Greece Documents pH1N1 Fatalities on Multiple Backgrounds during Early 2011

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked Excel for completeness in citation.

Publish Date : 2013-10-15
Last Update : 2013-11-18

Map - Active and Detailed

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57 HA Sequences

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On 2013-10-08, the National Influenza Centre for Northern Greece released a total of 57 pH1N1 Hemagglutinin sequence fragments at GISAID having 2 from early 2013, but with the larger set sampled during January and February 2011 [map]. All 57 patients sought medical attention.  The Neuraminidase segments were not released.  A total of 9 fatalities are documented and 6 subjects were under the age of 60 at the time of their death from Influenza.

Greek Fatalities

pH1N1 6 of 9 Greek Deaths Are Under Age 60 Clade Name Age ID  Clade2   GreeceThessaloniki410_52F_2013_01_31_f 52  EPI476396   Clade2   GreeceThessaloniki1391_47M_2011_02_21_VxX_f  47  EPI476395   None   GreeceThessaloniki1329_56F_2011_02_17_f 56  EPI476409   Clade2   GreeceThessaloniki1151_49F_2011_02_14_f 49  EPI476400   Clade5   GreeceThessaloniki1164_76M_2011_02_14_f 76  EPI476399   Clade2   GreeceGiannitsa1052_78F_2011_02_10_f 78  EPI476401   Clade2   GreeceThessaloniki678_56M_2011_02_07_f 56  EPI476398   Clade2   GreeceKavala470_46M_2011_02_01_f 46  EPI476406   Clade2   GreeceThessaloniki407_66M_2011_01_31_f 66  EPI476397

Genetic diversity and pathogenic vigor are demonstrated as these deaths are found on 3 separate backgrounds: 2 established clades and 1 off-clade death. Diversity in excess of 4 clades was circulating contemporaneously in that region during the 36 days of 2011 sampling.  Sequences covering hospitalisations total 4 in this deposit.

Greek Hospitalisations

pH1N1 100% of Greek InPatients Are Under Age 60 Clade Name Age ID  Clade2   GreeceKilkis1524_52F_2011_02_24_s 52  EPI474960   Clade2   GreeceThessaloniki1378_50M_2011_02_18_s  50  EPI475846   Clade2   GreeceThessaloniki1168_54F_2011_02_14_s 54  EPI475829   Clade2   GreeceThessaloniki287_56F_2011_01_27_s 56  EPI475853

The genetics of Vaccine Escape are evident in 3 sequences across 2 clades, including 2 fatalities.  HA 225N is shown on an unusual background in the area of Xanthi [EPI476404].  Dual infections signalled by mixtures feature on these fragments, including one of the fatalities.  The Komotini [EPI475900] sequence shows Clade1:189T crossing onto Clade2:188T.

Greek Vaccine Escape Early 2011

Vaccine Escape Diversity Type Observation Name ID  GenoTypic   VxX 155I   GreeceThessaloniki1391_47M_2011_02_21_VxX_f   EPI476395   GenoTypic   VxX 155I   GreeceThessaloniki839_59M_2011_02_08_VxX   EPI475899   GenoTypic   VxX 225N   GreeceXanthi265_50M_2011_01_27_VxX   EPI476404

We have annotated these HA fragments and placed them geographically throughout Greece for reference [map].

Isolate Metrics
Calendar Sample Month Count  2013-02  01  2013-01  01  2011-02  37  2011-01  18	Cladistics CladeName Count  Clade2:188T 48  Clade5:208K_219V 05  CrossClade:   188T_189T 01  UnCladed 01  Clade3:186P 01  Clade4:128D 01

Hemagglutinin Sequences

. . . . GreeceKavala464_48F_2013_02_01 (
. . . . . . . . A/Kavala/464/2011
. . . . . . . . Clade5:208K_219V

. . . . . . . . GISAID HA EPI475832

. . . . . . . . GISAID Isolate EPI_ISL_148171

. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn47L (CTg),

. . . . . . . . 100N,

. . . . . . . . syn102E (GAa),

. . . . . . . . syn170N (AAc),

. . . . . . . . 208K,

. . . . . . . . 219V,

. . . . . . . . syn221P (CCt),

. . . . . . . . 252L,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki410_52F_2013_01_31_f (
. . . . . . . . A/Thessaloniki/410/2011

