HA 158E in Cameroon Pair with Additional HA Changes Correlated to Anti-Viral Resistance

The UK National Institute for Medical Research published a group of sequences on 2010-12-30 at GISAID.  One group originated from the Centre Pasteur du Cameroun.

HA 158E, a polymorphism associated with Vaccine Escape, appears in two Cameroon sequences upon a highly plastic background that is demonstrated worldwide, including multiple non-adjacent, coastal areas of the United States and in Australia on a background that may be permissive to HA 230I.

This Cameroon background has additionally been conserved in domestic poultry Pandemic H1N1 from Canada.

The most recent sequence taken in April 2010, Cameroon10v_1090_2010_04_08, also carries HA syn223V just upstream of the 225 amino acid position that is so often tracked.  HA syn223V has been co-located with 454N in Texas45131774_2009_09_13.  454N and other changes at 454 are highly correlated to the most recent UK sequences on file and to a chain of sequences spanning Australia before the UK and Iran after the UKWhiteChapel4880374_2M_2010_11_28 sample.  The related hypermorphic Australian sequence, OzVictoria508_9F_2010_07_24, shares 8 changes with Cameroon.

Notice that the syn254P has been found on a Japanese TamiFlu Resistant sequence.  523A, which is found at various points on Vaccine Escape and TamiFlu Resistant sequences, is also contained within the potential UK donation reservoir from Australia.

Based on these updates from NIMR, potential exists for a 158E emergence in the UK.

GeneWurx has prepared an Excel spreadsheet investigating potential genetic acquisition in the currently uncharted severe Pandemic H1N1 wave in the UK.  In Version 2 of this spreadsheet, the Cameroon 158E sequence takes Column W and provides homology with potential predecessors to one UK White Chapel sequence of interest.

GeneWurx_UK_December_Emerging_Genetics_v2.xls

. . . . Cameroon10v_1090_2010_04_08 (
. . . . . . . . 35I,
. . . . . . . . 114L,
. . . . . . . . syn152I,
. . . . . . . . 158E,
. . . . . . . . syn219I,
. . . . . . . . syn223V [Thailand34_9913_2010_07_14,
. . . . . . . . . . . . . . Texas45131774_2009_09_13],
. . . . . . . . syn254P [Kumamoto2_2010_01_14_TmX],
. . . . . . . . syn276H,
. . . . . . . . syn402H,
. . . . . . . . syn419L,
. . . . . . . . syn456L,
. . . . . . . . 463V,
. . . . . . . . 523A [OzSydney217_2010_09_19 with 188T,
. . . . . . . . . . . . . OzVictoria508_9F_2010_07_24,
. . . . . . . . . . . . . Montana02_2010_04_07_VxX,
. . . . . . . . . . . . . Shizuoka_C21_2010_01_20_TmX])

. . . . Cameroon10v_813_2010_03_23 (
. . . . . . . . 35I,
. . . . . . . . syn152I,
. . . . . . . . 158E mix wt,
. . . . . . . . syn219I,
. . . . . . . . syn254P,
. . . . . . . . syn276H,
. . . . . . . . HA truncated after aa396)

