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PostPosted: Thu Oct 21, 2010 11:12 am 
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http://www.eurosurveillance.org/ViewArt ... leId=19692

Eurosurveillance, Volume 15, Issue 42, 21 October 2010
Research articles

A new pandemic influenza A(H1N1) genetic variant predominated in the winter 2010 influenza season in Australia, New Zealand and Singapore

I G Barr ()1, L Cui2, N Komadina1, R T Lee3, R T Lin2, Y Deng1, N Caldwell1, R Shaw1, S Maurer-Stroh3
1.World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
2.National Public Health Laboratory, Ministry of Health, Singapore
3.Bioinformatics Institute (BII), A*STAR, Singapore

Quote:
Citation style for this article: Barr IG, Cui L, Komadina N, Lee RT, Lin RT, Deng Y, Caldwell N, Shaw R, Maurer-Stroh S. A new pandemic influenza A(H1N1) genetic variant predominated in the winter 2010 influenza season in Australia, New Zealand and Singapore. Euro Surveill. 2010;15(42):pii=19692. Available online: http://www.eurosurveillance.org/ViewArt ... leId=19692

Date of submission: 14 September 2010

Pandemic H1N1 influenza virus is of global health concern and is currently the predominant influenza virus subtype circulating in the southern hemisphere 2010 winter. The virus has changed little since it emerged in 2009, however, in this report we describe several genetically distinct changes in the pandemic H1N1 influenza virus. These variants were first detected in Singapore in early 2010 and have subsequently spread through Australia and New Zealand. At this stage, these signature changes in the haemagglutinin and neuraminidase proteins have not resulted in significant antigenic changes which might make the current vaccine less effective, but such adaptive mutations should be carefully monitored as the northern hemisphere approaches its winter influenza season.

Since its emergence in early 2009 [1] the pandemic influenza A(H1N1) virus has remained closely related to one of the earliest viruses detected, A/California/7/2009, with little change in the viruses' genetic makeup in even the most variable genes, haemagglutinin (HA) and neuraminidase (NA). This lack of drift was reflected in the World Health Organization's (WHO) Vaccine formulation decisions which recommended an A/California/7/2009-like pandemic influenza A(H1N1) virus for both the southern hemisphere 2010 and the northern hemisphere 2010-11 influenza vaccines [2]. While some genetic variants have been reported such as the D222G (D239G numbering if starting at the first methionine) HA mutation which was linked with more severe outcomes following pandemic influenza virus infection [3] and a more commonly seen E391K change in the HA gene [4] during late 2009, no clear variant has predominated in a country or region and no vaccine update has been forthcoming. This report, however, describes the recent emergence in Singapore and subsequent spread of a genetic variant of the pandemic influenza A(H1N1) virus to Australia and New Zealand during their 2010 winter influenza season, where it now predominates and has been detected in some vaccine breakthroughs and fatal cases.

Genetic characterisation of the pandemic influenza A(H1N1) variant

We sequenced the HA, NA and other genes of 2010 pandemic influenza A(H1N1) viruses from Singapore, Australia, New Zealand and elsewhere using conventional Sanger sequencing. Viruses early in 2010 (January to April) from Singapore and Australia showed the E391K (numbering beginning at the first methionine in HA; equivalent to E374K if starting after the signal peptide sequence in HA at DTLC) change in the HA but were scattered throughout the phylogenetic trees for HA (Figure 1) and the whole genome (Figure 2).

Figure 1. Phylogenetic analysis of haemagglutinin sequences from recent pandemic influenza A(H1N1) viruses

Figure 2. Full genome maximum likelihood phylogenetic analysis of pandemic influenza A(H1N1) variants from Singapore, Australia and New Zealand and other non-redundant (<80% identity) strains

On 13 April 2010 an influenza A(H1N1) strain, A/Singapore/CC01/2010, was detected in Singapore that had further changes in HA (N142D; numbering beginning at the first M in HA; equivalent to N125D if starting after the signal peptide sequence in HA at DTLC) and in NA (M15I, N189S). Viruses with these changes then increased in frequency during May and June 2010 in Singapore and became the predominant viruses by mid-2010. Of the pandemic influenza viruses sequenced in Australia in 2010, those sampled in January and February mostly had the E391K change.

