225G Worldwide Tracking & Evaluation

[gsgs]

225G in pigs:

http://www.plosone.org/article/info%...l.pone.0009068


do you also have this ?
plosone loads very slowly, presumably due to the advertisement videos
maybe this link to the .pdf works better:
http://www.plosone.org/article/fetch...esentation=PDF


BTW. FT is also slower again recently for me. Slower than all the other forums
at least. Some seconds , tolerable , but sometimes I post to other boards
instead or don't post at all because of this.

[mixin]

Interesting that this PLoS study used egg passage.

I can't find a way to cut/paste this picture: Figure S6.

If I understand this correctly they innoculated with mixed signals D225X and Q226X (grT and crA).

In the sample taken from the directly innoculated pigs, D225X remained, but 226X reverted to Q226.

When transmitted to other pigs, both reverted to D225 (gat) and Q226 (caa)

So during transmission, it mutated from mixed signals to non-mutated signals?

But then in the lungs, on 1 and 2 days post-infection, it was still D225X and Q226 but on days 4 and 7, it changed to D225G and remained Q226.

Pig 3261 had to be put to death unexpectedly on day 17 due to welfare issues.

[mixin]

Here's the picture. HT to gs to use printscreen..

[mixin]

Brazil released a series of sequences from late last summer at GenBank.
These are all from deceased patients, some have D225 mutations (715, 716).

A/Rio de Janeiro/14601/2009 24-Aug-2009 gender M; age 23Y Nasopharyngeal aspirate
A4G(4),C537T(4),A716G(4),G930T(4),T1275C(4),C1408T (4)

A/Rio de Janeiro/4707/2009 23-Jul-2009 gender F; age 31Y Nasopharyngeal aspirate
A716G(4),G930T(4),C1408T(4),G1556A(4)

A/Rio de Janeiro/7131/2009 01-Aug-2009 gender F; age 16Y Nasopharyngeal aspirate
A4G(4),A232T(4),A716G(4),G930T(4),G1080A(4),C1408T (4)

A/Rio de Janeiro/7455/2009 04-Aug-2009 gender M; age 37Y Nasopharyngeal aspirate
A4G(4),A716G(4),G930T(4),A1272G(4),A1394C(4),C1408 T(4)

A/Bahia/15525/2009 05-Sep-2009 gender M; age 42Y Nasopharyngeal aspirate
T141C(4),G340A(4),T658A(4),G687A(4),G715R(4),A716R (4),C1408T(4),C1476Y(4),C1539Y(4),C1574Y(4)

A/Bahia/12606/2009 18-Aug-2009 gender F; age 38Y Nasopharyngeal secretion
C309A(4),G318A(4),T658A(4),A1281G(4),G1299A(4),C14 08T(4),

A/Rio Grande do Sul/9116/2009 02-Aug-2009 gender M; age 39Y Nasopharyngeal aspirate
G930T(4),A1260R(4),C1408T(4),

A/Minas Gerais/14602/2009 22-Aug-2009 gender F; age 36Y Nasopharyngeal secretion
T658A(4),C1408T(4),

A/Santa Catarina/6235/2009 26-Jul-2009 gender M; age 42Y Nasopharyngeal aspirate
G930T(4),C1408T(4),T1712C(4),C1713A(4),A1714G(4),G 1715A(4),A1717G(4),G1718C(4),C1719A(4),

[gsgs]

the first 4 don't have T658A thus are pre-Cancun.
Still 2 of them have A716G - yet another background,
yet another evidence that it developes in the host and
(usually) doesn't spread.

I'll update my South-America table in the genbank thread

[gsgs]

http://www.ncbi.nlm.nih.gov/pubmed/20367331
Quasispecies of the D225G Substitution in the Hemagglutinin of Pandemic
Influenza A(H1N1) 2009 Virus from Patients with Severe Disease in Hong Kong, China.
D225G substitution in 7 of 57 patients with severe disease and for 0 of 60 with mild disease

what does Nancy Cox say ?

[mixin]

Latest update for GenBank sequences with mutations at 716 = D225G and mixed signals. gs.

G >A/Mexico/InDRE4114,2009//
G >A/Mexico/InDRE4114,2009//
T >A/Monterrey/3,2009//
G >A/Abakan/02,2009//
G >A/Salekhard/01,2009//
G >A/Tomsk/07,2009//
G >A/Tomsk/08,2009//
G >A/Vladivostok/01,2009//
R >A/Sw/4/Mexico,2009/04/
R >A/Nebraska/02,2009/04/
G >A/NY/04,2009/04/
G >A/Mexico/3955,2009/04/02
R >A/CA/07,2009/04/09
R >A/Texas/04,2009/04/14
G >A/Texas/05,2009/04/15
R >A/CA/13,2009/04/21
R >A/Texas/10,2009/04/23
G >A/Texas/11,2009/04/23
R >A/NY/31,2009/04/24
R >A/NY/11,2009/04/25
G >A/Georgia/01,2009/04/27
T >A/Sw/Alberta/OTH-33-3,2009/05/03
G >A/Hiroshima/201,2009/06/17
M >A/CA/VRDL31,2009/06/17
G >A/CA/VRDL7,2009/06/17
G >A/CA/VRDL27,2009/06/27
G >A/Argentina/HNRG16,2009/06/29
R >A/Texas/42291877,2009/06/29
G >A/Sao Paulo/53206,2009/07/19
G >A/Rio de Janeiro/4707,2009/07/23
R >A/Finland/614,2009/07/24
R >A/Utah/42,2009/07/24
G >A/Utah/42,2009/07/24
G >A/Rio de Janeiro/5826,2009/07/28
G >A/Catalonia/NS1706,2009/07/29
N >A/Singapore/GP2312,2009/07/31
G >A/Pune/NIV9355,2009/08/
G >A/Rio de Janeiro/7131,2009/08/01
G >A/Sao Paulo/53225,2009/08/01
G >A/Catalonia/NS2001,2009/08/03
G >A/Catalonia/NS2008,2009/08/03
G >A/Rio de Janeiro/7455,2009/08/04
N >A/Singapore/GP2641,2009/08/05
N >A/Singapore/GP2651,2009/08/05
R >A/Norway/2924,2009/08/10
G >A/Rio de Janeiro/14601,2009/08/24
G >A/Roma/ISS1897,2009/08/27
G >A/Roma/ISS1941,2009/08/27
R >A/Nagano/RC1,2009/08/27
G >A/Pune/NIV10278,2009/09/
G >A/Norway/3206-3,2009/09/01
R >A/Bahia/15525,2009/09/05
G >A/Zhejiang-Yiwu/11,2009/09/06
G >A/Zhejiang/DTID-ZJU02,2009/09/07
G >A/Zhejiang/DTID-ZJU03,2009/09/07
R >A/Mexico/InDRE43149,2009/09/28
R >A/Mexico/InDRE50625,2009/10/31
G >A/Egypt/N14644,2009/11/01
R >A/Mexico/InDRE50617,2009/11/01
G >A/Bryansk/IIV2971,2009/11/11
G >A/Tver/IIV2969,2009/11/14
G >A/Thessaloniki/2502,2009/11/17
G >A/Kastoria/2636,2009/11/18
G >A/Thessaloniki/2812,2009/11/22
G >A/Perm/01,2009/11/25
G >A/Tver/IIV-183,2009/11/25
G >A/Taraz/01,2009/12/
G >A/IIV-Anadyr/177,2009/12/04
G >A/Yaroslavl/IIV-196,2009/12/04
G >A/Catalonia/NS092145684,2009/12/10
R >A/NY/7216,2009/12/21
G >A/Karasuk/01,2010/01/04
G >A/Kavala/219,2010/01/12
G >A/Thessaloniki/206,2010/01/12
G >A/Thessaloniki/225,2010/01/13
G >A/Orenburg/IIV-13,2010/03/02
716 mxha9 76 -:126 A:2971 G:52 M:1 N:3 R:18 T:2

[Ronan Kelly]

hattip HenryN @RLFT
Volume 16, Number 5–May 2010
Dispatch
Transmission of Hemagglutinin D222G Mutant Strain of Pandemic (H1N1) 2009 Virus
Simona Puzelli, Marzia Facchini, Domenico Spagnolo, Maria A. De Marco, Laura Calzoletti, Alessandro Zanetti, Roberto Fumagalli, Maria L. Tanzi, Antonio Cassone, Giovanni Rezza, Isabella Donatelli, and the Surveillance Group for Pandemic A (H1N1) 2009 Influenza Virus in Italy1
Author affiliations: National Institute of Health, Rome, Italy (S. Puzelli, M. Facchini, D. Spagnolo, M.A. De Marco, L. Calzoletti, A. Cassone, G. Rezza, I. Donatelli); Università degli Studi di Milano, Milan, Italy (A. Zanetti); Università degli Studi di Milano-Bicocca, Milan (R. Fumagalli); and Università degli Studi di Parma, Parma, Italy (M.L. Tanzi)

Suggested citation for this article

Abstract
A pandemic (H1N1) 2009 virus strain carrying the D222G mutation was identified in a severely ill man and was transmitted to a household contact. Only mild illness developed in the contact, despite his obesity and diabetes. The isolated virus reacted fully with an antiserum against the pandemic vaccine strain.
On November 20, 2009, the Norwegian Institute of Public Health reported to the World Health Organization a mutation in the hemagglutinin (HA) of pandemic (H1N1) 2009 virus, consisting in a change of aspartic acid (D) with glycine (G) at aa 222. The mutation had been detected in 3 patients (the first 2 fatal cases in the country and in 1 patient with severe pneumonia) among ≈70 other patients with pandemic (H1N1) 2009, suggesting that it was not widespread in Norway (1). The same mutation has been also detected in Brazil, China, Japan, Mexico, Ukraine, the United States, France, and Spain (1,2).

The D-to-G mutation among the 1918 influenza virus variants (3) correlated with a shift from α2-6–linked sialic acid preference to a dual α2-3/α2-6 specificity. However, whether such a mutation may alter receptor binding specificity in the pandemic (H1N1) 2009 virus is unknown.

Although several pandemic (H1N1) 2009 viral strains sharing this mutation were detected in fatal cases, the same mutation also was detected in some mild cases; conversely, viruses from numerous fatal cases have not shown the same mutation. Thus, the clinical and public health significance of this finding remains unclear. The mutation appears to occur sporadically and spontaneously. No links between the small number of patients infected with the mutated virus have been found, and the mutation did not appear to spread (4). On the basis of results from a retrospective HA1 sequence analysis performed on pandemic (H1N1) 2009 viral isolates in Italy, we report on a transmission event of this virus carrying the D222G mutation.

The Study
We reexamined the HA sequences of 130 influenza A (H1N1) virus strains identified from patients affected by pandemic (H1N1) 2009. The neuraminidase sequences of some of these viruses also have been analyzed.

Figure Link to picture:
http://www.cdc.gov/eid/content/16/5/863-F.htm
Figure. Phylogenetic relationships of hemagglutinin (HA) 1 sequences of pandemic (H1N1) 2009 viruses in Italy obtained from the National Influenza Centre (NIC)–Istituto Superiore di Sanità (ISS) and the National Center for Biotechnology Information...


