A/Chita/01, sampled from human lung in Russia with no identifying host gender or age, becomes the 5th distinct sequence on file for the previously discussed 4th permutation of the NA Dual Combination at amino acid positions 106 and 248. No HA was published for this sample, but the sample location points to fatality and 225G is suspect.
This PF11 sequence demonstrates 106V and 248D and is distinct from the four previous isolates with this characteristic pair:
2009-04 A/Toronto/3184
2009-04 A/Auckland/4
2009-07 A/Toronto/R8564
2009-05 A/Wisconsin/629-D00487
Chita01 is most similar (1417/1419) to Toronto3184, yet all 5 sequences with this pairing are distinct. 2 silent polymorphisms are found on Chita01, coding for syn257R and syn315G.
The NA Dual Combination of 106V and 248D is now found 5 times within ΣPF11:
2009-04 Canada and New Zealand
2009-05 Wisconsin
2009-07 Canada
2009-xx Russia
Showing posts with label NA Dual Combination. Show all posts
Showing posts with label NA Dual Combination. Show all posts
2009-11-09
225E Expectation in the Ukraine
PF11 SNP geographic analysis suggests that the Ukraine cases in the next two weeks may show a very similar genetic pattern to South America in August and the Mediterranean and Adriatic FlightPath in the past 8 weeks.
If the trend toward a higher infectivity of medical personnel continues as reported today of 687 doctors and 1,500 young specialists being ill, we would expect a higher death count in the coming days. Between 0.5% and 1.3% of all doctors in the country are ill (by region). Higher transmissibility is certain.
If a database of 100 sequences were to exist on the Ukraine, accurately cataloging a cross-reference of regions over 14 days of recent death and recovery cases, including major cities, rough expectations would indicate:
HA
225E
in moderate concentration (95% probability) with 206T
206T/225E/300S triplet
potential for introduction (1 sequence) (75% probability)
2E/206T/225E/298V quad combo
potential for appearance in very low count (1 to 2 sequences) (>25% probability)
2E/206T/225G/298V quad combo
potential for introduction (1 sequence) (<10% probability)
225G
potential, but certainly not widespread under current clinical reports (75% probability) with 206T
2E/206S/296H triplet
in low concentration (95% probability)
377K
potential for introduction (1 sequence) (25% probability)
270T
potential for introduction (1 sequence) (7% probability)
261V
potential for appearance in very low count (1 to 3 sequences) (>25% probability)
212 movement
potential for introduction (1 sequence) (7% probability)
208K
potential for introduction (1 sequence) (33% probability)
188/189/190 movement
potential for introduction (1 sequence) (>50% probability)
158E
potential for appearance in very low count (1 to 3 sequences) (>25% probability)
100N
potential for introduction (1 sequence) (>25% probability)
35I
potential for appearance in moderate count (<20% probability)
NA
106I, 248N pairing
potential in very low count (<20% probability)
106I, 248N, 286G triplet
potential for introduction (7% probability until the 8th week of the flashfire)
If the trend toward a higher infectivity of medical personnel continues as reported today of 687 doctors and 1,500 young specialists being ill, we would expect a higher death count in the coming days. Between 0.5% and 1.3% of all doctors in the country are ill (by region). Higher transmissibility is certain.
If a database of 100 sequences were to exist on the Ukraine, accurately cataloging a cross-reference of regions over 14 days of recent death and recovery cases, including major cities, rough expectations would indicate:
HA
225E
in moderate concentration (95% probability) with 206T
206T/225E/300S triplet
potential for introduction (1 sequence) (75% probability)
2E/206T/225E/298V quad combo
potential for appearance in very low count (1 to 2 sequences) (>25% probability)
2E/206T/225G/298V quad combo
potential for introduction (1 sequence) (<10% probability)
225G
potential, but certainly not widespread under current clinical reports (75% probability) with 206T
2E/206S/296H triplet
in low concentration (95% probability)
377K
potential for introduction (1 sequence) (25% probability)
270T
potential for introduction (1 sequence) (7% probability)
261V
potential for appearance in very low count (1 to 3 sequences) (>25% probability)
212 movement
potential for introduction (1 sequence) (7% probability)
208K
potential for introduction (1 sequence) (33% probability)
188/189/190 movement
potential for introduction (1 sequence) (>50% probability)
158E
potential for appearance in very low count (1 to 3 sequences) (>25% probability)
100N
potential for introduction (1 sequence) (>25% probability)
35I
potential for appearance in moderate count (<20% probability)
NA
106I, 248N pairing
potential in very low count (<20% probability)
106I, 248N, 286G triplet
potential for introduction (7% probability until the 8th week of the flashfire)
2009-11-02
225E on 45% of Catalonia HA Deposit from August and September
The Hospital Clinic of Barcelona, Spain deposited 21 HA/NA/MP segments at GenBank on Friday. The group as a whole demonstrates significant diversity and the velocity of change at residue 225 in the Receptor Binding Domain is remarkable.
