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 spreadsheet for completeness in citation.
Last Update
2011-07-18
The Cantacuzino Insttitute of Bucharest, Romania released sequences from 50 HA Segments and 2 unmatched NA segments at GenBank and GISAID on 2011-05-19. The sample dates span 452 days from 2009-11-12 to 2011-02-07. All 52 segment sequences are fragments and show extensive variation, including several with high Zoonotic Potential scores. Template crossing is documented in this deposit.
Diverse geography is represented across this batch and an overall heavy zoonotic homology is found. Animal reservoirs are represented including H9N2, H7N7, H5N1, H3N8 and H3N2. With the Romanian HA polymorphisms, homology is found to H9N2 Human & Avian, to H7N7 Human, Avian and Equine, to H5N1 Emergent Human, to H3N8 Avian and to H3N2 Emergent Human from H3N2 Avian, Feline & Canine. This group of sequences may, in time, be found to demonstrate significant zoonotic genetic re-seeding from the animal reservoirs at the 5’ ends of the fragments as well as the 3’ ends.
Zoonotic Potential
At least two sequences in this deposit demonstrate a 100% Zoonotic Potential score. H5N1 homology is found on RomaniaConstanta330_2010_01_05, a 201 amino HA fragment from Winter 2010. All 5 polymorphisms (2 Amino and 2 Silent) on this pH1N1 Romanian sequence are found in the H5N1 reservoir on various samples and the combination appears novel to pH1N1 and novel to H5N1. The superset of changes on RomaniaCluj14972_2009_12_23 (205aa frag) may also be accommodated by the influence of zoonotic reservoirs.
Receptor Binding Site - HA aa225
HA aa225 polymorphisms are found in 6 instances, 225N (3) & 225G (3).
RomaniaConstanta50378_2011_01_21 (296aa frag) affixes HA 225N on an 188T (Clade 2) background with 100N and syn#8V, a position significant to the emergent Upsilon pH1N1 Sub-Clade (Clade 1: 189T). RomaniaCarasSeverin663_2010_01_07 (173aa frag) carries 225N with 100N. A singlet HA 225N appears on RomaniaPrahova2704_2010_01_18 (175aa frag) approximately one year earlier.
Another winter 2010 sequence, RomaniaSuceava406_2010_01_05 (196aa span), carries 225G with 2 zoonotic polymorphisms having homology to H3N2, H3N8, H7N7 Human and H9N2 Human. On RomaniaBuzau14584_2009_12_21 (196aa frag), 225G is found with syn181G, a homology to H5N1 Human, H5N1 Emergent Avian and H9N2 Avian. HA syn168Y, a regional pH1N1 marker from Russian and Ukrainian fatalities, appears 4 times, including a pairing with 225G on RomaniaPrahova564_2010_01_06 (172aa frag) and a pairing with 100N on RomaniaMaramures13812_2009_12_15 (198aa frag).
HA Template Jumping
In addition, clade-defining elements are observed appearing on different clade backgrounds, including RomaniaBihor51551_54F_2011_01_31 on a Clade 2 (188T Tau) background with the addition of 189T (Clade 1). A Clade 5 (208K, 219V) background in 2011, RomaniaArad50090_2011_01_20 (287aa frag), received 188T (Clade 2).
Nine HA segment sequences spanning 2009_11_12 to 2010_01_26 measure zero polymorphisms.