All 130 strains had been obtained from clinical samples (nasal, pharyngeal, or nasopharyngeal swabs and/or tracheal aspirates) collected during May–November 2009 in the context of virologic surveillance conducted by the National Influenza Centre, in collaboration with the regional laboratory network. These samples were obtained to study the evolution of the pandemic strain. Forty-one HA gene sequences examined in the present study were retrieved from the National Center for Biotechnology Information, 3 from the Global Initiative on Sharing Avian Influenza Data database, and 86 HA sequences (47 directly from the clinical samples and 39 from cell culture supernatant) were obtained at the National Influenza Centre (NIC) with the following procedure. Viral RNAs were extracted by using the QIAamp Viral RNA Mini Kit (QIAGEN, Santa Clara, CA, USA) and amplified by reverse transcription–PCR (RT-PCR) (5). HA amplicons were sequenced by using the BigDye Terminator Cycle-Sequencing Ready Reaction (Applied Biosystems, Foster City, CA, USA) and ABI Prism 310 DNA sequencer (Applied Biosystems). All the NIC sequences were deposited in the GenBank database under the accession numbers reported in the Figure. Sequences were assembled and aligned using Lasergene package, version 4.0 (DNASTAR, Madison, WI, USA). BioEdit software version 4.0 (www.mbio.ncsu.edu/BioEdit/bioedit.html) of the MEGA software package (www.megasoftware.net) was used to estimate phylogenies from the nucleotide sequences and to construct phylogenetic trees by using the neighbor-joining algorithm and maximum-likelihood method.

Among 130 patients, 23 of whom had severe disease (i.e., requiring hospitalization), only 1 was infected with a virus showing the D222G change. The patient, a man 25 years of age from northern Italy, had a febrile illness on August 17. One week later, he was admitted to an intensive care unit with severe pneumonia and acute respiratory distress syndrome, which resolved after treatment with extracorporeal membrane oxygenation. Influenza A (H1N1) viral genome showing the D222G mutation was identified through direct sequencing of nasopharyngeal swab and tracheal aspirate collected on August 27. No sequence could be retrieved from a nasal wash, which was obtained the same day and was positive in real-time RT–PCR for pandemic (H1N1) 2009 virus. No viral growth was detected in MDCK cells seeded with both clinical samples.

To identify possible transmission chains of the mutated virus, we analyzed the genome of the viral strain detected in the throat swab of the father of the index case-patient, 55 years of age, who was obese and had diabetes. He became moderately ill on August 25 but did not require hospitalization or antiviral treatment. The virus isolated in MDCK cells from the sample obtained on August 27 had the same HA mutation, D222G. Viral strains from index and contact cases were susceptible to oseltamivir, as determined by lack of the specific oseltamivir-resistance marker (His274Tyr, N2 numbering) in neuraminidase sequences, which were identical in both viral strains. Additional samples analyzed from close contacts (i.e., 4 healthcare workers, 4 family members, and 2 friends) of the 2 patients all were negative for pandemic (H1N1) 2009 virus.

Comparison of the 2 HA1 sequences from the index case-patient and his father showed an additional substitution in the latter (G155E), which is located close to the receptor-binding pocket. Furthermore, sequence analyses showed that all virus strains containing a change in HA1 position 222 (D222G or D222E) also showed a second substitution in position 203 (D203T), when compared with the A/California/7/2009 vaccine strain (Figure). However, the effect of this second mutation on the HA receptor-binding properties is still unclear. The HA1 genes from the index and contact case-patients shared 2 additional nucleotide changes, 1 synonymous substitution (T504C, N1 numbering) not found in any other sequence analyzed in the present study and another nucleotide change resulting in an amino acid substitution (P297S, N1 numbering), detected only in a small number of sequences from Italy. Hemagglutination-inhibition test of the isolated virus did not show substantial reduction in its reactivity with an antiserum against pandemic (H1N1) 2009 vaccine, as compared with the reactivity of an influenza virus A/California/7/2009 strain not carrying the G155E mutation (Table). Link: http://www.cdc.gov/EID/content/16/5/863-T.htm


Conclusions
Identification of a pandemic (H1N1) 2009 virus strain carrying the D222G mutation and its association with the first fatal cases of influenza in Norway raised some concern about emergence of a viral strain with increased pathogenicity. No data have been reported on transmission capacity of this and other D222G variants, occasionally identified worldwide. Our findings suggest that the D222G mutated virus is to some extent transmissible. However, a number of close contacts were identified who did not acquire the infection.
Whether the mutated virus may have a lower fitness for receptors in the high respiratory tract, which may affect transmission, remains undefined. Furthermore, the mutation, which was first found in a severely affected man, was transmitted to a family member (father), who had only a mild illness, despite risk for severe infection. The HA1 sequence from this latter case presented an additional amino acid substitution (G155E), which was not found in any other sequence analyzed in our study and rarely detected among all sequences available from GenBank. Recent data suggest that amino acid substitution at this position may be critical for the switch from dual α2-3/α2-6 binding specificity to α2-6 linkage (6), which is preferentially recognized by human influenza viruses and expressed mainly in the upper respiratory tract. This change might be partially responsible for the milder influenza illness developed by the father of the index case-patient. In addition, the G155E mutation in laboratory-generated variants of pandemic (H1N1) 2009 virus has been associated with loss of antigenicity (7). In our study, the natural isolates of the virus carrying both the G155E and the D222G mutations had comparable antigenicity with the A/California/7/09-vaccine strain. Finally, our data do not support the association of the D222G mutation with severe disease.
Acknowledgments
We thank Tiziana Grisetti for editing the manuscript and F. Fazio for encouragement and support.

This study was supported by an Italian Ministry of Health research grant.

Dr Puzelli is a research biologist in the Department of Infectious, Parasitic and Immune-mediated Diseases at the National Institute of Health, Rome, Italy. Her research interests include molecular mechanisms of genetic variability of influenza viruses and antiviral susceptibility.

References
1.World Health Organization. Public health significance of virus mutation detected in Norway. Pandemic (H1N1) 2009. Briefing note 17 [cited 2009 Nov 20]. http://www.who.int/csr/disease/swine...ng_20091120/en
2.European Centre for Disease Prevention and Control Daily Update. Pandemic (H1N1) 2009 [cited 2009 Nov 30]. http://ecdc.europa.eu/en/healthtopic...rt_0900hrs.pdf
3.Stevens J, Blixt O, Glaser L, Taubenberger JK, Palese P, Paulson JC, et al. Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol. 2006;355:1143–55. PubMed DOI
4.World Health Organization. Preliminary review of D222G amino acid substitution in the haemagglutinin of pandemic influenza A (H1N1) 2009 viruses [cited 2010 Mar 22]. http://www.who.int/csr/resources/pub.../en/index.html
5.Surveillance Group for New Influenza A. Virological surveillance of human cases of influenza A(H1N1)v virus in Italy: preliminary results. Euro Surveill. 2009;14:19247.
6.Takahashi T, Hashimoto A, Maruyama M, Ishida H, Kiso M, Kawaoka Y, et al. Identification of amino acid residues of influenza A virus H3 HA contributing to the recognition of molecular species of sialic acid. FEBS Lett. 2009;583:3171–4. PubMed DOI
7.Chen Z, Wang W, Zhou H, Suguitan AL Jr, Shambaugh C, Kim L, et al. Generation of live attenuated novel influenza virus A/California/7/09 (H1N1) vaccines with high yield in embryonated chicken eggs. J Virol. 2010;84:44–51.
Figure
Figure. Phylogenetic relationships of hemagglutinin (HA) 1 sequences of pandemic (H1N1) 2009 viruses in Italy obtained from the National Influenza Centre (NIC)–Istituto Superiore di Sanità (ISS) and the National Center for Biotechnology Information...

Table Link: http://www.cdc.gov/EID/content/16/5/863-T.htm
Table. Hemagglutination-inhibition test results of pandemic (H1N1) 2009 viruses, Italy

Suggested Citation for this Article
Puzelli S, Facchini M, Spagnolo D, De Marco MA, Calzoletti L, Zanetti A, et al. Transmission of hemagglutinin D222G mutant strain of pandemic (H1N1) 2009 virus. Emerg Infect Dis [serial on the Internet]. 2010 May [date cited]. http://www.cdc.gov/EID/content/16/5/863.htm

DOI: 10.3201/eid1605.091858



1Members of the Surveillance Group for Pandemic A(H1N1) 2009 Influenza Virus in Italy: Istituto Superiore di Sanitá (ISS) (National Institute of Health): Livia Di Trani, Annapina Palmieri, and Concetta Fabiani; Regional Laboratories (director name in parentheses): Istituto di ricovero e cura a carattere scientifico, Rome (Maria R. Capobianchi); Catholic University, Rome (Giovanni Fadda); Padua (Giorgio Palù); Florence (Alberta Azzi); Palermo (Fabio Tramuto); Triest (Pierlanfranco D'Agaro); Cosenza (Cristina Giraldi); Naples (Ciro Esposito); Ancona (Patrizia Bagnarelli); Turin (Valeria Ghisetti); and Genoa (Filippo Ansaldi).
http://www.cdc.gov/eid/content/16/5/863.htm

[mixin]

Updated mutations at 715 = D225N

C:\gs>travel1 mxha9 715
T >A/Monterrey/3,2009//
R >A/Sw/4/Mexico,2009/04/
R >A/South Carolina/09,2009/04/26
R >A/Arizona/04,2009/04/27
A >A/Argentina/HNRG8,2009/06/11
A >A/NY/4099,2009/06/13
A >A/NY/4576,2009/07/08
A >A/Texas/43132503,2009/07/13
R >A/Utah/42,2009/07/24
A >A/Sao Paulo/53838,2009/08/01
A >A/Sao Paulo/53845,2009/08/02
A >A/Malaysia/8860,2009/08/08
R >A/Mexico/InDRE36529,2009/08/08
R >A/Nagano/RC1,2009/08/27
A >A/Nagano/RC1,2009/08/27
R >A/Bahia/15525,2009/09/05
R >A/Mexico/InDRE41741,2009/09/14
R >A/Mexico/InDRE50625,2009/10/31
A >A/Egypt/N14648,2009/11/
R >A/Mexico/InDRE50617,2009/11/01
A >A/Russia/100,2009/11/01
A >A/Orenburg/IIV2974,2009/11/16
A >A/Ankara/26,2009/11/24
A >A/Yaroslavl/IIV-198,2009/12/05
24 -:126 A:13 G:3023 R:10 T:1

[gsgs]

http://www.ncbi.nlm.nih.gov/pubmed/20718801
Surveillance of autopsy cases for D222G in Alberta, Canada
some specimens from autopsy patients were positive for D222N, none were positive for D222G

[tetano]

Clin Microbiol Infect. 2010 Oct 14. doi: 10.1111/j.1469-0691.2010.03403.x. [Epub ahead of print]
Severe outcome of influenza A/H1N1/09v infection associated with 222G/N polymorphisms in the haemagglutinin: a multicenter study.

Baldanti F, Campanini G, Piralla A, Rovida F, Braschi A, Mojoli F, Iotti G, Belliato M, Conaldi PG, Arcadipane A, Pariani E, Zanetti A, Minoli L, Emmi V.