Viruses with the dual HA mutation (E391K and N142D) were first detected in late April 2010 (e.g. A/Brisbane/10/2010, sample date 29 April 2010), and by June 2010, viruses with these HA (and NA) changes predominated. In the North and South Islands of New Zealand, viruses that were collected in July and August 2010 also showed this dual change in the HA along with the NA changes. Viruses with these genetic characteristics in the HA protein have only been detected sporadically in some other countries (e.g. Guam; Figure 1, Table 1), and the complete set of changes in HA and NA has not yet been reported in the northern hemisphere to date in 2010.

Table 1. Frequency of amino acid changes at positions 391 and 142 in the haemagglutinin gene of pandemic influenza A(H1N1) viruses obtained in 2010 (n=172)

These variant viruses have also been associated with several vaccine breakthroughs and a number of fatalities in both Singapore and Australia (labelled 'dec' in Figure 1). Examination of other gene segments of several pandemic influenza A(H1N1) variants showed that the other six segments were all very similar to the A/California/7/2009 strain (nucleotide identity ranged from >99% to 100%) with no evidence of gene reassorting between the pandemic influenza (H1N1) virus and seasonal influenza A(H1N1) or H3N2 viruses or another influenza A subtype. Nevertheless, as marked in the whole genome phylogenetic tree (Figure 2), some additional mutations in the other gene segments (PB2, PB1, NP, NS1) appeared commonly among the recent variant strains, but the significance of these changes remains to be determined.

To further investigate the importance of these surface antigen mutations, we built a structural homology model of HA from the A/Brisbane/10/2010(H1N1) virus based on the template structure of A/California/04/2009(H1N1) (PDB:3LZG) [5] using MODELLER with loop refinement [6] and ProQ [7] for model quality control. In Figure 3, we superimpose our model with the complex of the antigenically similar HA of the 1918 influenza A(H1) virus bound to an antibody that recognises the classical Sa epitope (PDB:3LZF) [5]. We show that N142D is centrally located in this epitope, which led us to further investigate the effect of the mutation on antigenic properties with haemagglutination inhibition assays.

Figure 3. Structural model of influenza A/Brisbane/10/2010(H1N1) haemagglutinin

Adding to the possibility of the N142D mutation affecting antigenicity, the equivalent mutation N129D(H3)/N124D(H5) in influenza A/Mallard/Pennsylvania/10218/84(H5N2) virus was previously reported to cause antigenic drift as an escape mutant [8]. However, the findings in the context of avian H5 may not be easily transferable to the swine-origin H1. Generally, a single mutation will only partially affect antigenicity as typically several mutations in the same epitope are needed to seriously alter vaccine efficacy.

An additional mutation in the HA sequence, D111N, was common among samples from New Zealand, and an equivalent mutation in avian influenza has been reported to be related to a shift in host specificity (from avian towards human) which could hypothetically mean a small fitness advantage in the human host [9]. The equivalent mutation (referred to as D94N in [9]) enhanced binding of HA to the human-type SA--2,6-Gal receptor and decreased binding to the avian-type SA--2,3-Gal receptor. It was also observed that the mutation was able to enhance HA-mediated membrane fusion in mammalian cells. Structurally, D111N is located on the outside of the bottom of the sialic acid binding pocket with the side chain pointing to the outside (Figure 3) and the mechanism that causes the reported effect is not fully clear.