Sequences
SortKeys:
SequenceDate Desc,
SequenceID Asc,
SegmentID Asc
. . . . RomaniaNeamt51999_2011_02_07 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317512
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . syn34N (AAt),
. . . . . . . . 146G,
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa287)
. . . . RomaniaBucuresti52010_2011_02_04 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317528
. . . . . . . . 11 Polymorphisms (6 Amino and 5 Silent)
. . . . . . . . syn47L (CTg),
. . . . . . . . syn66G (GGg) [H5N1 wt, H6, H9N2],
. . . . . . . . syn82I (ATc),
. . . . . . . . syn93C (TGc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H5N1 Avian Domestic & Wild],
. . . . . . . . . . . . . . . . . [H9N2 Avian Emergent 2009],
. . . . . . . . 100N,
. . . . . . . . 141Q,
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBihor51551_54F_2011_01_31 (
. . . . . . . . Clade 2: 188T crossing with Clade 1: 189T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317529
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBrasov49666_2011_01_30 (
. . . . . . . . Clade 3: 186P
. . . . . . . . GISAID HA EPI317530
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . syn212K (AAa),
. . . . . . . . syn214K (AAa),
. . . . . . . . syn272D (GAc) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian Emergent 2010],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBucuresti50820_2011_01_30 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317532
. . . . . . . . 7 Polymorphisms (4 Amino and 3 Silent)
. . . . . . . . syn31H (CAt),
. . . . . . . . 73F,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn283Q (CAa),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaArad51247_2011_01_29 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317518
. . . . . . . . 10 Polymorphisms (5 Amino and 5 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn292S (AGt),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaArad51034_2011_01_29 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317531
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaSalaj51422_2011_01_28 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317505
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . 174R,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)
. . . . RomaniaCluj51505_2011_01_27 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317504
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaMures51180_2011_01_27 (
. . . . . . . . Clade 5: 208K, 219V
. . . . . . . . GISAID HA EPI317506
. . . . . . . . 9 Polymorphisms (4 Amino and 5 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . syn170N (AAc),
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . syn276H (CAt),
. . . . . . . . HA Truncated after aa295)
. . . . RomaniaBucuresti51194_2011_01_26 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317507
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn107Q (CAg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)
. . . . RomaniaPrahova50643_2011_01_26 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317510
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa287)
. . . . RomaniaBucuresti50823_2011_01_26 (
. . . . . . . . Clade 4: 128D
. . . . . . . . GISAID HA EPI317533
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . 107L,
. . . . . . . . 128D,
. . . . . . . . HA Truncated after aa295)
. . . . RomaniaCalarasi2225_2011_01_21 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317508
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn107Q (CAg),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . HA Truncated after aa295)
. . . . RomaniaConstanta50378_2011_01_21 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317525
. . . . . . . . 9 Polymorphisms (5 Amino and 4 Silent)
. . . . . . . . syn#8V (GTg),
. . . . . . . . syn32S (TCc),
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 210G,
. . . . . . . . 225N,
. . . . . . . . syn232Y (TAc),
. . . . . . . . syn277D (GAc),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaArad50090_2011_01_20 (
. . . . . . . . Clade 5: 208K, 219V crossing with Clade 2: 188T
. . . . . . . . GISAID HA EPI317509
. . . . . . . . 8 Polymorphisms (5 Amino and 3 Silent)
. . . . . . . . syn36L (tTA),