  Molecular Virology Unit  Intensive Care Unit I  Intensive Care Unit II, Fondazione IRCCS Policlinico San Matteo, Pavia  Institute of Microbiology and Virology  Intensive Care Unit, ISSMET, Palermo  Dipartimento di Sanità Pubblica-Microbiologia-Virologia, Università degli Studi di Milano, Milan  Institute of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy.
Abstract

In a multicenter study influenza A/H1N1/09v 222G/N variants were more frequently detected in patients admitted to intensive care unit (ICU) for invasive mechanical ventilation or extracorporeal membrane oxygenation (ECMO) (10/23; 43.5%) than in patients hospitalized in other units (2/27; 7.4%) and community patients (0/81; 0.0%) (p<0.01). A significantly higher virus load (p=0.02) in the lower vs upper respiratory tract was observed. Predominance of 222G/N variants in the lower respiratory tract (40% of total virus population) vs upper respiratory tract (10%) was shown by clonal analysis of HA sequences in paired nasal swab and bronchoalveolar lavage samples. The time from illness onset to sampling was significantly longer in patients with severe infection vs community patients (p<0.001). Conclusions: i) 222G/N variants showed increased virulence; ii) mutant variants were likely selected in individual patients, iii) the longer duration of illness might have favored the emergence of adaptive mutations through multiple replication cycles.
Copyright © 2010 European Society of Clinical Microbiology and Infectious.

PMID: 20946414 [PubMed - as supplied by publisher]

http://www.ncbi.nlm.nih.gov/pubmed/20946414

[NS1]

HA 225G with 158E Series in Jiangsu China
http://pf11.blogspot.com/2010/12/ha-...n-jiangsu.html

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 fatal 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 158E and 225G amino acid combination came to be of interest to GeneWurx due to the variant sub-species produced from this Ukrainian sample. As additional sequences emerged in a similar geography including RussiaBelgorod2_2010_03_15 as predicted with 230I, emergent behaviour around these amino acid positions was noted for closer surveillance and the diverse nucleotide coding for 225G (Gga) from an overlay of 225G (GgT) onto a 225E (GAa) substrate was packaged onto the corresponding watch list.

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 our 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-PF11_Ω 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,
. . . . . . . . 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)

[NS1]

HA 225G Paired with 156E & 188T in Diverse Deposit from Australia
http://pf11.blogspot.com/2010/12/ha-...n-diverse.html

Last Updated 2010-12-16

A WHO Collaborating Centre for Reference and Research on Influenza released a large group of sequences at GISAID on 2010-12-14 primarily from Australia. 225G appears on two different backgrounds during the same timeframe, one with the H7N7 polymorphism that has been associated with viral conjunctivitis, 188T. OzBrisbane209_51F_2010_08_09 also demonstrates a 156E polymorphism just upstream from the section at aa158 and aa159 that has produced so many "Low Reactor" / Vaccine Escape strains.

156E was found in the 1976 Swine Flu with 225G, but until now has not been documented in the pH1N1 with 225G, though the individual change has been located in 9 sequences [New Zealand, Japan (2), China 2010, Hungary, Germany (2) and the United States (2)]. Changes at residues 156, 157 and 158 are known to increase viral replication speed and success on the pandemic H1N1 background. At the MedImmune growth speed experiments preparing for the 2009 Live Attenuated Influenza Vaccine, the combination of 156E and 225G created the highest pathological output (V5-153E) (J Virol. 2010 January; 84(1): 44–51). Though the V5-153E strain produced the most beneficial viral output, the lineage was impeached due to a 16 fold titers reduction in the antigenicity tests indicating a profound level of "Low Reactor".

This Brisbane sample has not yet been tagged for Vaccine Escape.

As a set of coincident events, several zoonotic Influenza reservoirs have also gained 156E in recent years. This group of reservoirs appears to parallel individual changes coming into the human H1N1 pandemic. H5N1 human cases in Vietnam carry this change from 2004. The most current updates of Avian sequences from Egypt H5N1 in 2009 up to July 2010 demonstrate emergent 156E with 225G (Ggg). One particular Egyptian bird, ckEgypt10135ss_2010_03, shows 156E, 225G and a variant coding for syn338G (GGg).

H3N8 equine and swine samples are on record producing this emergent change. H7N3 and H7N7 each provide material for nucleotide donation at the first codon base while an extensive percentage of the H10N7 sequences on file carry the 156E. A hybrid swine H1N1 sequence from Iowa,
swIowa44837_1_2009_11_08_xL, was recently published after a one year lag with 156E, 188R, 225N, 230I & syn346G.

This Brisbane strain is emergent and aggregates 225G with markers found throughout the coastal United States during late 2009 and 2010. On a similar note, a sub-clade may perhaps be forming from Jiangsu Province, China using 225G paired with 158E and a change at amino acid position 454.

The 215T found in the sequence from the 9 year old boy, Sydney202_9M_2010_07_18, confirms an increase in the genetic diversity of the post-pandemic reservoir found during the official pandemic on an eastern European sequence, PolandWarsawINS316_2009_12_08.

As we have previously reported, 100% of the Hemagglutinin positions between 186 and 248, including antigenic areas of the Receptor Binding Domain (RBD/RBS), are on record as polymorphic. No position in that range is stable. Many positions rate multiple changes. Protein revision is documented at 60 of the 63 positions (95%), engaging the potential for antibody resistance (natural immune escape and vaccine escape).

. . . . OzBrisbane209_51F_2010_08_09 (
. . . . . . . . 156E [H2N3, H3N8, H5N1, H10N7],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 225G,
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [OzVictoria670_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,
. . . . . . . . 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)

. . . . Sydney202_9M_2010_07_18 (
. . . . . . . . 34D,
. . . . . . . . syn44L,
. . . . . . . . 97N,
. . . . . . . . syn106E,
. . . . . . . . 128D,
. . . . . . . . 215T [PolandWarsawINS316_2009_12_08]
. . . . . . . . 225G,
. . . . . . . . 253A,
. . . . . . . . syn362S,
. . . . . . . . 377K,
. . . . . . . . 439G [Guangdong5024_2009_10_20])

Supporting Sequences

. . . . 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])

. . . . India8910_2010_05_08 (
. . . . . . . . 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])

. . . . Texas45131774_2009_09_13 (
. . . . . . . . syn223V [H5N1, H6N1],
. . . . . . . . 454N [H7N3, H7N7, H9N2]
. . . . . . . . . . . . . . [IndiaPune9355_2009_08 with 225G,
. . . . . . . . . . . . . . IndiaBlore236_2009_06 with 226R,
. . . . . . . . . . . . . . SouthCarolina18_2009_09_16_VxX with 224K,
. . . . . . . . . . . . . . FL_Pen210_2009_11_10 with 225E])

. . . . PolandWarsawINS316_2009_12_08 (
. . . . . . . . 22I,
. . . . . . . . syn92T,
. . . . . . . . 119M,
. . . . . . . . 165N,
. . . . . . . . syn178V,
. . . . . . . . syn186S,
. . . . . . . . 215T,
. . . . . . . . syn256Y,
. . . . . . . . syn275V,
. . . . . . . . 463V)

[Giuseppe Michieli]

Source: Eurosurveillance: http://www.eurosurveillance.org/View...rticleId=19760 also at FT.

Images URL:

(1) Influenza A H1N1 (2009) phylogenetic tree, http://www.eurosurveillance.org/imag...IS_Fig3new.jpg
(2) Influenza B, phylogenetic tree, http://www.eurosurveillance.org/imag...LLIS_Fig4-.jpg

[1]


[2]


-
------

[NS1]

UK Fatality Sequences Relate to US and Iran

The US CDC today released a small set of sequences at GISAID spanning June to November 2010. As the UK Severe Wave is the current topic of interest, we have profiled 6 of these sequences from today against the UK Fatality Sequences that have been published.  Five of the sequences are from the United States and one is from Bangladesh.

Previously, the UK HPA released a small group of sequences in two deposits at GISAID related to the present severe wave filling the ICU wards in the UK. A concurrent paper ¹ was published in early January with a phylogenetic tree. Several of the fatalities noted on the HPA Ellis Figure3 ¹ phylogenetic tree have been included in the two sequence deposits.

So that focus may occur at the clinical outcomes of highest priority, GeneWurx has prepared a fresh phylogenetic tree with annotation in progress that may prove useful to those investigating the ongoing divergency within this zoonoticly active pH1N1 viral reservoir.  UK Fatalities, UK Severe cases (225G), UK potential Vaccine Escape cases (158E, 159K) and cases from the US, Australia, Iran and Bangladesh are profiled.

GeneWurx_Global_Spread_of_Divergence_UK_US_Iran_v0 .jpg

The GeneWurx annotation for the full HPA Ellis Figure3 ¹ has been recently revised and Version 5 of the Emerging Genetics spreadsheet is available with several additions including two of the recent US sequences of interest and the Bangladeshi sequence.

• UK_2010_Phylo_ELLIS_Fig3new_4_GISAID_Notated_2011_ 01_13.JPG


• GeneWurx_UK_December_Emerging_Genetics_v5.xls

A pattern that has been expected is demonstrated in Kentucky09_40F_2010_11_01 with 158E, 188T and 225G on a similar background as the OzBrisbane209_51F_2010_08_09 sequence carrying 156E, 188T and 225G.  Though these two sequences share extensive homology, the tree and polymorphism details will show that overall the reservoir is diversifying and creating branches with minimal leaf count by acquiring and recombining rare and novel polymorphisms also found in animal reservoirs.

US Sequences

. . . . Indiana05_78F_2010_06_11 (
. . . . . . . . 100N,
. . . . . . . . 115K,
. . . . . . . . syn270I,
. . . . . . . . 377K)

. . . . Indiana06_9M_2010_07_29 (
. . . . . . . . #11V,
. . . . . . . . #8A,
. . . . . . . . syn36L,
. . . . . . . . syn99I,
. . . . . . . . 233H,
. . . . . . . . syn256Y,
. . . . . . . . syn282C,
. . . . . . . . syn283Q,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn428L,
. . . . . . . . 522A)

. . . . Kentucky08_xF_2010_10_11 (
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . Utah05_29F_2010_10_12 (
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 289M,
. . . . . . . . syn297N,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 396I,
. . . . . . . . 454N,
. . . . . . . . syn478C)

. . . . Kentucky09_40F_2010_11_01 (
. . . . . . . . 17G,
. . . . . . . . 100N,
. . . . . . . . 158E,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . syn452V,
. . . . . . . . 454N,
. . . . . . . . syn467C)

Bangladesh Sequence

. . . . Bangladesh8003_27M_2010_09_16 (
. . . . . . . . syn12A,
. . . . . . . . 137T,
. . . . . . . . 186P,
. . . . . . . . 225N mix wt,
. . . . . . . . syn297N,
. . . . . . . . syn326S,
. . . . . . . . syn383N,
. . . . . . . . syn388K,
. . . . . . . . 444K,
. . . . . . . . 447S,
. . . . . . . . syn474C)

UK Fatality Sequences

. . . . UKEngland5040499_2010_12_f (
[match GhanaFS10_4259_2010_08_27 less 213S]
. . . . . . . . 100N,
. . . . . . . . 188T,
. . . . . . . . 213S,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn537S)

