The astoundingly alacritous and accurate Hospital Clinic of Spain today released a number of very contemporary sequences at GenBank, including 10 HA, 10 NA and 11 MP segments sampled from 2009-10-26 to 2009-10-29.
225E is found in 6 of the 10 Hemagglutinin sequences. No 225G, 225N or 226R are found in these 10 sequences. All 10 sequences display 206T.
225E is Fixed and Conserved, I'd say.
Several new faces come into the PF11 reservoir with this deposit and among the 10 sequences we find the following amino acid codings, several of which you've watched emerge and then have tracked with us:
33I, 35I, 71G, 225E, 264D, 298V, 377K, 387D, 447K, 463T, 480K, 519N.
As you can see from the amino acid codings list, Influenza Flux is at work and recombinations are being recycled in the Mediterranean and Adriatic geographies.
CatS1600, CatS1604, CatS1605, CatS1606, CatS1620, CatS1632, CatS1637 and CatS1650 appear at first glance to be novel in HA permutation to ΣPF11 at GenBank. Across 3 days in one country, the Hospital Clinic samples 8 distinct HA segments springing at one time that are novel to the worldwide reservoir and co-existent with at least 2 previously discussed circulating strains.
CatS1641 and CatS1651 are each characterised with independent homology to earlier Catalonia strains and, on CatS1651, with recent Singapore entries as well.
10 sequences with 10 distinct HA segments in 1 geography during 1 time period of 3 days.
The Hydra Effect has never been more evident.
Due to time limitations, this analysis is far from complete and may involve error. As always, we invite independent verification on this short study.
Showing posts with label 298V. Show all posts
Showing posts with label 298V. 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 Trend Continues in Spain Through October 2009
The Hospital Clinic of Barcelona, Spain continued a strong professional showing this evening by depositing 41 sequences at GenBank covering the month of October 2009, including 14 HA and NA segments. The Spanish officials and medical community must be highly commended for continuing to provide research data of the highest calibre and timeliness during this early stage of the pandemic.
The velocity of change at amino acid residue 225 in the Receptor Binding Domain from October in Spain parallels our report from yesterday on August and September. These samples are contemporary, dating from 2009-10-05 to several in the third week of October (up to 2009-10-22). 6 of 14 specimens (43%) demonstrate 225E paired with 206T. As of this accumulation, Spain shows 37 instances of 225E with no 206S and 3 instances of 225G with 206T.
Additional unique faces also enter ΣPF11 with the Hospital Clinic's October sequences. 26 total polymorphisms within the antigens, HA and NA, spread across 13 amino acid positions generates branching on the Spanish tree in directions that may be suggestive of critical human fitness paths occurring throughout the world.
Of particular interest is the potential cluster:
Clinical information would be very useful in this matter. We are compelled by this Spanish cluster because a very striking HA homology has been circulating in North America since early August. The H8N4 strains may have donated 377K to the H5N1 along the flightpath with a surveillance lag not yet chronicling the event.
HA Amino Acid Codings to 3 Novel Polymorphisms and 8 Rare Signals
CatS1533, CatS1547.
Rare to ΣPF11.
Found in 10 other sequences including recent TamiFlu-Resistant US sequence, A/Texas/47.
Progenitors may include:
H5N1 Avian
H5N1 Human
71G
CatS1478, CatS1587.
CatS1436 and NY80 are the lone ΣPF11 peers.
88L
CatS1533.
Novel to ΣPF11.
89N
CatS1589.
Novel to ΣPF11.
100N
CatS1589.
Rare to ΣPF11.
Found in A/Sao Paulo/55312 and Argentina7953 from the INEI/CII Influenza Virus Sequencing Site.
Progenitors may include:
H1N1 Swine 2009
H1N2 Swine
142T
CatS1574.
CatS1411 is the singular ΣPF11 peer.
225E
CatS1478, CatS1479, CatS1490, CatS1545, CatS1587, CatS1592.
Presently velocitised within recent ΣPF11.
298V
CatS1478, CatS1479, CatS1587.
Unique to Catalonia within ΣPF11.
CatNS2001, CatNS2008, CatS1237, CatS1248, CatS1286, CatS1369, CatS1436.
373H
CatS1525, CatS1589.
Unique to Catalonia within ΣPF11.
