Last Updated 2011-01-16
The WHO Chinese National Influenza Center in Beijing deposited a full set of gene segment sequences on 2011-01-14 from a 3M sample taken in Jiangsu Province during the first week of the year. The Hong Kong Ministry of Health issued a notification that the boy was on long-term steroid treatment for chronic kidney disease.
Preliminary review shows that ChinaJiangsu1_3M_2011_01_04 carries a novel Hemagglutinin most closely related to late decade swine from Asia. The captivating factor is that this swine-like HA also demonstrates homology at least 25 recent genetic acquisitions into the human pH1N1 reservoir related to the UK Severe Wave and associated sequences on the highly divergent and hyper-zoonotic emerging sub-clades.
GeneWurx has prepared a spreadsheet for collaboration detailing the preliminarily recognised pH1N1 homologies to this most recent sequence in the database, ChinaJiangsu1_3M_2011_01_04. Several additional matches are not yet vetted for the spreadsheet, including syn338G, syn343G, syn346G, syn353G and syn363G. Each must be investigated as variant silent codings to changes in pH1N1 at the same amino acid position.
GeneWurx_Novel_HA_Jiangsu1_3M_2011_01_04_v0.xls
Showing posts with label China. Show all posts
Showing posts with label China. Show all posts
2010-12-15
HA 225G with 158E Series in Jiangsu China
Last Updated 2010-12-15
The Jiangsu Provincial Center for Disease Prevention and Control released a small set of sequences at GenBank on 2010-12-06 from the late 2009 pH1N1 reservoir. These sequences are related to several of the most recent and most concerning Chinese sequences on file that also came from Jiangsu. In an unusual presentation, the early sequences appear to be more elaborate genetically than the later group. Are we seeing the PF11 reservoir select the most useful revisions to continue attacking humans while dropping extraneous or sub-optimal genetic material?
Recall that the Ukraine produced an early Vaccine Escape strain, UkrLvivN6_26M_2009_10_27_xL_VxX_f, that carried only one amino acid change, 225G, and one silent change, syn413K. A variant passage of that same UkrLvivN6 patient created a sequence, UkrLvivN6_2009_10_27_C3C1_xL_f, with an additional amino acid change producing the following polymorphisms.
UkrLvivN6_2009_10_27_C3C1_xL_f
The Chinese sequences discussed today have a limited set of metadata, and are perhaps more highly correlated than they appear. A slight possibility for duplicate submission exists. Six geographically-sited sequences with this type of combination is a set worthy of investigation. Although some potential exists for errors in the names and dates of these Chinese sequences, the data at hand suggests that a sub-clade may be emerging in the Jiangsu region with five polymorphisms traveling together in a group that boasts rarity and Vaccine Escape documentation.
Jiangsu province is on the east coast of China and boasts the highest population density of any province in the country. Water covers 18% of the province with another 68% as low-lying plains. Jiangsu is also known as the “land of water” due to a thousand kilometer coast line with the Yellow Sea, the Yangtze River passing through the south, an extensive irrigation system and the canals found throughout several of the cities. Nanjing, the capital, is situated within the Yangtze River Delta. [Jiangsu, Nanjing]
With this deposit, polymorphisms at amino acid position 454 may now be correlated with RBD changes. An affinity exists in the aa223 to aa226 range and with HA 188T. These Chinese sequences carry the 158E revision that is useful for infecting the human upper respiratory tract and the 225G that is equally as useful in deep lung infection.
The recent 230I bearing sequence from Russia also demonstrates that 158E and 225G combination. A more current sequence from Australia, OzBrisbane209_51F_2010_08_09, shows a tendency toward this framing via domaining with 156E and matching the 225G while also carrying the H7N7 viral conjunctivitis-correlated polymorphism of HA 188T. Perhaps the SNP coding for the Southern Hemisphere 156E will be discovered in the animal reservoir of H7N7 or H9N2, paralleling the potential donor pools for 188T and 454N onto the human pandemic.
Declaration of Pandemic conclusion via press release has not effectively prevented emergent behaviour in this zoonoticly-active disease reservoir. Influenza Flux is apparently ongoing as the world remains in a pre-PF11Ω phase.
An enterprising question might be, “How many Hydra strains of Vaccine Escape capacity will co-circulate in this Northern Hemisphere winter?”