. . . . UKWhiteChapel4880374_2M_2010_11_28_f (
. . . . . . . . 0A [Arizona05_2010_05_01
. . . . . . . . . . . . . . . with syn338G & 377K,
. . . . . . . . . . Alabama08_2009_12_04
. . . . . . . . . . . . . . . with syn226Q, 310A mix & 506V,
. . . . . . . . . . RussiaPerm_ZTS_2009_11_30
. . . . . . . . . . . . . . . with 377K & syn475D,
. . . . . . . . . . RussiaBelgorod01_2009_11_30,
. . . . . . . . . . RussiaBelgorod05_2009_11_30,
. . . . . . . . . . Boston634_2009_11_09
. . . . . . . . . . . . . . . with 100N & syn270I],
. . . . . . . . syn55L [S9, H5N1],
. . . . . . . . . . . . . . [Iran16273_2009_11_22 with 226R
. . . . . . . . . . . . . . NZ_Waikato2_2010_01_04 with 233H,
. . . . . . . . . . . . . . tkOntarioFAV117_1C_2009_12_07, et al],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [OzBrisbane209_51F_2010_08_09
. . . . . . . . . . . . . . . . . . . . with 156E & 225G,
. . . . . . . . . . . . . . . Arizona05_2010_05_11 with 0A,
. . . . . . . . . . . . . . . Swine Asia 2005 with 0A, et al]
. . . . . . . . 377K,
. . . . . . . . 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, et al],
. . . . . . . . syn529L)

. . . . UKCambridge118_4F_2010_11_19_f (
. . . . . . . . syn118E,
. . . . . . . . 137T [41 sequences at GISAID],
. . . . . . . . syn163K,
. . . . . . . . 186P,
. . . . . . . . syn251L,
. . . . . . . . syn293L,
. . . . . . . . syn363G [21 sequences at GISAID],
. . . . . . . . syn455Q,
. . . . . . . . syn474C,
. . . . . . . . 504G,
. . . . . . . . 513V)

. . . . UKEngland4500186_2010_11_f (
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . 190Y [Avian H6N1],
. . . . . . . . . . [SwedenMalmoe1_2010_01_01_xL
. . . . . . . . . . . . with 377K, syn413K,
. . . . . . . . . . Brasil7450_2009_07_22
. . . . . . . . . . . . with 157E mix wt],
. . . . . . . . 377G [H2N3],
. . . . . . . . . . . . . [H5N1 Human Egypt Preschool 2009, H5N1 Human Indonesia 2005],
. . . . . . . . . . . . . [H6N1 2009],
. . . . . . . . . . . . . [US Swine 1957-1978],
. . . . . . . . . . . . . [IranBandarAbbas5096_2010_10_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C,
. . . . . . . . . . . . . Florida13_2010_08_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C, 512M,
. . . . . . . . . . . . . . Iowa05_2010_05_04
. . . . . . . . . . . . . . . . . . . with 208K, syn516I,
. . . . . . . . . . . . . . swSouthDakota1_2010_04_27,
. . . . . . . . . . . . . . TexasAF2647_2010_04_11
. . . . . . . . . . . . . . . . . . . with 200S, syn214K, syn276H,
. . . . . . . . . . . . . . swIowa02999_2010_04_01,
. . . . . . . . . . . . . . UtahAF2653_2010_03_14
. . . . . . . . . . . . . . . . . . . with syn253V,
. . . . . . . . . . . . . . North Carolina05_2010_02_24
. . . . . . . . . . . . . . . . . . . with 259V,
. . . . . . . . . . . . . . Kentucky04_2010_02_22
. . . . . . . . . . . . . . . . . . . with syn488D,
. . . . . . . . . . . . . . Minnesota02_2010_02_17
. . . . . . . . . . . . . . . . . . . with 259V, 509D,
. . . . . . . . . . . . . . SouthCarolina01_2010_01_27
. . . . . . . . . . . . . . . . . . . with syn238E, syn488D,
. . . . . . . . . . . . . . AnasPlatBelgium04328_pcs17_2010_01_21
. . . . . . . . . . . . . . . . . . . with syn474C,
. . . . . . . . . . . . . . GermanyAF2208_2010_01_20
. . . . . . . . . . . . . . . . . . . with #1T, 225E,
. . . . . . . . . . . . . . NorthCarolina03_2010_01_20
. . . . . . . . . . . . . . . . . . . with 225G mix, 259V, syn275V,
. . . . . . . . . . . . . . NewMexico01_2010_01_05
. . . . . . . . . . . . . . . . . . . with 430I, syn445V, syn490P,
. . . . . . . . . . . . . . swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . with #1T, 0A, 189T, syn338G,
. . . . . . . . . . . . . . . . . . . . . . syn451K, syn474C, syn456L, syn529L,
. . . . . . . . . . . . . . Moldova5053_2009_12_11
. . . . . . . . . . . . . . . . . . with 173R, 176I, 225A, 225G mix wt, syn286K,
. . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . with syn297N, syn343G, 471H,
. . . . . . . . . . . . . . KoreaAF2411_2009_11_11
. . . . . . . . . . . . . . . . . . . with 237I, syn286K,
. . . . . . . . . . . . . . England94840077_2009_11
. . . . . . . . . . . . . . . . . . . with 259T,
. . . . . . . . . . . . . . BahrainN11892_2009_10
. . . . . . . . . . . . . . . . . . . with 208K,
. . . . . . . . . . . . . . Nevada16_2009_10_02
. . . . . . . . . . . . . . . . . . . with 464R mix wt,
. . . . . . . . . . . . . . Tasmania2005_2009_07_03
. . . . . . . . . . . . . . . . . . . with 289M,
. . . . . . . . . . . . . . Texas42303371_2009
. . . . . . . . . . . . . . . . . . . with syn456L, syn507K],
. . . . . . . . syn408E,
. . . . . . . . syn474C,
. . . . . . . . 512M,
. . . . . . . . 530I)

. . . . UKEngland4640543_2010_11_f (
[match to UKEngland4940476_2010_12 less 225G plus 190G]
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 190G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

. . . . UKWhiteChapel4780352_5M_2010_10_26_f (
. . . . . . . . syn58C,
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . syn131S,
. . . . . . . . syn210S,
. . . . . . . . 377K)

. . . . UKEngland4380108_2010_10_f (
. . . . . . . . syn67N,
. . . . . . . . 100N,
. . . . . . . . 128D,
. . . . . . . . 144V [Boston703 and Ireland],
. . . . . . . . 224K,
. . . . . . . . syn235T,
. . . . . . . . 377K,
. . . . . . . . 529M)

. . . . UKBirmingham3220137_44F_2010_08_07_f (
. . . . . . . . #8A,
. . . . . . . . 175K,
. . . . . . . . 311E,
. . . . . . . . 377K,
. . . . . . . . syn385V,
. . . . . . . . syn451K,
. . . . . . . . syn454S,
. . . . . . . . syn494E,
. . . . . . . . 537G)

Severe Sequences

. . . . UKEngland4940476_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg) [Regional Marker 2009 (tTA)]
. . . . . . . . . . . . . . . . . . . . [TexasAF2588_2009_10_04,
. . . . . . . . . . . . . . . . . . . . TexasJMS404_2010_01_08],
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [H6N1]
. . . . . . . . . . . . . . . [Regional Marker UK 2009]
. . . . . . . . . . . . . . . [UKEngland4880378_2010_12 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland4640543_2010_11_f with syn179L, 188T, 190G
. . . . . . . . . . . . . . . UKEngland4920303_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland142_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland4860049_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . UKEngland126_2010_11 with syn179L, 188T,
. . . . . . . . . . . . . . . NZChristchurch8_2010_07_08
. . . . . . . . . . . . . . . . . . . with syn44L, 97N, syn99I, syn106E, 128D,
. . . . . . . . . . . . . . . . . . . . . . . syn214K, 253A, syn362S, 377K,
. . . . . . . . . . . . . . . Calif06_2010_04_05 with 269V
. . . . . . . . . . . . . . . Hawaii08_2010_04_12
. . . . . . . . . . . . . . . . . . . with 159D, 269V, 312R, 313K,
. . . . . . . . . . . . . . . Ethiopia13_2010_02_10
. . . . . . . . . . . . . . . . . . . with 100N, syn163K, 269V, 324I, syn360Q, syn455Q,
. . . . . . . . . . . . . . . Philippines824_2010_02_17 with 165N,
. . . . . . . . . . . . . . . Kosova876_2009_12_22,
. . . . . . . . . . . . . . . RussiaYakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . . Netherlands2143_2009_11_16 with syn179L (tTA),
. . . . . . . . . . . . . . . RussiaYaroslavl_CHMV_2009_11_10_f with 224K & 225G mix
. . . . . . . . . . . . . . . AntwerpINS221_2009_10_28 with syn179L (tTA)],
. . . . . . . . 454N)

. . . . UKEngland4880378_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)

Potential Vaccine Escape Sequences

[Diversity with Vaccine Escape Potential]

. . . . UKEngland106_2010_11 (
. . . . . . . . 0A,
. . . . . . . . syn55L,
. . . . . . . . 158E mix wt,
. . . . . . . . 188T,
. . . . . . . . syn258F,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 452I [],
. . . . . . . . 454N,
. . . . . . . . syn529L)

. . . . UKEngland3380426_2010_08 (
. . . . . . . . syn44L,
. . . . . . . . syn106E,
. . . . . . . . 128D,
. . . . . . . . 159K [NY3230_2010_01_25 with 100N, syn177L, syn231N],
. . . . . . . . 377K)

Iran Sequences

. . . . IranShahriar5336_2010_12_06 (
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . syn297N [H3N8 gadwallRussiaAltai1325_2007_09],
. . . . . . . . . . . . . . . [H5N1],
. . . . . . . . . . . . . . . [Wisconsin08_2010_08_10
. . . . . . . . . . . . . . . . . . . . . . with 39R, syn78S, 137T, 186P, syn297N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn326S, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn413K, 444K, syn474C,
. . . . . . . . . . . . . . . CalifVRDL2_2010_01_11
. . . . . . . . . . . . . . . . . . . . . . with syn121P & 502K,
. . . . . . . . . . . . . . . YaroslavlIIV196_2009_12_04_f
. . . . . . . . . . . . . . . . . . . . . . with syn159N, 225G,
. . . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . . . . with syn343G, 377G, 471H,
. . . . . . . . . . . . . . . Brussels243_2009_11_09
. . . . . . . . . . . . . . . . . . . . . . with syn44L, syn159N & syn323N,
. . . . . . . . . . . . . . . Australia6_2009_07_18
. . . . . . . . . . . . . . . . . . . . . . with syn159N, 233H]
. . . . . . . . syn326S [Wisconsin08_2010_08_10
. . . . . . . . . . . . . . . . . . . . . . with 39R, syn78S, 137T, 186P, syn297N,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn326S, syn346G, syn388K,
. . . . . . . . . . . . . . . . . . . . . . . . . . syn413K, 444K, syn474C,
. . . . . . . . . . . . . . . Zhongyuan1643_2009_11_16
. . . . . . . . . . . . . . . . . . . . . . with 208G],
. . . . . . . . syn383N [H3N8],
. . . . . . . . syn388K [H3N8, H5N1, S7],
. . . . . . . . . . . . . . . [OzVictoria508_2010_07_24
. . . . . . . . . . . . . . . . . . . . . . . with 238D,
. . . . . . . . . . . . . . . swIowa44837_1_2009_11_08_xL
. . . . . . . . . . . . . . . . . . . . . . . with 188R, 225N & 230I,
. . . . . . . . . . . . . . . Utah20_C2_2_2009_07_25_VxX
. . . . . . . . . . . . . . . . . . . . . . . with 159D & 227G, et al],
. . . . . . . . syn411N (AAc) [H7N3 & H7N7 donor ATc],
. . . . . . . . 444K (AAg) [H3N8 gAg],
. . . . . . . . syn474C [H3N8, Avian H1N1 2010],
. . . . . . . . . . . . . . . [Michigan10_2009_06_03 with 137T, 225N, et al])

