2010-05-09
pH1N1 Demonstrates 95% Instability In Critical Genetics Range with Extensive Bird Flu Inclusions
More than 95% of the Hemagglutinin positions between 186 and 246, including antigenic areas of the Receptor Binding Domain (RBD/RBS), are on record as polymorphic. Only 3 positions in that range are stable. Many positions rate multiple changes. Protein revision is documented at 45 of the 61 positions (73.8%), engaging the potential for antibody resistance (natural immune escape and vaccine escape).
Please recall from earlier analyses (linked in the ultimate paragraph) that individual single nucleotide polymorphisms (SNPs) have been correlated to escape events (low reactor).
The list presented today is certainly not comprehensive. Only one section is discussed from one gene segment (HA) covering 61 contiguous amino acid positions. The extensive variation in that short range is detailed in the data listing.
Viral revision is also rapidly occurring in additional HA antigenic areas outside the range of positions documented in this analysis. The Neuraminidase of the human pandemic H1N1 reservoir is also acquiring revisions with homology to Avian and Equine influenza at a ratio to total changes even higher than that of the Hemagglutinin being surveyed in this analysis.
The viral reservoir backing this present H1N1 flu pandemic is far from stable and is actively acquiring new genetics. Current data does not indicate an immediate direction toward stability.
A previous version of this listing may be referenced for tracking. Please review details on the causality behind this particular study in the earliest version.
186S synonymous (TCc) Russia61, BZSP53823_2009_08_01_f,
. . . . BadenWurttemberg8_2010, TexasJMS387_2009_12_08,
. . . . KO_Daegu1873_2009_12_16_TmX,
. . . . H9N2 (cCc, cac)
186P (cCT) CalifVRDL7, UkraineChernihiv857, Ankara17
. . . . Thessaloniki791_2010 mix (225G, syn233Y, 324I, 377K)
186F (TtT) Ankara26
187T synonymous (ACc) Berlin164, Iran572, BeijingXicheng11649,
. . . . S5, 1918,
. . . . H9N2
187A (gCT) TexasJMS405_2009, TexasJMS406_2009,
. . . . H5N1 (gaT)
188T (AcT) swThaiCURA75_2010_01,
. . . . H6N1 dkHK202_1977, dkKOS17_2003,
. . . . H7N7 extensive including human fatality
188S synonymous (AGc) NY6943_xL
188N SC16, SC31, NY3502, ME15, CatS1187, Milan433, Kaifu4142,
. . . . Bilthoven4360903023, Japan, China,
. . . . swHK_NS1809_2009_12_03 (189T), swHK_NS1810_2009_12_03
. . . . S5, H5N1
188I Growing in US on cross-linked background (4), BZSP53823 (186S),
. . . . H1N1 (1943, 46, 51)
189A synonymous (GCc), Georgia01_2010, Georgia 2010 (+5),
. . . . swOR4060
189V (GtT) Sydney2503, Texas46172731,
. . . . Sask, H6N1 mallMaryland887_2002
189S (tCT) Wisc1434
189T (aCT) Extensive in US incl NY7020 (77N), on cross-linkage (4) incl