The samples are primarily from August and September, as late as 2009-09-30. One sample is earlier, from July. 9 of 20 specimens (45%) in this deposit that were sampled in August and September demonstrate 225E paired with 206T. As of this accumulation, Spain shows 31 instances of 225E with no 206S and 3 instances of 225G with 206T. Additionally, several unique faces enter ΣPF11 with the Hospital Clinic's latest deposit.
HA Amino Acid Codings to 3 Novel Polymorphisms and 6 Rare Signals
CatS1305, CatS1411, CatS1414, CatS1435.
Rare to ΣPF11.
Found in 6 other sequences including recent TamiFlu-Resistant US sequence, A/Texas/47.
Progenitors may include:
H5N1 Avian
H5N1 Human
71G
CatS1436.
NY80 is the singular ΣPF11 peer.
142T
CatS1411.
Novel to ΣPF11.
188N
CatS1369.
CatS1187 and Niigata700 are the lone ΣPF11 peers.
193G
CatS1384.
Novel to ΣPF11.
225E
CatS1300, CatS1304, CatS1331, CatS1333, CatS1350, CatS1369, CatS1379, CatS1436, CatS1453.
Presently velocitised within recent ΣPF11.
240R
CatS1436.
Novel to ΣPF11.
Progenitors may include:
Zhuhai/790/2008
H1N2 Swine
298V
CatS1369, CatS1436.
Unique to Catalonia within ΣPF11.
CatNS2001, CatNS2008, CatS1237, CatS1248, CatS1286.
373H
CatS1353.
Unique to Catalonia within ΣPF11.
CatS1285.
Neuraminidase Triple Combination
106I, 248D, 286S 20 Sequences
106V, 248D, 286S CatS1369.
The pattern shown by CatS1369 is found in 4 other instances within ΣPF11. Three of those were very early in the pandemic and the most recent is A/Toronto/R8564 from a 7F in early July.
This Neuraminidase group displays some variety with exception in three sequences.
NA Amino Acid Codings to 4 Polymorphisms
CatS1402.
369T
CatS1307, CatS1402.
386D
CatS1384.
395R
CatS1402.
The samples are primarily from August and September, as late as 2009-09-30. One sample is earlier, from July. 9 of 20 specimens (45%) in this deposit that were sampled in August and September demonstrate 225E paired with 206T. As of this accumulation, Spain shows 31 instances of 225E with no 206S and 3 instances of 225G with 206T. Additionally, several unique faces enter ΣPF11 with the Hospital Clinic's latest deposit.
HA Amino Acid Codings to 3 Novel Polymorphisms and 6 Rare Signals
- 35I
- 71G
- 142T
- 188N
- 193G
- 225E
- 240R
- 298V
- 373H
CatS1305, CatS1411, CatS1414, CatS1435.
Rare to ΣPF11.
Found in 6 other sequences including recent TamiFlu-Resistant US sequence, A/Texas/47.
Progenitors may include:
H5N1 Avian
H5N1 Human
71G
CatS1436.
NY80 is the singular ΣPF11 peer.
142T
CatS1411.
Novel to ΣPF11.
188N
CatS1369.
CatS1187 and Niigata700 are the lone ΣPF11 peers.
193G
CatS1384.
Novel to ΣPF11.
225E
CatS1300, CatS1304, CatS1331, CatS1333, CatS1350, CatS1369, CatS1379, CatS1436, CatS1453.
Presently velocitised within recent ΣPF11.
240R
CatS1436.
Novel to ΣPF11.
Progenitors may include:
Zhuhai/790/2008
H1N2 Swine
298V
CatS1369, CatS1436.
Unique to Catalonia within ΣPF11.
CatNS2001, CatNS2008, CatS1237, CatS1248, CatS1286.
373H
CatS1353.
Unique to Catalonia within ΣPF11.
CatS1285.
Neuraminidase Triple Combination
106I, 248D, 286S 20 Sequences
106V, 248D, 286S CatS1369.
The pattern shown by CatS1369 is found in 4 other instances within ΣPF11. Three of those were very early in the pandemic and the most recent is A/Toronto/R8564 from a 7F in early July.
This Neuraminidase group displays some variety with exception in three sequences.
NA Amino Acid Codings to 4 Polymorphisms
- 321V
- 369T
- 386D
- 395R
CatS1402.
