
. . . . . . . . 59S,
. . . . . . . . 377K,
. . . . . . . . syn494E (GAa))

. . . . swThailandCU_RA75_2010_01 (
. . . . . . . . GISAID EPI255118
. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)
. . . . . . . . 188T,
. . . . . . . . 263D,
. . . . . . . . syn350G (GGg),
. . . . . . . . 414I,
. . . . . . . . syn484N (AAc))

. . . . KoreaDaejeon1871_2009_12_15 (
. . . . . . . . GISAID EPI254654
. . . . . . . . 4 Polymorphisms (4 Amino and 0 Silent)
. . . . . . . . 25R,
. . . . . . . . 59S,
. . . . . . . . 131P,
. . . . . . . . 158E)

. . . . TexasAF2623_2009_12_13 (
. . . . . . . . GISAID EPI281756
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 57E,
. . . . . . . . 59S,
. . . . . . . . 100N,
. . . . . . . . syn137A (GCt),
. . . . . . . . syn270I (ATc),
. . . . . . . . 377K,
. . . . . . . . HA Truncated after aa386)

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HA 230I RBS Polymorphism Potential in Mexico

Current trending indicates a reportable potential for the M230I polymorphism spreading on the Hemagglutinin of PF11. This Receptor Binding Domain change may enhance Vaccine Escape from the currently selected vaccine target candidate, CA/07 X181. 

For those who are following the prediction on February 25, 2010, the pandemic reservoir now shows multiple instances of multiple encodings for 230I.  Model adjustment and data transparency allowed a second set of detailed geographic predictions on 2010-08-09 that have also found traction.

The 230I bearing sequences meeting the prediction are documented in the detailed discussion on Vaccine Escape that demonstrates a 100% change rate in the pandemic influenza (pH1N1) reservoir at the critical HA genetics range between amino acid positions 186 and 248.  95% of the amino acid positions have notated revisions.

Expectations for the M230I polymorphism, that first came to our notice for zoonotic concern on the H5N1 human fatality cluster, have now been revised based on the most current public data.  The GeneWurx RnR model approximates that HA 230I will appear in the PF11 RBS according to the following geographic probabilities.

• 20% probability in Mexico sampled by 2011-06-30.
• 55% probability in Mexico sampled by 2011-09-30.

• 10% or less probability of HA 230I conserving across PF11 by 2011-09-30.
• 17% probability of HA 230I conserving on one or more Hydrae by 2011-09-30.

These probabilities will be updated as additional data is made public.  Transparency at this post-pandemic stage is essential to formulate viable responses for the risk groups.  Release of sequences and clinical data of a finer detail and higher quantity will allow information-based decisions.

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Scandinavia Accumulates Superset on Emergent 188T Background

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked spreadsheet for completeness in citation.

Last Updated
2011-03-29

On 2011-03-20, the Statens Serum Institut of Copenhagen, Denmark published 6 pH1N1 sequences at GenBank sampled in a time period spanning approximately 3 weeks from late December 2010 until mid January 2011. Five of the six HA sequences demonstrate the 188T of the first pH1N1 emergent nucleotide coding having a second base revision (AcT) and two of those Denmark 188T sequences additionally carry HA 225G.

Denmark120_2010_12_20 and Denmark20_2011_01_04 with 188T and 225G demonstrate ongoing transmission of a template having 6 revisions (100N, syn179L, 188T, syn338G, syn448L, 454N) that congealed during November and December across published cases in at least nine American states and in severe and fatal UK cases. The backgrounds with 188T have exhibited experimentally and practically determined Vaccine Escape, as have backgrounds carrying 225G individually. The final silent revision at HA 448L on this particular 188T template appears to correlate with RBD revisions (190G, 221L, 224K) and to revisions at known Vaccine Escape amino acid positions (158E, 159D, 188T (AcT), 225G).

• GeneWurx_UK_December_Emerging_Genetics_v6.xls
• 
  
  
  
• 
  
   

A potentially related, contemporary sequence from Sweden was sampled one day after Denmark120_2010_12_20.  SwedenHalmstad1_23F_2010_12_21, from the adjacent European geography, is the first published on this 188T background to carry HA 230I.  The Halmstad sequence also revised at a known Vaccine Escape position to 159K.  As the 188T bearing sub-clades represent over 50% of all GISAID-published, human pH1N1 sequences between October 2010 and March 2011, the "swl" lineage appears to have widespread 188T seeding that is attractant to additional polymorphic accommodation from zoonotic sources.

Though Scandinavia is now the only published geography with the polymorphic superset of 159K, 188T, 225G and 230I on similar backgrounds, GeneWurx analysis suggests that a signal with 188T, 225G and 230I has reportable probability in Scandinavia and several other regions worldwide.  Consideration must be given to this potential template (188T, 225G, 230I) also carrying a revision from aa156 to aa159.  In a parallel, transmitting sub-clade, 189T, 225G and 230I show potential for convergence and / or expansion with 165N and / or 158E.