. . . . IranBandarAbbas5096_2010_10_02 (
. . . . . . . . 72P,
. . . . . . . . 137T (aCA) [H3N8 donor aAT, aGT, aGC],
. . . . . . . . 186P [Avian H12 2008, 2009], [Avian H1N1],
. . . . . . . . syn318A,
. . . . . . . . 377G [H2N3],
. . . . . . . . . . . . . [H5N1 Human Egypt Preschool 2009, H5N1 Human Indonesia 2005],
. . . . . . . . . . . . . [H6N1 2009],
. . . . . . . . . . . . . [US Swine 1957-1978],
. . . . . . . . . . . . . [Florida13_2010_08_02
. . . . . . . . . . . . . . . . . . . with 137T, 186P, syn474C, 512M,
. . . . . . . . . . . . . . Iowa05_2010_05_04
. . . . . . . . . . . . . . . . . . . with 208K, syn516I,
. . . . . . . . . . . . . . swSouthDakota1_2010_04_27,
. . . . . . . . . . . . . . TexasAF2647_2010_04_11
. . . . . . . . . . . . . . . . . . . with 200S, syn214K, syn276H,
. . . . . . . . . . . . . . swIowa02999_2010_04_01,
. . . . . . . . . . . . . . UtahAF2653_2010_03_14
. . . . . . . . . . . . . . . . . . . with syn253V,
. . . . . . . . . . . . . . North Carolina05_2010_02_24
. . . . . . . . . . . . . . . . . . . with 259V,
. . . . . . . . . . . . . . Kentucky04_2010_02_22
. . . . . . . . . . . . . . . . . . . with syn488D,
. . . . . . . . . . . . . . Minnesota02_2010_02_17
. . . . . . . . . . . . . . . . . . . with 259V, 509D,
. . . . . . . . . . . . . . SouthCarolina01_2010_01_27
. . . . . . . . . . . . . . . . . . . with syn238E, syn488D,
. . . . . . . . . . . . . . AnasPlatBelgium04328_pcs17_2010_01_21
. . . . . . . . . . . . . . . . . . . with syn474C,
. . . . . . . . . . . . . . GermanyAF2208_2010_01_20
. . . . . . . . . . . . . . . . . . . with #1T, 225E,
. . . . . . . . . . . . . . NorthCarolina03_2010_01_20
. . . . . . . . . . . . . . . . . . . with 225G mix, 259V, syn275V,
. . . . . . . . . . . . . . NewMexico01_2010_01_05
. . . . . . . . . . . . . . . . . . . with 430I, syn445V, syn490P,
. . . . . . . . . . . . . . swThailandCU_CHK4_2009_01
. . . . . . . . . . . . . . . . . . with #1T, 0A, 189T, syn338G,
. . . . . . . . . . . . . . . . . . . . . . syn451K, syn474C, syn456L, syn529L,
. . . . . . . . . . . . . . Moldova5053_2009_12_11
. . . . . . . . . . . . . . . . . . with 173R, 176I, 225A, 225G mix wt, syn286K,
. . . . . . . . . . . . . . WiscD0128_2009_11_15
. . . . . . . . . . . . . . . . . . . with syn297N, syn343G, 471H,
. . . . . . . . . . . . . . KoreaAF2411_2009_11_11
. . . . . . . . . . . . . . . . . . . with 237I, syn286K,
. . . . . . . . . . . . . . England94840077_2009_11
. . . . . . . . . . . . . . . . . . . with 259T,
. . . . . . . . . . . . . . BahrainN11892_2009_10
. . . . . . . . . . . . . . . . . . . with 208K,
. . . . . . . . . . . . . . Nevada16_2009_10_02
. . . . . . . . . . . . . . . . . . . with 464R mix wt,
. . . . . . . . . . . . . . Tasmania2005_2009_07_03
. . . . . . . . . . . . . . . . . . . with 289M,
. . . . . . . . . . . . . . Texas42303371_2009
. . . . . . . . . . . . . . . . . . . with syn456L, syn507K],
. . . . . . . . syn449Y (TAc) [H3N8 Ttc],
. . . . . . . . syn474C [H3N8])

. . . . IranKaraj5327_2010_12_06 (
. . . . . . . . syn34N [JapanKanagawa74_2010_10_16, et al],
. . . . . . . . 146G [JapanKanagawa74_2010_10_16, et al],
. . . . . . . . 188T,
. . . . . . . . 200T,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . 454N,
. . . . . . . . syn465N [OzBrisbane209_51F_2010_08_09,
. . . . . . . . . . . . . . . . . . . . with 156E & 225G,
. . . . . . . . . . . . . . CalifVRDL131_2009_12_30, et al],
. . . . . . . . syn538F [Brunei218_2010 with 188T])

Australia Sequence

. . . . OzBrisbane209_51F_2010_08_09 (
. . . . . . . . 156E [H2N3, H3N8, H5N1, H10N7],
. . . . . . . . 188T [H6N1, H7N7],
. . . . . . . . 225G,
. . . . . . . . syn338G [H3N8, H4, H5, H6, sw],
. . . . . . . . . . . . . . . [OzVictoria670_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,
. . . . . . . . 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)


1. Ellis J, Galiano M, Pebody R, Lackenby A, Thompson C, Bermingham A, McLean E, Zhao H, Bolotin S, Dar O, Watson JM, Zambon M. Virological analysis of fatal influenza cases in the United Kingdom during the early wave of influenza in winter 2010/11. Euro Surveill. 2011;16(1):pii=19760. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19760

[mixin]

Disclaimer: I am not a scientist, researcher, programmer or file converter so there could be an occassional error.

I finally have the ability to search submissions from both GISAID and Genbank. Thanks to gs for the hours and hours he spent helping me with this.

To tell the difference between my GISAID isolates and his from Genbank, mine include the method of passage and the collection date is a little different.

This first group contains the mutations that give D225N.

R >A/Castro/12274/2010,2010/05/14,E3/E1
R >A/Moldova/351/2010,2010/01/18,clinical sample
A >A/Christchurch/16/2010,2010/07/12,E2
R >A/Hong Kong/2166/2010,2010/07/13,E1
A >A/Hong Kong/2172/2010,2010/07/12,E3
A >A/Christchurch/16/2010,2010/07/12,E2/E2
A >A/Christchurch/16/2010,2010/07/12,E2/E1
A >A/Kenya/3872/2010,2010/07/13,E3
R >A/Bangladesh/8003/2010,2010/09/16,C2/C1
A >A/Alborz/5607/2010,2010/12/01,E2/E1
A >A/YOKOHAMA/1357/2009,2009/10/06,MDCK 2 +2,
A >A/NIIGATA/1371/2009,2009/11/06,MDCK 2 +1
A >A/YAMAGATA/721/2009,2009/12/08,MDCK 1 +3
A >A/India/4725/2009,2009/06/10,X2/C2
A >A/Neimenggu-Hangjinhouqi/SWL51/2009,2009/11/02,E2
A >A/Fujian-Gulou/SWL11951/2009,2009/11/16,E2
R >A/Ukraine/01/2009,2009/10/28,Original
A >A/Ukraine/02/2009,2009/10/28,Original
R >A/Stockholm/92/2009,2009/08/27,original
R >A/Moldova/G-152/2009,2009/10/23,clinical sample
R >A/Kyiv/377/2009,2009/11/07,lung wash
R >A/Chernihiv/452/2009,2009/11/07,lung wash
R >A/Lviv/425/2009,2009/11/07,lung autopsy
R >A/Lviv/639/2009,2009/11/11,lung autopsy
R >A/Azores/13092/2009,2009/11/12,nasopharyngeal swab
R >A/Rivne/836/2009,2009/11/13,lung autopsy
R >A/Chernivtsi/842/2009,2009/11/11,lung autopsy
R >A/Lviv/420/2009,2009/11/09,lung autopsy
A >A/Lviv/646/2009,2009/11/10,lung autopsy
A >A/Lviv/638/2009,2009/11/08,lung autopsy
R >A/Azores/13091/2009,2009/11/20,bronchial wash
R >A/Ivano-Frankivsk/237/2009,2009/10/26,lung autopsy
R >A/Lviv/421/2009,2009/11/09,lung autopsy
R >A/Lviv/645/2009,2009/11/01,lung autopsy
R >A/Rivne/214/2009,2009/10/30,lung autopsy
A >A/Chernivtsi/844/2009,2009/11/11,lung autopsy
R >A/Cherkasy/744/2009,2009/11/01,lung autopsy
R >A/Chernihiv/859/2009,2009/11/14,lung autopsy
A >A/Baden-Wurttemberg/502/2009,2009/12/06,SIAT3, SIAT1
A >A/Ireland/M79555/2009,2009/11/11,pm lung
A >A/Ireland/M79556/2009,2009/11/11,pm lung
R >A/Arizona/04/2009,2009/04/27,E2
R >A/South Carolina/09/2009,2009/04/26,E2
R >A/Utah/42/2009,2009/07/24,Original
A >A/Michigan/10/2009,2009/06/03,C1-1
A >A/Michigan/10/2009,2009/06/03,C1-2
R >A/North Carolina/42/2009,2009/10/14,IR
A >A/South Carolina/47/2009,2009/11/05,E2
R >A/SYDNEY/2501/2009,2009/07/07,original specimen
A >A/VICTORIA/2125/2009,2009/11/08,Clinical Specimen
A >A/Perth/431/2009,2009/07/28,MDCK2
T >A/Monterrey/3/2009
R >A/Sw/4/Mexico/2009/04/
R >A/South Carolina/09/2009/04/26
R >A/Arizona/04/2009/04/27
A >A/Argentina/HNRG8/2009/06/11
A >A/NY/4099/2009/06/13
A >A/NY/4576/2009/07/08
A >A/Texas/43132503/2009/07/13
R >A/Utah/42/2009/07/24
A >A/Sao Paulo/53838/2009/08/01
A >A/Sao Paulo/53845/2009/08/02
A >A/Malaysia/8860/2009/08/08
R >A/Mexico/InDRE36529/2009/08/08
R >A/Nagano/RC1/2009/08/27
A >A/Nagano/RC1/2009/08/27
R >A/Bahia/15525/2009/09/05
R >A/Mexico/InDRE41741/2009/09/14
R >A/Mexico/InDRE50625/2009/10/31
A >A/Ulyanovsk/CRIE-SHTA/2009/10/31
A >A/Egypt/N14648/2009/11/
R >A/Mexico/InDRE50617/2009/11/01
A >A/Russia/100/2009/11/01
A >A/Netherlands/2457b/2009/11/07
A >A/Moscow oblast/CRIE-STV/2009/11/09
A >A/Orenburg/IIV2974/2009/11/16
R >A/Orel/CRIE-AAP/2009/11/20
R >A/Moscow/CRIE-TYD/2009/11/23
A >A/Tambov/CRIE-SPN/2009/11/24
R >A/Ivanovo/CRIE-RNA/2009/11/24
A >A/Ankara/26/2009/11/24
R >A/Tambov/CRIE-LLA/2009/11/30
A >A/Netherlands/2629/2009/12/04
A >A/Yaroslavl/IIV-198/2009/12/05
715  haall 84   -:132 A:42 G:9143 R:41 T:1