. . . . . . . . GISAID HA EPI476396

. . . . . . . . GISAID Isolate EPI_ISL_148268

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn174K (AAg),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 200V mix wt,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKilkis1524_52F_2011_02_24_s (
. . . . . . . . A/Kilkis/1524/2011 

. . . . . . . . GISAID HA EPI474960

. . . . . . . . GISAID Isolate EPI_ISL_148032

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn160S (TCg),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1391_47M_2011_02_21_VxX_f (
. . . . . . . . A/Thessaloniki/1391/2011

. . . . . . . . GISAID HA EPI476395

. . . . . . . . GISAID Isolate EPI_ISL_148267

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 155I [H5N1],

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1378_50M_2011_02_18_s (
. . . . . . . . A/Thessaloniki/1378/2011

. . . . . . . . GISAID HA EPI475846

. . . . . . . . GISAID Isolate EPI_ISL_148185

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1329_56F_2011_02_17_f (
. . . . . . . . A/Thessaloniki/1329/2011

. . . . . . . . GISAID HA EPI476409

. . . . . . . . GISAID Isolate EPI_ISL_148281
. . . . . . . . Off-Clade Fatality

. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn52P (CCc),

. . . . . . . . 54R [avH1N1],

. . . . . . . . 58W,

. . . . . . . . syn62G (GGg),

. . . . . . . . 64V [avH1N1, H7N7, H9N2],

. . . . . . . . 65R,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . syn286K (AAa),

. . . . . . . . 303L [H13N2],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceAlexandroupolis1290_79M_2011_02_16 (
. . . . . . . . A/Alexandroupolis/1290/2011

. . . . . . . . GISAID HA EPI476393

. . . . . . . . GISAID Isolate EPI_ISL_148265

. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn163K (AAa),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . syn192Q (CAg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceAlexandroupolis1219_46M_2011_02_15 (
. . . . . . . . A/Alexandroupolis/1219/2011

. . . . . . . . GISAID HA EPI475845

. . . . . . . . GISAID Isolate EPI_ISL_148184

. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn163K (AAa),

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . syn192Q (CAg),

. . . . . . . . 241E [H5N1, avH1N1farm, H13N2],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1151_49F_2011_02_14_f (
. . . . . . . . A/Thessaloniki/1151/2011

. . . . . . . . GISAID HA EPI476400

. . . . . . . . GISAID Isolate EPI_ISL_148272

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . syn304G (GGg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1164_76M_2011_02_14_f (
. . . . . . . . A/Thessaloniki/1164/2011
. . . . . . . . Clade5:208K_219V

. . . . . . . . GISAID HA EPI476399

. . . . . . . . GISAID Isolate EPI_ISL_148271

. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn47L (CTg),

. . . . . . . . 100N,

. . . . . . . . syn102E (GAa),

. . . . . . . . syn170N (AAc),

. . . . . . . . 208K,

. . . . . . . . 219V,

. . . . . . . . syn221P (CCt),

. . . . . . . . 252L,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1168_54F_2011_02_14_s (
. . . . . . . . A/Thessaloniki/1168/2011

. . . . . . . . GISAID HA EPI475829

. . . . . . . . GISAID Isolate EPI_ISL_148168

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 116M,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki1167_76M_2011_02_14 (
. . . . . . . . A/Thessaloniki/1167/2011

. . . . . . . . GISAID HA EPI475828

. . . . . . . . GISAID Isolate EPI_ISL_148167

. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn62G (GGt),

. . . . . . . . 100N,

. . . . . . . . 173R [avH7N9 2011, H5N1, avH1N1],

. . . . . . . . 188T,

. . . . . . . . syn239P (CCa),

. . . . . . . . syn304G (GGg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceGiannitsa1052_78F_2011_02_10_f (
. . . . . . . . A/Giannitsa/1052/2011

. . . . . . . . GISAID HA EPI476401

. . . . . . . . GISAID Isolate EPI_ISL_148273

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 276Y,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki983_77F_2011_02_09 (
. . . . . . . . A/Thessaloniki/983/2011