. . . . . . . . syn47L (CTg),
. . . . . . . . 100N,
. . . . . . . . syn102E (GAa) [H1N1 Avian
. . . . . . . . . . . . . . . . . . . . . . with extensive pH1N1υ polymorphisms],
. . . . . . . . . . . . . . . . . . . [H5N1 wt],
. . . . . . . . . . . . . . . . . . . [H9N2 Early Human wt, Human 2008],
. . . . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . . . . . . . . . . . . [H10N7 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . with 87N, 100N, syn102E,
. . . . . . . . . . . . . . . . . . . . . . . . 156E, 157E, 163T, 165N,
. . . . . . . . . . . . . . . . . . . . . . . . syn177L, 188T, syn221P, syn207S, syn213F,
. . . . . . . . . . . . . . . . . . . . . . . . 225G, 230I, 233H, 237I, syn239P,
. . . . . . . . . . . . . . . . . . . . . . . . syn338G, syn346G, syn356H,
. . . . . . . . . . . . . . . . . . . . . . . . syn390N, syn391T],
. . . . . . . . 188T,
. . . . . . . . 208K,
. . . . . . . . 219V,
. . . . . . . . 252L,
. . . . . . . . HA Truncated after aa287)
. . . . RomaniaTimis49900_2011_01_19 (
. . . . . . . . GISAID HA EPI317501
. . . . . . . . 3 Polymorphisms (1 Amino and 2 Silent)
. . . . . . . . syn60I (ATc),
. . . . . . . . syn273T (ACg),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaMaramures49545_2011_01_15 (
. . . . . . . . Clade 2: 188T
. . . . . . . . GISAID HA EPI317502
. . . . . . . . 3 Polymorphisms (3 Amino and 0 Silent)
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaIasi48801_2011_01_11 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317511
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 38G,
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . syn292S (AGt),
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBucuresti48333_2011_01_09 (
. . . . . . . . Clade 2: 188T
. . . . . . . . Sub-Clade Tau: 100N, syn179L, 188T,
. . . . . . . . . . . . . . . . Tau Imputed: syn338G, syn448L, 454N
. . . . . . . . GISAID HA EPI317503
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBihor48551_2011_01_09 (
. . . . . . . . GISAID NA EPI317527
. . . . . . . . 5 Polymorphisms (1 Amino and 4 Silent)
. . . . . . . . NA Truncated before aa253,
. . . . . . . . syn307N (AAt),
. . . . . . . . syn312Y (TAc),
. . . . . . . . 369K,
. . . . . . . . syn377P (CCa),
. . . . . . . . syn416D (GAc),
. . . . . . . . NA Truncated after aa435)
. . . . RomaniaIasi47959_2010_12_31 (
. . . . . . . . GISAID NA EPI317526
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . NA Truncated before aa253,
. . . . . . . . syn330D (GAc),
. . . . . . . . 386S,
. . . . . . . . NA Truncated after aa435)
. . . . RomaniaPrahova3261_2010_01_26 (
. . . . . . . . GISAID HA EPI317487
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaIasi2807_2010_01_19 (
. . . . . . . . GISAID HA EPI317486
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn279N (AAc),
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaPrahova2704_2010_01_18 (
. . . . . . . . GISAID HA EPI317485
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . 225N,
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaNeamt2058_2010_01_13 (
. . . . . . . . GISAID HA EPI317484
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn140P (CCc),
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaCarasSeverin663_2010_01_07 (
. . . . . . . . GISAID HA EPI317491
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . 100N,
. . . . . . . . 225N,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa273)
. . . . RomaniaBistritaNasaud677_2010_01_07 (
. . . . . . . . GISAID HA EPI317492
. . . . . . . . 4 Polymorphisms (1 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa93,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 100N,
. . . . . . . . syn220R (AGg) [H1N1 Avian with extensive pH1N1 polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human],
. . . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . . . . . . . . . . . [WSN_1933],
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa273)
. . . . RomaniaIlfov481_2010_01_06 (
. . . . . . . . GISAID HA EPI317488
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa137,
. . . . . . . . syn167S (TCt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)
. . . . RomaniaPrahova564_2010_01_06 (
. . . . . . . . GISAID HA EPI317489