Polymorphism jumping appears to be occurring bi-directionally between the transmitting 189T sub-clade and the emergent 188T sub-clades.

. . . . Denmark120_2010_12_20 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N)

. . . . Denmark20_2011_01_04 (
. . . . . . . . HA truncated before aa1,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T [SwedenHalmstad1_23F_2010_12_21
. . . . . . . . . . . . . . . . with 100N, 159K, 230I,
. . . . . . . . . . . . . . . . . . . . syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . 454N, syn537S],
. . . . . . . . 225G mix wt,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [UKEngland4940476_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4880378_2010_12_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4920303_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland142_2010_11_severe
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland126_2010_11
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 221L, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . UKEngland4860049_2010_11
. . . . . . . . . . . . . . . . . . . . with 0A, 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . syn210S, syn338G, 377K,
. . . . . . . . . . . . . . . . . . . . . . . . 454N, 528I,
. . . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . . with 159D, 269V,
. . . . . . . . . . . . . . . . . . . . . . . . 312R, 313K, 377K,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S],
. . . . . . . . 454N,
. . . . . . . . syn541C)

Supporting Sequences

From GISAID database (GISAID Citation).

. . . . SwedenHalmstad1_23F_2010_12_21 (
. . . . . . . . 100N [Slovakia1625_56X_2010_03_30_xL
. . . . . . . . . . . . . . . . . . . . with 230I],
. . . . . . . . 159K [UKEngland4940476_2010_08
. . . . . . . . . . . . . . . . . . . . with 128D, 377K,
. . . . . . . . . . . . . NY3230_2010_01_25
. . . . . . . . . . . . . . . . . . . . with 100N, syn231N],
. . . . . . . . 188T,
. . . . . . . . 230I,
. . . . . . . . syn245F [RussiaBelgorod2_2010_03_15
. . . . . . . . . . . . . . . . . . . . with 158E, 225G, 230I & syn343G],
. . . . . . . . 280A [MXinDRE797_2010_TmX
. . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . with 156E, 225N, 230I & syn346G],
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S [UKEngland5040499_2010_12_f])

. . . . UKEngland142_2010_11_severe (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . UKEngland126_2010_11 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 221L,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . UKEngland4860049_2010_11 (
. . . . . . . . 0A,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn210S,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N,
. . . . . . . . 528I)

. . . . Hawaii08_2010_04_12
. . . . . . . . 159D mix wt,
. . . . . . . . 269V,
. . . . . . . . syn288A,
. . . . . . . . 312R,
. . . . . . . . 313K,
. . . . . . . . 377K,
. . . . . . . . syn448L [England4940476_2010_12,
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Kentucky09_2010_11_01
. . . . . . . . . . . . . . . . . . . . with 100N, 158E, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . England4640543_2010_11_f
. . . . . . . . . . . . . . . . . . . . with 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . . . . . . . . . 190G, syn338G, 377K, 454N,
. . . . . . . . . . . . . . . . Yakutsk_EAV_2009_11_18
. . . . . . . . . . . . . . . . . . . . with syn348V,
. . . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f
. . . . . . . . . . . . . . . . . . . . with 224K, 225G, syn348V, syn542S])

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Vaccine Escape Signal 188T Takes Another Genetic Step and Transmits

On 2011-02-23 the National Institute of Infectious Diseases (NIID) of Japan submitted a small series of 8 sequences from Japan and South Korea. The 4 partial HA sequences originating from the Korean CDC include 2 from late 2010 carrying a novel, second-step 188T coding.

GeneWurx has discussed the relationship of the original zoonotic 188T change [H7N7 human fatality] and Immune / Vaccine Escape within the pH1N1 reservoir. This Korean novel third base revision (T->C) builds onto the earlier second base revision (G->C) that created the original 188T (AcT).

Step1 = AGT->AcT - From pH1N1 wild type to original pH1N1 188T
Step2 = AcT->Acc - From pH1N1 188T (AcT) to Korean alternate pH1N1 188T

This second step amendment creates an alternate codon (Acc) to the widely circulating (148 full signal sequences), documented Vaccine Escape 188T version (AcT) on a background similar to existing sub-clades.

Donors for the third base change required to create this alternate pH1N1 188T are found in H7N3 and H7N7, the same reservoirs that likely donated the second base for the original pH1N1 188T. The H7N7 reservoir carries the alternate codon (Acc) extensively in Avian species including the recent worldwide geographies of Egypt (2004-2006), Sweden (2005), Italy (2006) and Poland (2009). Of note, the alternate codon also appears to have been popular across Europe in Avian species at the beginning of the 20th century (1902-1927) within the H7N7 serotype and extensive in late 20th century Equine species with H7N7.