369T
CatS1307, CatS1402.
386D
CatS1384.
395R
CatS1402.
2009-10-30
Matching Pair of Human-Fit NA Novelty Emerges Independently in Two Distinct Locales during August 2009
The University of Padova deposited 23 Neuraminidase segments at GenBank yesterday. One particularly merits discussion. We were keyed to the sequence by the rare 106I and 248N human pairing, but even more human fitness acquisition was at work upon review. The NA of A/Italy/180, sampled in August 2009 from a 47M, brings another unique face into ΣPF11.
NA Amino Acid Codings to 1 Novel Polymorphism and 2 Independent Co-Emergent Signals
Neuraminidase Triple Combination
106I, 248N, 286S
Only 25 sequences currently match the 146 amino acids from 106I to 248N, including the Italy134 sequence recently profiled demonstrating the NA Triple Combination herald for Pandemic 2.0.
This new Italian sequence is a marvel in itself, but the argument against random mutation gains strength upon a similar and apparently independent co-emergence. Two perfectly novel introductions paired onto two divergent backgrounds in two different geographies suggest a randomness redundancy.
A/Catalonia/S1276, sampled 2009-08-19 from a 13F, also demonstrates two of the three novel introductions, but onto a separate NA background. CatS1276 is a perfect nucleotide match to Italy180 except at 742G generating 248D (1216 of 1217 aligned residues). Like many of the Catalonia sequences, the initial 47 amino acids of CatS1276 are absent or we might find the 45K there as well. Even without the full sequence, CatS1276 is unique and stand-alone within ΣPF11 due to the swine 248D conjoined with 386D and C1276T.
45K
Novel to ΣPF11.
Progenitors may include:
A/Washington/03/2009 H1N1 with HA 230I & NA 386D, syn426L
A/New Jersey/30/2008 H1N1 with HA 230I & NA 386D, syn426L
A/Thailand/271/2005 H1N1 with HA 225G, 261N, 263D, 270T & NA:45K, syn346V
386D
CatS1276 is the singular ΣPF11 peer.
Progenitors may include:
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Consensus)
Avian H1N1
syn426L
CatS1276 is the singular ΣPF11 peer.
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Extensive)
Swine H1N1 1990-1999
WSN33
Paired genetic introductions onto disparate backgrounds are not a spline for randomness. Perhaps a less random examination of the database at hand would provide additional observational evidence for a new school of logic? Without question, human-fit genetics from previous Seasonal H1N1 and H3N2 are being gained by the Hydra pandemic strains. In this case, the sub-segment acquisitions are precise and clear.
NA Amino Acid Codings to 1 Novel Polymorphism and 2 Independent Co-Emergent Signals
- 45K
- 386D
- 426L (synonymous C1276T)
Neuraminidase Triple Combination
106I, 248N, 286S
Only 25 sequences currently match the 146 amino acids from 106I to 248N, including the Italy134 sequence recently profiled demonstrating the NA Triple Combination herald for Pandemic 2.0.
This new Italian sequence is a marvel in itself, but the argument against random mutation gains strength upon a similar and apparently independent co-emergence. Two perfectly novel introductions paired onto two divergent backgrounds in two different geographies suggest a randomness redundancy.
A/Catalonia/S1276, sampled 2009-08-19 from a 13F, also demonstrates two of the three novel introductions, but onto a separate NA background. CatS1276 is a perfect nucleotide match to Italy180 except at 742G generating 248D (1216 of 1217 aligned residues). Like many of the Catalonia sequences, the initial 47 amino acids of CatS1276 are absent or we might find the 45K there as well. Even without the full sequence, CatS1276 is unique and stand-alone within ΣPF11 due to the swine 248D conjoined with 386D and C1276T.
45K
Novel to ΣPF11.
Progenitors may include:
A/Washington/03/2009 H1N1 with HA 230I & NA 386D, syn426L
A/New Jersey/30/2008 H1N1 with HA 230I & NA 386D, syn426L
A/Thailand/271/2005 H1N1 with HA 225G, 261N, 263D, 270T & NA:45K, syn346V
386D
CatS1276 is the singular ΣPF11 peer.
Progenitors may include:
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Consensus)
Avian H1N1
syn426L
CatS1276 is the singular ΣPF11 peer.
Seasonal H1N1 2005, 2006, 2007, 2008 and 2009 (Extensive)
Swine H1N1 1990-1999
WSN33
Paired genetic introductions onto disparate backgrounds are not a spline for randomness. Perhaps a less random examination of the database at hand would provide additional observational evidence for a new school of logic? Without question, human-fit genetics from previous Seasonal H1N1 and H3N2 are being gained by the Hydra pandemic strains. In this case, the sub-segment acquisitions are precise and clear.