This group gives mutations for D225G

G >A/Zhejiang-Haishu/SWL1289/2010,2010/02/11,E1
G >A/Arizona/04/2010,2010/04/03,C1
G >A/Florida/04/2010,2010/03/18,E2
G >A/Florida/04/2010,2010/03/18,CX/C1
G >A/Saratov/07/2010,2010/02/01,E2
G >A/Saratov/07/2010,2010/02/01,E2/E1
G >A/St. Petersburg/204/2010,2010/02/08,E2
G >A/St. Petersburg/204/2010,2010/02/08,E2/E1
G >A/Wisconsin/04/2010,2010/02/22,E3
G >A/Kentucky/06/2010,2010/04/06,MX/C1
G >A/Brazil/8546/2010,2010/03/04,C1
R >A/Moldova/351/2010,2010/01/18,clinical sample
G >A/Belgorod/2/2010,2010/03/15,E1, E1
G >A/Victoria/502/2010,2010/06/20,E3
R >A/Montana/01/2010,2010/04/04,E2
G >A/Brazil/1394/2010,2010/03/25,C1
G >A/St. Petersburg/204/2010,2010/02/08,E2/E2
G >A/Hong Kong/2200/2010,2010/07/14,MDCK2, MDCK1
G >A/Pennsylvania/07/2010,2010/08/12,C1
G >A/SYDNEY/202/2010,2010/07/18,mdckx,mdck1
G >A/BRISBANE/209/2010,2010/08/09,MDCK4
G >A/Venezuela/27/2010,2010/01/29,C1
G >A/England/4880378/2010,2010/12/01,original
G >A/England/4940476/2010,2010/12/01,original
G >A/Kentucky/09/2010,2010/11/01,E2
G >A/Saudi Arabia/4270/2009,2009/07/28,C1
G >A/Tianjin/SWL4/2009,2009/06/11,E3
G >A/NAGANO/RC1/2009,2009/08/27,MDCK1
G >A/India/8489/2009,2009/10/20,X3/C1
R >A/KathmanduBGN/21-2/2009,2009/11/30,nasal swab
R >A/YAMAGUCHI/247/2009,2009/12/01,MDCK 2
G >A/Egypt-Vacsera/138/2009,2009/12/01,E1,E1
R >A/Laos/138/2009,2009/08/22,C2
G >A/Iran/572/2009,2009/12/01,Ex, E1
R >A/Iran/20001/2009,2009/12/01,Ex, E1
G >A/Georgia/4484/2009,2009/12/21,clinical specimen
G >A/Turkey/TR-20/2009,2009/10/31,SIAT1, SIAT3
R >A/Shanxi-Linxian/SWL323/2009,2009/11/04,C1
G >A/Guangdong-Luohu/SWL1755/2009,2009/11/05,E2
G >A/Zhejiang/SWL3/2009,2009/09/06,C2
G >A/Georgia/4484/2009,2009/12/21,SIAT4
R >A/TOKYO/99946/2009,2009/11/05,E1 +1
G >A/Lviv/N2/2009,2009/10/28,lungs
G >A/Ternopil/N10/2009,2009/10/28,lungs
G >A/Ternopil/N11/2009,2009/10/27,lungs
G >A/Lviv/N6/2009,2009/10/27,throat swab
G >A/Stockholm/48/2009,2009/07/15,original
R >A/Stockholm/92/2009,2009/08/27,original
R >A/Dnipropetrovsk/273/2009,2009/11/05,MDCK1
R >A/Moldova/G-152/2009,2009/10/23,clinical sample
V >A/Kyiv/377/2009,2009/11/07,lung wash
R >A/Chernihiv/452/2009,2009/11/07,lung wash
G >A/Ivano-Frankivsk/240/2009,2009/10/29,lung autopsy
R >A/Lviv/425/2009,2009/11/07,lung autopsy
G >A/Kyiv/251/2009,2009/11/04,lung autopsy
G >A/Ivano-Frankivsk/239/2009,2009/10/28,lung autopsy
G >A/Rivne/516/2009,2009/11/10,lung autopsy 
R >A/Lviv/639/2009,2009/11/11,lung autopsy
R >A/Zakarpatska/830/2009,2009/11/12,lung autopsy
R >A/Rivne/836/2009,2009/11/13,lung autopsy
R >A/Chernivtsi/842/2009,2009/11/11,lung autopsy
R >A/Lviv/420/2009,2009/11/09,lung autopsy
R >A/Azores/13091/2009,2009/11/20,bronchial wash
R >A/Ivano-Frankivsk/237/2009,2009/10/26,lung autopsy
R >A/Lviv/421/2009,2009/11/09,lung autopsy
R >A/Lviv/645/2009,2009/11/01,lung autopsy
R >A/Rivne/214/2009,2009/10/30,lung autopsy
R >A/Sumy/797/2009,2009/11/13,lung autopsy
R >A/Cherkasy/744/2009,2009/11/01,lung autopsy
G >A/Volin/226/2009,2009/11/05,Siat3
G >A/Rivne/214/2009,2009/10/30,Siat4
R >A/Chernihiv/859/2009,2009/11/14,lung autopsy
R >A/Chernihiv/856/2009,2009/11/13,lung autopsy
R >A/Chernihiv/855/2009,2009/11/11,lung autopsy
R >A/Chernihiv/857/2009,2009/11/14,lung autopsy
G >A/Voronezh/01/2009,2009/11/30,E1/E1
R >A/France/6808/09,2009/11/01,C1, SIAT2
G >A/Latvia/12-1488/2009,2009/12/29,MDCKx
G >A/Latvia/12-2498/2009,2009/12/07,MDCKx
G >A/Iceland/162/2009,2009/10/21,MDCK2
G >A/Iceland/176/2009,2009/11/01,MDCK2
G >A/Denmark/1900/2009,2009/12/01,MDCK3, SIAT1
G >A/Iceland/162/2009,2009/10/21,MDCK2, SIAT3
G >A/Latvia/12-1488/2009,2009/12/29,MDCKx, SIAT1
G >A/Moldova/3163/2009,2009/11/23,clinical sample
G >A/Moldova/3245/2009,2009/11/25,clinical sample
V >A/Moldova/5053/2009,2009/12/11,clinical sample
G >A/ENG/671/2009,2009/07/01,c1
G >A/ENG/94640080/2009,2009/11/04,original
G >A/ENG/93960032/2009,2009/09/10,original
G >A/SC/10/2009,2009/06/01,original
G >A/ENG/93780689/2009,2009/09/01,c1
G >A/ENG/1005/2009,2009/09/01,c1
R >A/ENG/94620048/2009,2009/10/01,original
R >A/California/07/2009,2009/04/09,E2
G >A/Mexico/3955/2009,2009/04/03,E2
G >A/New York/04/2009,2009/04/01,E2
R >A/New York/11/2009,2009/04/25,E2
R >A/New York/31/2009,2009/04/24,E2
G >A/Georgia/01/2009,2009/04/27,C1
R >A/Nebraska/02/2009,2009/04/01,E2
R >A/Texas/04/2009,2009/04/14,X/E2
G >A/Texas/11/2009,2009/04/23,E2
R >A/Texas/10/2009,2009/04/23,E2
R >A/California/13/2009,2009/04/21,E2
G >A/Texas/05/2009,2009/04/15,X/E2
G >A/Illinois/10/2009,2009/07/31,C4
G >A/Indiana/09/2009,2009/04/22,E2
R >A/Massachusetts/16/2009,2009/06/15,C1
G >A/Utah/42/2009,2009/07/24,M1
R >A/Utah/42/2009,2009/07/24,Original
G >A/Costa Rica/3149/2009,2009/07/13,X1/C1
G >A/Michigan/25/2009,2009/10/14,C1
G >A/Utah/42/2009,2009/07/24,M1/C1
G >A/Mexico/3956/2009,2009/04/03,Original
R >A/North Carolina/39/2009,2009/10/15,IR
G >A/North Carolina/49/2009,2009/10/16,M1/C1
G >A/North Carolina/53/2009,2009/10/18,M1/C1
G >A/Washington/68/2009,2009/10/14,X/C2
G >A/Jamaica/6261/2009,2009/07/07,C1
G >A/Uruguay/755/2009,2009/07/22,C1
G >A/SYDNEY/2503/2009,2009/07/12,original specimen
R >A/SOUTH AUSTRALIA/2016/2009,2009/07/16,MDCKX,MDCK1
G >A/Perth/261/2009,2009/08/12,MDCKX,MDCK1
T >A/Monterrey/3/2009
G >A/Mexico/InDRE4114/2009
G >A/Mexico/InDRE4114/2009
G >A/Vladivostok/01/2009
G >A/Abakan/02/2009
G >A/Tomsk/07/2009
G >A/Salekhard/01/2009
G >A/Tomsk/08/2009
R >A/Sw/4/Mexico/2009/04/
R >A/Nebraska/02/2009/04/
G >A/NY/04/2009/04/
G >A/Mexico/3955/2009/04/02
R >A/CA/07/2009/04/09
R >A/Texas/04/2009/04/14
G >A/Texas/05/2009/04/15
R >A/CA/13/2009/04/21
R >A/Texas/10/2009/04/23
G >A/Texas/11/2009/04/23
R >A/NY/31/2009/04/24
R >A/NY/11/2009/04/25
G >A/Georgia/01/2009/04/27
G >A/Mexico city/CIA11/2009/05/02
T >A/Sw/Alberta/OTH-33-3/2009/05/03
G >A/Mexico city/CIA10/2009/05/03
R >A/Boston/109/2009/06/15
G >A/Hiroshima/201/2009/06/17
G >A/CA/VRDL7/2009/06/17
M >A/CA/VRDL31/2009/06/17
G >A/CA/VRDL27/2009/06/27
G >A/Argentina/HNRG16/2009/06/29
R >A/Texas/42291877/2009/06/29
G >A/Sao Paulo/53206/2009/07/19
G >A/Rio de Janeiro/4707/2009/07/23
R >A/Finland/614/2009/07/24
R >A/Utah/42/2009/07/24
G >A/Utah/42/2009/07/24
G >A/Rio de Janeiro/5826/2009/07/28
G >A/Catalonia/NS1706/2009/07/29
N >A/Singapore/GP2312/2009/07/31
G >A/Pune/NIV9355/2009/08/
G >A/Mum/NIV9312/2009/08/
G >A/Rio de Janeiro/7131/2009/08/01
G >A/Sao Paulo/53225/2009/08/01
G >A/Catalonia/NS2001/2009/08/03
G >A/Catalonia/NS2008/2009/08/03
G >A/Rio de Janeiro/7455/2009/08/04
N >A/Singapore/GP2641/2009/08/05
N >A/Singapore/GP2651/2009/08/05
R >A/Norway/2924/2009/08/10
G >A/Orenburg/CRIE-VNV/2009/08/16
G >A/Rio de Janeiro/14601/2009/08/24
G >A/Roma/ISS1897/2009/08/27
G >A/Roma/ISS1941/2009/08/27
R >A/Nagano/RC1/2009/08/27
G >A/Pune/NIV10278/2009/09/
G >A/Netherlands/1064b/2009/09/01
G >A/Norway/3206-3/2009/09/01
R >A/Bahia/15525/2009/09/05
G >A/South Carolina/WRSP520/2009/09/05
G >A/Zhejiang-Yiwu/11/2009/09/06
G >A/Zhejiang/DTID-ZJU02/2009/09/07
G >A/Zhejiang/DTID-ZJU03/2009/09/07
G >A/Nsk/NIV10348/2009/09/07
R >A/Mexico/InDRE43149/2009/09/28
R >A/Moscow/CRIE-BVA/2009/10/24
R >A/Mexico/InDRE50625/2009/10/31
R >A/Kaluga/CRIE-INV/2009/11/
R >A/Ivanovo/CRIE-AMV/2009/11/
G >A/Moscow oblast/CRIE-DEI/2009/11/
G >A/Egypt/N14644/2009/11/01
R >A/Mexico/InDRE50617/2009/11/01
G >A/Moscow oblast/CRIE-OAM/2009/11/02
R >A/Lipetsk/CRIE-BVV/2009/11/10
R >A/Yaroslavl/CRIE-CHMV/2009/11/10
G >A/Bryansk/IIV2971/2009/11/11
G >A/Tver/IIV2969/2009/11/14
G >A/Thessaloniki/2502/2009/11/17
G >A/Netherlands/2243/2009/11/17
C >A/Madrid/INS296/2009/11/17
G >A/Kastoria/2636/2009/11/18
G >A/Ivanovo/CRIE-BOV/2009/11/18
G >A/Ivanovo/CRIE-AIV/2009/11/18
R >A/Orel/CRIE-AAP/2009/11/20
G >A/Ivanovo/CRIE-STV1/2009/11/21
G >A/Thessaloniki/2812/2009/11/22
G >A/Moscow/CRIE-CHSN/2009/11/23
R >A/Moscow oblast/CRIE-KMA/2009/11/23
G >A/Ulyanovsk/CRIE-BAA/2009/11/23
R >A/Moscow/CRIE-TYD/2009/11/23
R >A/Ivanovo/CRIE-RNA/2009/11/24
G >A/Perm/01/2009/11/25
G >A/Tver/IIV-183/2009/11/25
R >A/Tambov/CRIE-LLA/2009/11/30
G >A/Taraz/01/2009/12/
G >A/Yaroslavl/IIV-196/2009/12/04
G >A/IIV-Anadyr/177/2009/12/04
G >A/Catalonia/NS092145684/2009/12/10
R >A/NY/7216/2009/12/21
G >A/Iran/1519/2009/12/23
G >A/CA/VRDL131/2009/12/30
G >A/Egypt/N00267/2010/01/
G >A/Karasuk/01/2010/01/04
G >A/Kavala/219/2010/01/12
G >A/Thessaloniki/206/2010/01/12
G >A/Thessaloniki/225/2010/01/13
G >A/Tunisia/1064/2010/01/18
G >A/Orenburg/IIV-13/2010/03/02
G >A/Orenburg/IIV-13/2010/03/02
R >A/Singapore/SS003/2010/04/
R >A/Singapore/SS004/2010/04/
R >A/Bahia/231/2010/04/01
G >A/Nanjing/2/2010/06/30
G >A/Nanjing/1/2010/06/30
716  haall 244   -:132 A:8983 C:1 G:159 M:1 N:3 R:76 T:2 V:2