. . . . ChinaJiangsuNanjing1_2010_06_30 (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuNanjing2_2010_06_30 (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsu1_2009_11_20_re (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsu2_2009_11_13_re (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuS61_2009_11_10 (
. . . . . . . . 54R,
. . . . . . . . 84G [Unique to GenBank PF11],
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 211R [swOR4060_2009_12_31],
. . . . . . . . 225G,
. . . . . . . . syn319T [MississippiAF2473_2010_03_04 with 60T, 225E,
. . . . . . . . . . . . . . . FloridaAF2199_2010_03_11 with 60T, 225E,
. . . . . . . . . . . . . . . YaroslavlIIV196_2009_12_04_f with 225G
. . . . . . . . . . . . . . . SpainCatS1236_2009_08_13 with 225E,
. . . . . . . . . . . . . . . Finland612_2009_07_21 with 225E,
. . . . . . . . . . . . . . . KazAstana818_2009_07,
. . . . . . . . . . . . . . . KazAlmati01_2009 with 225E],
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuS62_2009_11_10 (
. . . . . . . . 60T [MississippiAF2473_2010_03_04 with 225E, syn319T,
. . . . . . . . . . . FloridaAF2199_2010_03_11 with 225E, syn319T],
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 481G,
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
Supporting Sequences
. . . . RussiaBelgorod2_2010_03_15 (
. . . . . . . . syn13N [WiscD0459_2009_12_18_xL
. . . . . . . . . . . . . . . . . . with 189T, 324I & 499K,
. . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . with syn338G],
. . . . . . . . 77N [tn, swine, S5]
. . . . . . . . . . . [JapanOsaka60_2010_07_02
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . Maryland04_2010_02_08
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . ShandongShizhongSWL24_2010_01_24,
. . . . . . . . . . . NY7020_2009_12_14
. . . . . . . . . . . . . . . . with syn166K & 189T,
. . . . . . . . . . . CalifVRDL115_2009_12_04
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . JapanAF2267_2009_11_09
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . NevadaAF2490_2009_11_02
. . . . . . . . . . . . . . . . with 100N & syn270I,
. . . . . . . . . . . AlaskaAF2093_2009_11_02
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . Russia74_2009_11_01_xL,
. . . . . . . . . . . ThailandTHB0441_2009_07_28,
. . . . . . . . . . . Lisboa40_2009_06_23,
. . . . . . . . . . . AnhuiSWL1_2009_06_18
. . . . . . . . . . . . . . . . with 275I,
. . . . . . . . . . . Lithuania1942_2009,
. . . . . . . . . . . swKoreaSCJ10_2009_12,
. . . . . . . . . . . swKoreaSCJ09_2009_12]
. . . . . . . . 158E mix,
. . . . . . . . 225G (Gga) stepwise from 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . [PNG_Goroka17_2010_04_14,
. . . . . . . . . . . . AthensINS398_2010_01_24,
. . . . . . . . . . . . AthensINS339_2009_12_30,
. . . . . . . . . . . . Kaliningrad01_11M_2009_11_02
. . . . . . . . . . . . . . . . . . with 225E & 226R,
. . . . . . . . . . . . KaliningradCRIE_DA_2009_09_26,
. . . . . . . . . . . . KaliningradCRIE_KG_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_SHD_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_MA_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_ZD_2009_09_25],
. . . . . . . . syn245F [H2N3, H5N1, H7N7, H10N7, H11]
. . . . . . . . . . . . . . [SingON2416_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with syn166K & 300P,
. . . . . . . . . . . . . . . EgyptAswan2288_2009_11_02
. . . . . . . . . . . . . . . . . . . . . with 189T],
. . . . . . . . 300S [H7N3, H7N7 (tCt)],
. . . . . . . . 305N (AAc) [ThaiChiangRai226_2M_2010_03_04
. . . . . . . . . . . . . . . . . . . . . . . with 270T,
. . . . . . . . . . . . . . . . . . Brunei5_52M_2010,
. . . . . . . . . . . . . . . . . . SouthCarolinaAF2562_2009_11_15 (AAt),
. . . . . . . . . . . . . . . . . . DenmarkAalborgINS133_2009_12_02 (AAt)],
. . . . . . . . syn343G [H3N8, H5N1, H6N1, H7N3, H7N7, H10N7, H11, 1918],
. . . . . . . . . . . . . . . [Thuringen189_2009_11_24_xL,
. . . . . . . . . . . . . . . Thuringen227_11_17_xL])
. . . . Brisbane209_51F_2010_08_09 (
. . . . . . . . 156E,
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 225G,
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [Victoria670_30M_2010_11_14
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . Emergent across Australia
. . . . . . . . . . . . . . . . . . . . . during late 2010 season,
. . . . . . . . . . . . . . . Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . OZVictoria512_2010_07_30
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . NZChristchurch15_2010_07_12
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . India5107_2010_06_28
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . MississippiAF2474_2010_03_10
. . . . . . . . . . . . . . . . . . . . . with syn235T,
. . . . . . . . . . . . . . . FloridaAF2197_2010_03_07
. . . . . . . . . . . . . . . . . . . . . with 156T,
. . . . . . . . . . . . . . . CalifVRDL9_2010_02_09