GeneWurx expects additional attraction of genetic data from animal based influenza serotypes like H3N8, H5N1, H7N3, H7N7 and H9N2 onto these backgrounds.

This novel revision is found in the adjacent provinces of Chungbuk and Gyeonggi demonstrating geographic spread in less than 3 weeks, suggesting transmissibility and fitness of the additional 188T coding. The unique pH1N1 coding for 188T signals continued viral genetic revision at a point already having an established Immune Escape and Vaccine Escape history (188T). The amino acid position 188 had previously come under selective pressure and successfully revised to evade the vaccines and the natural immunity. The viral strains appear to be revising at a rate higher than necessary according to the accepted concept of selection.

Each of the Korean pH1N1 sequences with the unique 188T codon displays markers related to currently circulating pH1N1 sub-clades carrying the original 188T coding; however, extensive additional rare polymorphisms are found on each of the Korean sequences under investigation though the HA is missing approximately 200 proteins from the 3’ end (truncated after amino acid position 348). Though the two Korean sequences share 5 polymorphisms (syn1A, 100N, 188T, syn271S and syn338G), the earlier of the two, Gyeonggi2623_2010_11_24, is more complex with 6 additional changes including a 158E mixture that has been previously related to Vaccine Escape.

The Chungbuk2826_2010_12_14 sequence from 3 weeks later carries 2 additional changes not found on the Gyeonggi pattern. Several of the rare polymorphisms from these two sequences are also found in animal influenza reservoirs [H3N8, H5N1, H9N2], a clear demonstration that the most current pH1N1 sequences show a human reservoir that is hyper-morphic and hyper-zoonotic at a time period when public health officials continue to assure citizens that the circulating flu is unchanged.

Nothing could be further from the Truth.


. . . . Chungbuk2826_2010_12_14 (
. . . . . . . . syn1A (GCc) [Georgia4573_2009_12_23],
. . . . . . . . syn31H (CAt) [31 GISAID],
. . . . . . . . . . . . . . . . . . . [Conserved Asia],
. . . . . . . . 100N,
. . . . . . . . 173R [19 GISAID],
. . . . . . . . 188T (Acc) [H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [Unique to PF11 Korea 2010 (2)],
. . . . . . . . syn271S (TCg) [OzDarwin43_2010_07_23
. . . . . . . . . . . . . . . . . . . . . . . . . . . . with 166N, syn239P,
. . . . . . . . . . . . . . . . . . . . . CalifSD_INS105_2009_11_04
. . . . . . . . . . . . . . . . . . . . . . . . . . . . with syn103E],
. . . . . . . . . . . . . . . . . . . . . [swine HK 2001 with 100N, syn258F],
. . . . . . . . . . . . . . . . . . . . . [swine Colorado 2001 (ATg)],
. . . . . . . . syn327I (ATc) mix wt [43 GISAID],
. . . . . . . . syn338G,
. . . . . . . . HA truncated after aa348)

. . . . Gyeonggi2623_2010_11_24 (
. . . . . . . . syn1A (GCc) [Georgia4573_2009_12_23],
. . . . . . . . 100N,
. . . . . . . . syn108L (TTa) [15 GISAID],
. . . . . . . . . . . . . . . . . . . [US, US Military],
. . . . . . . . . . . . . . . . . . . [Sri Lanka 2010, China],
. . . . . . . . . . . . . . . . . . . [Canada, Europe, Abu Dhabi],
. . . . . . . . . . . . . . . . . . . [swine Asia, swine US],
. . . . . . . . 158E mix wt,
. . . . . . . . syn175E [83 GISAID
. . . . . . . . . . . . . . . [Worldwide, primarily 2009],
. . . . . . . . . . . . . . . [2010 Australia, Costa Rica, China Widespread],
. . . . . . . . 188T (Acc) [H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [Unique to PF11 Korea 2010 (2)],
. . . . . . . . syn239P (CCa) [H3N8, H9N2],
. . . . . . . . . . . . . . . . . . . . . [30 GISAID],
. . . . . . . . . . . . . . . . . . . . . [Widespread US, US Military],
. . . . . . . . . . . . . . . . . . . . . [Asia, Russia, Europe],
. . . . . . . . syn258F (TTt) [16 GISAID],
. . . . . . . . . . . . . . . . . . . . . [US, US Military],
. . . . . . . . . . . . . . . . . . . . . [South America],
. . . . . . . . . . . . . . . . . . . . . [Japan, Russia, Europe],
. . . . . . . . . . . . . . . . . . . . . [swine HK 2001],
. . . . . . . . syn271S (TCg) [OzDarwin43_2010_07_23
. . . . . . . . . . . . . . . . . . . . . . . . . . . . with 166N, syn239P,
. . . . . . . . . . . . . . . . . . . . . CalifSD_INS105_2009_11_04
. . . . . . . . . . . . . . . . . . . . . . . . . . . . with syn103E],
. . . . . . . . . . . . . . . . . . . . . [swine HK 2001 with 100N, syn258F],
. . . . . . . . . . . . . . . . . . . . . [swine Colorado 2001 (ATg)],
. . . . . . . . syn337A (GCa) [H5N1 Avian Japan 2007-2008],
. . . . . . . . . . . . . . . . . . . . . [Unique to PF11],
. . . . . . . . syn338G,
. . . . . . . . HA truncated after aa348)