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . syn168Y (TAt),
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa272)
. . . . RomaniaGalati591_2010_01_06 (
. . . . . . . . GISAID HA EPI317490
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa110,
. . . . . . . . HA Truncated after aa276)
. . . . RomaniaConstanta330_2010_01_05 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI317480
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa92,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 127S [H5N1 Egypt wt],
. . . . . . . . 166E [H5N1 Egypt Emergent Human 2010],
. . . . . . . . syn181G (GGa) [H5N1 Egypt Human 2007, 2009],
. . . . . . . . . . . . . . . . . . . . . . [H5N1 Avian Emergent 2010],
. . . . . . . . . . . . . . . . . . . . . . [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . . with 39E, syn42G, 296R mix wt],
. . . . . . . . syn258F (TTt) [pH1N1 rare GISAID (under 30)],
. . . . . . . . . . . . . . . . . . [pH1N1 GISAID Low Homology to this Sequence],
. . . . . . . . . . . . . . . . . . [pH1N1 GISAID 4 with VxX Markers],
. . . . . . . . . . . . . . . . . . [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Human 2009 (Tat)],
. . . . . . . . HA Truncated after aa293)
. . . . RomaniaSuceava406_2010_01_05 (
. . . . . . . . GISAID HA EPI317481
. . . . . . . . 4 Polymorphisms (3 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa101,
. . . . . . . . 225G,
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)
. . . . RomaniaBotosani169_2010_01_03 (
. . . . . . . . GISAID HA EPI317479
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . 93F,
. . . . . . . . syn95P (CCc) [H1N1 Avian wt],
. . . . . . . . . . . . . . . . . [H3N2 Human and Avian wt (agc)],
. . . . . . . . . . . . . . . . . [H9N2 Early Human],
. . . . . . . . . . . . . . . . . [H9N2 Avian wt],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 99L,
. . . . . . . . 100V,
. . . . . . . . HA Truncated after aa289)
. . . . RomaniaOlt114_2010_01_02 (
. . . . . . . . GISAID HA EPI317465
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaOlt119_2010_01_02 (
. . . . . . . . GISAID HA EPI317466
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaBotosani15520_2009_12_30 (
. . . . . . . . GISAID HA EPI317476
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaCluj15569_2009_12_30 (
. . . . . . . . GISAID HA EPI317477
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . 100N,
. . . . . . . . 111L [H3N2 Human and Avian wt (cTa)],
. . . . . . . . . . . . . [H9N2 Avian Emergent with pH1N1 polymorphisms (tct)],
. . . . . . . . syn251L (tTA),
. . . . . . . . syn270I (ATc),
. . . . . . . . HA Truncated after aa280)
. . . . RomaniaBraila15575_2009_12_30 (
. . . . . . . . GISAID HA EPI317478
. . . . . . . . 5 Polymorphisms (2 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa97,
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn135V (GTg),
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBotosani15033_2009_12_26 (
. . . . . . . . GISAID HA EPI317474
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa100,
. . . . . . . . HA Truncated after aa291)
. . . . RomaniaDambovita15050_2009_12_26 (
. . . . . . . . GISAID HA EPI317475
. . . . . . . . 2 Polymorphisms (1 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . HA Truncated after aa288)
. . . . RomaniaCluj14972_2009_12_23 (
. . . . . . . . Zoonotic Potential: 100%
. . . . . . . . GISAID HA EPI317473
. . . . . . . . 6 Polymorphisms (3 Amino and 3 Silent)
. . . . . . . . HA Truncated before aa91,
. . . . . . . . 91S [H3N2 Asia Avian],
. . . . . . . . . . . [H3N2 Human wt (aGc)],
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn272D (GAc) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . . [H3N2 Avian],
. . . . . . . . . . . . . . . . . . [H5N1 Egypt Avian Emergent 2010],
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaIasi14805_2009_12_22 (
. . . . . . . . GISAID HA EPI317471
. . . . . . . . 1 Polymorphisms (0 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa96,
. . . . . . . . syn96G (GGg) [H1N1 Avian with pH1N1 Upsilon polymorphisms],
. . . . . . . . . . . . . . . . . [H5N1 Human and Avian wt],
. . . . . . . . . . . . . . . . . [H9N2 Human and Avian wt],
. . . . . . . . HA Truncated after aa291)
. . . . RomaniaIlfov14852_2009_12_22 (
