HA 223E and 223M in Early Pandemic Suggest Correlation to H5N1 and H3N8 Polymorphisms

On 2010-11-29, a WHO Collaborating Centre for Reference and Research on Influenza deposited an aged sequence from an early Dalby pH1N1 sample, 2009-08-27, originated at the Queensland Health Scientific Services of Australia. The OzBrisbane2014_2009_08_27 sequence was published with no age, gender, antigenic characterisation or drug resistance information.

OzBrisbane2014_2009_08_27 carries a very early genetic revision in the Receptor Binding Domain just upstream of the much discussed amino acid position 225. The 223E on this sequence marks a novel instance at a position with very few recorded changes (223M).  This viral reservoir began to cycle through tested Immune Escape RBD changes at a very young age, though this data has only recently been made public. Protein revision is documented at 58 of the 63 amino acid positions (92%) within a critical Receptor Binding Domain area slotting from 186 to 248.

Zoonotic Influenza serotypes have also demonstrated changes corresponding to amino acid position 223, in animals and in humans.

H3N8 is consistently 223V, matching the amino acid value in the pH1N1 reservoir, except for two recent equine sequences from 2008 Egypt [eqEgypt6066NAMRU3VSVRI_2008] and 2009 Japan [eqYokohamaaq19_2009] that each revised at the first nucleotide from G to A, gTC->aTC producing 223I, Isoleucine.

H5N1 is also consistently 223V, except in a very small number of cases that show a similar first base revision of G to A, gTA->aTA producing also 223I, Isoleucine. These H5N1 cases with a revision at amino acid position 223 include at least 2 of the 2006 Gharbiyah, Egypt human death cluster [Egypt14724_2006 & Egypt14725_2006], avian samples from 2007 Egypt [ckEgypt1892N3_HK49_2007], an adult female from 2009 in Kafr El Sheikh, Egypt [EgyptN03434_33F_2009_04_15] and 2 Viet human cases [VietCL100_2004 & VietJPHN30321_2005].

H7N3 and H7N7 are also remarkably consistent as 223V, with a similar variation to H3N8 and H5N1 on H7N7 equine samples worldwide from 1956 to 1977. These older equine samples primarily show the now familiar first base revision of G to A, gTA->aTA (15) producing 223I, Isoleucine. A parallel situation occurs in the H11 reservoir with two sequences of birds from Ohio (1987 and 2001) moving from G to A, gTA->aTA.

That same G to A first base nucleotide revision onto a Pandemic H1N1 background, gTG->aTG, may have produced the 223M found in a human pH1N1 case from California early in the pandemic, California33_2009_08_06. The potential donor for the 223E remains unresolved. The probability is very low for true mutation / sloppy polymerase being involved because patterning throughout the remainder of the sequence leads to other considerations.

Influenza Flux is not necessarily a one-way street. Today’s donor may be tomorrow’s recipient. This particular zoonotic serotype variation pattern around amino acid position 223 that is overlaying onto human pH1N1 is but the tip of the iceburg considering the inter-serotype dynamics (animal <=> human) that GeneWurx.com has carefully documented over the past 20 months.

With 2 of the most recent H5N1 human cases (Hong Kong and Indonesia) presenting several novel and important clinical signals, a meritorious investigation would determine potential pH1N1 and H5N1 genetic interaction. The creation of a lower CFR H5N1 reservoir like Egypt of 2009 and other similar H5N1 genetics may begin allowing a more consistent and longer human incubation period like these two recent “walking H5N1” patients.

A longer human incubation period, with a commensurate slower burn through the H5N1 human host, increases the potential for co-infection with pH1N1. Co-infection, especially with pH1N1, creates the distinct risk of further human adaptation. PF11 is certainly considered capable of effective transmission. Thereby, a slightly more adept human H5N1, as seen in these 2 recent cases, may further optimise H2H (Human to Human) transmission genetics for the traditional Avian Influenza serotypes.

These reservoirs appear to be working in tandem and in earnest.