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

2011 Novel Jiangsu HA from Swine Signals Zoonotic Flux

Last Updated 2011-01-16

The WHO Chinese National Influenza Center in Beijing deposited a full set of gene segment sequences on 2011-01-14 from a 3M sample taken in Jiangsu Province during the first week of the year.  The Hong Kong Ministry of Health issued a notification that the boy was on long-term steroid treatment for chronic kidney disease.

Preliminary review shows that ChinaJiangsu1_3M_2011_01_04 carries a novel Hemagglutinin most closely related to late decade swine from Asia.  The captivating factor is that this swine-like HA also demonstrates homology at least 25 recent genetic acquisitions into the human pH1N1 reservoir related to the UK Severe Wave and associated sequences on the highly divergent and hyper-zoonotic emerging sub-clades.

GeneWurx has prepared a spreadsheet for collaboration detailing the preliminarily recognised pH1N1 homologies to this most recent sequence in the database, ChinaJiangsu1_3M_2011_01_04.  Several additional matches are not yet vetted for the spreadsheet, including syn338G, syn343G, syn346G, syn353G and syn363G.  Each must be investigated as variant silent codings to changes in pH1N1 at the same amino acid position.

GeneWurx_Novel_HA_Jiangsu1_3M_2011_01_04_v0.xls

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

UK Fatality Sequences Relate to US and Iran

The US CDC today released a small set of sequences at GISAID spanning June to November 2010. As the UK Severe Wave is the current topic of interest, we have profiled 6 of these sequences from today against the UK Fatality Sequences that have been published.  Five of the sequences are from the United States and one is from Bangladesh.

Previously, the UK HPA released a small group of sequences in two deposits at GISAID related to the present severe wave filling the ICU wards in the UK. A concurrent paper ¹ was published in early January with a phylogenetic tree. Several of the fatalities noted on the HPA Ellis Figure3 ¹ phylogenetic tree have been included in the two sequence deposits.

So that focus may occur at the clinical outcomes of highest priority, GeneWurx has prepared a fresh phylogenetic tree with annotation in progress that may prove useful to those investigating the ongoing divergency within this zoonoticly active pH1N1 viral reservoir.  UK Fatalities, UK Severe cases (225G), UK potential Vaccine Escape cases (158E, 159K) and cases from the US, Australia, Iran and Bangladesh are profiled.

GeneWurx_Global_Spread_of_Divergence_UK_US_Iran_v0.jpg

The GeneWurx annotation for the full HPA Ellis Figure3 ¹ has been recently revised and Version 5 of the Emerging Genetics spreadsheet is available with several additions including two of the recent US sequences of interest and the Bangladeshi sequence.

• UK_2010_Phylo_ELLIS_Fig3new_4_GISAID_Notated_2011_01_13.JPG
• GeneWurx_UK_December_Emerging_Genetics_v5.xls

A pattern that has been expected is demonstrated in Kentucky09_40F_2010_11_01 with 158E, 188T and 225G on a similar background as the OzBrisbane209_51F_2010_08_09 sequence carrying 156E, 188T and 225G.  Though these two sequences share extensive homology, the tree and polymorphism details will show that overall the reservoir is diversifying and creating branches with minimal leaf count by acquiring and recombining rare and novel polymorphisms also found in animal reservoirs.

US Sequences

. . . . Indiana05_78F_2010_06_11 (
. . . . . . . . 100N,
. . . . . . . . 115K,
. . . . . . . . syn270I,
. . . . . . . . 377K)

. . . . Indiana06_9M_2010_07_29 (
. . . . . . . . #11V,
. . . . . . . . #8A,
. . . . . . . . syn36L,
. . . . . . . . syn99I,
. . . . . . . . 233H,
. . . . . . . . syn256Y,
. . . . . . . . syn282C,
. . . . . . . . syn283Q,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn428L,
. . . . . . . . 522A)

. . . . Kentucky08_xF_2010_10_11 (
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . Utah05_29F_2010_10_12 (
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 289M,
. . . . . . . . syn297N,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 396I,
. . . . . . . . 454N,
. . . . . . . . syn478C)

. . . . Kentucky09_40F_2010_11_01 (
. . . . . . . . 17G,
. . . . . . . . 100N,
. . . . . . . . 158E,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . syn452V,
. . . . . . . . 454N,
. . . . . . . . syn467C)