. . . . NY6943_xL, Ontario328474, Aswan2288, China,
. . . . swHK_NS1809_2009_12_03 (188N)
. . . . 1918, H5N1 2009, H6N1, H9N2 2008
190D synonymous (GAt) Nebraska02_2010, Milan326, UkraineZakarpatska830,
. . . . AfghanN09833_2009_08
. . . . 1918, H1N1 (1943, 51)
190Y SwedenMalmoe1_2010_01_01, H6N1 (tTG)
191R (CgA) Chengdu18 (131P), GuangdongSWL28 (192H, 199N)
192H (CAt) GuangdongSWL28 (191R, 199N),
. . . . Avian H2N3 (agt), H3N8 (act), H6N1 (aAt, gat, gct)
192Q synonymous (CAg) RomaISS50 (227V), Nebraska01_2010,
. . . . H1N1 (1943, 46)
193S synonymous (AGc) US 2010 (4), SC18_VxX, NM11, NM13,
. . . . Wisc (5), DC_INS28,
. . . . CalifVRDL11_2010, CalifVRDL13_2010,
. . . . AfghanN10765_2009_09, Milan294, Japan 2010,
. . . . H3N8 AGc aplatBelgium12827_2007,
. . . . H6N1 AGc chkTaiwan0706_2003,
. . . . H9N2 Aac dkViet2009,
. . . . H11Nx Aac dkViet2009
193G (gGT) AR08, Cal_SDINS04, Kansas26,
. . . . H5N1 (gGg), H3N8 (gaT, gac, gaa), H11 (gac, gat)
193N (AaT) Washington72,
. . . . H3N8, H6N1, H9N2, H11
193R (cGT) catItaly304678_1_2009_12_17_f, Origin Unknown
194I (aTC) NC38E3, VA27, SC18, Bangladesh3009, StPete59, StPete99,
. . . . Thessaloniki788_2010 (syn233Y, 324I, 377K),
. . . . China (3),
. . . . H5N1
194L synonymous (CTa) Japan4081, tn,
. . . . H9N2 2008 (tTa),
. . . . H6N1 ckTaiwan1205_2001, tkBC2_1997 (CTa)
194L synonymous (CTt) TexasJMS385_2009, CalifVRDL36,
. . . . WiscD0675, WiscD0891, WiscD1237,
. . . . EgyptN11640_2009_10, Iran572,
. . . . H5N1,
. . . . H9N2 dkVietnamOIE2327_2009
195Y synonymous (TAc) Guayaquil4 (206S),
. . . . swOR4060, tkDeutsche, swDeutsche,
. . . . Avian H2N3,
. . . . Avian and Equine H3N8 emergent,
. . . . H5N1 gsEgyptR4_2007,
. . . . H6N1,
. . . . H7N7 2004-2009,
. . . . H9N2 99%,
. . . . H11 90%
196Q synonymous (CAa) Wisc (3), Moldova (3), Malaysia (2), China,
. . . . Milan326, Pavia (6), Ankara18, NordrheinWestfalen106,
. . . . swOR4060,
. . . . Avian H2N3,
. . . . H5N1
197T (AcT) Malaysia4039, swH1N2
198A synonymous (GCc) KO_Seoul1870_2009_12_18_TmX
198V Malaysia5283, Malaysia9117
198G (GgA) BeijingXuanwu1945 (86T, 178M), Tomsk07 (131P, 225G)
. . . . WSN33,
. . . . H3N8 eqHeilongjiang10_2008,
. . . . H6N1,
. . . . H7N7 ext
199N (aAT) GuangdongSWL28, Milan80, Milan83, Iceland176,
. . . . S9, S7, M7, Sask, H5 (aCT),
. . . . H1N1 (1943, 46, 51) (aCT)
199D synonymous (GAc) swine Illinois, H5, H9N2
200A synonymous (GCc) swOR4060, S5
200T (aCA) FL31, RomaniaTimis2018, Australia (6), Asia (15),
. . . . MilanUSHR1, Bilthoven4360901004,
. . . . ShizuokaC247_2009_11_08, H5, KO_Seoul1785_2009_11_TmX,
. . . . NepalNP09A294,
. . . . KuwaitN12991_2009_08_24,
. . . . tkDeutsche, swDeutsche,
. . . . H9N2
200S (tCA) NY1999_2010_01_18, NY0461, NY6945, NY5276,
. . . . NC57, SC46, WiscD0780, WiscS1338, NJ11, DC_INS31,