. . . . OzBrisbane2014_2009_08_27 (
. . . . . . . . 3T [GhanaFS1966_2010_04-06,
. . . . . . . . . . . Taiwan27_2010_03_01
. . . . . . . . . . . . . . . .with 189T, 218T, syn305K, 404D, syn494E,
. . . . . . . . . . . NY04_2010_02_25
. . . . . . . . . . . . . . . .with 100N, syn232Y, syn270I, 437N, syn484N,
. . . . . . . . . . . England1054_2009_12 with 225E,
. . . . . . . . . . . RussiaStPeter99_2009_11_30
. . . . . . . . . . . . . . . .with 225E, syn325P,
. . . . . . . . . . . SichuanWuhouSWL4401_2009_11_29 with syn413K,
. . . . . . . . . . . MarylandAF2457_2009_11_12,
. . . . . . . . . . . Mississippi03_2009_09_25,
. . . . . . . . . . . HongKong24705_2009_09_13,
. . . . . . . . . . . Netherlands1039_2009_08_25 with 430I,
. . . . . . . . . . . California36_2009_08_22 with syn413K,
. . . . . . . . . . . Suriname7534_2009_08_13,
. . . . . . . . . . . HenanSWL14_2009_07_17 with 225E,
. . . . . . . . . . . Surinam08_2009_06_11,
. . . . . . . . . . . Surinam02_2009_06_09,
. . . . . . . . . . . CanadaQCRV1759_2009_05_07,
. . . . . . . . . . . Ireland1_2009_05],
. . . . . . . . 223E mix wt [Unique to GISAID; Unique to GenBank],
. . . . . . . . 269V,
. . . . . . . . 414I)

Supporting Sequences

. . . . OzBrisbane2015_2009_08_28 (
. . . . . . . . 97N mix wt,
. . . . . . . . 269V,
. . . . . . . . 414I)

. . . . California33_2009_08_06 (
. . . . . . . . 223M,
. . . . . . . . 262K,
. . . . . . . . 285T,
. . . . . . . . 502K [UkrTernopilN10_2009_10_28_xL_f with 225G,
. . . . . . . . . . . Oz_Victoria800_2010_06_02,
. . . . . . . . . . . SingGP2362_2010_05_18,
. . . . . . . . . . . Scandinavia (7),
. . . . . . . . . . . CalifVRDL2_2010_01_11,
. . . . . . . . . . . Michigan21_2009_08_07,
. . . . . . . . . . . SouthCarolina36_2009_09_02,
. . . . . . . . . . . SouthCarolina38_2009_09_17,
. . . . . . . . . . . Haiti534_2009_10_19,
. . . . . . . . . . . AlgeriaG2902_2009_12_09 mix with 225E,
. . . . . . . . . . . Egypt114_2009_12_06 with 225E,
. . . . . . . . . . . JapanPR1070_2009_07_10,
. . . . . . . . . . . ThailandTHB0438_2009_07_28,
. . . . . . . . . . . Jiangyin34_2009_08_16,
. . . . . . . . . . . GuangxiLongan1870_2009_12_16])

. . . . swAlbertaOTH33_24_2009_05_03 (
. . . . . . . . 196H,
. . . . . . . . syn216E [H9N2],
. . . . . . . . 223M,
. . . . . . . . syn456L [H5N1])

. . . . swAlbertaOTH33_21_2009_05_05 (
. . . . . . . . 68R,
. . . . . . . . 223M,
. . . . . . . . 299V)

. . . . NY04_2010_02_25 (
. . . . . . . . 3T [OzBrisbane2014_2009_08_27, et al],
. . . . . . . . 50E,
. . . . . . . . syn53L [H2, H5N1 Viet Human, Avian, Civet, H6N1],
. . . . . . . . . . . . . . [TexasJMS380_2009_11_27 with 25R,
. . . . . . . . . . . . . . Tambov_SPN_2009_11_24_f with 225N],
. . . . . . . . 100N,
. . . . . . . . syn232Y,
. . . . . . . . syn270I,
. . . . . . . . 377K,
. . . . . . . . 437N,
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])

. . . . TexasJMS380_2009_11_27 (
. . . . . . . . 25R,
. . . . . . . . syn53L [H2, H5N1 Viet Human, Avian, Civet, H6N1])

. . . . Tambov_SPN_2009_11_24_f (
. . . . . . . . syn6L [H3N8],
. . . . . . . . 19I [H3N8],
. . . . . . . . syn53L [H2, H5N1 Viet Human, Avian, Civet, H6N1],
. . . . . . . . syn177L [H3N8, H6, H7N7],
. . . . . . . . 225N,
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn542S [H2, H5, H9N2])

