US Capital, New York and Wisconsin Add 15 Recent Samples to the Cross-Linked Background

Cross-Linked Silent HA and NA Polymorphisms Correlated with Fatal 225G Cases in the Ukraine and Russia

• HA:syn413K encoded from A1281G, AAa->AAg
• NA:syn407V encoded from T1221C, GTt->GTc

 PF11 Sequences Demonstrating Cross Segment Linkage

• Iraq8529E3  with HA 131L, 160L, 194I, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8529M1 with HA 131L, 160L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8531     with HA 130E, 131L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Australia Victoria2129 with potential H5N2 inclusions and NA 454S 
• Australia Victoria2130 with NA 454S
• Ukraine Kyiv377 with mixture of 225D, 225G, 225N, 225S, 225T and 225A
• Ukraine Lviv673
• Ukraine Lviv682
• Ukraine Cherkasy332
• Ukraine Cherkasy333
• Ukraine Cherkasy346
• Ukraine Chernihiv855L with mixture of wt 225D / 225G and additional 1918 Markers (syn238E & 324I), Fatal outcome 
• Ukraine Chernihiv856 with mixture of wt 225D / 225G , Fatal outcome 
• Ukraine Chernihiv857 with mixture of wt 225D / 225G and additional 1918 Markers (186P, syn238E, 324I & G796A), Fatal outcome 
• Ukraine Chernihiv858, Fatal outcome 
• Ukraine Dnipropetrovsk260
• Ukraine Dnipropetrovsk267
• Ukraine Dnipropetrovsk268
• Ukraine Dnipropetrovsk272
• Ukraine Dnipropetrovsk273 with mixture of wt 225D and 225G
• Ukraine Dnipropetrovsk274
• Ukraine Dnipropetrovsk1124
• Ukraine Dnipropetrovsk1171
• Ukraine LvivN2 with 225G
• Ukraine LvivN6 with 225G
• Ukraine TernopilN10 with 225G
• Ukraine TernopilN11 with 225G
• Ukraine Volin226 with 225G
• MoldovaG120
• MoldovaG140
• MoldovaG181
• MoldovaG182
• MoldovaG191
• HA and NA Norway2924 with mixture of wt 225D and 225G
• HA and NA Norway3364-2
• HA and NA Denmark AarhusINS82 with syn177L and 324I
• HA and NA Denmark CopenhagenINS95 with 69K, syn157K and 176I
• HA and NA Denmark CopenhagenINS98
• HA and NA Poland WarsawINS100 with 324I and 377K
• HA and NA Greece AthensINS85 with syn57C, syn233Y, 324I and 377K
• HA and NA CatNS7362 TamiFlu Resistant
• HA and NA CatS1096
• HA and NA CatS1162
• HA and NA CatS1179
• HA and NA CatS1181
• HA and NA CatS1267
• HA and NA CatS1268
• HA and NA CatS1402
• HA and NA CatS1501
• HA and NA CatS1687
• HA and NA CatS1748
• HA and NA CatS1751
• HA and NA CatS1761
• HA and NA CatS1827
• HA and NA CatS1935
• HA and NA CatS2120 with multiple swine markers
• HA and NA CatS2151 with swine markers and 165N (TamiFlu Resistant CatNS7632 and Russian 225G Salekhard01)
• HA and NA Guangdong02
• HA and NA Guangdong05
• HA and NA SingaporeON1156
• HA and NA India BloreNIV236 with 226R, syn372Q, 454N and 550T
• HA and NA Sweden Stockholm31
• Sweden Malmoe1 from 2010 with 190Y, 324I and 377K
• Sweden Gothenburg2 with 146G, 324I (1918) and markers found extensively in Moldova and Russia 
• HA and NA Russia4 with syn238E and 324I (1918)
• HA and NA Russia12 with 324I (1918)
• HA and NA Russia14
• HA and NA Russia19 with 324I (1918)
• HA and NA Russia74
• HA and NA Russia149
• HA and NA Russia165
• HA and NA Russia171 with 165N
• HA and NA Russia178
• HA and NA Russia180 with 165N, syn239P and 264G
• HA and NA Russia190
• HA and NA Russia191
• HA and NA Kurgan01 with HA 214E (MoldovaG168, G176, G188) and NA mixture at 407 (Fatal 225G Abakan02) 
• HA and NA Omsk02 
• HA and NA Tver2969 with 225G, Fatal outcome
• HA and NA Salekhard01 with 165N and 225G, presumptive Fatal outcome
• HA and NA Orenburg2974 with 225N, potential Fatal outcome
• HA and NA Perm01 with 131P, 225G and 324I, presumptive Fatal outcome
• HA and NA District of ColumbiaINS43 with 22I, syn157K and 176I *
• HA and NA NY3702
• HA and NA NY3715
• HA and NA NY3828
• HA and NA NY4398 *
• HA and NA NY4977 with 189T *
• HA and NA NY5086 with 22I, syn157K, 176I and 264T *
• HA and NA NY5186 *
• HA and NA NY5227 with 189T *
• HA and NA NY5931 with 22I, syn157K, 176I and 262K *
• United States NewYork96
• HA and NA RhodeIsland08
• HA and NA Texas42102708
• HA and NA Texas45072128
• HA and NA Texas45122886
• HA and NA WiscD0544 with 22I, syn157K and 176I *
• HA and NA WiscD0853 with 22I, syn157K, 176I, 188I, 231K and 277N *
• HA and NA WiscD1915 with 22I, syn157K, 176I, 188I, 231K and 277N *
• HA and NA WiscD1987 with 189T and 324I *
• HA and NA WiscD2060 with 22I, syn157K and 176I *
• HA and NA WiscD2337 with 22I, syn157K, 176I, 188I, 231K, 277N and 285S *
• HA and NA WiscS1252 with 189T and 324I *
• HA and NA WiscS1416 with 22I, syn157K, 176I, 188I, 231K, 277N and syn366A *
• United States Kentucky19 from an 18 year old subject with HA 298V
• United States Indiana20 from a 10M subject with 5 Avian H5N1 markers
• US Private Sequence TamiFlu Resistant  
• United States NorthCarolina37 from a 24F subject with HA 298V
• United States NorthCarolina44 from a 50M subject with 6 Avian H5N1 markers
• United States NorthCarolina46_C2     from a 39F subject with HA 298V
• United States NorthCarolina46_C2C1 from a 39F subject with HA 298V
• HA and NA swine/NC/34752 with 298V 
• HA and NA swine/OR4060 Emergent Non-PF11 Lineage of H1N1 2009-12-31 *