HA D111N is almost exclusively found in combination with another mutation, HA V267A, which is located at an internal beta sheet below the receptor binding pocket facing the Sa epitope (Figure 2). Exchanging valine for the smaller alanine at this position creates a small cavity which may slightly alter the surface of the epitope on top and could add to the effects of N142D. However, so far the HA D111N and V267A mutations have only occurred in a close temporal and geographic context (four in New Zealand and three in eastern Australia in July and August 2010, see Figure 1) and their increased local occurrence may simply be due to founder effects.

Two additional mutations occurred in the NA sequence, M15I and N189S, which were predominant in viruses from Singapore and Australia by mid-2010. NA M15I is located in the signal peptide region. The signal peptide is the motif required for cell surface expression of the viral protein and its existence and quality can be predicted with the programme SignalP 3.0 [10]. For the NA M15I mutation, the prediction score (D-score) increases from 0.326 for M15 to 0.404 for I15. This could hypothetically indicate that the mutated version represents a better signal peptide with potentially increasing secretion and surface expression efficiency, but this needs to be further tested experimentally. NA N189S on the other hand is located at the bottom side of the NA structure, far away from the sialic acid- and drug-binding pocket and any phenotypic change cannot easily be predicted.

Antigenic analysis of variant viruses

While genetic differences were apparent in this variant group of pandemic influenza A(H1N1) viruses, when they were assessed for antigenic variation in haemagglutination inhibition assays (HI) using ferret antisera raised to A/California/7/2009-like viruses and viruses from the new variant group (e.g. A/Singapore/548/2010, A/Brisbane10/2010), no differences in titres were apparent, indicating that these viruses were not antigenically distinguishable from the reference and vaccine virus A/California/7/2009 (Table 2).

Table 2. Antigenic reactivity of pandemic influenza A(H1N1) variants compared to the A/California/7/2009-like viruses using haemagglutination inhibition assay

Further antigenic analysis was performed using a small human serum panel (n=48) containing pre- and post-vaccination sera from Australian adults (24 subjects between the age of 18 and 59 years) and elderly subjects (24 subjects over the age of 60 years) who were given a single dose of inactivated 2010 Australian seasonal influenza vaccine (CSL Fluvax; CSL Limited, Australia) which contained an A/California/7/2009-like pandemic influenza A(H1N1) virus, an A/Perth/16/2009-like A(H3N2) virus and a B/Brisbane/60/2008-like B virus. The geometric mean HI titre (GMT) in the sera of all vaccinated subjects was reduced by 53% when tested against an egg-grown A/Brisbane/10/2010 virus (one of the genetically variant viruses) compared to the GMT obtained against egg-grown wildtype A/California/7/2009 virus. Despite some reduction in HI titres with human post-vaccination sera, there were no clear differences with ferret sera, suggesting that there are no major antigenic differences in these variant viruses at this stage in their evolution and that they still share most of their antigenic properties with the early pandemic influenza A(H1N1) viruses.

Discussion

While the 2009 pandemic has recently been downgraded by the WHO [11], the pandemic influenza A(H1N1) virus still remains the predominant influenza virus in most countries including those in the southern hemisphere that recently experienced their winter influenza season (with the exception of South Africa where influenza B and A(H3N2) viruses have predominated in 2010) [11]. To date there has been little change detected in either the genetic or antigenic characteristics of the pandemic H1N1 influenza virus in the nearly 18 months that it has infected humans. No clear variant has appeared apart from minor changes occurring in the HA, NA and other viral genes during this time. Recently however a genetically distinct variant containing several signature amino acid changes in both the HA and NA genes has emerged in Singapore, Australia and New Zealand, coinciding with the winter influenza season in the latter two countries. While the combination of HA mutations at E391K and N142D has been seen sporadically in isolates in Korea and the United States in November 2009 (ADM21270, ADM21278, ADL59660, ADD74728), the first appearance of the double HA and double NA change has been in April in Singapore (A/Singapore/CC01/2010). Similar viruses have also been detected in Guam (A/Guam/2/2010(H1N1)) and Thailand (A/Bangkok/INS428/2010(H1N1)) in March 2010; they were lacking the NA mutations but at least partially shared the changes in other segments (PB2 K660R, NS1 M93I, PB1 T257A and A652V, NP K452R) which makes these strains closely related to A/Singapore/GP329/2010 which was isolated in January 2010. Strains with the full set of characteristic mutations of the new variant have not yet been reported in other regions and have not appeared in genetic databases to date.