. . . . Ukraine123_2010_02_14_xL (
. . . . . . . . syn0T [BangkokINS427_27M_2010_03_04
. . . . . . . . . . . . . . . . . with syn209Y, syn232Y, syn490P & syn506V,
. . . . . . . . . . . . . DenmarkHvidovreINS290_20F_2009_11_27
. . . . . . . . . . . . . . . . . with 35I, syn490P, 502K & 526T,
. . . . . . . . . . . . . LaReunion3479_2009
. . . . . . . . . . . . . . . . . with syn97D, syn139C & 225E]
. . . . . . . . 186P,
. . . . . . . . 208K,
. . . . . . . . 230I (ATa),
. . . . . . . . syn238E [Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . WiscD2424_2009_12_15
. . . . . . . . . . . . . . . . . . . with 225E, 300S & 463T,
. . . . . . . . . . . . . . . Netherlands2629_2009_12_04_xL
. . . . . . . . . . . . . . . . . . . with 225N, syn233Y, 324I, syn413K & 507E,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . JapanNagasakiHA64_2009_11_27
. . . . . . . . . . . . . . . . . . . with syn35L, syn92T, 200T, 324I & 513V,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K & syn484N,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Orel_KAI1_2009_11_05
. . . . . . . . . . . . . . . . . . . with 280A, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL
. . . . . . . . . . . . . . . . . . . with syn103E, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus220_2009_11,
. . . . . . . . . . . . . . . Belarus360_2009_11,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . Belarus131_2009_10,
. . . . . . . . . . . . . . . GuamNHRC0032_2009_09_14
. . . . . . . . . . . . . . . . . . . with 89G,
. . . . . . . . . . . . . . . Managua5295_02_2009_07_23,
. . . . . . . . . . . . . . . ThailandTHA0364_2009_07_22
. . . . . . . . . . . . . . . . . . . with #12E, 37N, 296H & syn348V,
. . . . . . . . . . . . . . . Missouri02_2009_05_01
. . . . . . . . . . . . . . . . . . . with syn215P, syn377E, syn456L & syn523V,
. . . . . . . . . . . . . . . Bayern62S3_2009_04_29_VxX
. . . . . . . . . . . . . . . . . . . with 158E mix & syn238E,
. . . . . . . . . . . . . . . GermanyRegensburg01_2009_04_27
. . . . . . . . . . . . . . . . . . . with syn456L,
. . . . . . . . . . . . . . . GermanyRegensburgD6_2009
. . . . . . . . . . . . . . . . . . . with syn456L],
. . . . . . . . 252M [Fixed in 2010 Illinois swine with 119M,
. . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . Seoul2883_2009_12_02,
. . . . . . . . . . . . . Seoul1829_2009_11_26,
. . . . . . . . . . . . . LagosWRAIR1982N_2009_11_23,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984N_2009_11_18,
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . LagosWRAIR1984T_2009_11_18
. . . . . . . . . . . . . . . . . . . with syn164L, syn244T [u], syn291T,
. . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 324I,
. . . . . . . . . . . . . . . . . . . . . . . syn413K, syn431L, syn484N,
. . . . . . . . . . . . . Texas45132202_2009_09_13,
. . . . . . . . . . . . . Ancona86_2009_08_31
. . . . . . . . . . . . . . . . . . . with 225E & 300S,
. . . . . . . . . . . . . TurkeyAnkara17_2009_08,
. . . . . . . . . . . . . BZ_SaoPaulo43812_2009_07_03_f],
. . . . . . . . 289V [HK1881_2010_04_18,
. . . . . . . . . . . . . EstoniaTallinnINS431_2010_02_05,
. . . . . . . . . . . . . Luxembourg184_2010_01_25,
. . . . . . . . . . . . . Saarland21_2009_12_11,
. . . . . . . . . . . . . IndiaPune21115_2009_12 with 233H,
. . . . . . . . . . . . . Hiroshima457 _2009_11_02,
. . . . . . . . . . . . . JiangsuNanjinggulouSWL11146_2009_09_17,
. . . . . . . . . . . . . Kobe91993_2009_08_18,
. . . . . . . . . . . . . Kobe91992_2009_08_17,
. . . . . . . . . . . . . UK_Glascow_SC10_2009_06 with 225G,
. . . . . . . . . . . . . UK_Glascow_SC19_2009_06,
. . . . . . . . . . . . . UK_Glascow_SC20_2009_06],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn431L [Emergent],
. . . . . . . . . . . . . . . [OZ_Grafton2_20F_2010_08_05
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . OZ_Perth504_5M_2010_07_07
. . . . . . . . . . . . . . . . . . . . . . . with 128D, syn173G & syn273T,
. . . . . . . . . . . . . . . swIllinois03037_2010_06_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . swIowa03032_2010_06_04
. . . . . . . . . . . . . . . . . . . . . . . with 77G,
. . . . . . . . . . . . . . . PNG_Goroka16_1F__2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka16E3_1F_2010_04_07
. . . . . . . . . . . . . . . . . . . . . . . with 77G, 186P, 204M, syn205G & 252L,