Supporting Sequences

. . . . OzVictoria508_9F_2010_07_24 (
. . . . . . . . 35I [H5N1],
. . . . . . . . 88P [H2N3, H5N1, H11],
. . . . . . . . . . . [HunanHechengSWL1616_2009-11-23,
. . . . . . . . . . . KoreaAF2376_2009_10_27
. . . . . . . . . . . . . . . with 280A and 290K
. . . . . . . . . . . Nevada15_9F_2009_09_10
. . . . . . . . . . . . . . . with 22I, 225E, 256F, 299Y,
. . . . . . . . . . . . . . . . . . 299Y, 300S, syn384S,
. . . . . . . . . . . GermanyCologne13_2009_06_29
. . . . . . . . . . . . . . . with 35I, 38V, syn108L,
. . . . . . . . . . . . . . . . . . syn205G, 206s, syn276H],
. . . . . . . . syn102E [SingON2407_2009_12_13,
. . . . . . . . . . . . . . . Singapore544_2009_12_10,
. . . . . . . . . . . . . . . Brussels243_2009_11_09
. . . . . . . . . . . . . . . . . . . . with syn44L and 89G],
. . . . . . . . syn152I [CalifVRDL115_2009_12_04,
. . . . . . . . . . . . . . . NY6939_2009_12_11,
. . . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07
. . . . . . . . . . . . . . . . . . . . with 35I, syn219I, syn276H,
. . . . . . . . . . . . . . . . . . . . . . . syn456L, 463V, 523A,
. . . . . . . . . . . . . . . England1050_2009_12,
. . . . . . . . . . . . . . . Scotland103_2009_12,
. . . . . . . . . . . . . . . England1051_2009_12,
. . . . . . . . . . . . . . . ItalyAncona451_2009_11_27_f,
. . . . . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . . . . DC_114_2009_11_04,
. . . . . . . . . . . . . . . England94800096_2009_11,
. . . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . . . . IndiaPune6196_2009_08,
. . . . . . . . . . . . . . . IndiaDhule9433_2009_08,
. . . . . . . . . . . . . . . SantoDomingoWR1057N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1058N_2009_07_02,
. . . . . . . . . . . . . . . SantoDomingoWR1059N_2009_06_30],
. . . . . . . . 206S,
. . . . . . . . syn219I [CalifVRDL115_2009_12_04
. . . . . . . . . . . . . . . . . with 35I, syn152I, syn276H,
. . . . . . . . . . . . . . . . . . . . syn456L, 463V, 523A,
. . . . . . . . . . . . . . FL_Pen213_2009_11_17
. . . . . . . . . . . . . . . . . . . . with 35I, syn152I, 273A,
. . . . . . . . . . . . . . . . . . . . syn456L, 463V, 523A,
. . . . . . . . . . . . . . CalifVRDL107_2009_11_15
. . . . . . . . . . . . . . . . . . . . with 35I, syn152I, syn276H,
. . . . . . . . . . . . . . . . . . . . syn456L, 463V, 523A,
. . . . . . . . 238D (GAc) [H2N3, H7N3, H7N7],
. . . . . . . . . . . . . . . . . . [Belgorod2_2010-03-15 (GAt),
. . . . . . . . . . . . . . . . . . Kaliningrad01_2009_11_02 (GAt)
. . . . . . . . . . . . . . . . . . . . . . . . with 225E and 226R,
. . . . . . . . . . . . . . . . . . AthensINS398_2010-01-24 GAt),
. . . . . . . . . . . . . . . . . . KaliningradCRIE_DA_2009-09-26 (GAt),
. . . . . . . . . . . . . . . . . . KaliningradCRIE_KG_2009-09-25 (GAt),
. . . . . . . . . . . . . . . . . . KaliningradCRIE_MA_2009-09-25 (GAt),
. . . . . . . . . . . . . . . . . . KaliningradCRIE_SHD_2009-09-25 (GAt),