. . . . China,
. . . . MadridINS186 (373H), OdenseINS177 (286E)
. . . . cheetahCA30954
. . . . H11 Avian tCt ext, tCc ext including dkViet2009
201H (cAT) Wisc1140, Darwin2140,
. . . . H3N8 (cAa, cga), H7N7 (cta, ctg)
202A (GcT) MXinDRE797 2010 TmX (280A, syn321L, 324I), IA14, KY25,
. . . . HK34360, Guangdong2282 (131P, 230I, 244I, 275A),
. . . . LiaoningShuncheng1145, LiaoningShuncheng1148 (131P, 230I, 244I, 275A),
. . . . Bilthoven4310901550 (89G), Bilthoven4360903104 (89G),
. . . . H9N2 (AcA, AcG)
202V synonymous (GTa) JiangsuXiaguan1411
202V synonymous (GTc) YAMAGATA778, YAMAGATA803, swIllinois,
. . . . H1N1 (1943, 46, 51)
203S (TcT) Non-PF11 Sask, S9, S7, M7, 1918, WSN33
204V synonymous (GTa) PA31, SHIZUOKA1573, 1918, S7
204V synonymous (GTa) TexasJMS367_2009_11_12, PA31,
. . . . AfghanN10767_2009_09, AfghanN10974_2009_09,
. . . . KuwaitN13111_2009_09_23,
. . . . Shizuoka1573, Niedersachsen34, RheinlandPfalz86,
. . . . 1918, S9, S7, M7, Sask,
. . . . H9N2 Israel 2009, H9N2 Iran 2008
205G synonymous (GGa) Texas76C2, Wisc (4),
. . . . AfghanN09836_2009_08, TurkeyTR19_2009 (233H)
. . . . Slovenia5662, Slovenia5711,
. . . . Iceland162M (225G), Iceland162Siat3 (225G),
. . . . tkDeutsche, swDeutsche,
. . . . S5, H3N8 (tCa), H9N2 (GCa), H6N1 (GGa), H7N7 (GGa)
205E (GaG) BadenWurttemberg8_2010, ShizuokaC247_2009_11_08
. . . . Alabama03_2010_03_01 mix,
. . . . H11 (Gat), H7N7 (Gaa), H7N7 dkVictoria1976 (GaG)
205W (tGG) Brno216_2009
206A CatS1161
206T (ACA) Extensive
206T (ACt) Georgia670_2010 (Europe)
207S synonymous (TCg) California01_2010,
. . . . Avian H2N3,
. . . . H7N7 mallCalHKWF1971_2007 plus 5
208K (AaA) US, UK, Canada, HK, MX, Italy (2), Australia (12), Asia (5),
. . . . BahrainN11890_2009_10, BahrainN11892_2009_10, Dakar 2010 (3)
. . . . Cyprus5870_2010 (214R, 225E, 324I),
. . . . swOR4060
208S Australia43, Australia45, H6N1
208G (gGA) NY6292, HubeiWuchang1407,
. . . . Avian H4N6, H9N2 (gaA)
208T Norway3440
208R synonymous (AGg) TexasJMS385_2009
209Y synonymous (TAt) ShanxiWanbolin337
209D NorthDakota15
210S synonymous (AGt) Bogota0466N, Malaysia9131, H9N2 (Aat)
210G (gGC) Bilthoven4360903119 (225E)
210N Texas76C2, H1N1 (1943, 46, 51)
211K (AAa) synonymous MXinDRE50617 (225G), Niedersachsen330
211R swOR4060_2009_12_31, 1918, H1N1 (1943, 46, 51)
212R swOR4060_2009_12_31, 1918, H1N1 (1943, 46, 51)
212E Vlad01 (225G), Argentina8574_41, IN21, HI30, Malaysia4039,
. . . . Latvia122498 (225G), Iwate1093
212N ME15
212T Anadyr177_F (225G), CA07X179, CA07X181
212K synonymous (AAa) NY1999_2010_01_18, NY0461, TexasJMS404_2009,
. . . . AfghanN11216_2009_10_16
213L TX15, Iowa04_2010, H5N1
213F synonymous (TTt) NY3230_2010_01_25 (100N, 159K), StPete99 (225E),
. . . . Sachsen156, IsraelMF4683, Georgia4805 (35I), Georgia670_2010 (165R)