. . . . . . . . GISAID HA EPI476392

. . . . . . . . GISAID Isolate EPI_ISL_148264

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki774_46M_2011_02_08 (
. . . . . . . . A/Thessaloniki/774/2011

. . . . . . . . GISAID HA EPI476402

. . . . . . . . GISAID Isolate EPI_ISL_148274

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceAlexandroupolis819_79M_2011_02_08 (
. . . . . . . . A/Alexandroupolis/819/2011
. . . . . . . . Clade5:208K_219V

. . . . . . . . GISAID HA EPI476391

. . . . . . . . GISAID Isolate EPI_ISL_148263

. . . . . . . . 10 Polymorphisms (4 Amino and 6 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn47L (CTg),

. . . . . . . . 100N,

. . . . . . . . syn102E (GAa),

. . . . . . . . syn162P (CCg),

. . . . . . . . syn170N (AAc),

. . . . . . . . 208K,

. . . . . . . . 219V,

. . . . . . . . syn221P (CCt),

. . . . . . . . 252L,

. . . . . . . . syn319T (ACg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki839_59M_2011_02_08_VxX (
. . . . . . . . A/Thessaloniki/839/2011

. . . . . . . . GISAID HA EPI475899

. . . . . . . . GISAID Isolate EPI_ISL_148198

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn118E (GAa),

. . . . . . . . 155I [H5N1],

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceFlorina807_53F_2011_02_08 (
. . . . . . . . A/Florina/807/2011

. . . . . . . . GISAID HA EPI475851

. . . . . . . . GISAID Isolate EPI_ISL_148190

. . . . . . . . 5 Polymorphisms (4 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn24E (GAg),

. . . . . . . . 87I [pH1N1 TamiFlu Resistance NA 247N],

. . . . . . . . 100N,

. . . . . . . . 110P mix wt,

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceXanthi803_62M_2011_02_08 (
. . . . . . . . A/Xanthi/803/2011

. . . . . . . . GISAID HA EPI475849

. . . . . . . . GISAID Isolate EPI_ISL_148188

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn42G (GGa),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceAlexandroupolis815_46x_2011_02_08 (
. . . . . . . . A/Alexandroupolis/815/2011

. . . . . . . . GISAID HA EPI475844

. . . . . . . . GISAID Isolate EPI_ISL_148183

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki677_79M_2011_02_07 (
. . . . . . . . A/Thessaloniki/677/2011

. . . . . . . . GISAID HA EPI476407

. . . . . . . . GISAID Isolate EPI_ISL_148279

. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 39R,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 226R,

. . . . . . . . 318G,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki678_56M_2011_02_07_f (
. . . . . . . . A/Thessaloniki/678/2011

. . . . . . . . GISAID HA EPI476398

. . . . . . . . GISAID Isolate EPI_ISL_148270

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki672_59M_2011_02_07 (
. . . . . . . . A/Thessaloniki/672/2011

. . . . . . . . GISAID HA EPI475857

. . . . . . . . GISAID Isolate EPI_ISL_148196

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki712_47M_2011_02_07 (
. . . . . . . . A/Thessaloniki/712/2011

. . . . . . . . GISAID HA EPI475843

. . . . . . . . GISAID Isolate EPI_ISL_148182

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . syn284T (ACg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceSerres663_60M_2011_02_04 (
. . . . . . . . A/Serres/663/2011

. . . . . . . . GISAID HA EPI475856

. . . . . . . . GISAID Isolate EPI_ISL_148195

. . . . . . . . 5 Polymorphisms (4 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 136S [H5N1, avH1N1, zH3N2, H9N2],

. . . . . . . . 146G,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki657_57M_2011_02_04 (
. . . . . . . . A/Thessaloniki/657/2011

. . . . . . . . GISAID HA EPI475855

. . . . . . . . GISAID Isolate EPI_ISL_148194

. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 173R [avH7N9 2011, H5N1, avH1N1],

. . . . . . . . 188T,

. . . . . . . . syn239P (CCa),

. . . . . . . . syn276H (CAt),

. . . . . . . . syn304G (GGg),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki654_64M_2011_02_04 (
. . . . . . . . A/Thessaloniki/654/2011