113 sequences have encircled the globe as of 2010-03-24 * with high fidelity carrying a cross-segment paired set of background markers matching and contributing to fatal cases in the Ukraine and Russia.  225G appears in 14 on this background; 225N once and 225E precisely zero.  The first occasion of 226R entered the list this week retrospectively due to sequence release delay with a June 2009 case from India.

The 15 newest entries represent a diverse geography within the United States of ΣPF11 infections, including 1 entry for Washington D.C., the nation's capital, 6 from New York and 7 from Wisconsin.  The final entry is an H1N1 swine from Oregon that documents an emergent non-PF11 lineage building onto this cross segment linkage.

The available data, though sparse, requires the simple evaluation that this pandemic reservoir is not approaching stasis. The background continues to widen within the existing clades adding polymorphisms from H5N1 and 1918 strains demonstrating that ΣPF11 is far from reaching Omega status.   Movement onto this cross-linked background has accelerated recently, now encompassing 2% of all available pandemic sequences.

Areas covered include Texas (3), the Northeastern United States (11), Wisconsin (7), Oregon, Washington D.C., Kentucky, Indiana, North Carolina (5), China (2), Singapore, India, Australia (2), the Ukraine (23), Moldova (5), Russia (18), Iraq (3), Denmark(3), Norway (2), Sweden (3), Poland, Greece and extensive penetration in Spain (17 sequences).

