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)

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