. . . . . . . . . . . . . . . . . . . . . with syn193S,
. . . . . . . . . . . . . . . Georgia06_2010_02_05
. . . . . . . . . . . . . . . . . . . . . with syn161Y,
. . . . . . . . . . . . . . . NY4662_2010_02_03
. . . . . . . . . . . . . . . . . . . . . with 97N, syn276H, syn283Q, syn304G,
. . . . . . . . . . . . . . . TexasJMS406_2010_01_10
. . . . . . . . . . . . . . . . . . . . . with 187A, syn193S, syn283Q,
. . . . . . . . . . . . . . . TexasJMS405_2010_01_09
. . . . . . . . . . . . . . . . . . . . . with 187A, syn283Q,
. . . . . . . . . . . . . . . CalifVRDL131_2009_12_30
. . . . . . . . . . . . . . . . . . . . . with 225G, syn455Q,
. . . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . . . . with syn13N,
. . . . . . . . . . . . . . . Vienna291_2009_11_19
. . . . . . . . . . . . . . . catOregon29573_2009_11_09
. . . . . . . . . . . . . . . . . . . . . with 226R, syn283Q,
. . . . . . . . . . . . . . . Calif_SanDiegoINS63_2009_10_26
. . . . . . . . . . . . . . . . . . . . . with syn283Q, et al],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2],
. . . . . . . . . . [Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . FL_Pen210_2009_11_10
. . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . SouthCarolina18_2009_09_16_VxX
. . . . . . . . . . . . . . . . . . with 159D, 224K,
. . . . . . . . . . Texas45131774_2009_09_13
. . . . . . . . . . . . . . . . . . with syn223V,
. . . . . . . . . . IndiaPune9355_2009_08
. . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . IndiaBlore236_2009_06_xL
. . . . . . . . . . . . . . . . . . with 226R, et al],
. . . . . . . . syn465N)
The Jiangsu Provincial Center for Disease Prevention and Control released a small set of sequences at GenBank on 2010-12-06 from the late 2009 pH1N1 reservoir. These sequences are related to several of the most recent and most concerning Chinese sequences on file that also came from Jiangsu. In an unusual presentation, the early sequences appear to be more elaborate genetically than the later group. Are we seeing the PF11 reservoir select the most useful revisions to continue attacking humans while dropping extraneous or sub-optimal genetic material?
Recall that the Ukraine produced an early Vaccine Escape strain, UkrLvivN6_26M_2009_10_27_xL_VxX_f, that carried only one amino acid change, 225G, and one silent change, syn413K. A variant passage of that same UkrLvivN6 patient created a sequence, UkrLvivN6_2009_10_27_C3C1_xL_f, with an additional amino acid change producing the following polymorphisms.
UkrLvivN6_2009_10_27_C3C1_xL_f
- 158E
- 225G
- syn413K (AAg) - synonymous cross-linkage (xL) marker
The Chinese sequences discussed today have a limited set of metadata, and are perhaps more highly correlated than they appear. A slight possibility for duplicate submission exists. Six geographically-sited sequences with this type of combination is a set worthy of investigation. Although some potential exists for errors in the names and dates of these Chinese sequences, the data at hand suggests that a sub-clade may be emerging in the Jiangsu region with five polymorphisms traveling together in a group that boasts rarity and Vaccine Escape documentation.
Jiangsu province is on the east coast of China and boasts the highest population density of any province in the country. Water covers 18% of the province with another 68% as low-lying plains. Jiangsu is also known as the “land of water” due to a thousand kilometer coast line with the Yellow Sea, the Yangtze River passing through the south, an extensive irrigation system and the canals found throughout several of the cities. Nanjing, the capital, is situated within the Yangtze River Delta. [Jiangsu, Nanjing]
With this deposit, polymorphisms at amino acid position 454 may now be correlated with RBD changes. An affinity exists in the aa223 to aa226 range and with HA 188T. These Chinese sequences carry the 158E revision that is useful for infecting the human upper respiratory tract and the 225G that is equally as useful in deep lung infection.
The recent 230I bearing sequence from Russia also demonstrates that 158E and 225G combination. A more current sequence from Australia, OzBrisbane209_51F_2010_08_09, shows a tendency toward this framing via domaining with 156E and matching the 225G while also carrying the H7N7 viral conjunctivitis-correlated polymorphism of HA 188T. Perhaps the SNP coding for the Southern Hemisphere 156E will be discovered in the animal reservoir of H7N7 or H9N2, paralleling the potential donor pools for 188T and 454N onto the human pandemic.
Declaration of Pandemic conclusion via press release has not effectively prevented emergent behaviour in this zoonoticly-active disease reservoir. Influenza Flux is apparently ongoing as the world remains in a pre-PF11Ω phase.
An enterprising question might be, “How many Hydra strains of Vaccine Escape capacity will co-circulate in this Northern Hemisphere winter?”
