225A Appears In Madrid Spain Pandemic Influenza

The very effective contributors to The NIAID Influenza Genome Sequencing Consortium deposited a contemporaneous set of sequences at GISAID this week covering a significant number of data points over geography and emerging trends in pandemic RnR * polymorphism.

225A is found for the first time on an unmixed trace in this pandemic on Madrid296_2009_11_17, having previously been discussed on an unusual sequence from the Ukraine. The HA of UkrKyiv377_2009_11_07_xL only revised at two protein positions, the syn413K for cross-linkage and amino residue 225 (rvT coding up to 6 values).  These multiple, mixed traces at the first and second nucleotides of the codon represent the only documented prior instance of potential 225A in this pandemic reservoir.

Additionally, a narrow slice of the data in this directed review further suggests a peculiar behaviour that our team has postulated in the past 3 months within this present pandemic reservoir (PF11). Spain and Greece provide an active working ground for this particular genetic acquisition cycle behaviour.

Notice that the reservoir appears to individually conserve polymorphisms on strains having few revisions (generalised / consensus strains) from time to time, even after the given polymorphism has appeared on a significant count of sequences having numerous polymorphisms.  This apparent reversal of progressive genetic acquisition may have purpose. 

Preservation behaviour for future recombination using / by creating a type of "universal donor" template is suggested.  This step-wise method of storing an important piece of data for later usage in a labile format is not entirely novel in biology.  Ease of access / transfer / adoption may be increased as a function of the homology / identity of the two interchanging viral strains.  “Mix and match” becomes more organised and discrete in this scenario. Ergo, a generalised virus with only a single revision or a minimal revision count may be more successful as an overlay for material transfer.

Note that Madrid300_2009_11_30 carries only the 373H.  Similarly, notice that syn372Q (in a similar domain) is found on Russian fatality sequences that have no change other than the cross-linkage syn413K.  The syn372Q is also found upon a 225G and a fatal 225N case in the same area, Ulyanovsk. 

Is a similar function within the same sequence area (372, 373) being preserved in Spain, Greece, Portugal, Belgium, Germany and Australia using the 373H?

Is the Madrid296_2009_11_17 pairing of 225A (in its first recorded occurrence) with 373H another of the reservoir's conservation storage templates that will be referenced for later antigenic escape?

. . . . Athens357_2009_12_26 (
. . . . . . . . 1S,
. . . . . . . . 92M,
. . . . . . . . syn181G [H9N2],
. . . . . . . . . . . . . . . [Lisboa2_2010_01_04,
. . . . . . . . . . . . . . . Rome632_2009_11_23, et al],
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02])

. . . . Athens358_2009_12_26 (
. . . . . . . . syn179L (CTt) [TexasJMS404_2010_01_08 (tTA)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . with syn66G,
. . . . . . . . . . . . . . . . . . . . . Netherlands2143_2009_11_16 (tTA),
. . . . . . . . . . . . . . . . . . . . . Odense143_2009_11_11 (tTA)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . with 48K, 269V,
. . . . . . . . . . . . . . . . . . . . . UkrPoltava746_2009_11_09_f (tTA),
. . . . . . . . . . . . . . . . . . . . . UkrCherkasy745_2009_11_01_f (tTA),
. . . . . . . . . . . . . . . . . . . . . Antwerp221_2009_10_28 (tTA)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . with 259T,
. . . . . . . . . . . . . . . . . . . . . JapanAF2244_2009_10_14 (CTg),
. . . . . . . . . . . . . . . . . . . . . ColoradoAF2139_2009_10_06 (CTg)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . with syn311K, 324I,
. . . . . . . . . . . . . . . . . . . . . NY4981_2009_10_05 (CTg)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . with syn311K, 324I,
. . . . . . . . . . . . . . . . . . . . . ThailandPMKD0030_2009_09_25 (tTA),
. . . . . . . . . . . . . . . . . . . . . WiscS0143_2009_06_02 (CTg),
. . . . . . . . . . . . . . . . . . . . . WiscD1725_2009_06_01 (CTg),
. . . . . . . . . . . . . . . . . . . . . WiscD0117_2009_05_28 (CTg)]
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02])