Bangladesh Sequence

. . . . Bangladesh8003_27M_2010_09_16 (
. . . . . . . . syn12A,
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . 225N mix wt,
. . . . . . . . syn297N,
. . . . . . . . syn326S,
. . . . . . . . syn383N,
. . . . . . . . syn388K,
. . . . . . . . 444K,
. . . . . . . . 447S,
. . . . . . . . syn474C)

UK Fatality Sequences

. . . . UKEngland5040499_2010_12_f (
[match GhanaFS10_4259_2010_08_27 less 213S]
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 213S,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S)

. . . . UKWhiteChapel4880374_2M_2010_11_28_f (
. . . . . . . . 0A [Arizona05_2010_05_01
. . . . . . . . . . . . . . . with syn338G & 377K,
. . . . . . . . . . Alabama08_2009_12_04
. . . . . . . . . . . . . . . with syn226Q, 310A mix & 506V,
. . . . . . . . . . RussiaPerm_ZTS_2009_11_30
. . . . . . . . . . . . . . . with 377K & syn475D,
. . . . . . . . . . RussiaBelgorod01_2009_11_30,
. . . . . . . . . . RussiaBelgorod05_2009_11_30,
. . . . . . . . . . Boston634_2009_11_09
. . . . . . . . . . . . . . . with 100N & syn270I],
. . . . . . . . syn55L [S9, H5N1],
. . . . . . . . . . . . . . [Iran16273_2009_11_22 with 226R
. . . . . . . . . . . . . . NZ_Waikato2_2010_01_04 with 233H,
. . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07, et al],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [OzBrisbane209_51F_2010_08_09
. . . . . . . . . . . . . . . . . . . . with 156E & 225G,
. . . . . . . . . . . . . . . Arizona05_2010_05_11 with 0A,
. . . . . . . . . . . . . . . Swine Asia 2005 with 0A, et al]
. . . . . . . . 377K,
. . . . . . . . 454N [H7N3, H7N7, H9N2]
. . . . . . . . . . [Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . FL_Pen210_2009_11_10
. . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . SouthCarolina18_2009_09_16_VxX
. . . . . . . . . . . . . . . . . . with 159D, 224K, et al],
. . . . . . . . syn529L)

. . . . UKCambridge118_4F_2010_11_19_f (
. . . . . . . . syn118E,
. . . . . . . . 137T [41 sequences at GISAID],
. . . . . . . . syn163K,
. . . . . . . . 186P,
. . . . . . . . syn251L,
. . . . . . . . syn293L,
. . . . . . . . syn363G [21 sequences at GISAID],
. . . . . . . . syn455Q,
. . . . . . . . syn474C,
. . . . . . . . 504G,
. . . . . . . . 513V)

. . . . UKEngland4500186_2010_11_f (
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . 190Y [Avian H6N1],
. . . . . . . . . . [SwedenMalmoe1_2010_01_01_xL
. . . . . . . . . . . . with 377K, syn413K,
. . . . . . . . . . Brasil7450_2009_07_22
. . . . . . . . . . . . with 157E mix wt],
. . . . . . . . 377G [H2N3],
. . . . . . . . . . . . . [H5N1 Human Egypt Preschool 2009, H5N1 Human Indonesia 2005],
. . . . . . . . . . . . . [H6N1 2009],
. . . . . . . . . . . . . [US Swine 1957-1978],
. . . . . . . . . . . . . [IranBandarAbbas5096_2010_10_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C,
. . . . . . . . . . . . . Florida13_2010_08_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C, 512M,
. . . . . . . . . . . . . . Iowa05_2010_05_04
. . . . . . . . . . . . . . . . . . . with 208K, syn516I,
. . . . . . . . . . . . . . swSouthDakota1_2010_04_27,
. . . . . . . . . . . . . . TexasAF2647_2010_04_11
. . . . . . . . . . . . . . . . . . . with 200S, syn214K, syn276H,
. . . . . . . . . . . . . . swIowa02999_2010_04_01,
. . . . . . . . . . . . . . UtahAF2653_2010_03_14
. . . . . . . . . . . . . . . . . . . with syn253V,
. . . . . . . . . . . . . . North Carolina05_2010_02_24
. . . . . . . . . . . . . . . . . . . with 259V,
. . . . . . . . . . . . . . Kentucky04_2010_02_22
. . . . . . . . . . . . . . . . . . . with syn488D,
. . . . . . . . . . . . . . Minnesota02_2010_02_17
. . . . . . . . . . . . . . . . . . . with 259V, 509D,
. . . . . . . . . . . . . . SouthCarolina01_2010_01_27
. . . . . . . . . . . . . . . . . . . with syn238E, syn488D,
. . . . . . . . . . . . . . AnasPlatBelgium04328_pcs17_2010_01_21
. . . . . . . . . . . . . . . . . . . with syn474C,
. . . . . . . . . . . . . . GermanyAF2208_2010_01_20
. . . . . . . . . . . . . . . . . . . with #1T, 225E,
. . . . . . . . . . . . . . NorthCarolina03_2010_01_20
. . . . . . . . . . . . . . . . . . . with 225G mix, 259V, syn275V,
. . . . . . . . . . . . . . NewMexico01_2010_01_05
. . . . . . . . . . . . . . . . . . . with 430I, syn445V, syn490P,
. . . . . . . . . . . . . . swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . with #1T, 0A, 189T, syn338G,
. . . . . . . . . . . . . . . . . . . . . . syn451K, syn474C, syn456L, syn529L,
. . . . . . . . . . . . . . Moldova5053_2009_12_11
. . . . . . . . . . . . . . . . . . with 173R, 176I, 225A, 225G mix wt, syn286K,
. . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . with syn297N, syn343G, 471H,
. . . . . . . . . . . . . . KoreaAF2411_2009_11_11
. . . . . . . . . . . . . . . . . . . with 237I, syn286K,
. . . . . . . . . . . . . . England94840077_2009_11
. . . . . . . . . . . . . . . . . . . with 259T,
. . . . . . . . . . . . . . BahrainN11892_2009_10
. . . . . . . . . . . . . . . . . . . with 208K,
. . . . . . . . . . . . . . Nevada16_2009_10_02
. . . . . . . . . . . . . . . . . . . with 464R mix wt,
. . . . . . . . . . . . . . Tasmania2005_2009_07_03
. . . . . . . . . . . . . . . . . . . with 289M,
. . . . . . . . . . . . . . Texas42303371_2009
. . . . . . . . . . . . . . . . . . . with syn456L, syn507K],
. . . . . . . . syn408E,
. . . . . . . . syn474C,
. . . . . . . . 512M,
. . . . . . . . 530I)