. . . . . . . . GISAID HA EPI475848

. . . . . . . . GISAID Isolate EPI_ISL_148187

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceNaousa626_62M_2011_02_04 (
. . . . . . . . A/Naousa/626/2011

. . . . . . . . GISAID HA EPI475838

. . . . . . . . GISAID Isolate EPI_ISL_148177

. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn55L (TTa),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKavala564_58M_2011_02_03 (
. . . . . . . . A/Kavala/564/2011

. . . . . . . . GISAID HA EPI475837

. . . . . . . . GISAID Isolate EPI_ISL_148176

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 188T,

. . . . . . . . syn245F (TTt),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKilkis533_76M_2011_02_02 (
. . . . . . . . A/Kilkis/533/2011

. . . . . . . . GISAID HA EPI476390

. . . . . . . . GISAID Isolate EPI_ISL_148262

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki516_51M_2011_02_02 (
. . . . . . . . A/Thessaloniki/516/2011

. . . . . . . . GISAID HA EPI475915

. . . . . . . . GISAID Isolate EPI_ISL_148213

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn25K (AAa),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceGrevena552_47M_2011_02_02 (
. . . . . . . . A/Grevena/552/2011

. . . . . . . . GISAID HA EPI475836

. . . . . . . . GISAID Isolate EPI_ISL_148175

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn34N (AAt),

. . . . . . . . syn122K (AAa),

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki515_64M_2011_02_02 (
. . . . . . . . A/Thessaloniki/515/2011

. . . . . . . . GISAID HA EPI475831

. . . . . . . . GISAID Isolate EPI_ISL_148170

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 49E [pH1N1 TamiFlu Resistant NA 247N],

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKavala470_46M_2011_02_01_f (
. . . . . . . . A/Kavala/470/2011

. . . . . . . . GISAID HA EPI476406

. . . . . . . . GISAID Isolate EPI_ISL_148278

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 174R [pH1N1 TamiFlu Resistance NA 247N, H13N2],

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKavala463_52M_2011_02_01 (
. . . . . . . . A/Kavala/463/2011

. . . . . . . . GISAID HA EPI476403

. . . . . . . . GISAID Isolate EPI_ISL_148275

. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 25R [Emergent H7N9 wt],

. . . . . . . . syn34N (AAt),

. . . . . . . . 100N,

. . . . . . . . 146G,

. . . . . . . . 188T,

. . . . . . . . 200T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki508_52M_2011_02_01 (
. . . . . . . . A/Thessaloniki/508/2011

. . . . . . . . GISAID HA EPI475908

. . . . . . . . GISAID Isolate EPI_ISL_148207

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 305E [H5N1 wt],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKavala469_50F_2011_02_01 (
. . . . . . . . A/Kavala/469/2011

. . . . . . . . GISAID HA EPI475841

. . . . . . . . GISAID Isolate EPI_ISL_148180

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki506_48F_2011_02_01 (
. . . . . . . . A/Thessaloniki/506/2011

. . . . . . . . GISAID HA EPI475834

. . . . . . . . GISAID Isolate EPI_ISL_148173

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki503_50F_2011_02_01 (
. . . . . . . . A/Thessaloniki/503/2011

. . . . . . . . GISAID HA EPI475833

. . . . . . . . GISAID Isolate EPI_ISL_148172

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 188T,

. . . . . . . . syn245F (TTt),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki407_66M_2011_01_31_f (
. . . . . . . . A/Thessaloniki/407/2011

. . . . . . . . GISAID HA EPI476397

. . . . . . . . GISAID Isolate EPI_ISL_148269

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki446_76M_2011_01_31 (
. . . . . . . . A/Thessaloniki/446/2011

. . . . . . . . GISAID HA EPI475920

. . . . . . . . GISAID Isolate EPI_ISL_148217

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki451_51M_2011_01_31 (
. . . . . . . . A/Thessaloniki/451/2011

. . . . . . . . GISAID HA EPI475903

. . . . . . . . GISAID Isolate EPI_ISL_148202

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki447_56M_2011_01_31 (
. . . . . . . . A/Thessaloniki/447/2011

. . . . . . . . GISAID HA EPI475839

. . . . . . . . GISAID Isolate EPI_ISL_148178

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 293F,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki453_47M_2011_01_31 (
. . . . . . . . A/Thessaloniki/453/2011