CatS1285, CatS1353.
377K
CatS1515, CatS1554.
Novel to ΣPF11.
Progenitors may include:
H8N4 Avian
H6N1 Avian
504N
CatS1525, CatS1589.
A/Gifu-C/67 is the singular ΣPF11 peer.
Progenitors may include:
H1N1 Avian
H1N2 Swine
Neuraminidase Triple Combination
106I, 248D, 286S
All October sequences.
The Neuraminidase displays strong homology with exception in only three sequences.
NA Amino Acid Codings to 2 Novel Polymorphisms
CatS1515.
Identical in HA and MP segments to CatS1554.
Novel to ΣPF11.
Progenitors unknown, but adjacent residue 162 is highly active in:
H5N1 Human
H5N1 Avian
H1N1 Human
H1N1 Avian
H3N2 Human
442I
CatS1525, CatS1589.
Novel to ΣPF11.
Progenitors may include:
H5N1 Human
H5N1 Avian
H1N1 Swine
WSN33
The velocity of change at amino acid residue 225 in the Receptor Binding Domain from October in Spain parallels our report from yesterday on August and September. These samples are contemporary, dating from 2009-10-05 to several in the third week of October (up to 2009-10-22). 6 of 14 specimens (43%) demonstrate 225E paired with 206T. As of this accumulation, Spain shows 37 instances of 225E with no 206S and 3 instances of 225G with 206T.
Additional unique faces also enter ΣPF11 with the Hospital Clinic's October sequences. 26 total polymorphisms within the antigens, HA and NA, spread across 13 amino acid positions generates branching on the Spanish tree in directions that may be suggestive of critical human fitness paths occurring throughout the world.
Of particular interest is the potential cluster:
- A/Catalonia/S1515, HA, NA, MP, sampled on 2009-10-13, 14F
- A/Catalonia/S1554, HA, NA, MP, sampled on 2009-10-20, 1F
Clinical information would be very useful in this matter. We are compelled by this Spanish cluster because a very striking HA homology has been circulating in North America since early August. The H8N4 strains may have donated 377K to the H5N1 along the flightpath with a surveillance lag not yet chronicling the event.
HA Amino Acid Codings to 3 Novel Polymorphisms and 8 Rare Signals
- 35I
- 71G
- 88L
- 89N
- 100N
- 142T
- 225E
- 298V
- 373H
- 504N
CatS1533, CatS1547.
Rare to ΣPF11.
Found in 10 other sequences including recent TamiFlu-Resistant US sequence, A/Texas/47.
Progenitors may include:
H5N1 Avian
H5N1 Human
71G
CatS1478, CatS1587.
CatS1436 and NY80 are the lone ΣPF11 peers.
88L
CatS1533.
Novel to ΣPF11.
89N
CatS1589.
Novel to ΣPF11.
100N
CatS1589.
Rare to ΣPF11.
Found in A/Sao Paulo/55312 and Argentina7953 from the INEI/CII Influenza Virus Sequencing Site.
Progenitors may include:
H1N1 Swine 2009
H1N2 Swine
142T
CatS1574.
CatS1411 is the singular ΣPF11 peer.
225E
CatS1478, CatS1479, CatS1490, CatS1545, CatS1587, CatS1592.
Presently velocitised within recent ΣPF11.
298V
CatS1478, CatS1479, CatS1587.
Unique to Catalonia within ΣPF11.
CatNS2001, CatNS2008, CatS1237, CatS1248, CatS1286, CatS1369, CatS1436.
373H
CatS1525, CatS1589.
Unique to Catalonia within ΣPF11.
CatS1285, CatS1353.
377K
CatS1515, CatS1554.
Novel to ΣPF11.
Progenitors may include:
H8N4 Avian
H6N1 Avian
504N
CatS1525, CatS1589.
A/Gifu-C/67 is the singular ΣPF11 peer.
Progenitors may include:
H1N1 Avian
H1N2 Swine
Neuraminidase Triple Combination
106I, 248D, 286S
All October sequences.
The Neuraminidase displays strong homology with exception in only three sequences.
NA Amino Acid Codings to 2 Novel Polymorphisms
- 161C (synonymous T483C)
- 442I
CatS1515.
Identical in HA and MP segments to CatS1554.