. . . . ChinaJiangsuNanjing1_2010_06_30 (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuNanjing2_2010_06_30 (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsu1_2009_11_20_re (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsu2_2009_11_13_re (
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuS61_2009_11_10 (
. . . . . . . . 54R,
. . . . . . . . 84G [Unique to GenBank PF11],
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 211R [swOR4060_2009_12_31],
. . . . . . . . 225G,
. . . . . . . . syn319T [MississippiAF2473_2010_03_04 with 60T, 225E,
. . . . . . . . . . . . . . . FloridaAF2199_2010_03_11 with 60T, 225E,
. . . . . . . . . . . . . . . YaroslavlIIV196_2009_12_04_f with 225G
. . . . . . . . . . . . . . . SpainCatS1236_2009_08_13 with 225E,
. . . . . . . . . . . . . . . Finland612_2009_07_21 with 225E,
. . . . . . . . . . . . . . . KazAstana818_2009_07,
. . . . . . . . . . . . . . . KazAlmati01_2009 with 225E],
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
. . . . ChinaJiangsuS62_2009_11_10 (
. . . . . . . . 60T [MississippiAF2473_2010_03_04 with 225E, syn319T,
. . . . . . . . . . . FloridaAF2199_2010_03_11 with 225E, syn319T],
. . . . . . . . 131P,
. . . . . . . . 158E [H3N8, H5N1],
. . . . . . . . 225G,
. . . . . . . . 454G [Unique to PF11 Jiangsu],
. . . . . . . . 481G,
. . . . . . . . 488N [H3N8 2009, H6, H9N2, NewJersey01_2010_01_01])
Supporting Sequences
. . . . RussiaBelgorod2_2010_03_15 (
. . . . . . . . syn13N [WiscD0459_2009_12_18_xL
. . . . . . . . . . . . . . . . . . with 189T, 324I & 499K,
. . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . with syn338G],
. . . . . . . . 77N [tn, swine, S5]
. . . . . . . . . . . [JapanOsaka60_2010_07_02
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . Maryland04_2010_02_08
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . ShandongShizhongSWL24_2010_01_24,
. . . . . . . . . . . NY7020_2009_12_14
. . . . . . . . . . . . . . . . with syn166K & 189T,
. . . . . . . . . . . CalifVRDL115_2009_12_04
. . . . . . . . . . . . . . . . with syn276H,
. . . . . . . . . . . JapanAF2267_2009_11_09
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . NevadaAF2490_2009_11_02
. . . . . . . . . . . . . . . . with 100N & syn270I,
. . . . . . . . . . . AlaskaAF2093_2009_11_02
. . . . . . . . . . . . . . . . with 286E,
. . . . . . . . . . . Russia74_2009_11_01_xL,
. . . . . . . . . . . ThailandTHB0441_2009_07_28,
. . . . . . . . . . . Lisboa40_2009_06_23,
. . . . . . . . . . . AnhuiSWL1_2009_06_18
. . . . . . . . . . . . . . . . with 275I,
. . . . . . . . . . . Lithuania1942_2009,
. . . . . . . . . . . swKoreaSCJ10_2009_12,
. . . . . . . . . . . swKoreaSCJ09_2009_12]
. . . . . . . . 158E mix,
. . . . . . . . 225G (Gga) stepwise from 225E,
. . . . . . . . 230I (ATa),
. . . . . . . . 238D [H2N3, H7N3, H7N7, tn, swine],
. . . . . . . . . . . . [PNG_Goroka17_2010_04_14,
. . . . . . . . . . . . AthensINS398_2010_01_24,
. . . . . . . . . . . . AthensINS339_2009_12_30,
. . . . . . . . . . . . Kaliningrad01_11M_2009_11_02
. . . . . . . . . . . . . . . . . . with 225E & 226R,
. . . . . . . . . . . . KaliningradCRIE_DA_2009_09_26,
. . . . . . . . . . . . KaliningradCRIE_KG_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_SHD_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_MA_2009_09_25,
. . . . . . . . . . . . KaliningradCRIE_ZD_2009_09_25],
. . . . . . . . syn245F [H2N3, H5N1, H7N7, H10N7, H11]
. . . . . . . . . . . . . . [SingON2416_2009_12_15
. . . . . . . . . . . . . . . . . . . . . with syn166K & 300P,
. . . . . . . . . . . . . . . EgyptAswan2288_2009_11_02
. . . . . . . . . . . . . . . . . . . . . with 189T],
. . . . . . . . 300S [H7N3, H7N7 (tCt)],
. . . . . . . . 305N (AAc) [ThaiChiangRai226_2M_2010_03_04
. . . . . . . . . . . . . . . . . . . . . . . with 270T,
. . . . . . . . . . . . . . . . . . Brunei5_52M_2010,
. . . . . . . . . . . . . . . . . . SouthCarolinaAF2562_2009_11_15 (AAt),
. . . . . . . . . . . . . . . . . . DenmarkAalborgINS133_2009_12_02 (AAt)],
. . . . . . . . syn343G [H3N8, H5N1, H6N1, H7N3, H7N7, H10N7, H11, 1918],
. . . . . . . . . . . . . . . [Thuringen189_2009_11_24_xL,
. . . . . . . . . . . . . . . Thuringen227_11_17_xL])
. . . . Brisbane209_51F_2010_08_09 (
. . . . . . . . 156E,
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 225G,
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [Victoria670_30M_2010_11_14
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . Emergent across Australia
. . . . . . . . . . . . . . . . . . . . . during late 2010 season,
. . . . . . . . . . . . . . . Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . OZVictoria512_2010_07_30
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . NZChristchurch15_2010_07_12
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . India5107_2010_06_28
. . . . . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . . . . . . MississippiAF2474_2010_03_10
. . . . . . . . . . . . . . . . . . . . . with syn235T,
. . . . . . . . . . . . . . . FloridaAF2197_2010_03_07
. . . . . . . . . . . . . . . . . . . . . with 156T,
. . . . . . . . . . . . . . . CalifVRDL9_2010_02_09
. . . . . . . . . . . . . . . . . . . . . with syn193S,
. . . . . . . . . . . . . . . Georgia06_2010_02_05
. . . . . . . . . . . . . . . . . . . . . with syn161Y,
. . . . . . . . . . . . . . . NY4662_2010_02_03
. . . . . . . . . . . . . . . . . . . . . with 97N, syn276H, syn283Q, syn304G,
. . . . . . . . . . . . . . . TexasJMS406_2010_01_10
. . . . . . . . . . . . . . . . . . . . . with 187A, syn193S, syn283Q,
. . . . . . . . . . . . . . . TexasJMS405_2010_01_09
. . . . . . . . . . . . . . . . . . . . . with 187A, syn283Q,
. . . . . . . . . . . . . . . CalifVRDL131_2009_12_30
. . . . . . . . . . . . . . . . . . . . . with 225G, syn455Q,
. . . . . . . . . . . . . . . LouisianaAF2435_2009_11_30
. . . . . . . . . . . . . . . . . . . . . with syn13N,
. . . . . . . . . . . . . . . Vienna291_2009_11_19
. . . . . . . . . . . . . . . catOregon29573_2009_11_09
. . . . . . . . . . . . . . . . . . . . . with 226R, syn283Q,
. . . . . . . . . . . . . . . Calif_SanDiegoINS63_2009_10_26
. . . . . . . . . . . . . . . . . . . . . with syn283Q, et al],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2],
. . . . . . . . . . [Florida14_24M_2010_08_05
. . . . . . . . . . . . . . . . . . with 188T, 454N,
. . . . . . . . . . FL_Pen210_2009_11_10
. . . . . . . . . . . . . . . . . . with 225E,
. . . . . . . . . . SouthCarolina18_2009_09_16_VxX
. . . . . . . . . . . . . . . . . . with 159D, 224K,
. . . . . . . . . . Texas45131774_2009_09_13
. . . . . . . . . . . . . . . . . . with syn223V,
. . . . . . . . . . IndiaPune9355_2009_08
. . . . . . . . . . . . . . . . . . with 225G,
. . . . . . . . . . IndiaBlore236_2009_06_xL
. . . . . . . . . . . . . . . . . . with 226R, et al],
. . . . . . . . syn465N)
2010-09-24
Pandemic Influenza and Avian Influenza Conjunctivitis Presentation
Last Updated 2010-09-30
Large outbreaks of eye inflammation (conjunctivitis), including hemorrhagic conjunctivitis, have begun around the world this month with several regions registering case counts in the thousands. Viral infection is frequently associated with this type of highly contagious "Pink Eye" or "Red Eye". Early pandemic H1N1 cases document these types of eye redness in the patient symptomology.
One recent HA polymorphism found in the pandemic reservoir has been previously associated with viral conjunctivitis with and without classic influenza symptoms. The amino acid value of HA 188T is strongly correlated to conjunctivitis on the Netherlands human H7N7 outbreak during 2003, including zoonoses from commercial poultry operatons. One human fatality was recorded during that outbreak and that case sequence shows the HA 188T.
Avian influenza again may be communicating with the human pandemic H1N1 Hydrae. India today, 2010-09-30, is on record in a section of Mumbai as counting 2,500 cases of conjunctivitis this month. HA 188T is also found in India.
. . . . Florida14_24M_2010_08_05 (
. . . . . . . . 100N [H7N3, H7N7, H9N2],
. . . . . . . . syn161Y [H3N8 2009, H6N1, H9N2],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 442I mix,
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . OZVictoria512_2010_07_30 (
. . . . . . . . syn60I,
. . . . Thailand34_9912_2010_07_14 (
. . . . . . . . HA truncated after aa253)
. . . . Thailand34_9937_2010_07_14 (
. . . . . . . . 162Q [Unique to PF11 GenBank/GISAID],
. . . . NZChristchurch15_2010_07_12 (
. . . . . . . . 100N,
. . . . India5107_2010_06_28 (
. . . . . . . . syn60I,
. . . . India8910_2010_05_08 (
. . . . . . . . syn49G [H7N3, H7N7],
. . . . . . . . syn51A,
. . . . swThaiCURA75_2010_01 (
. . . . . . . . syn350G [H7N3, H7N7],
. . . . . . . . 414I,
The human post-pandemic reservoir continues to diversify and augment from a wide variety of avian, canine and equine sources. Sampling and sequence confirmation may corroborate that Mexico, China or Pakistan has HA 188T in the PF11 reservoir near the same geographies where the eye symptoms are occurring.