. . . . UKEngland4640543_2010_11_f (
[match to UKEngland4940476_2010_12 less 225G plus 190G]
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . UKWhiteChapel4780352_5M_2010_10_26_f (
. . . . . . . . syn58C,
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . syn131S,
. . . . . . . . syn210S,
. . . . . . . . 377K)

. . . . UKEngland4380108_2010_10_f (
. . . . . . . . syn67N,
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . 144V [Boston703 and Ireland],
. . . . . . . . 224K,
. . . . . . . . syn235T,
. . . . . . . . 377K,
. . . . . . . . 529M)

. . . . UKBirmingham3220137_44F_2010_08_07_f (
. . . . . . . . #8A,
. . . . . . . . 175K,
. . . . . . . . 311E,
. . . . . . . . 377K,
. . . . . . . . syn385V,
. . . . . . . . syn451K,
. . . . . . . . syn454S,
. . . . . . . . syn494E,
. . . . . . . . 537G)

Severe Sequences

. . . . UKEngland4940476_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg) [Regional Marker 2009 (tTA)]
. . . . . . . . . . . . . . . . . . . . [TexasAF2588_2009_10_04,
. . . . . . . . . . . . . . . . . . . . TexasJMS404_2010_01_08],
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [H6N1]
. . . . . . . . . . . . . . . [Regional Marker UK 2009]
. . . . . . . . . . . . . . . [UKEngland4880378_2010_12 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland4640543_2010_11_f with syn179L, 188T, 190G
. . . . . . . . . . . . . . . UKEngland4920303_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland142_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland4860049_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland126_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . NZChristchurch8_2010_07_08
. . . . . . . . . . . . . . . . . . . with syn44L, 97N, syn99I, syn106E, 128D,
. . . . . . . . . . . . . . . . . . . . . . . syn214K, 253A, syn362S, 377K,
. . . . . . . . . . . . . . . Calif06_2010_04_05 with 269V
. . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . with 159D, 269V, 312R, 313K,
. . . . . . . . . . . . . . . Ethiopia13_2010_02_10
. . . . . . . . . . . . . . . . . . . with 100N, syn163K, 269V, 324I, syn360Q, syn455Q,
. . . . . . . . . . . . . . . Philippines824_2010_02_17 with 165N,
. . . . . . . . . . . . . . . Kosova876_2009_12_22,
. . . . . . . . . . . . . . . RussiaYakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . . Netherlands2143_2009_11_16 with syn179L (tTA),
. . . . . . . . . . . . . . . RussiaYaroslavl_CHMV_2009_11_10_f with 224K & 225G mix
. . . . . . . . . . . . . . . AntwerpINS221_2009_10_28 with syn179L (tTA)],
. . . . . . . . 454N)

. . . . UKEngland4880378_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

Potential Vaccine Escape Sequences

[Diversity with Vaccine Escape Potential]

. . . . UKEngland106_2010_11 (
. . . . . . . . 0A,
. . . . . . . . syn55L,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . syn258F,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 452I [],
. . . . . . . . 454N,
. . . . . . . . syn529L)