. . . . . . . . GISAID HA EPI317472
. . . . . . . . 4 Polymorphisms (2 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa98,
. . . . . . . . 99M (ATg) [H1N1 Avian with pH1N1 polymorphisms],
. . . . . . . . . . . . . . . [H9N2 Human 2000],
. . . . . . . . . . . . . . . [H9N2 Asia and Europe Avian (gag)],
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . HA Truncated after aa296)
. . . . RomaniaBuzau14584_2009_12_21 (
. . . . . . . . GISAID HA EPI317470
. . . . . . . . 3 Polymorphisms (2 Amino and 1 Silent)
. . . . . . . . HA Truncated before aa97,
. . . . . . . . syn181G (GGa) [H5N1 Egypt Human 2007, 2009],
. . . . . . . . . . . . . . . . . . . . . . [H5N1 Avian Emergent 2010],
. . . . . . . . . . . . . . . . . . . . . . [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . . . . . with 39E, syn42G, 296R mix wt],
. . . . . . . . 182V,
. . . . . . . . 225G,
. . . . . . . . HA Truncated after aa293)
. . . . RomaniaMures14446_2009_12_20 (
. . . . . . . . GISAID HA EPI317469
. . . . . . . . 1 Polymorphisms (1 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa124,
. . . . . . . . 255K,
. . . . . . . . HA Truncated after aa268)
. . . . RomaniaMaramures13812_2009_12_15 (
. . . . . . . . GISAID HA EPI317468
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . HA Truncated before aa99,
. . . . . . . . 99R,
. . . . . . . . 100N,
. . . . . . . . syn168Y (TAt),
. . . . . . . . syn294P (CCc) [H3N2 Human emergent 2010 dropping 295F (TTc)],
. . . . . . . . . . . . . . . . . . [H3N2 Avian, Canine & Feline],
. . . . . . . . . . . . . . . . . . [H3N8 Avian wt],
. . . . . . . . . . . . . . . . . . [H7N7 Human, Avian and Equine wt],
. . . . . . . . . . . . . . . . . . [H9N2 Human 2009 with Upsilon polymorphisms],
. . . . . . . . 296R (Cgc) [H9N2 Avian 2008
. . . . . . . . . . . . . . . . . . . . with 39E, syn42G, syn181G, 296R mix wt],
. . . . . . . . 297S,
. . . . . . . . HA Truncated after aa297)
. . . . RomaniaHarghita12170_2009_12_08 (
. . . . . . . . GISAID HA EPI317467
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa114,
. . . . . . . . HA Truncated after aa273)
. . . . RomaniaIasi11140_2009_12_02 (
. . . . . . . . GISAID HA EPI317464
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa107,
. . . . . . . . HA Truncated after aa246)
. . . . RomaniaBotosani10121_2009_11_26 (
. . . . . . . . GISAID HA EPI317463
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa135,
. . . . . . . . HA Truncated after aa281)
. . . . RomaniaIasi9422_2009_11_22 (
. . . . . . . . GISAID HA EPI317483
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa105,
. . . . . . . . HA Truncated after aa272)
. . . . RomaniaBotosani8204_2009_11_12 (
. . . . . . . . GISAID HA EPI317482
. . . . . . . . 0 Polymorphisms (0 Amino and 0 Silent)
. . . . . . . . HA Truncated before aa107,
. . . . . . . . HA Truncated after aa280)
Showing posts with label Romania. Show all posts
Showing posts with label Romania. Show all posts
2011-06-07
HA 189T Upsilon in Czech Republic Recombines with 188T Tau SubClade
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 spreadsheet for completeness in citation.
Last Updated
2011-06-09
On 2011-06-06, the National Institute of Medical Research of the UK published 56 pH1N1 sequences at GISAID sampled in a time period spanning late 2010 to early 2011 with the geographic majority from Europe. A subclade bearing HA 189T that is 230I-permissive gains 3 members with this deposit, but more importantly the level of polymorphic subclade jumping has accelerated as previously discussed. The 3' end of a well-defined 188T-bearing subclade from fatal and severe cases in the UK has recombined onto the rare Upsilon subclade (53 sequences, 5.8% CFR).
The 3 additions to pH1N1υ are detailed, with the recombinant CzechRepublic32_xM_2011_01_18 shown first. Though 189T has been found upon 188T backgrounds in several pandemic geographies, this 189T Czech sequence marks the first fully defined, contiguous range, triple polymorphism recombination of 188T background markers onto the 189T Upsilon subclade.
Trailing the polymorphism lists of the 3 Upsilon additions, we also detail two of the several instances of the single polymorphism HA 189T arriving on a 188T background.