. . . . . . . . Clade3: 186P
. . . . . . . . GISAID HA EPI475835

. . . . . . . . GISAID Isolate EPI_ISL_148174
. . . . . . . . 7 Polymorphisms (3 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 69Q [Emergent H7N9 wt],

. . . . . . . . syn73L (CTt),

. . . . . . . . 137T,

. . . . . . . . syn163K (AAa),

. . . . . . . . 186P,

. . . . . . . . syn293L (CTt),

. . . . . . . . syn324V (GTt),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki329_46M_2011_01_28 (
. . . . . . . . A/Thessaloniki/329/2011

. . . . . . . . GISAID HA EPI475842

. . . . . . . . GISAID Isolate EPI_ISL_148181

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn58C (TGc),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceXanthi265_50M_2011_01_27_VxX (
. . . . . . . . A/Xanthi/265/2011

. . . . . . . . Clade5:208K_219V with 225N
. . . . . . . . GISAID HA EPI476404

. . . . . . . . GISAID Isolate EPI_ISL_148276
. . . . . . . . 10 Polymorphisms (6 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 33G,

. . . . . . . . syn47L (CTg),

. . . . . . . . 100N,

. . . . . . . . syn102E (GAa),

. . . . . . . . syn170N (AAc),

. . . . . . . . 208K,

. . . . . . . . 219V,

. . . . . . . . syn221P (CCt),

. . . . . . . . 225N,

. . . . . . . . 252L,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKomotini261_55M_2011_01_27 (
. . . . . . . . A/Komotini/261/2011

. . . . . . . . CrossClade:188T_189T
. . . . . . . . GISAID HA EPI475900

. . . . . . . . GISAID Isolate EPI_ISL_148199
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 188T,

. . . . . . . . 189T,

. . . . . . . . syn245F (TTt),

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki287_56F_2011_01_27_s (
. . . . . . . . A/Thessaloniki/287/2011

. . . . . . . . GISAID HA EPI475853

. . . . . . . . GISAID Isolate EPI_ISL_148192

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki268_57F_2011_01_27 (
. . . . . . . . A/Thessaloniki/268/2011

. . . . . . . . Clade5:208K_219V
. . . . . . . . GISAID HA EPI475852

. . . . . . . . GISAID Isolate EPI_ISL_148191

. . . . . . . . 8 Polymorphisms (4 Amino and 4 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn47L (CTg),

. . . . . . . . 100N,

. . . . . . . . syn102E (GAa),

. . . . . . . . syn170N (AAc),

. . . . . . . . 208K,

. . . . . . . . 219V,

. . . . . . . . syn221P (CCt),

. . . . . . . . 252L,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceNaousa225_58F_2011_01_26 (
. . . . . . . . A/Naousa/225/2011

. . . . . . . . GISAID HA EPI475854

. . . . . . . . GISAID Isolate EPI_ISL_148193

. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 8V [avH1N1farm, H5N1, H13N2],

. . . . . . . . syn21T (ACg),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 200V mix wt,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceKaterini199_51M_2011_01_25 (
. . . . . . . . A/Katerini/199/2011

. . . . . . . . GISAID HA EPI476408

. . . . . . . . GISAID Isolate EPI_ISL_148280

. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn92T (ACa),

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceSerres213_50M_2011_01_25 (
. . . . . . . . A/Serres/213/2011

. . . . . . . . Clade4: 128D
. . . . . . . . GISAID HA EPI475850

. . . . . . . . GISAID Isolate EPI_ISL_148189
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn60I (ATc),

. . . . . . . . 128D,

. . . . . . . . 318V [H5N1, avH1N1],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki174_49F_2011_01_24 (
. . . . . . . . A/Thessaloniki/174/2011

. . . . . . . . GISAID HA EPI476405

. . . . . . . . GISAID Isolate EPI_ISL_148277

. . . . . . . . 6 Polymorphisms (5 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 83G mix wt,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 253I,

. . . . . . . . 320E [pH1N1 HA 230I],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki164_61M_2011_01_24 (
. . . . . . . . A/Thessaloniki/164/2011