. . . . UKEngland3380426_2010_08 (
. . . . . . . . syn44L,
. . . . . . . . syn106E,
. . . . . . . . 128D,
. . . . . . . . 159K [NY3230_2010_01_25 with 100N, syn177L, syn231N],
. . . . . . . . 377K)

Iran Sequences

. . . . IranShahriar5336_2010_12_06 (
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . syn297N [H3N8 gadwallRussiaAltai1325_2007_09],
. . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . [Wisconsin08_2010_08_10
. . . . . . . . . . . . . . . . . . . . . . with 39R, syn78S, 137T, 186P, syn297N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn326S, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn413K, 444K, syn474C,
. . . . . . . . . . . . . . . CalifVRDL2_2010_01_11
. . . . . . . . . . . . . . . . . . . . . . with syn121P & 502K,
. . . . . . . . . . . . . . . YaroslavlIIV196_2009_12_04_f
. . . . . . . . . . . . . . . . . . . . . . with syn159N, 225G,
. . . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . . . . with syn343G, 377G, 471H,
. . . . . . . . . . . . . . . Brussels243_2009_11_09
. . . . . . . . . . . . . . . . . . . . . . with syn44L, syn159N & syn323N,
. . . . . . . . . . . . . . . Australia6_2009_07_18
. . . . . . . . . . . . . . . . . . . . . . with syn159N, 233H]
. . . . . . . . syn326S [Wisconsin08_2010_08_10
. . . . . . . . . . . . . . . . . . . . . . with 39R, syn78S, 137T, 186P, syn297N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn326S, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn413K, 444K, syn474C,
. . . . . . . . . . . . . . . Zhongyuan1643_2009_11_16
. . . . . . . . . . . . . . . . . . . . . . with 208G],
. . . . . . . . syn383N [H3N8],
. . . . . . . . syn388K [H3N8, H5N1, S7],
. . . . . . . . . . . . . . . [OzVictoria508_2010_07_24
. . . . . . . . . . . . . . . . . . . . . . . with 238D,
. . . . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . . . . with 188R, 225N & 230I,
. . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25_VxX
. . . . . . . . . . . . . . . . . . . . . . . with 159D & 227G, et al],
. . . . . . . . syn411N (AAc) [H7N3 & H7N7 donor ATc],
. . . . . . . . 444K (AAg) [H3N8 gAg],
. . . . . . . . syn474C [H3N8, Avian H1N1 2010],
. . . . . . . . . . . . . . . [Michigan10_2009_06_03 with 137T, 225N, et al])

. . . . IranBandarAbbas5096_2010_10_02 (
. . . . . . . . 72P,
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . syn318A,
. . . . . . . . 377G [H2N3],
. . . . . . . . . . . . . [H5N1 Human Egypt Preschool 2009, H5N1 Human Indonesia 2005],
. . . . . . . . . . . . . [H6N1 2009],
. . . . . . . . . . . . . [US Swine 1957-1978],
. . . . . . . . . . . . . [Florida13_2010_08_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C, 512M,
. . . . . . . . . . . . . . Iowa05_2010_05_04
. . . . . . . . . . . . . . . . . . . with 208K, syn516I,
. . . . . . . . . . . . . . swSouthDakota1_2010_04_27,
. . . . . . . . . . . . . . TexasAF2647_2010_04_11
. . . . . . . . . . . . . . . . . . . with 200S, syn214K, syn276H,
. . . . . . . . . . . . . . swIowa02999_2010_04_01,
. . . . . . . . . . . . . . UtahAF2653_2010_03_14
. . . . . . . . . . . . . . . . . . . with syn253V,
. . . . . . . . . . . . . . North Carolina05_2010_02_24
. . . . . . . . . . . . . . . . . . . with 259V,
. . . . . . . . . . . . . . Kentucky04_2010_02_22
. . . . . . . . . . . . . . . . . . . with syn488D,
. . . . . . . . . . . . . . Minnesota02_2010_02_17
. . . . . . . . . . . . . . . . . . . with 259V, 509D,
. . . . . . . . . . . . . . SouthCarolina01_2010_01_27
. . . . . . . . . . . . . . . . . . . with syn238E, syn488D,
. . . . . . . . . . . . . . AnasPlatBelgium04328_pcs17_2010_01_21
. . . . . . . . . . . . . . . . . . . with syn474C,
. . . . . . . . . . . . . . GermanyAF2208_2010_01_20
. . . . . . . . . . . . . . . . . . . with #1T, 225E,
. . . . . . . . . . . . . . NorthCarolina03_2010_01_20
. . . . . . . . . . . . . . . . . . . with 225G mix, 259V, syn275V,
. . . . . . . . . . . . . . NewMexico01_2010_01_05
. . . . . . . . . . . . . . . . . . . with 430I, syn445V, syn490P,
. . . . . . . . . . . . . . swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . with #1T, 0A, 189T, syn338G,
. . . . . . . . . . . . . . . . . . . . . . syn451K, syn474C, syn456L, syn529L,
. . . . . . . . . . . . . . Moldova5053_2009_12_11
. . . . . . . . . . . . . . . . . . with 173R, 176I, 225A, 225G mix wt, syn286K,
. . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . with syn297N, syn343G, 471H,
. . . . . . . . . . . . . . KoreaAF2411_2009_11_11
. . . . . . . . . . . . . . . . . . . with 237I, syn286K,
. . . . . . . . . . . . . . England94840077_2009_11
. . . . . . . . . . . . . . . . . . . with 259T,
. . . . . . . . . . . . . . BahrainN11892_2009_10
. . . . . . . . . . . . . . . . . . . with 208K,
. . . . . . . . . . . . . . Nevada16_2009_10_02
. . . . . . . . . . . . . . . . . . . with 464R mix wt,
. . . . . . . . . . . . . . Tasmania2005_2009_07_03
. . . . . . . . . . . . . . . . . . . with 289M,
. . . . . . . . . . . . . . Texas42303371_2009
. . . . . . . . . . . . . . . . . . . with syn456L, syn507K],
. . . . . . . . syn449Y (TAc) [H3N8 Ttc],
. . . . . . . . syn474C [H3N8])