. . . . . . . . . . . . . . . . . . KaliningradCRIE_ZD_2009-09-25 (GAt)],
. . . . . . . . syn247A [Belize8756_2009_10_08,
. . . . . . . . . . . . . . . Singapore93_2009_06_22]
. . . . . . . . syn254P,
. . . . . . . . 272G [Niigata19_2009_12_31,
. . . . . . . . . . . . GuangdongSWL36_2009_11_29],
. . . . . . . . syn276H [1918, S5],
. . . . . . . . syn388K [H5N1],
. . . . . . . . . . . . . . . [NagasakiHA_10_28_2010_03_23
. . . . . . . . . . . . . . . . . . . . . with 22I,
. . . . . . . . . . . . . . . NagasakiHA_10_26_2010_03_15
. . . . . . . . . . . . . . . . . . . . . with 22I, syn103E,
. . . . . . . . . . . . . . . NagasakiHA_10_24_2010_03_08
. . . . . . . . . . . . . . . . . . . . . with syn103E,
. . . . . . . . . . . . . . . GuangxiLonganSWL1990_2010_02_08
. . . . . . . . . . . . . . . . . . . . . with 453K, syn462E,
. . . . . . . . . . . . . . . JiangxiDonghuSWL15_2010_01_04
. . . . . . . . . . . . . . . . . . . . . with syn106E, 149R, syn456L (TTg),
. . . . . . . . . . . . . . . ViennaINS142_2009_11_26
. . . . . . . . . . . . . . . . . . . . . with syn97D, 99T,
. . . . . . . . . . . . . . . CzechUsti208_2009_11_25
. . . . . . . . . . . . . . . . . . . . . with 268T,
. . . . . . . . . . . . . . . GhanaFS_1921_2009_11_11,
. . . . . . . . . . . . . . . Alaska44_2009_11_17
. . . . . . . . . . . . . . . . . . . . . with syn275V, 276N,
. . . . . . . . . . . . . . . CalifVRDL76_2009_09_21
. . . . . . . . . . . . . . . . . . . . . with syn283Q,
. . . . . . . . . . . . . . . Taiwan206_2009_09_18,
. . . . . . . . . . . . . . . Taiwan177_2009_09_18,
. . . . . . . . . . . . . . . Taiwan167_2009_09_18,
. . . . . . . . . . . . . . . Taiwan156_2009_09_18,
. . . . . . . . . . . . . . . Taiwan143_2009_09_15
. . . . . . . . . . . . . . . . . . . . . with 205E mix,
. . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25_VxX
. . . . . . . . . . . . . . . . . . . . . with 159D, 206S, 227G
. . . . . . . . . . . . . . . Slovenia2687_2009_07_01
. . . . . . . . . . . . . . . . . . . . . with 35I, 206S],
. . . . . . . . syn456L [H5N1],
. . . . . . . . 463V,
. . . . . . . . 523A [Nebraska02_2010_03_11,
. . . . . . . . . . . . NagasakiHA1022_2010_03_01_syn413K,
. . . . . . . . . . . . DomRepublic3768_2009_12_15,
. . . . . . . . . . . . NY6939_2009_12_11,
. . . . . . . . . . . . CalifVRDL115_2009_12_04,
. . . . . . . . . . . . NY6607_2009_11_24,
. . . . . . . . . . . . RheinlandPfalz81_2009_11_23,
. . . . . . . . . . . . Berlin210_2009_11_16,
. . . . . . . . . . . . BadenWurttemberg511_2009_11_16,
. . . . . . . . . . . . CalifVRDL107_2009_11_15,
. . . . . . . . . . . . FL_Pensacola40_2009_11_09,
. . . . . . . . . . . . CalifVRDL101_2009_11_05,
. . . . . . . . . . . . DC114_2009_11_04,
. . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . NY5447_2009_10_23,
. . . . . . . . . . . . CalifVRDL84_2009_10_09,
. . . . . . . . . . . . CalifVRDL87_2009_10_09,
. . . . . . . . . . . . KuwaitN13013_2009_08_31_syn413K])