2009-09-14
NA Dual Combination 106I and 248N; 22 PF11 Sequences; 1 in United States
Human-fit Seasonal H1N1 from 2008 and 2009 typically demonstrates the H275Y TamiFlu Resistance marker and a NA Triple Combination at 106, 248 and 286:
106I, 248N, 286G
As of today, GenBank shows only one sequence on file from the United States demonstrating a match to the NA Dual Combination of 106I and 248N and the consensus interior region:
Europe, North America and Asia are now penetrated with the NA Dual Combination of 106I and 248N in the PF11 reservoir matching 2008 and 2009 H1N1 Seasonal Influenza and laying the groundwork for additional TamiFlu Resistance.
106I, 248N, 286G
As of today, GenBank shows only one sequence on file from the United States demonstrating a match to the NA Dual Combination of 106I and 248N and the consensus interior region:
- A/Louisiana/03, sampled on 2009-05-01 from a 1 year old female
- Italy (1: Italy127)
- Russia (2: Ekaterinburg01 & Almati01)
- US (1: Louisiana03)
- Asia (18)
- Japan (15, including TamiFlu Resistant Osaka180)
- China (2: Shanghai71T & Nanjing1)
- Korea (1: Korea01)
Europe, North America and Asia are now penetrated with the NA Dual Combination of 106I and 248N in the PF11 reservoir matching 2008 and 2009 H1N1 Seasonal Influenza and laying the groundwork for additional TamiFlu Resistance.
2009-09-09
NA 106V and 248D in April 2009 Toronto Sequence Released Today, Distinct
A/Toronto/3184, sampled in April 2009, now becomes the ultimate origin on file for the Northern Hemisphere for the previously discussed 4th permutation of the NA Dual Combination at amino acid positions 106 and 248.
This early PF11 sequence demonstrates 106V and 248D and appears distinct from the April 2009, A/Auckland/4, and the A/Toronto/R8564 specimen sampled in July that are the only other sequences in the PF11 reservoir on file with these two amino acid codings. The Toronto3184 NA is most similar (1422/1423) to a series from Stockholm, Zhejiang2 and Finland555 (all 106I).
The NA Dual Combination of 106V and 248D is found 3 times: New Zealand and Canada (April) and Canada (July).
This early PF11 sequence demonstrates 106V and 248D and appears distinct from the April 2009, A/Auckland/4, and the A/Toronto/R8564 specimen sampled in July that are the only other sequences in the PF11 reservoir on file with these two amino acid codings. The Toronto3184 NA is most similar (1422/1423) to a series from Stockholm, Zhejiang2 and Finland555 (all 106I).
The NA Dual Combination of 106V and 248D is found 3 times: New Zealand and Canada (April) and Canada (July).
2009-09-03
Toronto re-emergence of 4th PF11 Neuraminidase Permutation at positions 106 and 248
A/Toronto/R8564, sampled 2009-07-06, rescues the 4th permutation of the NA Dual Combination at amino acid positions 106 and 248. The PF11 sequence demonstrates 106V and 248D, a combination that was previously found only once within ΣPF11, early in the pandemic in April 2009, A/Auckland/4.
This re-emergence of the permutation returns a 4th version of the NA Dual Combination to activity on PF11.
The TorontoR8564 NA is an exact amino acid match to the Auckland4 sequence from April. The certain interchange that occurs between the two cities on a regular basis would lead us to investigate for re-assortment potential. However, re-assortment is impeached from this investigation due to the 2 polymorphisms at the nucleotide level:
Several Auckland sequences carry the G76A.
G355A is found in only 14 worldwide ΣPF11 strains: Toronto, China, Japan, Spain, Australia and 5 in the Southern United States.
The N1 backgrounds are widening in a fashion suggestive of non-random genetic acquisition with this completion of the permutation set concerning the NA Dual Combination at positions 106 and 248.
This re-emergence of the permutation returns a 4th version of the NA Dual Combination to activity on PF11.
The TorontoR8564 NA is an exact amino acid match to the Auckland4 sequence from April. The certain interchange that occurs between the two cities on a regular basis would lead us to investigate for re-assortment potential. However, re-assortment is impeached from this investigation due to the 2 polymorphisms at the nucleotide level:
Several Auckland sequences carry the G76A.
G355A is found in only 14 worldwide ΣPF11 strains: Toronto, China, Japan, Spain, Australia and 5 in the Southern United States.
The N1 backgrounds are widening in a fashion suggestive of non-random genetic acquisition with this completion of the permutation set concerning the NA Dual Combination at positions 106 and 248.
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