[sharon sanders]

hat tip Michael Coston -


Eurosurveillance: Debating The D222G/N Mutation In H1N1





# 5263


For well over a year there has been considerable debate among virologists, and other researchers, over the impact of an amino acid substitution seen in a small percentage of 2009 H1N1 samples.

The `Norway’ or D222G/N (D225G/Nin influenza H3 Numbering) mutation was first linked to more severe disease by Norwegian Scientists in November 2009, although patients carrying these strains can have mild illness as well.

While we’ve covered this territory a number of times over the past year, a brief (and hopefully simple) review is in order. If you are up to speed on receptor binding, and the history of the D222G/N variant, feel free to skip the next section.

This mutation involves a single amino acid change in the HA1 gene at position 222 from aspartic acid (D) to glycine (G) (or asparagine (N)).

The pdmH1N1 virus carrying this mutation appears to bind more readily to receptor cells (α2-3) found deeper in the lungs, whereas unmutated seasonal flu strains bind preferentially to the (α2-6) receptor cells found in the upper airway.

A virus’s ability to bind to specific cells is controlled by its RBD or Receptor Binding Domain; an area of its genetic code that allows it to attach to, and infect, specific types of host cells.

(A Very Simplified Illustration of RBDs)
Like a key into a padlock, the RBD must `fit’ in order to open the cell to infection.

The evidence for the D222G/N amino acid substitution driving increased virulence has been mixed, with the World Health Organization, the CDC, and the HPA continuing to investigate.

During the first week of January, Eurosurveillance printed a study looking at fatal and non-fatal cases of influenza in the UK (see Eurosurveillance: Analysis Of Fatal H1N1 Cases In The UK).

Ellis et al. reported that almost all of the virus samples tested in fatal and non-fatal cases during the early wave of the 2010/11 influenza season showed aspartic acid (D) at position 222.

In other words, no `Norway’ mutation.


Today, Eurosurveillance published a letter from an Italian researcher who has found a high percentage of D222G/N mutations in severely ill patients (43%) – particularly when taking virus samples from the lower respiratory tract (lungs).

You can read the entire letter at the link below.

Eurosurveillance, Volume 16, Issue 4, 27 January 2011
Letters
Letter to the editor. Virological analysis of fatal influenza cases in the United Kingdom during the early wave of influenza in winter 2010/11
F Baldanti

The point being, that if the UK researchers were only taking nasal (or upper respiratory) swabs, they might be missing some D222G/N mutations.

In a reply, the authors of the original study concede that in many cases, only upper respiratory swabs were available for this analysis, and that when possible, samples from the lower respiratory system would be useful.

Eurosurveillance, Volume 16, Issue 4, 27 January 2011
Letters
Authors’ reply. Virological analysis of fatal influenza cases in the United Kingdom during the early wave of influenza in winter 2010/11
J Ellis , M Galiano, R Pebody, A Lackenby, CI Thompson, A Bermingham, E McLean, H Zhao, S Bolotin, O Dar, J M Watson, M Zambon

This scholarly debate isn’t over, of course. As Ellis et al. state in their reply:

The selection and emergence of the D222G mutation as a cause or consequence of more severe lower respiratory tract infection is still to be resolved.

Emergence of this mutant is likely to exacerbate severity of disease, but by itself, may be neither necessary nor sufficient to account for a severe disease outcome, which is invariably a balance between virus virulence factors and host immune response capability.

It will take more samples, more research, and more time to determine the truth in the matter.

And even if this mutation should eventually be linked to higher virulence, its ultimate impact on public health will ride on how just prevalent this D222G/N is among the H1N1 viruses in circulation.

Stay tuned. There’s a lot left for us to discover.

[alert]

Published Date: 2013-01-17 17:10:27
Subject: PRO/EDR> Influenza (08): (Norway) emergence of D222G variant & severity
Archive Number: 20130117.1503366

INFLUENZA (08): (NORWAY) EMERGENCE OF D222G VARIANT AND SEVERITY
************************************************** **************
A ProMED-mail post
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International Society for Infectious Diseases
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Date: Thu 17 Jan 2013
Source: Eurosurveillance, Volume 18, Issue 3 [summarised & edited]
http://www.eurosurveillance.org/View...rticleId=20369


Title: Within-patient emergence of the influenza A(H1N1)pdm09 HA1 D222G variant and clear association with severe disease, Norway. By: Rykkvin R, Kilander A, Dudman SG, Hungnes O. At: Department of Virology, Norwegian Institute of Public Health, Oslo, Norway

Summary
--------
The association between a particular mutation in the HA1 subunit of the influenza virus haemagglutinin, D222G, and severe and fatal disease in cases of influenza A(H1N1)pdm09 in Norway during the 2009 pandemic was investigated using pyrosequencing. The prevalence of the variant among fatal cases was 8/26 and among severe non-fatal cases 5/52. No D222G mutations were found among the 381 mild cases. This difference could not be attributed to sampling differences, such as body location of sampling, or duration of illness. In cases with mutant virus where clinical specimens from different days of illness were available, transition from wild-type to mutant virus was commonly observed (4/5), indicating that the mutant virus emerged sporadically in individual patients. In patients with paired samples from both the upper and lower respiratory tract (n=8), the same viral genotypes were detected in both locations. In most of the D222G cases (11/13), the mutant virus was found as a quasi-species.

Introduction
----------
Infection with the pandemic influenza A(H1N1) virus that emerged in 2009 led to mild disease in the vast majority of cases; however, there was also an unusual occurrence of viral pneumonia, severe disease and death in younger age groups than commonly observed for seasonal influenza [1]. In a large proportion of severe cases, conditions predisposing for severe disease have been identified [2], and host factors, therefore, appear to strongly influence the clinical outcome of infection. On the other hand, this novel virus of zoonotic origin differed from the previous seasonal A(H1N1) virus in the resulting disease profile; thus, viral determinants of pathogenicity must also be involved, e.g. it has been shown to be more pneumotropic than seasonal A(H1N1) virus in a ferret model [3]. It is important to understand better what viral and host-related factors determine the observed dichotomous pathogenicity profile.

The 1st cases of influenza A(H1N1)pdm09 virus infection in Norway were recorded in early May 2009, shortly after emergence in Mexico, but cases were few and scattered across the country until mid-summer [2009]. A limited influenza epidemic took place in late July/early August 2009, followed by a comparatively calm period leading up to a major epidemic that surpassed all previous peaks recorded in the current surveillance system. The epidemic reached its highest point in early November 2009, and by the end of 2009, it had mostly subsided.

As part of the intensified surveillance carried out during the 2009 influenza pandemic, the national reference laboratory for human influenza at the Norwegian Institute of Public Health received a large number of respiratory specimens from confirmed and possible cases of influenza A(H1N1)pdm09. In late November 2009, we noticed that a particular amino acid substitution -- aspartic acid (D) to glycine (G) in the viral haemagglutinin (HA) glycoprotein subunit HA1 at position 222 (D222G) -- appeared in fatal cases, while we did not find it in the numerous mild cases analysed. Realising that a similar pattern seemed to be taking place in the Ukraine (R. Daniels, personal communication, November 2009) and given that the mutation had been shown to influence viral receptor specificity in another influenza A(H1N1) virus [4], it was decided to notify international public health authorities and other national authorities about this possible pathogenicity determinant to expedite assessment of it [5]. A preliminary review in January 2010 of D222G amino acid substitution in the HA of influenza A(H1N1)pdm09 viruses from the World Health Organization (WHO) stated that mutations, including those leading to the D222G substitution in the HA, had appeared sporadically since the 1st emergence of influenza A(H1N1)pdm09 viruses and that the substitutions in HA had been reported in viruses obtained from cases of mild to severe to fatal illnesses but that such viruses had neither formed distinct phylogenetic clustering nor been associated with consistent changes in virus antigenicity [6].