Novel to ΣPF11.
Progenitors unknown, but adjacent residue 162 is highly active in:
H5N1 Human
H5N1 Avian
H1N1 Human
H1N1 Avian
H3N2 Human
442I
CatS1525, CatS1589.
Novel to ΣPF11.
Progenitors may include:
H5N1 Human
H5N1 Avian
H1N1 Swine
WSN33
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.
2009-10-02
H5N1 and 1918 Receptor Binding Domain Change, HA 225G, Emerges On Two Sub-Clades in Spain
Spain deposited 239 sequences today at GenBank.
A/Catalonia/NS1706, sampled on 2009-07-29, Segment 4 (HA) and Segment 6 (NA)
A/Catalonia/NS2001, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)
A/Catalonia/NS2008, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)
225G is found on these 3 Spanish Hemagglutinins as in the 2 Sao Paulo cases during the same late July to early August timeframe. On the CatNS1706 specimen, 206S is paired with the 225G; whereas, the Brasilian deaths were 206T and 225G similar to CatNS2001 and CatNS2008. During the same timeframe, two cities more than 5,000 miles distant with an ocean between them each have emergence of multiple novel sub-clades for their geography related to the Receptor Binding Domain residue 225. Consider seasonality and your puzzlement is enhanced.
225G is consensus for H5N1, is carried on NewYork1918 and only appears in 8 other PF11 sequences across the US and Mexico.
SaoPaulo53206
SaoPaulo53225
MX3955
MXInDRE4114
NY04
GA01
TX05
TX11
225X is demonstrated several times in the US proximal to 225G in area and time.
NY11
NY31
TX10
CA13
NE02
CatNS2001 and CatNS2008 also feature HA 298V, a potential reversion to swine sequences or to 2008 Seasonal. Because 206T is featured in these two sequences and 206T is exclusive of 296H, we may perhaps postulate a secondary acquisition pathway for an unidentified human-fit, trait-enhancing domain (HA296:301).
Three additional sequences in this deposit carry the pair of 206T and 298V:
An Intra-Segment Exclusivity exists within the Catalonia specimens between 206S and 225E. 24 of 25 Catalonia 225E specimens carry 206T, all but the unusual CatS1161 with 206A.
Neuraminidase Quadruple Combination
Non-Random Acquisition Acceleration appears to be underway in potential trait-enhancing domains of both Antigen segments. Influenza Flux is a two way street with clearly defined lanes and many points of ingress.
The Hydra Effect is demonstrated in the phylogenic trees of Brasil and Spain. When your tree is all branches with only a few leaves at each tip, you aren’t going to get much protection from the sun unless you decided very early to be standing on just the right spot when the perfect light of noon arrives.
A/Catalonia/NS2001, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)
A/Catalonia/NS2008, sampled on 2009-08-03, Segment 4 (HA) and Segment 6 (NA)
225G is consensus for H5N1, is carried on NewYork1918 and only appears in 8 other PF11 sequences across the US and Mexico.
SaoPaulo53225
MX3955
MXInDRE4114
NY04
GA01
TX05
TX11
NY31
TX10
CA13
NE02
Three additional sequences in this deposit carry the pair of 206T and 298V:
- A/Catalonia/S1237, HA, sampled 2009-08-13
- A/Catalonia/S1248, HA, sampled 2009-08-18
- A/Catalonia/S1286, HA, sampled 2009-08-25
An Intra-Segment Exclusivity exists within the Catalonia specimens between 206S and 225E. 24 of 25 Catalonia 225E specimens carry 206T, all but the unusual CatS1161 with 206A.
Neuraminidase Quadruple Combination
- CatNS1706 = 106V, 248N, 275H, 286G
- CatNS2001 = 106I, 248D, 275H, 286S
- CatNS2008 = 106I, 248D, 275H, 286S
- CatNS1237 = 106I, 248D, 275H, 286S
- CatNS1248 = 106I, 248D, 275H, 286S
- CatNS1286 = 106I, 248D, 275H, 286S
The Hydra Effect is demonstrated in the phylogenic trees of Brasil and Spain. When your tree is all branches with only a few leaves at each tip, you aren’t going to get much protection from the sun unless you decided very early to be standing on just the right spot when the perfect light of noon arrives.
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