. . . . . . . . GISAID HA EPI475830

. . . . . . . . GISAID Isolate EPI_ISL_148169

. . . . . . . . 5 Polymorphisms (3 Amino and 2 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . syn52P (CCc) mix wt,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 262K [Emergent H7N9 wt],

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki118_52M_2011_01_21 (
. . . . . . . . A/Thessaloniki/118/2011

. . . . . . . . GISAID HA EPI475847

. . . . . . . . GISAID Isolate EPI_ISL_148186

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki73_36F_2011_01_19 (
. . . . . . . . A/Thessaloniki/73/2011

. . . . . . . . GISAID HA EPI476394

. . . . . . . . GISAID Isolate EPI_ISL_148266

. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . HA Truncated after aa330)

. . . . GreeceThessaloniki63_60M_2011_01_19 (
. . . . . . . . A/Thessaloniki/63/2011

. . . . . . . . GISAID HA EPI475840

. . . . . . . . GISAID Isolate EPI_ISL_148179

. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)

. . . . . . . . HA Truncated before aa4,

. . . . . . . . 100N,

. . . . . . . . 119V [H5N1],

. . . . . . . . 188T,

. . . . . . . . syn245F (TTt),

. . . . . . . . HA Truncated after aa330)

Please visit GeneWurx.com for insight into the latest published studies.

pH1N1 Influenza Hemagglutinin Segments elucidated at 2013-10-15-10_39_00_540770 by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

Publication Copyright 2007-2013 GeneWurx.com, All Rights Reserved.

Vaccine Escape in Sao Paulo, Brazil on July 2013 pH1N1 Case

Sequences discussed in this analysis are variously stored publicly at GenBank and at GISAID. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GenBank and from GISAID’s EpiFlu™ Database on which this research is based. A GISAID-generated list is detailed in a linked Excel for completeness in citation.

Publish Date : 2013-10-04
Last Update : 2014-01-09

Geographic Distribution

---

1 Sequence

---

On 2013-10-03, the Instituto Adolfo Lutz of Brazil released one pH1N1 Hemagglutinin sequence at GISAID sampled from a 53 year old female in early July.  The Neuraminidase segment was not released.  The patient is documented as having been vaccinated in 2013.

Vaccine Escape Diversity
Type	Observation	Count
PhenoTypic	Vaccinated 2013	01

This Vaccine Escape case from Sao Paulo, Brazil [map] is on a genetic background in wide circulation around the world.  That background is expected to be prominent in form during the Northern Hemisphere 2013 season.

Cladistics
CladeName	Count
Clade2:188T	01

HA Polymorphisms

. . . . BrazilSaoPaulo55023_53F_2013_07_10_VxX_s (
. . . . . . . . A/Sao Paulo/55023/2013

. . . . . . . . Vaccinated 2013

. . . . . . . . GISAID HA EPI475776

. . . . . . . . GISAID Isolate EPI_ISL_148145

. . . . . . . . 23 Polymorphisms (9 Amino and 14 Silent)

. . . . . . . . syn42G (GGt),

. . . . . . . . syn77S (AGt),

. . . . . . . . 100N,

. . . . . . . . syn141H (CAc),

. . . . . . . . syn165S (AGt),

. . . . . . . . 166Q,

. . . . . . . . syn179L (CTg),

. . . . . . . . 188T,

. . . . . . . . 259T,

. . . . . . . . 286E,

. . . . . . . . syn308K (AAg),

. . . . . . . . syn318A (GCa),

. . . . . . . . syn333F (TTc),

. . . . . . . . syn338G (GGc),

. . . . . . . . syn372Q (CAa),

. . . . . . . . 377K,

. . . . . . . . syn383N (AAc),

. . . . . . . . syn396V (GTg),

. . . . . . . . syn448L (TTg),

. . . . . . . . 454N,

. . . . . . . . 482I,

. . . . . . . . 502K,

. . . . . . . . syn537S (AGc))

Please visit GeneWurx.com for insight into the latest published studies.

pH1N1 Influenza Hemagglutinin Segment elucidated at 2013-10-04-09_29_00_087350  by GeneWurx see.PolyDetector v0, Copyright 2007-2013.

Publication Copyright 2007-2013 GeneWurx.com, All Rights Reserved.