Since the 1st account of our findings in Norway [7], investigations into the occurrence of this mutation resulted in an increasing number of reports [8-28]. While the prevalence of this mutation varied between the reporting countries, in most studies, the 222G mutation is primarily found in severe and fatal cases. One of the 1st larger studies came from a group in Hong Kong, who analysed this amino acid position in severe and non-severe cases of influenza A(H1N1)pdm09 [13]. Nine (4.1 percent) of 219 severe or fatal cases of pandemic influenza had the mutation in contrast to none of 239 non-severe cases.

Data from these reports indicated that the D222G mutation was absent or uncommon in viruses that were in sustained circulation. However, one case of transmission of a 222G virus was reported [9], but the transmitted virus in this case had acquired an additional mutation that may have influenced receptor binding characteristics.

To further investigate the sporadic occurrence of the 222G mutant influenza virus, we performed a more in-depth analysis of an expanded data set. Our original data set [7] included 266 cases, while the expanded set comprised 462 cases. The present study included assessment of the majority of the fatal cases in Norway as well as of a larger number of samples from severe non-fatal and mild cases collected throughout the pandemic.

We studied the prevalence of HA1 222 mutations within different clinical outcome groups, in serially collected specimens, in upper versus lower respiratory tract and in early versus late specimens. We also analysed age and sex distribution and examined the characteristics of the fatal cases.

We further compared the mutant viruses phylogenetically and looked for the presence of mutant quasi-species and oseltamivir resistance.

[Interested readers should access the original document via the source URL to view the full text describing the methods, figures, the tabulated data, and references.]

Discussion
---------
In the present study, we provide further epidemiological evidence of the association between the D222G mutation in HA1 of influenza A(H1N1)pdm09 virus and severe or fatal clinical course. Furthermore, we present evidence that the mutated viruses emerge in individual patients after the onset of illness and demonstrate the presence of mutant virus in both the upper and lower respiratory tract. We also address some potential biases that could conceivably confound the analysis. The Norwegian cases of infection with HA1 222G genotype viruses have occurred sporadically and do not cluster epidemiologically or in phylogenetic analysis.

As observed by others, the D222G substitution has been observed to occur sporadically in the laboratory when specimens containing predominantly wild-type virus are subjected to virus isolation in eggs or mammalian cell lines [6,13,35].We therefore based our analysis on viral sequences obtained from the primary clinical specimens.

The 222G viruses appear to be rare among circulating strains, but are still quite frequent in patients with severe disease, who are not epidemiologically linked. A likely explanation is that the presence of mutant viruses in these particular individuals experiencing severe disease is due to selective upgrowth of mutant genomes during infection. In all 4 222G cases where we could analyse both early and late specimens, we observed a transition from wild-type to mutant virus, which lends support to the hypothesis that the presence of the mutant is due to sporadic emergence rather than widespread circulation.

In our analysis, we could not distinguish between upgrowth from a rare quasi-species, which may be present at inapparent levels in many more cases, and upgrowth from de novo mutation events. The 222G genotype appears to occur as sporadic mutations with no or little onward transmission, rather than through persistence as a circulating variant. If this is the case, the likelihood of finding mutant viruses is expected to increase during the course of infection. Conceivably, since the severe cases, including those that were fatal, tended to be sampled later in their course of illness than mild cases, the higher occurrence of mutations could alternatively be explained purely as a sampling artifact and not as a marker of virulence. But if the occurrence of the mutation was merely a function of time since infection, there should be no difference in the frequency of 222G mutant in specimens from mild versus severe cases, if taken equally late in infection. Our results show that the significant difference remained even when all early specimens were excluded: thus the difference in sampling day can be ruled out as an alternative explanation for the pattern observed.

In several of the cases, simultaneous specimens were available from different body locations. In all of these pairs/sets, the same genotypes were observed, but with differences in the ratio of mutant versus wild type in patients harbouring quasi-species. Other studies have identified D222G quasi-species mainly in endotracheal aspirate or broncheoalveolar lavage (BAL) samples and less frequently in nasopharyngeal aspirate samples [12,14,20]. This discrepancy could be due to the use of different analytical methods. Lower rates of mutant versus wild type in nasal swabs may not have been revealed by conventional sequencing. This was demonstrated by Baldanti et al [14]. In D222G/N cases with available paired nasal swabs and BAL samples, the authors found D222G/N in only one of 4 cases using direct sequencing, but this proportion increased to 3 of 4 cases using clonal analysis. From our study, we cannot exclude the possibility that the occurrence of the mutation as a quasi-species, together with the wild-type, is due to a complementary function of the wild-type. This phenomenon might change if the mutant virus were to develop another fitness-compensatory mutation that permits the mutant to replicate and spread in pure form. This possibility needs to be further studied.

In addition to its possible biological importance, the fact that the majority of the cases with 222G mutants carried a mixture of 222D- and 222G-encoding viral genomes, usually with predominance of the wild-type 222D, makes it likely that many influenza A(H1N1)pdm09 cases worldwide carrying D222G mutant viruses could have been missed in analyses that are not sensitive to minor nucleic acid species or where only the majority nucleotide is recorded in the published sequence.

Selleri et al analysed influenza A(H1N1)pdm09 viral quasi-species and the polymorphism at codon 222 by ultra-deep pyrosequencing [28]. Codon 222 polymorphism was detected in 40.7 percent of patients by ultra-deep pyrosequencing and in only 7.1 percent by conventional sequencing. They found that the frequency of polymorphism was significantly higher in samples collected from patients with severe manifestations than in those patients with moderate-mild manifestations. The D222G/N/A mutations were detected as either minor or predominant variants only in severe cases, whereas D222E was equally represented in severe and moderate-mild infections.

The question of whether the presence of mutant viruses in lower airways is underestimated due to lack of sampling in the lower respiratory tract was investigated by Baldanti et al [14]. Paired nasal swabs and BAL samples from patients admitted to intensive care units for mechanical ventilation or extracorporeal membrane oxygenation were compared with samples from patients with pneumonia not requiring mechanical ventilation and from community patients. By combining data from nasal swabs and BAL samples, the frequency of D222G/N mutants in patients with severe infections increased to 43 percent, as compared with 7.8 percent and 0 percent in patients with moderate and mild infections, respectively [14]. Baldanti et al also showed that the viral RNA levels were significantly higher in BAL samples than those in nasal swabs [14]. Piralla et al. described the same finding, suggesting higher virus replication in the lower respiratory tract [20].

Watanabe et al. have characterised 2 of the Norwegian virus isolates included in our study, namely A/Norway/3568/2009 (Norway3568) and A/Norway/3487-2/2009 (Norway3487) [34]. The viruses were isolates from a fatal case (Norway3487) and a mild case (Norway3568): the viruses differ by only 10 amino acids, and none of the amino acid changes known to affect virulence were found in PB2, PB1-F2, HA, or NS1, except for an amino acid change to 222G in HA1, in Norway3487. More efficient viral replication in cultured cells and delayed virus clearance from ferret respiratory organs was observed for Norway3487 virus (isolated from a severe case), as compared with Norway3568 (isolated from a mild case). To some extent, Norway3487 virus caused more severe lung damage in non-human primates than did Norway3568 virus. Moreover, the authors found that PB2 derived from Norway3487 contributed to higher polymerase activity, possibly leading to more efficient viral replication in vitro and in vivo, which in turn also could play a role in the increased lung damage.

In our analysis, all cases with detectable 222G mutant viruses had severe illness, and the prevalence of 222G increased with the degree of severe outcome. If the conditions for virus growth in lower airways are favourable to 222G mutants and the likelihood of upgrowth of mutant virus increases with duration of infection, it follows that individuals who fail to limit infection to upper airways and fail to eliminate the infection rapidly stand a greater risk of acquiring mutant viruses. Regardless of virulence, such a mechanism may contribute to the observed pattern of mutants being found primarily in severe cases. However, if the mutant viruses are also more virulent, an increased probability of emergence in patients who already have a long-lasting infection involving the lower respiratory tract probably constitutes a vicious circle phenomenon, which underscores the importance of treatment that helps persons with elevated risk to clear the infection rapidly.

The concept of D222G being a determinant of virulence is supported by a growing body of evidence from in vitro and animal studies including non-human primates [36-45]. Increased tropism of D222G mutant virus for type II pneumocytes [44] may result in more efficient infection, reducing the availability of progenitor cells for essential lung functions and regeneration and thus leading to severe pulmonary impairment. Increased viral titres in the lungs also trigger stronger inflammatory responses, augmenting tissue damage and delaying healing in the infected lungs [44].

While one instance of transmission of 222G mutant virus has been documented [9], the transmitted virus in this case had acquired an additional mutation, (G155E) that may have counteracted the putative 222G-induced receptor-binding changes [46], and there are no indications that effective sustained transmission has taken place. In our data set, one of the patients with mutant viruses was the likely source of infection of a healthcare worker. However, this occurred early in the course of illness: virus from an early specimen, as well as the virus collected from the healthcare worker, was wild type.

In light of the fact that 222G mutant viruses are and remain substantially less transmissible than corresponding wild-type viruses, their immediate public health impact is limited to the individual cases in whom such mutants occur and the fact that they may possibly contribute to the severity of illness. Similar to the apparent situation with avian influenza A(H5N1) virus infection in humans, tropism of 222G mutant viruses for lung cells may contribute to both increased virulence and impaired transmissibility, which may thus be linked traits [47]. On the other hand, when the H275Y neuraminidase mutation conferring oseltamivir resistance in seasonal influenza A(H1N1) viruses was 1st identified, this mutation also correlated with impaired viral fitness [48], a situation that was abruptly changed with the global emergence of high-fitness resistant viruses during the 2007/08 influenza season [49]. Similarly, further adaptation of the newly emerged A(H1N1)pdm09 virus to humans as host species may conceivably lead to compensatory mutations that render the 222G mutants more transmissible, or lead to other changes that influence pathogenicity. The evolution of these viruses, therefore, needs to be closely monitored in a framework that ensures that virological and clinical data are taken into account.

--
Communicated by:
ProMED-mail from HealthMap alerts


[This study shows that 222G viruses appear to be rare among circulating strains but are still quite frequent in patients with severe disease who are not epidemiologically linked. A likely explanation is that the presence of mutant viruses in these particular individuals experiencing severe disease is due to selective upgrowth of mutant genomes during infection. In all 4 222G cases where the authors could analyse both early and late specimens, they observed a transition from wild-type to mutant virus, which lends support to the hypothesis that the presence of the mutant is due to sporadic emergence rather than widespread circulation. However, the observations that 222G mutant viruses are and remain substantially less transmissible than corresponding wild-type viruses suggest that their immediate public health impact is limited to the individual cases in whom such mutants occur. - Mod.CP