A deposit made 2011-06-05 at GenBank from Fondazione IRCCS Policlinico San Matteo in Pavia, Italy demonstrates another particular instance of subclade elasticity. A similar crossing of the Czech pH1N1 Tau and Upsilon subclades is found in reverse on a Palermo HA segment sampled via a deep lung wash from a patient suffering Acute Respiratory Distress Syndrome (ARDS). This 188T Tau subclade sequence, ItalyPalermo02_2011_01_31_severe, takes an 189T from Upsilon and then adds a 208K from an emerging tertiary subclade, resulting in a single 225G-bearing Italian HA segment holding data from three dominant subclades.
These developments suggest the merit of sampling and directly sequencing a wider variety of sources and tissue types. The investigators from Pavia have now established a working benchmark for accurately surfacing the actual causative strain sequences from severely ill patients.
On 2011-05-19, the Cantacuzino Institute of Bucharest, Romania deposited 52 sequences at GenBank, representing partial segments (several with potential 3' end recombination from non-pH1N1 primer-matching strains). A similar adoption of HA 189T onto a known circulating 188T background occurred on RomaniaBihor51551_54F_2011_01_31 with the unusual HA 296R unique to this Romanian deposit and a single 2009 Malaysian HA. Recall that the polymorphism HA 296H was correlated to numerous fatalities during the early pandemic in Brasil.
Co-location of these transferable components within zoonotic reservoirs provides ample opportunity for exchange. Expectations should be reset for future pH1N1 antigenic variation as these three dominant subclades continue to demonstrate active cooperation in developing viable Vaccine Escape polymorphisms and then sharing them when perfected.
Upsilon
. . . . CzechRepublic32_xM_2011_01_18 (
. . . . . . . . GISAID HA EPI319447
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 218T [Texas03_M1C2_38M_2010_06_01],
. . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . AlgeriaG388_1F_2010_12_21 (
. . . . . . . . GISAID HA EPI319430
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn118E (GAa),
. . . . . . . . syn158G (GGg),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc))
. . . . Estonia55236_30M_2011_03_02 (
. . . . . . . . GISAID HA EPI319464
. . . . . . . . 13 Polymorphisms (5 Amino and 8 Silent)
. . . . . . . . 34D,
. . . . . . . . 42W,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc),
. . . . . . . . syn469E (GAg))
Italy
. . . . ItalyPalermo02_2011_01_31_severe (
. . . . . . . . GenBank HA JN017179
. . . . . . . . BronchoAlveolar Lavage
. . . . . . . . 12 Polymorphisms (7 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . syn116R (AGa),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . 208K,
. . . . . . . . 225G,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn428L (tTG),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
Romania
. . . . RomaniaBihor51551_54F_2011_01_31 (
. . . . . . . . GenBank HA CY090796
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 296R [GISAID Rare 11 – Romania (10) & 2009 Malaysia],
. . . . . . . . HA Truncated after aa296)
Last Updated
2011-06-09
On 2011-06-06, the National Institute of Medical Research of the UK published 56 pH1N1 sequences at GISAID sampled in a time period spanning late 2010 to early 2011 with the geographic majority from Europe. A subclade bearing HA 189T that is 230I-permissive gains 3 members with this deposit, but more importantly the level of polymorphic subclade jumping has accelerated as previously discussed. The 3' end of a well-defined 188T-bearing subclade from fatal and severe cases in the UK has recombined onto the rare Upsilon subclade (53 sequences, 5.8% CFR).
The 3 additions to pH1N1υ are detailed, with the recombinant CzechRepublic32_xM_2011_01_18 shown first. Though 189T has been found upon 188T backgrounds in several pandemic geographies, this 189T Czech sequence marks the first fully defined, contiguous range, triple polymorphism recombination of 188T background markers onto the 189T Upsilon subclade.
Trailing the polymorphism lists of the 3 Upsilon additions, we also detail two of the several instances of the single polymorphism HA 189T arriving on a 188T background.