Receptor Binding Site (RBS) changes at 225 are associated with fatality, 225G and 225N at a rate higher than 225E.

If LvivN6 is officially confirmed as a vaccine escape event, these cross-segment pairs may be surveilled as potential future effectors of vaccine efficacy failure.

Previous Study on this Topic:

• 2010-03-22 Cross-Linked Background Includes 226R Strain from India and Sweden Entry with novel 190Y
• 2010-03-17 Cross-Linked Background Supporting Fatal 225G Cases Penetrates 3 New Countries: Poland, Denmark and Greece
• 2010-01-28 Ukraine - 100% of New Sequences with Required HA and NA on Cross-Linked Background; 225G on 6 of 11; 1918 Markers Coalesce
• 2010-01-19 Fatal Ukraine Cross Segment Linkage Extends in the US, Iraq and Australia (HA syn413K and NA syn407V)
• 2010-01-01 HA syn413K and NA syn407V Cross Segment Linkage Increases Range and Penetration
• 2009-12-04 Spain Introduces 2 November Sequences with Cross-Segment Pairing from Fatal Cases in the Ukraine
• 2009-11-28 Ukraine and Spain Cross-Linked HA and NA Silent Changes Circle the Globe
• 2009-11-26 The Ukraine, Norway and Spain Share Paired HA and NA Changes

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

Cross-Linked Background Includes 226R Strain from India and Sweden Entry with novel 190Y

Cross-Linked Silent HA and NA Polymorphisms Correlated with Fatal 225G Cases in the Ukraine and Russia

• HA:syn413K encoded from A1281G, AAa->AAg
• NA:syn407V encoded from T1221C, GTt->GTc