. . . . CalifVRDL115_2009_12_04 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 77N,
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)

. . . . FL_Pen213_2009_11_17 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . 273A,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)

. . . . CalifVRDL107_2009_11_15 (
. . . . . . . . . . . . 35I [H5N1],
. . . . . . . . . . . . 39N,
. . . . . . . . . . . . syn152I,
. . . . . . . . . . . . syn219I,
. . . . . . . . . . . . syn276H [1918, S5],
. . . . . . . . . . . . syn456L [H5N1],
. . . . . . . . . . . . 463V,
. . . . . . . . . . . . 523A)

. . . . KoreaAF2376_2009_10_27 (
. . . . . . . . 88P [H2N3, H5N1, H11],
. . . . . . . . . . . . [Victoria508_2010_07_24 with ext changes,
. . . . . . . . . . . HunanHechengSWL1616_2009-11-23,
. . . . . . . . . . . Nevada15_9F_2009_09_10,
. . . . . . . . . . . GermanyCologne13_2009_06_29],
. . . . . . . . 131P,
. . . . . . . . 280A,
. . . . . . . . 290K [HunanHechengSWL1617_2009_11_23],
. . . . . . . . HA truncated after aa386)

. . . . Nevada15_9F_2009_09_10 (
. . . . . . . . 22I,
. . . . . . . . 88P,
. . . . . . . . 225E,
. . . . . . . . 256F,
. . . . . . . . 299Y,
. . . . . . . . 300S,
. . . . . . . . syn384S)

. . . . GermanyCologne13_2009_06_29 (
. . . . . . . . HA truncated until aa28,
. . . . . . . . 35I,
. . . . . . . . 38V,
. . . . . . . . 88P,
. . . . . . . . syn108L,
. . . . . . . . syn205G,
. . . . . . . . 206S,
. . . . . . . . syn276H,
. . . . . . . . HA truncated after aa321)

. . . . Texas45131774_2009_09_13 (
. . . . . . . . syn223V [H5N1, H6N1],
. . . . . . . . 454N [H7N3, H7N7, H9N2]
. . . . . . . . . . . . . . [IndiaPune9355_2009_08 with 225G,
. . . . . . . . . . . . . . IndiaBlore236_2009_06 with 226R,
. . . . . . . . . . . . . . SouthCarolina18_2009_09_16_VxX,
. . . . . . . . . . . . . . FL_Pen210_2009_11_10 with 225E]),

. . . . Shizuoka_C21_2010_01_20_TmX (
. . . . . . . . 22I,
. . . . . . . . syn149K,
. . . . . . . . syn413K,
. . . . . . . . 523A [Extensive US 2010 April & May (10),
. . . . . . . . . . . . on entirely different background,
. . . . . . . . . . . . including Montana02_2010_04_07_VxX]),