It remains to be seen whether this variant will continue to predominate for the rest of the influenza season in Oceania and in other parts of the southern hemisphere and then spread to the northern hemisphere or merely die out. Already this variant virus has been associated with several vaccine breakthroughs in teenagers and adults vaccinated in 2010 with monovalent pandemic influenza vaccine as well as a number of fatal cases from whom the variant virus was isolated. Unfortunately we did not have access to the comprehensive patient records that may have enabled us to determine the relative frequency of vaccine breakthroughs with this variant compared to the non-variant. This information is important to eliminate other confounding factors such as the age of the vaccinee, time since they were vaccinated or if they were taking immuosuppressive drugs, all of which might impact on their level of protection following vaccination. It is therefore not known at this time if the amino acid changes in this variant virus are responsible for these vaccine breakthroughs or deaths, or if they are simply a result of this virus genotype being the predominant virus in circulation during this period. The HA and NA amino acid changes seen in the variant are present both in the original clinical samples and in viruses isolated in MDCK cells and are retained in viruses isolated directly in embryonated hens eggs. Careful studies are underway to determine if the variant viruses grow better than other influenza A/California/7/2009-like viruses but preliminary data indicate that these variant viruses grow as well or better than viruses without these characteristic amino acid changes both in MDCK cell culture and in embryonated hens eggs (data not shown) and this may make them useful vaccine virus seeds. If confirmed this may also explain the rapid spread and predominance of this variant virus. Further animal and human transmission and growth studies will be required to support this initial finding.

Conclusions

A new genetic variant of the pandemic influenza (H1N1) virus has emerged in Singapore, Australia and New Zealand in the second and third quarters of 2010 that does not appear at this stage to represent a significant antigenic change for the virus. However, it may represent the start of more dramatic antigenic drift of the pandemic influenza A(H1N1) viruses that may require a vaccine update sooner than might have been expected, with a new human influenza virus.

Acknowledgements
The authors would like to thank the WHO National Influenza Centres and other laboratories for supplying viruses used in this study, Chua Sin Ying for help with the Bioinformatics analysis and Shiau Pheng Phuah, Shu Meng, Meng Li Teo for their technical support. The Melbourne WHO Collaborating Centre for Reference and Research on Influenza is supported by the Australian Government Department of Health and Ageing.

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PostPosted: Thu Oct 21, 2010 1:49 pm 
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Another link along the same lines.

http://uk.news.yahoo.com/22/20101021/ts ... 1ccfa.html

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PostPosted: Thu Oct 21, 2010 4:21 pm 
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Location: Pittsburgh, PA USA
This is old news. N142D pedigree profile (N126D using H3 numbering)