Large outbreaks of eye inflammation (conjunctivitis), including hemorrhagic conjunctivitis, have begun around the world this month with several regions registering case counts in the thousands. Viral infection is frequently associated with this type of highly contagious "Pink Eye" or "Red Eye". Early pandemic H1N1 cases document these types of eye redness in the patient symptomology.
One recent HA polymorphism found in the pandemic reservoir has been previously associated with viral conjunctivitis with and without classic influenza symptoms. The amino acid value of HA 188T is strongly correlated to conjunctivitis on the Netherlands human H7N7 outbreak during 2003, including zoonoses from commercial poultry operatons. One human fatality was recorded during that outbreak and that case sequence shows the HA 188T.
- Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in the Netherlands.
- Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome.
Avian influenza again may be communicating with the human pandemic H1N1 Hydrae. India today, 2010-09-30, is on record in a section of Mumbai as counting 2,500 cases of conjunctivitis this month. HA 188T is also found in India.
. . . . Florida14_24M_2010_08_05 (
. . . . . . . . 100N [H7N3, H7N7, H9N2],
. . . . . . . . syn161Y [H3N8 2009, H6N1, H9N2],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 442I mix,
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . OZVictoria512_2010_07_30 (
. . . . . . . . syn60I,
. . . . . . . . 100N [H7N3, H7N7, H9N2],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn285P,. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . Thailand34_9912_2010_07_14 (
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 200T, . . . . . . . . HA truncated after aa253)
. . . . Thailand34_9937_2010_07_14 (
. . . . . . . . 162Q [Unique to PF11 GenBank/GISAID],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . HA truncated after aa253). . . . NZChristchurch15_2010_07_12 (
. . . . . . . . 100N,
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . India5107_2010_06_28 (
. . . . . . . . syn60I,
. . . . . . . . 100N [H7N3, H7N7, H9N2],
. . . . . . . . syn135V,
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . . . . . syn49G [H7N3, H7N7],
. . . . . . . . syn51A,
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . 377K [H9N2],
. . . . . . . . 454N [H7N3, H7N7, H9N2])
. . . . swThaiCURA75_2010_01 (
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 263D, . . . . . . . . syn350G [H7N3, H7N7],
. . . . . . . . 414I,
. . . . . . . . syn484N [H3N8, H4, H5N1 (E/A/H), H6, H7N7, H9N2, H11])
The human post-pandemic reservoir continues to diversify and augment from a wide variety of avian, canine and equine sources. Sampling and sequence confirmation may corroborate that Mexico, China or Pakistan has HA 188T in the PF11 reservoir near the same geographies where the eye symptoms are occurring.
2009-11-14
Zhejiang University Releases Second 225G from September; 100% Homology to First
A/Zhejiang/DTID-ZJU03, sampled on 2009-09-07, was deposited today at GenBank. A 100% homology at the HA to the earlier profiled A/Zhejiang/DTID-ZJU02 is demonstrated. The cases were sampled the same day.
225G now appears on 3 sequences from China.
225G now appears on 3 sequences from China.
2009-10-19
225G in Receptor Binding Domain Traveled to China without Vaccine Pairing of 206S
The expected Hydra Effect on Hemagglutinin patterns are being validated with the latest sequence deposits. Multiple antigenic heads continue to arise within single geographic areas while the march from Southern Hemisphere winter strains (May-July 2009) into the Northern Hemisphere ΣPF11 lays distinct markers.
Two sequences today from China carry the Receptor Binding Domain polymorphism coding for 225G similar to the fatal cases during the South American winter. These sequences represent the first movement of 225G into China and the second into Asia after Hiroshima201, although we have observed 225E in one instance, Changsha78.
This incursion of 225G makes Zhejiang Province one of very few geographic locales to represent both vaccine RBD polymorphisms as 226R was demonstrated mid-summer in A/Zhejiang/DTID-ZJU01/2009.
Let's examine the new Yiwu HA segments for this analysis:
These two Zhejiang province cases were sampled in September making the sequences contemporary for evaluation of the genetic acquisition cycle pertinent to North America today. Each case continues the recent affinity of 206T with 225G. Nine of fourteen instances of 225G on record within ΣPF11 are paired with 206T and only one isolated sequence after April has 206S in the pairing. You will note that the live vaccine is based on an early finding in Texas and Mexico (Texas05 pairing of 206S / 225G). The current sequences continue to demonstrate a directional movement away from those four early Texas and Mexican strains from April.
The Yiwu11 case, 41F, is specifically noted as having "severe symptoms". Confidence is increased that these sequences are valid due to independent verification. The two sequences were managed from separate labs though the hosts were apparently from the same city, Yiwu, and suffered during the same time frame.
Each of the two HA sequences represent a novel introduction into ΣPF11. Yiwu11's closest GenBank match is 1758 of 1774 nucleotides and ZJU02's closest match is Yiwu11. The two sequences are an exact nucleotide match (1759/1759) at all alignable positions (sequence truncation at Yiwu11 head and ZJU02 tail), potentially representing perfect transmission in Asia of 225G. The Catalonia sequences from Spain in early August initiated the first and only previously recorded perfect segment transmission of a 206T / 225G pairing. The Brasil deaths share amino acid homology, but varied at a silent SNP coding for Lysine at residue 222 (222K).