 PF11 Sequences Demonstrating Cross Segment Linkage

• Iraq8529E3  with HA 131L, 160L, 194I, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8529M1 with HA 131L, 160L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Iraq8531     with HA 130E, 131L, 298V and syn419L (Kentucky19 and 225G Utah42)
• Australia Victoria2129 with potential H5N2 inclusions and NA 454S 
• Australia Victoria2130 with NA 454S
• Ukraine Kyiv377 with mixture of 225D, 225G, 225N, 225S, 225T and 225A
• Ukraine Lviv673
• Ukraine Lviv682
• Ukraine Cherkasy332
• Ukraine Cherkasy333
• Ukraine Cherkasy346
• Ukraine Chernihiv855L with mixture of wt 225D / 225G and additional 1918 Markers (syn238E & 324I), Fatal outcome 
• Ukraine Chernihiv856 with mixture of wt 225D / 225G , Fatal outcome 
• Ukraine Chernihiv857 with mixture of wt 225D / 225G and additional 1918 Markers (186P, syn238E, 324I & G796A), Fatal outcome 
• Ukraine Chernihiv858, Fatal outcome 
• Ukraine Dnipropetrovsk260
• Ukraine Dnipropetrovsk267
• Ukraine Dnipropetrovsk268
• Ukraine Dnipropetrovsk272
• Ukraine Dnipropetrovsk273 with mixture of wt 225D and 225G
• Ukraine Dnipropetrovsk274
• Ukraine Dnipropetrovsk1124
• Ukraine Dnipropetrovsk1171
• Ukraine LvivN2 with 225G
• Ukraine LvivN6 with 225G
• Ukraine TernopilN10 with 225G
• Ukraine TernopilN11 with 225G
• Ukraine Volin226 with 225G
• MoldovaG120
• MoldovaG140
• MoldovaG181
• MoldovaG182
• MoldovaG191
• HA and NA Norway2924 with mixture of wt 225D and 225G
• HA and NA Norway3364-2
• HA and NA Denmark AarhusINS82 with syn177L and 324I
• HA and NA Denmark CopenhagenINS95 with 69K, syn157K and 176I
• HA and NA Denmark CopenhagenINS98
• HA and NA Poland WarsawINS100 with 324I and 377K
• HA and NA Greece AthensINS85 with syn57C, syn233Y, 324I and 377K
• HA and NA CatNS7362 TamiFlu Resistant
• HA and NA CatS1096
• HA and NA CatS1162
• HA and NA CatS1179
• HA and NA CatS1181
• HA and NA CatS1267
• HA and NA CatS1268
• HA and NA CatS1402
• HA and NA CatS1501
• HA and NA CatS1687
• HA and NA CatS1748
• HA and NA CatS1751
• HA and NA CatS1761
• HA and NA CatS1827
• HA and NA CatS1935
• HA and NA CatS2120 with multiple swine markers
• HA and NA CatS2151 with swine markers and 165N (TamiFlu Resistant CatNS7632 and Russian 225G Salekhard01)
• HA and NA Guangdong02
• HA and NA Guangdong05
• HA and NA SingaporeON1156
• HA and NA India BloreNIV236 with 226R, syn372Q, 454N and 550T *
• HA and NA Sweden Stockholm31
• Sweden Malmoe1 from 2010 with 190Y, 324I and 377K *
• Sweden Gothenburg2 with 146G, 324I (1918) and markers found extensively in Moldova and Russia 
• HA and NA Russia4 with syn238E and 324I (1918)
• HA and NA Russia12 with 324I (1918)
• HA and NA Russia14
• HA and NA Russia19 with 324I (1918)
• HA and NA Russia74
• HA and NA Russia149
• HA and NA Russia165
• HA and NA Russia171 with 165N
• HA and NA Russia178
• HA and NA Russia180 with 165N, syn239P and 264G
• HA and NA Russia190
• HA and NA Russia191
• HA and NA Kurgan01 with HA 214E (MoldovaG168, G176, G188) and NA mixture at 407 (Fatal 225G Abakan02) 
• HA and NA Omsk02 
• HA and NA Tver2969 with 225G, Fatal outcome
• HA and NA Salekhard01 with 165N and 225G, presumptive Fatal outcome
• HA and NA Orenburg2974 with 225N, potential Fatal outcome
• HA and NA Perm01 with 131P, 225G and 324I, presumptive Fatal outcome
• HA and NA NY3702
• HA and NA NY3715
• HA and NA NY3828
• United States NewYork96
• HA and NA RhodeIsland08
• HA and NA Texas42102708
• HA and NA Texas45072128
• HA and NA Texas45122886
• United States Kentucky19 from an 18 year old subject with HA 298V
• United States Indiana20 from a 10M subject with 5 Avian H5N1 markers
• US Private Sequence TamiFlu Resistant  
• United States NorthCarolina37 from a 24F subject with HA 298V
• United States NorthCarolina44 from a 50M subject with 6 Avian H5N1 markers
• United States NorthCarolina46_C2     from a 39F subject with HA 298V
• United States NorthCarolina46_C2C1 from a 39F subject with HA 298V
• HA and NA swine/NC/34752 with 298V 

98 sequences have encircled the globe as of 2010-03-19 * with high fidelity carrying a cross-segment paired set of background markers matching and contributing to fatal cases in the Ukraine and Russia.  225G appears in 14 on this background; 225N once and 225E precisely zero.  The first occasion of 226R now enters our list retrospectively due to sequence release delay with a June 2009 case from India.

These 2 newest entries represent a very early case of ΣPF11 in an Indian individual who travelled extensively and a very recent case in Sweden from January 2010. All data guides us to the position that this pandemic reservoir is not approaching stasis. The background continues to widen within the existing clades demonstrating that ΣPF11 is far from reaching Omega status.

Areas covered include Texas (3), the Northeastern United States (5), Kentucky, Indiana, North Carolina (5), China (2), Singapore, India, Australia (2), the Ukraine (23), Moldova (5), Russia (18), Iraq (3), Denmark(3), Norway (2), Sweden (3), Poland, Greece and extensive penetration in Spain (17 sequences).