A deposit made 2011-06-05 at GenBank from Fondazione IRCCS Policlinico San Matteo in Pavia, Italy demonstrates another particular instance of subclade elasticity. A similar crossing of the Czech pH1N1 Tau and Upsilon subclades is found in reverse on a Palermo HA segment sampled via a deep lung wash from a patient suffering Acute Respiratory Distress Syndrome (ARDS). This 188T Tau subclade sequence, ItalyPalermo02_2011_01_31_severe, takes an 189T from Upsilon and then adds a 208K from an emerging tertiary subclade, resulting in a single 225G-bearing Italian HA segment holding data from three dominant subclades.
These developments suggest the merit of sampling and directly sequencing a wider variety of sources and tissue types. The investigators from Pavia have now established a working benchmark for accurately surfacing the actual causative strain sequences from severely ill patients.
On 2011-05-19, the Cantacuzino Institute of Bucharest, Romania deposited 52 sequences at GenBank, representing partial segments (several with potential 3' end recombination from non-pH1N1 primer-matching strains). A similar adoption of HA 189T onto a known circulating 188T background occurred on RomaniaBihor51551_54F_2011_01_31 with the unusual HA 296R unique to this Romanian deposit and a single 2009 Malaysian HA. Recall that the polymorphism HA 296H was correlated to numerous fatalities during the early pandemic in Brasil.
Co-location of these transferable components within zoonotic reservoirs provides ample opportunity for exchange. Expectations should be reset for future pH1N1 antigenic variation as these three dominant subclades continue to demonstrate active cooperation in developing viable Vaccine Escape polymorphisms and then sharing them when perfected.
Upsilon
. . . . CzechRepublic32_xM_2011_01_18 (
. . . . . . . . GISAID HA EPI319447
. . . . . . . . 13 Polymorphisms (6 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 218T [Texas03_M1C2_38M_2010_06_01],
. . . . . . . . . . . . . [H5N1 Egypt Human 2009],
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . 377K,
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
. . . . AlgeriaG388_1F_2010_12_21 (
. . . . . . . . GISAID HA EPI319430
. . . . . . . . 11 Polymorphisms (4 Amino and 7 Silent)
. . . . . . . . 34D,
. . . . . . . . syn118E (GAa),
. . . . . . . . syn158G (GGg),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc))
. . . . Estonia55236_30M_2011_03_02 (
. . . . . . . . GISAID HA EPI319464
. . . . . . . . 13 Polymorphisms (5 Amino and 8 Silent)
. . . . . . . . 34D,
. . . . . . . . 42W,
. . . . . . . . syn87S (AGc),
. . . . . . . . syn118E (GAa),
. . . . . . . . 165N,
. . . . . . . . 189T,
. . . . . . . . syn213F (TTt),
. . . . . . . . 275I,
. . . . . . . . syn287G (GGg),
. . . . . . . . syn305K (AAg),
. . . . . . . . syn346G (GGa),
. . . . . . . . syn397G (GGc),
. . . . . . . . syn469E (GAg))
Italy
. . . . ItalyPalermo02_2011_01_31_severe (
. . . . . . . . GenBank HA JN017179
. . . . . . . . BronchoAlveolar Lavage
. . . . . . . . 12 Polymorphisms (7 Amino and 5 Silent)
. . . . . . . . 100N,
. . . . . . . . syn116R (AGa),
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . 208K,
. . . . . . . . 225G,
. . . . . . . . syn338G (GGc),
. . . . . . . . 377K,
. . . . . . . . syn428L (tTG),
. . . . . . . . syn448L (TTg),
. . . . . . . . 454N)
Romania
. . . . RomaniaBihor51551_54F_2011_01_31 (
. . . . . . . . GenBank HA CY090796
. . . . . . . . 6 Polymorphisms (4 Amino and 2 Silent)
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg),
. . . . . . . . 188T,
. . . . . . . . 189T,
. . . . . . . . syn215P (CCa),
. . . . . . . . 296R [GISAID Rare 11 – Romania (10) & 2009 Malaysia],
. . . . . . . . HA Truncated after aa296)
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