If a cluster is in effect with these two sequences, then we may be observing a foundational, well-passaged, human-fit strain in the Northern Hemisphere heralding Pandemic 2.0 Influenza. Only time will tell.
A correlation is also emerging in consideration of geography and population ethnicity with nine of the fourteen 225G cases in areas with a substantial Hispanic population. The ethnic profiles of the individual cases are not identified. Yiwu is a burgeoning commodities trading area with a substantial immigrant population including import/export workers from South America. If we note that NY and Georgia have Hispanic populations, then only Hiroshima remains as a potential non-Hispanic area. At any rate, the correlation of 225G to areas with Hispanic human genotypes bears scrutiny for pathogen-host interaction at the genetic level.
Recall that other human-fit genetic advances are recorded in the Zhejiang Province recently. Of minor note, the Neuraminidase segments of Yiwu11 and ZJU02 are also novel to the reservoir though the amino acid levels match widely. A third base SNP that merits attention has now spanned from the original introduction in A/Netherlands/602 to ZJU02, A408G coding at residue 136 for a synonymous Glutamine (136Q). Movement at this amino acid position is implicated in Relenza resistence (136K), though the synonymous change from the Netherlands and Zhejiang is not accorded trait enhancement in the literature.
This advancing Antigenic Diversity and movement of 225G separated from the 206S into a highly populated country prior to winter should generate a call for wider surveillance and more rapid deposition of sequences.
Two sequences today from China carry the Receptor Binding Domain polymorphism coding for 225G similar to the fatal cases during the South American winter. These sequences represent the first movement of 225G into China and the second into Asia after Hiroshima201, although we have observed 225E in one instance, Changsha78.
This incursion of 225G makes Zhejiang Province one of very few geographic locales to represent both vaccine RBD polymorphisms as 226R was demonstrated mid-summer in A/Zhejiang/DTID-ZJU01/2009.
Let's examine the new Yiwu HA segments for this analysis:
These two Zhejiang province cases were sampled in September making the sequences contemporary for evaluation of the genetic acquisition cycle pertinent to North America today. Each case continues the recent affinity of 206T with 225G. Nine of fourteen instances of 225G on record within ΣPF11 are paired with 206T and only one isolated sequence after April has 206S in the pairing. You will note that the live vaccine is based on an early finding in Texas and Mexico (Texas05 pairing of 206S / 225G). The current sequences continue to demonstrate a directional movement away from those four early Texas and Mexican strains from April.
The Yiwu11 case, 41F, is specifically noted as having "severe symptoms". Confidence is increased that these sequences are valid due to independent verification. The two sequences were managed from separate labs though the hosts were apparently from the same city, Yiwu, and suffered during the same time frame.
Each of the two HA sequences represent a novel introduction into ΣPF11. Yiwu11's closest GenBank match is 1758 of 1774 nucleotides and ZJU02's closest match is Yiwu11. The two sequences are an exact nucleotide match (1759/1759) at all alignable positions (sequence truncation at Yiwu11 head and ZJU02 tail), potentially representing perfect transmission in Asia of 225G. The Catalonia sequences from Spain in early August initiated the first and only previously recorded perfect segment transmission of a 206T / 225G pairing. The Brasil deaths share amino acid homology, but varied at a silent SNP coding for Lysine at residue 222 (222K).
If a cluster is in effect with these two sequences, then we may be observing a foundational, well-passaged, human-fit strain in the Northern Hemisphere heralding Pandemic 2.0 Influenza. Only time will tell.
A correlation is also emerging in consideration of geography and population ethnicity with nine of the fourteen 225G cases in areas with a substantial Hispanic population. The ethnic profiles of the individual cases are not identified. Yiwu is a burgeoning commodities trading area with a substantial immigrant population including import/export workers from South America. If we note that NY and Georgia have Hispanic populations, then only Hiroshima remains as a potential non-Hispanic area. At any rate, the correlation of 225G to areas with Hispanic human genotypes bears scrutiny for pathogen-host interaction at the genetic level.
Recall that other human-fit genetic advances are recorded in the Zhejiang Province recently. Of minor note, the Neuraminidase segments of Yiwu11 and ZJU02 are also novel to the reservoir though the amino acid levels match widely. A third base SNP that merits attention has now spanned from the original introduction in A/Netherlands/602 to ZJU02, A408G coding at residue 136 for a synonymous Glutamine (136Q). Movement at this amino acid position is implicated in Relenza resistence (136K), though the synonymous change from the Netherlands and Zhejiang is not accorded trait enhancement in the literature.
This advancing Antigenic Diversity and movement of 225G separated from the 206S into a highly populated country prior to winter should generate a call for wider surveillance and more rapid deposition of sequences.