214K synonymous (AAa) CalifVRDL81 (100N, 135I), San DiegoINS101_2009, NM13,
. . . . Iran20001, Iraq2587, CatS1937, ENG620,
. . . . China22811, GuangdongFutian1480,
. . . . NagasakiHA1015_2010_02_01 (135E, 377K),
. . . . NagasakiHA1017_2010_02_08 (135E, 377K, syn496A, 550K),
. . . . S5, H9N2
214E Kurgan01, Moldova (3), swOR4060_2009_12_31
214N ENG92960012, SHIZUOKA1514, Hessen48
214Q Wisc0936 (237L)
214R (AgG) Cyprus5870_2010 (208K, 225E, 324I)
215P synonymous (CCa) NY2372_2010_01_20 (233H), San DiegoINS101_2009,
. . . . Kuwait (4), SC33, Eng616, BZ_Bahia15525_42M_f (RRT),
. . . . NepalNP09A284, Thai0440, GuangdongyunchengSWL51,
. . . . swHK_2299_2009_10_22, swHK_NS1583_2009_10_22
215P synonymous (CCt) NY_WC37RG, MO02, Eng256, Lisboa171 (324I, 373H)
216E synonymous (GAg) BadenWurttemberg490_xL, Hamburg14_xL,
. . . . Thuringen189_xL, Thuringen227_xL, Bilthoven4360903109,
. . . . Moldova (4), Belarus, Bosnia (3, 225G),
. . . . Bulgaria1369 (99T), Ostrava221_2010,
. . . . Iraq2587, Indiana,
. . . . tn, H9N2 (GTg)
217M (ATg) CalifVRDL99 (syn97D, syn147F, 377K, syn429L)
218A synonymous (GCg) Belarus, GhanaN12987_2009_10,
. . . . H9N2 (GGg), H6N1
218A synonymous (GCt) Nebraska02_2010, Iraq2587,
. . . . WSN33
218E Texas77 (159S, syn173G, 275A, 377K, 454I)
218S (tCA) Georgia07_2010 mix
218T (aCA) Hiroshima201 (225G), KuwaitN12991_2009_08_24
. . . . BelgiumG4751_2009 mix, Latvia237_2010 mix (377K)
218V (GTa) GuangdongyunchengSWL51, Malaysia (2 mix wt)
218V (GTc) swIll02930, 2931, 2932, 2937 (2009-12-29, 30)
219I synonymous (ATt) Calif_SDINS35, CalifVRDL84 (35I), NY6939 (35I),
. . . . Ancona451_f, Lyon2490, Poitiers3691 (35I), Valladolid35 (35I),
. . . . RheinlandPfalz81, Berlin210, BadenWurttemberg511,
. . . . Saarland21 (35I), Luxembourg184_2010 (35I), Luxembourg251_2010 (35I),
. . . . Dakar 2010 (4, 35I), Cameroon463 (35I),
. . . . H5N1 (Act), H6N1 (gct, gat)
219T (AcA) Wisc0134 (225E), Ontario315107 (225E),
. . . . RomaISS223, TessenderloINS191,
. . . . Korea3623_2009_11_09 (131P, 226R, 280A),
. . . . swOR4060_2009_12_31
220R synonymous (AGg) Florida02_2010, Mexico476, MexCtCIA4,
. . . . Malaysia9451,
. . . . H6N1
221P synonymous (CCa) WiscD0780
221P synonymous (CCt) Non-PF11 tkDeutsche, swDeutsche
222R (AgA) ThaiTHB0405, ThaiTHB0408
223V synonymous (GTa) Utah59, ThaiTHB0390
. . . . H1N1 (1943, 1946, 1951),
. . . . H6N1 mallSweden30/2005
223M CA33
224K SC18_VxX, Melbourne1_1946
224M NY5186
225D synonymous (GAc) HubeiWuchang1418,
. . . . swHK_NS1809_2009_12_03, swHK_NS1810_2009_12_03
225N BZ_SP53838, Ukraine mix wt, Victoria2125, Malaysia8860
. . . . Neimenggu-Hangjinhouqi51, EgyptN14648_2009_11,
. . . . IrelandM79555, IrelandM79556,
. . . . BadenWurttemberg502, et al
225E Extensive on multiple backgrounds, incl Kuwait, Ghana and Egypt.