This particular cross linked background pattern may precurse 225G and mixtures of 225D / 225G.  The Orenburg2974 sequence from Russia carries 225N on this background.  Receptor Binding Site (RBS) changes at 225 are associated with fatality, 225G and 225N at a rate higher than 225E.

If LvivN6 is officially confirmed as a vaccine escape event, these cross-segment pairs may be surveilled as potential future effectors of vaccine efficacy failure.

Previous Study on this Topic:

• 2010-03-17 Cross-Linked Background Supporting Fatal 225G Cases Penetrates 3 New Countries: Poland, Denmark and Greece
• 2010-01-28 Ukraine - 100% of New Sequences with Required HA and NA on Cross-Linked Background; 225G on 6 of 11; 1918 Markers Coalesce
• 2010-01-19 Fatal Ukraine Cross Segment Linkage Extends in the US, Iraq and Australia (HA syn413K and NA syn407V)
• 2010-01-01 HA syn413K and NA syn407V Cross Segment Linkage Increases Range and Penetration
• 2009-12-04 Spain Introduces 2 November Sequences with Cross-Segment Pairing from Fatal Cases in the Ukraine
• 2009-11-28 Ukraine and Spain Cross-Linked HA and NA Silent Changes Circle the Globe
• 2009-11-26 The Ukraine, Norway and Spain Share Paired HA and NA Changes

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

SingaporeTLL10 HA demonstrates 3 H5N1 amino acids: 206T, 226R and 261V

A/Singapore/TLL10, sample 2009-07-27, is a first on the PF11 background.

SingTLL10 is the first on PF11 to carry 261V, though movement at that position has been documented in Italy51 and Italy53 with 261G and a downstream 263D entered PF11 with Tomsk01 and then continued with 3 Thai sequences (ThaiCU-H9, ThaiCU-B938, ThaiCU-H276).

261V is wild type for H5N1 including Anhui02 that carries all three of the amino acid changes mentioned here for SingTLL10:

• 206T
• 226R
• 261V

H5N1 Anhui02 is a potential donor for 296H that seems to track primarily to 206T bearing strains.

This expansion deeper into Southern Asia with 226R brings the number of sequences bearing the H5N1 match into double digits.  RBD changes matching H5N1 demand scrutiny.  For background, please read an earlier 226R Study.

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

United States (NorthEast) HA Diversity at 206; 296H Intra-Segment Exclusivity Continues

A pair of sequences each from Pennsylvania and Rhode Island deposited at GenBank on 2009-09-10 demonstrate continued Hemagglutinin diversity within single geographies and similar time frames.  Multiple PF11 sub-clades in the United States and worldwide show ongoing human fitness and co-existance ability producing a Hydra Effect.

• A/Pennsylvania/06 (PA06) demonstrates 206S and 296H
• A/Pennsylvania/14 (PA14) demonstrates 206T and 296Q,  218X

• A/Rhode Island/07 (RI07) demonstrates 206S and 296H
• A/Rhode Island/08 (RI08) demonstrates 206T and 296Q

• A/Massachusetts/10 (MA10) demonstrates 206S and 296H
• A/Indiana/17 (IN17) demonstrates 206S and 296H

As of this moment, the Intra-Segment Exclusivity between 296H and 206T continues on the PF11 background.  Pennsylvania, Rhode Island and Massachusetts have observed candidate donors of 206T; however, the genetic diversity of 206S with 296H remains in those states and with similar occassion in many international locales.

The highly correlative 2E is found in the 4 referenced 296H Hemagglutinins in this United States deposit.

PA06, RI07, MA10 and IN17 are an exact nucleotide match to A/Italy/127 from 2009-06-17, the only PF11 sequence in the world to carry the 256L on Neuraminidase (with 106I/248N). 

The rare 256L is originally found on the 1918 Brevig Mission sequence.  256L candidate donors include many H3N2 2008 Seasonal Influenza specimens and several H1N2 2008 swine from Oklahoma and Texas.