. . . . Kumamoto2_2010_01_14_TmX (
. . . . . . . . syn10Y [China22811_2009_12
. . . . . . . . . . . . . . . . . . . with 14 HA changes],
. . . . . . . . 252L [Maryland03_2010_01_13,
. . . . . . . . . . . . Guangdong2361_2009_11_25],
. . . . . . . . syn254P [1918, tn, H5N1]),
. . . . . . . . . . . . . . [Ancona451_2009_11_27_f,
. . . . . . . . . . . . . . Iran15583_2009_11_21
. . . . . . . . . . . . . . . . . . with 16 HA (226R) + 3 NA changes,
. . . . . . . . . . . . . . Iran16677_2009_11_24],
. . . . . . . . syn320G [H5N1],
. . . . . . . . . . . . . . [Yamagata307_2009_09_24
. . . . . . . . . . . . . . . . . . . with 123T, syn134G,
. . . . . . . . . . . . . . Moscow_ION_2009_07_16,
. . . . . . . . . . . . . . Bolivia1263_2009_07_14 with syn107Q,
. . . . . . . . . . . . . . Mie41_2009_07_11 with syn107Q]
. . . . . . . . syn366A (GCa) [H5N1],
. . . . . . . . . . . . . . [Unique to PF11 Asia,
. . . . . . . . . . . . . . Netherlands2143_2009_11_16,
. . . . . . . . . . . . . . Maryland31_2009_11_09,
. . . . . . . . . . . . . . Calif_SD35_2009_10_26,
. . . . . . . . . . . . . . NY5297_2009_10_22,
. . . . . . . . . . . . . . NorthCarolina53_2009_10_18,
. . . . . . . . . . . . . . Stockholm67_2009_07_17,
. . . . . . . . . . . . . . MauritusMPn_2009_07_01,
. . . . . . . . . . . . . . MauritusMPt_2009_07_01,
. . . . . . . . . . . . . . ENG92860032_2009_07,
. . . . . . . . . . . . . . ENG520_2009_06,
. . . . . . . . . . . . . . ENG507_2009_06,
. . . . . . . . . . . . . . WiscS1416_2009_10_26_xL (GCt),
. . . . . . . . . . . . . . TexasJMS385_2009_12_04 (GCt)],
. . . . . . . . syn390N [H2, H3N8, H5, H6, H7N3, H7N7, H9N2, H11],
. . . . . . . . . . . . . . [Calif09_2010_05_11,
. . . . . . . . . . . . . . NY7480_2010_03_01,
. . . . . . . . . . . . . . NY03_2010_02_09,
. . . . . . . . . . . . . . Texas01_2010_01_13,
. . . . . . . . . . . . . . TexasJMS400_2009_12_31,
. . . . . . . . . . . . . . TexasJMS399_2009_12_31,
. . . . . . . . . . . . . . TexasJMS398_2009_12_30,
. . . . . . . . . . . . . . TexasJMS397_2009_12_30,
. . . . . . . . . . . . . . Washington73_2009_12_14,
. . . . . . . . . . . . . . NY6937_2009_12_11,
. . . . . . . . . . . . . . Bishkek03_2009_11_28
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S, 175D,
. . . . . . . . . . . . . . Tomsk06_2009_11_22,
. . . . . . . . . . . . . . Russia200_2009_11_01
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S, 175D,
. . . . . . . . . . . . . . NY5196_2009_10_20,
. . . . . . . . . . . . . . NY5141_2009_10_16
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . ENG94280034_2009_10_06,
. . . . . . . . . . . . . . Texas45093846_2009,
. . . . . . . . . . . . . . Texas45024243_2009,
. . . . . . . . . . . . . . AfghanistanN10786_2009_09_07
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . AfghanistanN10760_2009_09
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . AfghanistanN09787_2009_08
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . Nepal (Nov)
. . . . . . . . . . . . . . NeimengguHuimin11560_2009_12_30,
. . . . . . . . . . . . . . Kentucky16_2009_07_30],
. . . . . . . . syn466G [H5N1, tn],
. . . . . . . . . . . . . . [Unique to PF11 Japan,
. . . . . . . . . . . . . . ChongqingYuzhong11307_2009_12_15
. . . . . . . . . . . . . .. . . . . . . . . . with 219V,
. . . . . . . . . . . . . . NY6864_2009_12_02
. . . . . . . . . . . . . .. . . . . . . . . . with 530I,
. . . . . . . . . . . . . . NY6909_2009_11_29
. . . . . . . . . . . . . .. . . . . . . . . . with 530I,
. . . . . . . . . . . . . . GuangdongHaizhu1644_2009_11_25,
. . . . . . . . . . . . . . NY6675_2009_11_24
. . . . . . . . . . . . . .. . . . . . . . . . with 530I,
. . . . . . . . . . . . . . DC46_2009_11_03
. . . . . . . . . . . . . .. . . . . . . . . . with 530I,
. . . . . . . . . . . . . . NY4995_2009_10_04
. . . . . . . . . . . . . .. . . . . . . . . . with 530I,
. . . . . . . . . . . . . . CalifVRDL75_2009_09_19
. . . . . . . . . . . . . .. . . . . . . . . . with 119M,
. . . . . . . . . . . . . . Texas45130742_2009_09_13,
. . . . . . . . . . . . . .. . . . . . . . . . with syn227E,
. . . . . . . . . . . . . . Texas45132788_2009_09_13,
. . . . . . . . . . . . . . Texas45120922_2009_09_12,
. . . . . . . . . . . . . . Texas45122282_2009_09_12,
. . . . . . . . . . . . . . Texas45113882_2009_09_11],
. . . . . . . . syn548C [H5N1, 1918, tn]
. . . . . . . . . . . . . . [Unique to PF11 Asia,
. . . . . . . . . . . . . . Bishkek03_2009_11_28
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S, 175D,
. . . . . . . . . . . . . . Russia200_2009_11_01
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S, 175D,
. . . . . . . . . . . . . . NY5141_2009_10_16
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . AfghanistanN10786_2009_09_07
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . AfghanistanN10760_2009_09
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S,
. . . . . . . . . . . . . . AfghanistanN09787_2009_08
. . . . . . . . . . . . . .. . . . . . . . . . with syn131S])

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