. . . . IranKaraj5327_2010_12_06 (
. . . . . . . . syn34N [JapanKanagawa74_2010_10_16, et al],
. . . . . . . . 146G [JapanKanagawa74_2010_10_16, et al],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N [OzBrisbane209_51F_2010_08_09,
. . . . . . . . . . . . . . . . . . . . with 156E & 225G,
. . . . . . . . . . . . . . CalifVRDL131_2009_12_30, et al],
. . . . . . . . syn538F [Brunei218_2010 with 188T])

Australia Sequence

. . . . OzBrisbane209_51F_2010_08_09 (
. . . . . . . . 156E [H2N3, H3N8, H5N1, H10N7],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 225G,
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [OzVictoria670_30M_2010_11_14
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . Emergent across Australia
. . . . . . . . . . . . . . . . . . . . . during late 2010 season,
. . . . . . . . . . . . . . . Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . OZVictoria512_2010_07_30
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . NZChristchurch15_2010_07_12
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . India5107_2010_06_28
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . MississippiAF2474_2010_03_10
. . . . . . . . . . . . . . . . . . . . . with syn235T,
. . . . . . . . . . . . . . . FloridaAF2197_2010_03_07
. . . . . . . . . . . . . . . . . . . . . with 156T,
. . . . . . . . . . . . . . . CalifVRDL9_2010_02_09
. . . . . . . . . . . . . . . . . . . . . with syn193S,
. . . . . . . . . . . . . . . Georgia06_2010_02_05
. . . . . . . . . . . . . . . . . . . . . with syn161Y,
. . . . . . . . . . . . . . . NY4662_2010_02_03
. . . . . . . . . . . . . . . . . . . . . with 97N, syn276H, syn283Q, syn304G,
. . . . . . . . . . . . . . . TexasJMS406_2010_01_10
. . . . . . . . . . . . . . . . . . . . . with 187A, syn193S, syn283Q,
. . . . . . . . . . . . . . . TexasJMS405_2010_01_09
. . . . . . . . . . . . . . . . . . . . . with 187A, syn283Q,
. . . . . . . . . . . . . . . CalifVRDL131_2009_12_30
. . . . . . . . . . . . . . . . . . . . . with 225G, syn455Q,
. . . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . . . . with syn13N,
. . . . . . . . . . . . . . . Vienna291_2009_11_19
. . . . . . . . . . . . . . . catOregon29573_2009_11_09
. . . . . . . . . . . . . . . . . . . . . with 226R, syn283Q,
. . . . . . . . . . . . . . . Calif_SanDiegoINS63_2009_10_26
. . . . . . . . . . . . . . . . . . . . . with syn283Q, et al],
. . . . . . . . 377K,
. . . . . . . . 454N [H7N3, H7N7, H9N2]
. . . . . . . . . . [Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . FL_Pen210_2009_11_10
. . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . SouthCarolina18_2009_09_16_VxX
. . . . . . . . . . . . . . . . . . with 159D, 224K,
. . . . . . . . . . Texas45131774_2009_09_13
. . . . . . . . . . . . . . . . . . with syn223V,
. . . . . . . . . . IndiaPune9355_2009_08
. . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . IndiaBlore236_2009_06_xL
. . . . . . . . . . . . . . . . . . with 226R, et al],
. . . . . . . . syn465N)


1. Ellis J, Galiano M, Pebody R, Lackenby A, Thompson C, Bermingham A, McLean E, Zhao H, Bolotin S, Dar O, Watson JM, Zambon M. Virological analysis of fatal influenza cases in the United Kingdom during the early wave of influenza in winter 2010/11. Euro Surveill. 2011;16(1):pii=19760. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19760

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