2009-10-07
Antigenic Diversity Increases with 7 Novel H1 SNPs from Chengdu and Jiangyin
On 2009-10-06 China deposited 22 Hemagglutinin sequences and 23 matching partial Neuraminidase sequences from the areas of Chengdu and Jiangyin sampled respectively on 2009-07-26 and 2009-08-16. The two sets of sequences are from patients that were students at boarding schools during an outbreak. The Neuraminidase segments are far too limited in data for evaluation. The HA segments are remarkable due to the fact that 100% of the distinguishable SNPs are, on first inspection, novel introductions to ΣPF11. These wild type changes directly upstream and downstream of the Receptor Binding Domain may increase the velocity of vaccine escape.
HA Amino Acid Codings to 7 Novel Polymorphisms and 1 Mixed Signal
76T
Novel to ΣPF11.
All Jiangyin (10 sequences).
Progenitors may include:
Korea swine 2006 H1N2 (2 Entries)
Iowa human swine worker 2005 H1N1 (IA/CEID23/2005)
131P
Novel to ΣPF11.
All Chengdu (12 sequences).
Progenitor unknown.
191R
Novel to ΣPF11.
Chengdu18
Progenitor unknown.
Further inspection required:
Quail/Nanchang/12-340/2000 H1N1
Beijing/262/95 H1N1 (FluMist Vaccine Virus)
With the 3 residue deletion producing E130del (similar to S129del in several human H5N1 sub-clade 2.2.1.2), a conformational proximity may exist at 192R for alignment and / or transposition onto Chengdu18 residue 191. These two donor candidates also carry M230I, though the Chinese Quail is the only Avian H1N1 sequence on file with this human-fit RBD change. Chengdu is approximately 1,100 miles west of Lake Poyang (Nanchang) with a series of inland lakes and rivers on the flightpath.
238K
Novel to ΣPF11.
Chengdu04
Progenitors may include:
Seasonal 2008 H1N1 (1 Entry)
Seasonal 2005 H1N1 (2 Entries)
Guangdong swine 2009 H1N1
NC swine 2008 H1N1 (8 Entries)
PR8_34
LabVir_hvPR8_34
H5N1 Sub-clade 2.2
259V
Novel to ΣPF11.
Jiangyin01
Jiangyin15
Jiangyin16
Jiangyin17
Progenitors may include:
Seasonal 2006 H1N1 (South Carolina/2)
264X
Indistinguishable amino acid.
Jiangyin68
286N
Novel to ΣPF11.
Chengdu40
Progenitors may include:
Swine H1N1 2003-2007 (NC, Ohio, Kansas)
502K
Novel to ΣPF11.
Jiangyin34
Progenitors may include:
red-winged tinamou/Argentina/MP1/2008 H1N1
with HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G
Seasonal 2009 H1N1
Seasonal 2007 H1N1
WSN33
HA Amino Acid Codings to 7 Novel Polymorphisms and 1 Mixed Signal
- 76T
- 131P
- 191R
- 238K
- 259V
- 264X
- 286N
- 502K
76T
Novel to ΣPF11.
All Jiangyin (10 sequences).
Progenitors may include:
Korea swine 2006 H1N2 (2 Entries)
Iowa human swine worker 2005 H1N1 (IA/CEID23/2005)
131P
Novel to ΣPF11.
All Chengdu (12 sequences).
Progenitor unknown.
191R
Novel to ΣPF11.
Chengdu18
Progenitor unknown.
Further inspection required:
Quail/Nanchang/12-340/2000 H1N1
Beijing/262/95 H1N1 (FluMist Vaccine Virus)
With the 3 residue deletion producing E130del (similar to S129del in several human H5N1 sub-clade 2.2.1.2), a conformational proximity may exist at 192R for alignment and / or transposition onto Chengdu18 residue 191. These two donor candidates also carry M230I, though the Chinese Quail is the only Avian H1N1 sequence on file with this human-fit RBD change. Chengdu is approximately 1,100 miles west of Lake Poyang (Nanchang) with a series of inland lakes and rivers on the flightpath.
238K
Novel to ΣPF11.
Chengdu04
Progenitors may include:
Seasonal 2008 H1N1 (1 Entry)
Seasonal 2005 H1N1 (2 Entries)
Guangdong swine 2009 H1N1
NC swine 2008 H1N1 (8 Entries)
PR8_34
LabVir_hvPR8_34
H5N1 Sub-clade 2.2
259V
Novel to ΣPF11.
Jiangyin01
Jiangyin15
Jiangyin16
Jiangyin17
Progenitors may include:
Seasonal 2006 H1N1 (South Carolina/2)
264X
Indistinguishable amino acid.
Jiangyin68
286N
Novel to ΣPF11.
Chengdu40
Progenitors may include:
Swine H1N1 2003-2007 (NC, Ohio, Kansas)
502K
Novel to ΣPF11.
Jiangyin34
Progenitors may include:
red-winged tinamou/Argentina/MP1/2008 H1N1
with HA 225G, 277N, 286H, 298V / NA 106I, 248N, 286G
Seasonal 2009 H1N1
Seasonal 2007 H1N1
WSN33
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