RI07 on Segment 6 (Neuraminidase) is an exact nucleotide match to a pivotal sequence that will be detailed later from Germany, A/Bayern/66.  The IN17 NA also tracks to RI07 and Bayern66 at 1409 of 1410 nucleotide positions.  Bayern66 is strongly related to the HA of the Russian and Northern European heralds of HA:226R, Omsk01, Ekaterinburg01 and Finland553 and to the HA of Tomsk01.

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

HA:237I Downstream from RBD in TaiwanT1821 and 4 Russian Specimens

A rare Isoleucine, 237I, occurs within ΣPF11 downstream from the Receptor Binding Domain in A/Taiwan/T1821 sampled 2009-05-30 and in 4 Russian sequences.  206T is shared in all five 237I sequences.

Three of the four Russian sequences are from Moscow and were sampled on 2009-05-26 in the same week as the Taiwan sequence.  The fourth is Irkutsk02 that also carries the RBD polymorphism 226R.

An intra-segment exclusivity exists between 206S and 237I at this time upon PF11 backgrounds.

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

Russian Sequences, Omsk01 & Ekaterinburg01, show 2nd unique Quadruple Cross-Segment Combination (QC2)

Two of the sequences released by Russia's Vector lab in the past 7 days demonstrate another unique Cross-Segment Quadruple Combination (QC2) very similar to the combination (QC1) recently noted in the discussion on the Vector released Kazakhstani entry, Almati01.

Please review the sequences from the two samples for validation of this finding.

• HA / NA : A/Omsk/01/2009
• HA / NA : A/Ekaterinburg/01/2009

This introduction on the PF11 background carries a quadruple set of amino acids crossing Hemagglutinin and Neuraminidase:

        QC2

• HA 206T
• HA 226R
• NA 106I
• NA 248N

Omsk01 also carries NA:127S matching a polymorphic position with TamiFlu resistant Washington28.  Ekaterinburg01 shows NA:259D that appears unique at this time within ΣPF11.  Initial studies indicated that reassortment is impeached as a mechanism for these genetic acquisitions.

The QC2 changes, of course, are not fixed in the geography, as other sequences from the areas demonstrate considerable variation.  Movement within and around the Receptor Binding Domain (RBD) continues to draw our focus.

A University of Wisconsin-Madison study in 2008 found that Glutamine (Q) at 226 mediates the Binding Affinity for SAα2,6Gal (Sialic Acid α2,6) and, in turn, lowers infectivity levels in primary epithelial cells for humans compared to Leucine at that position (226L).  I am not aware of conclusive studies comparing 226Q to 226R in this regard.  Please contact me if you have applicable studies.

226R on PF11 Background (9)

• Omsk01
• Irkutsk02
• Ekater01
• Finland553 with HA:206T and NA:106I
• Lishui01
• ZhejiangDTID-ZJU01
• Texas17
• MX4603
• MXInDRE4487

Mixed signals or absent data for residue 226 appear in 13 ΣPF11 sequences across the US and Mexico.

At any rate, ΣPF11 in Eurasia and the Americas is now varying away from a stable, low infectivity position in the Receptor Binding Domain to an amino acid found in H5N1 at 226 (A/Anhui/2/2005/H5N1).  And I remind you that Anhui2 carries 206T and 296H which we are seeing persistently emerge throughout the world including clustering in Italy and the Northeastern United States.

Scrutiny is required here.

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

China - Lishui01 PF11 Carries Human-Fit Seasonal Marker at 324

A/Lishui/01/2009 from July 2009 appears to be the first Chinese PF11 sample to carry the robust signal of 324I on HA, a human-fit polymorphism carried on Seasonal H1N1 2008 and 2009 backgrounds as well as 1918 specimens. 

The Lishui HA also shows the rare PF11 226R.  The recent ZhejiangDTID-ZJU01, Ekaterinburg01 and Finland553 carry this polymorphism that profiled early within ΣPF11 in one Texas and two Mexico samples.

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