. . . . Denmark1341 (158E, 264V), Cyprus5870_2010 (208K, 214R, 324I),
. . . . LaReunion3479, Morocco1088H (300S)
225G LvivN6_VxX with syn413K, UkDnip273 (GgT mix wt),
. . . . YaroslavlIIV196_2009_12_04_f (89G & 4 silent H5N1 changes),
. . . . TurkeyTR20 (324I), Thessaloniki791_2010 mix (186P, syn233Y, 324I, 377K),
. . . . Latvia121488_2009 (377K), Georgia4484_2009 (158E, 377K),
. . . . Iceland162M, Iceland162Siat3, Denmark1900,
. . . . China mix,
. . . . NY7216 (148F),
. . . . H1N1 (1943, 46, 51),
. . . . H6N1,
. . . . H9N2
225G (Gga) RomaISS1897 & 1941, EgyptVacsera138,
. . . . EgyptN14644_2009_11_01, ex225E all with 300S, H6N1
225E+226R Russia (3), GermanyBY74, swMX4
226R synonymous (CAg) Alabama08, Texas45033567, Texas45131305,
. . . . S7, M7, S5, tn
226R Alabama01_2010, Trabzon01 (Turkey), GermanyMVHGW4_2009_12,
. . . . Korea3623_2009_11_09 (131P, 280A), China,
. . . . catItaly304678_2_2009_12_17_f, et al
227E synonymous (GAg) Wisc (10), Texas45130742,
. . . . Paris2573, Paris2590,
. . . . Avian H2 (Ggg)
227A swOR4060_2009_12_31, tkDeutsche, swDeutsche,
. . . . NJ11_1976_X53A, 1918,
. . . . H1N1 (1943, 46, 51)
227V (GtA) RomaISS50
227G (GgA) Utah20_VxX mix, Avian H2
228G synonymous (GGa) Arizona06, Lisboa108 (225E, syn346G),
. . . . Valladolid35 (35I),
. . . . GhanaFS1982 (syn139C, 206T, 261K, 296H, syn346G, 377K),
. . . . GhanaFS2206 (syn139C, 206T, 261K, 296H, syn346G),
. . . . ShanxiPingding351
. . . . S9, S7, M7, S5,
. . . . H5N1
229R synonymous (AGg) swMX04 (225G, 226R), SichuanDongqu1818,
. . . . H6N1
230I (ATc) Sask, S9, S7, H6N1 (4), H7N7
230I (ATa) Wisc0337_2009_12_15 (275A, 377K),
. . . . H1N1 (1943, 46, 51),
. . . . H5N1 Gharbiyah 80% CFR,
. . . . H3N8
230I (ATt) Guangdong2282 (131P, 202A, 244I, 275A),
. . . . LiaoningShuncheng1148 (131P, 202A, 244I, 275A),
. . . . H5N1, H6N1,
. . . . H7N7,
. . . . H9N2
230V (gTG) TexasJMS369_2009
231N synonymous (AAt) NY3230_2010_01_25 (100N, 159K),
. . . . CalifVRDL36 mix (273K), Lisboa104
231D Ankara05, OSAKA2143, GuangxiQinnan1187,
. . . . H6N1,
. . . . H9N2 2008
231K (AAa) Wisc0853, Wisc1915, Wisc2337
. . . . WiscD0740 (22I, 176I, 188I, 277N, syn413K)
232Y synonymous (TAc) NY7216 (148F, 225G), TexasJMS386_2009,
. . . . Florida30, PuertoRico51,
. . . . S9, S7, M7, Sask,
. . . . H5N1, H6N1,
. . . . H9N2