. . . . . . . . . . . . . . . PNG_Goroka15_2010_02_24
. . . . . . . . . . . . . . . . . . . . . . . with 77G & 252L,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL,
. . . . . . . . . . . . . . . HainanDinganSWL123_2010_01_08,
. . . . . . . . . . . . . . . swOregon10_004060_2009_12_31
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . AthensINS359_2009_12_26
. . . . . . . . . . . . . . . . . . . . . . . with syn189A,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f,
. . . . . . . . . . . . . . . SpainCatS1632_2009_10_28,
. . . . . . . . . . . . . . . swHongKong2314_2009_10_22,
. . . . . . . . . . . . . . . ItalyAncona05_2009_07-12
. . . . . . . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . . . . . . England673_2009_07
. . . . . . . . . . . . . . . . . . . . . . . with 225E],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11]),
. . . . . . . . . . . . . . . [NY04_2010_02_25
. . . . . . . . . . . . . . . . . . . with 3T, 50E, syn53L, 100N, syn232Y,
. . . . . . . . . . . . . . . . . . . . . . . syn270I, 377K, 437N,
. . . . . . . . . . . . . . . RussiaStPeter204E2E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2E1_2010_02_08_VxX,
. . . . . . . . . . . . . . . RussiaStPeter204E2_2010_02_08_VxX,
. . . . . . . . . . . . . . . Saratov07E2E1_2010_02_01_VxX,
. . . . . . . . . . . . . . . Saratov07E2_2010_02_01_VxX,
. . . . . . . . . . . . . . . Ukraine122_2010_01_15_xL
. . . . . . . . . . . . . . . . . . . with 186P, 252M, 324I, syn413K,
. . . . . . . . . . . . . . . . . . . . . . syn431L & syn484N,
. . . . . . . . . . . . . . . RussiaAnadyrIIV177_2009_12_04_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . Arkhangelsk_GNY_2009_11_25_xL_f
. . . . . . . . . . . . . . . . . . . with 324I, syn413K, 437N & syn484N,
. . . . . . . . . . . . . . . MoscowCHSN_2009_11_23_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I & syn413K,
. . . . . . . . . . . . . . . DenmarkHvidovreINS141_2009_11_20_xL
. . . . . . . . . . . . . . . . . . . with syn23L, 324I, syn413K, syn484N & syn549R,
. . . . . . . . . . . . . . . RussiaStPeterVMN_2009_11_19_f,
. . . . . . . . . . . . . . . UkrChernihiv857_2009_11_14_xL_f
. . . . . . . . . . . . . . . . . . . with 186P, 225G, syn238E, 252M,
. . . . . . . . . . . . . . . . . . . . . . . 324I, syn413K, syn431L,
. . . . . . . . . . . . . . . UkrChernihiv855L_2009_11_11_xL_f,
. . . . . . . . . . . . . . . Lipetsk_BVV_2009_11_10_xL_f
. . . . . . . . . . . . . . . . . . . with 225G, 324I, syn413K & syn484N,
. . . . . . . . . . . . . . . OrelKAI1_2009_11_05,
. . . . . . . . . . . . . . . Russia4_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia14_2009_11_01_xL,
. . . . . . . . . . . . . . . Russia191_2009_11_01_xL,
. . . . . . . . . . . . . . . EgyptN14648_2009_11
. . . . . . . . . . . . . . . . . . . with 225N, syn238E, 324I & syn413K,
. . . . . . . . . . . . . . . RussiaStPeterRII96_2009_10_29
. . . . . . . . . . . . . . . . . . . with 187N,
. . . . . . . . . . . . . . . NizhniNovgorodMEV_2009_07_30,
. . . . . . . . . . . . . . . ItalyAncona15_2009_07_17,
. . . . . . . . . . . . . . . Fixed in Thai Swine including
. . . . . . . . . . . . . . . . . . . swThaiCU_RA75_2010_01 with 188T],
. . . . . . . . syn500R [Unique to GenBank/GISAID]),

. . . . Saratov07E2_24X_2010_02_01_xL_VxX (
. . . . . . . . 158E mix,
. . . . . . . . 225G,
. . . . . . . . syn235T [H3N8],
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn419L (CTt),
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])

. . . . Saratov07E2E1_24X_2010_02_01_ xL_VxX (
. . . . . . . . 47I mix,
. . . . . . . . 157E,
. . . . . . . . 158E mix,
. . . . . . . . 225G,
. . . . . . . . syn235T [H3N8],
. . . . . . . . syn238E,
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn419L (CTt),
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])

. . . . RussiaStPeter204E2_2010_02_08_ xL_VxX (
. . . . . . . . 157E,
. . . . . . . . 225G,
. . . . . . . . syn238E,
. . . . . . . . syn240G
. . . . . . . . 324I,
. . . . . . . . 275F,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])

. . . . AnadyrIIV177_2009_12_04_xL_f (
. . . . . . . . 212T [H3N8],
. . . . . . . . 225G,
. . . . . . . . syn238E [H2, H4],
. . . . . . . . 324I,
. . . . . . . . syn413K [H2, H5N1, H9N2],
. . . . . . . . syn484N [H3N8, H4, H5, H6, H7N7, H9N2, H11])

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