. . . . Munich364_2009_12_04 (
. . . . . . . . #1V,
. . . . . . . . syn181G [H9N2],
. . . . . . . . . . . . . . . [Lisboa2_2010_01_04,
. . . . . . . . . . . . . . . Rome632_2009_11_23, et al],
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02],
. . . . . . . . syn396V,
. . . . . . . . syn477T)

. . . . Munich363_2009_11_30 (
. . . . . . . . 165R [Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . with syn181G],
. . . . . . . . syn181G [H9N2],
. . . . . . . . . . . . . . . [Lisboa2_2010_01_04,
. . . . . . . . . . . . . . . Rome632_2009_11_23, et al],
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02],
. . . . . . . . syn488D,
. . . . . . . . syn514Y)

. . . . Madrid300_2009_11_30 (
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02])

. . . . Madrid299_2009_11_26 (
. . . . . . . . 128I,
. . . . . . . . 235I,
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02],
. . . . . . . . syn453R)

. . . . Madrid298_2009_11_24 (
. . . . . . . . 0I [H9N2],
. . . . . . . . .  [Lisboa2_2010_01_04,
. . . . . . . . . Latvia12_649_2009_12_09,
. . . . . . . . . NY7426_2009_12_08,
. . . . . . . . . Tambov_FOS_2009_12_01_xL,
. . . . . . . . . Slovenia5555_2009_12,
. . . . . . . . . Slovenia5559_2009_12,
. . . . . . . . . Ivanovo_RNA_2009_11_24_xL_f with 225G, 225N,
. . . . . . . . . Stockholm107_2009_11_24,
. . . . . . . . . GD_Yuncheng51_2009_11_19,
. . . . . . . . . Guangdong1271_2009_11_19,
. . . . . . . . . Austria528378_2009_11_19,
. . . . . . . . . Latvia11_1133_2009_11_16,
. . . . . . . . . Latvia11_1133M_2009_11_16,
. . . . . . . . . Latvia11_575_2009_11_11,
. . . . . . . . . England94600039_2009_10_27,
. . . . . . . . . SwedenUmea8_2009_10_07,
. . . . . . . . . Managua2323_02_2009_08_18,
. . . . . . . . . Utah20_C2_2_2009_07_25_VxX with 159D, 227G,
. . . . . . . . . Texas42163291_2009_06_16,
. . . . . . . . . Marseille3416_2009],
. . . . . . . . syn181G [H9N2],
. . . . . . . . . . . . . . . [Lisboa2_2010_01_04,
. . . . . . . . . . . . . . . Rome632_2009_11_23, et al],
. . . . . . . . 233H [NC Duke TmX Fatality cluster,
. . . . . . . . . . . . Rome632_2009_11_23 with syn181G],
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02],
. . . . . . . . 504N [England735_2009_10,
. . . . . . . . . . . . England1023_2009_09,
. . . . . . . . . . . . England (11),
. . . . . . . . . . . . Scotland94420091_2009_08_11])

. . . . Madrid296_2009_11_17 (
. . . . . . . . 225A [Unique to PF11],
. . . . . . . . 373H [Perth500_2010_02_17 with 165N,
. . . . . . . . . . . . . Tessenderlo191_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with 165R, syn181G,
. . . . . . . . . . . . . Lisboa171_2009_12_02])

Please refer to additional studies for further genetic analyses, including the survey on amino acid revisions potentially related to Vaccine Escape.  A hyper-morphic, TamiFlu-resistant sequence from the state of Washington in Spring 2010 has recently been profiled with similar zoonotic influences.


* Rare, not Random.

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