233Y synonymous (TAt) AthensINS85,
. . . . Thessaloniki788_2010 (194I, 324I, 377K),
. . . . Thessaloniki791_2010 mix (186P, 225G, 324I, 377K),
. . . . Hiroshima645,
. . . . H6N1,
. . . . H9N2 2008
233H (cAC) NC Duke TmX cluster (5, mix, 225G, 225N), NY2372_2010_01_20,
. . . . AZ17 & Australia6, TurkeyTR19_2009 (syn205G),
. . . . swHK_189_2010_01_07
235A CatNS7632, CalifVRDL55
235I Wisc2489
236L synonymous (CTg) Wisc0099, H9N2 (gTg)
236V Eng93120020, ENG645, H9N2, H6N1
237I Delaware02_2010, Cal_SDINS69, England (2),
. . . . Russia (4), Asia (4), MadridINS185 (447K)
237L Wisc0936 (214Q), 1918, H1N1 (1943, 46, 51),
. . . . tn, H5N1, H6N1,
. . . . H9N2
237V synonymous (GTg) Pennsylvania31, KuwaitN13111_2009_09_23,
. . . . AfghanN10767_2009_09, AfghanN10974_2009_09,
. . . . H9N2 (TTg), M7 (CTg)
238G (GgG) AthensINS161 (89G, 152L)
238D Kaliningrad01 (225E+226R), tn
238K (aAG) Wisc2485 (225E), DjiboutiN13142_2009_12_08, Spain (3),
. . . . OrenburgIIV13_2010_03_02_xL_f (225G), China,
. . . . swOR4060,
. . . . H1N1 Iowa_1943,
. . . . H5N1, H6N1,
. . . . H9N2 2008
238E synonymous (GAa) Extensive Wisc2424, EgyptN14648_2009_11,
. . . . Latvia122498, ThaiTHA0364, ShanxiChengqu547,
. . . . Cyprus5800_2010, HvidovreINS141,
. . . . SC01_2010, MN01_2010,
. . . . H9N2 (aAa), H6N1 (aAa)
239P synonymous (CCt) ENG621, NY6939, swOR4060_2009_12_31
239P synonymous (CCa) Ancona508PG, Russia180, Australia60,
. . . . MS09, NV20, ME01_2010, tn,
. . . . H6N1
. . . . H9N2
240G synonymous (GGg) DC_INS24,
. . . . S9, S7, M7, Sask,
. . . . H6N1 (GGg),
. . . . H9N2
240G synonymous (GGc) Wisc0636,
. . . . H9N2 (GGc)
240E (GaA) Brandenburg34
241D synonymous (GAt) CatS1943, Colombia4117, swIll (3), S7, M7, tn, H5
241G NH17, ENG93040048
241E China22811, H9N2 (CAa, CAg), H6N1 (GAa, GAg)
242K synonymous (AAg) swOR4060_2009_12_31
244I ThaiCU_H9, Shiga1, Guangdong2282 (131P, 202A, 230I, 275A),
. . . . LiaoningShuncheng1148 (131P, 202A, 230I, 275A),
. . . . Ancona02, Stockholm29,
. . . . Alabama03_2010,
. . . . H1N1 (1946, 51), S9, S7, M7, Sask
244T synonymous (ACt) CatS1935, CatS2120
245F synonymous (TTt) Aswan2288 (189T, 377K)
246E synonymous (GAg) NorthCarolina56 (100N, syn137A, 377K),
. . . . S7, M7, 1918, tn,
. . . . H5N1
246G (GgA) Iceland163_2009 mix (159D)
The truth is in the sequences.
No comments:
Post a Comment