EPI279911 A/Stockholm/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279893 A/Hong Kong2203/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279232 A/DARWIN/36/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279217 A/GRAFTON/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279214 A/CANBERRA/200/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279211 A/TOWNSVILLE/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279201 A/VICTORIA/817/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279186 A/DARWIN/47/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279168 A/PERTH/518/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279165 A/PERTH/504/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279162 A/VICTORIA/808/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279158 A/CHRISTCHURCH/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279157 A/CHRISTCHURCH/6/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279155 A/CHRISTCHURCH/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279153 A/DARWIN/51A/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279135 A/WELLINGTON/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279132 A/WELLINGTON/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279129 A/SOUTH AUCKLAND/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279121 A/WAIKATO/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279118 A/WELLINGTON/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279115 A/SOUTH AUCKLAND/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279101 A/BRISBANE/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279098 A/BRISBANE/20/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279097 A/BRISBANE/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279096 A/BRISBANE/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279095 A/BRISBANE/15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279094 A/CHRISTCHURCH/24/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279093 A/CHRISTCHURCH/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279090 A/CHRISTCHURCH/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279089 A/CHRISTCHURCH/20/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279088 A/CHRISTCHURCH/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279085 A/CHRISTCHURCH/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279084 A/CHRISTCHURCH/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279082 A/CHRISTCHURCH/14/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279081 A/CHRISTCHURCH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279079 A/CHRISTCHURCH/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279077 A/CHRISTCHURCH/4/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279076 A/CHRISTCHURCH/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279075 A/CHRISTCHURCH/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279072 A/BRISBANE/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279069 A/BRISBANE/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279068 A/BRISBANE/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279067 A/VICTORIA/514/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279063 A/VICTORIA/804/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279059 A/VICTORIA/507/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279058 A/VICTORIA/509/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279056 A/DARWIN/46/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279053 A/DARWIN/44/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279043 A/SINGAPORE/572/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279038 A/SINGAPORE/584/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279035 A/DARWIN/35/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279032 A/PERTH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279024 A/VICTORIA/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279015 A/DARWIN/29/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279012 A/DARWIN/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279009 A/DARWIN/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279006 A/DARWIN/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279003 A/DARWIN/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279000 A/DARWIN/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278860 A/Hong Kong/2166/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278844 A/Alabama/06/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278693 A/KOBE/181/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278605 A/Christchurch/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278603 A/Christchurch/8/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278601 A/Christchurch/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278599 A/Victoria/502/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278595 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278580 A/Norway/445/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278204 A/Korea/AF2414/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278196 A/Korea/AF2406/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277873 A/Mexico City/WR1668T/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277566 A/AICHI/116/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277268 A/Bangkok/INS428/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276627 A/Georgia/AF2205/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276454 A/ENG/837/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273876 A/Hong Kong/1880/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI273638 A/Arizona/04/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272642 A/YOKOHAMA/67/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272049 A/VICTORIA/800/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271945 A/SINGAPORE/548/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271772 A/Singapore/SS004/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271770 A/Singapore/SS003/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269960 A/Brisbane/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI269921 A/Guam/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI267672 A/Netherlands/1064b/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI265956 A/Stockholm/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263450 A/Singapore/GP999/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263409 A/Singapore/GP2362/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI262453 A/Kenya/0042/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258256 A/Zhejiang-Haishu/SWL1289/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258164 A/Fujian-Licheng/SWL126/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258112 A/Fujian-Siming/SWL1163/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258056 A/Fujian-Gulou/SWL1549/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258032 A/Fujian-Gulou/SWL1338/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257896 A/Guangdong-Chancheng/SWL178/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257888 A/Fujian-Gulou/SWL1338/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257884 A/Fujian-Gulou/SWL52/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI253751 A/Berlin/88/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI252386 A/Ontario/304434/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Thu Oct 21, 2010 4:28 pm 
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Posts: 48101
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Recent updates

EPI287184 A/OITA/61/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI284009 A/Thailand/34-9936/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI281927 A/New York/INS317/2009 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280338 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280317 A/Santiago/17389/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Thu Oct 21, 2010 4:58 pm 
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Location: Pittsburgh, PA USA
D95N at GISAID and Genbank
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280317 A/Santiago/17389/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279201 A/VICTORIA/817/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279158 A/CHRISTCHURCH/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279157 A/CHRISTCHURCH/6/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279135 A/WELLINGTON/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279132 A/WELLINGTON/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279118 A/WELLINGTON/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279096 A/BRISBANE/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279095 A/BRISBANE/15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279094 A/CHRISTCHURCH/24/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279093 A/CHRISTCHURCH/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279090 A/CHRISTCHURCH/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279089 A/CHRISTCHURCH/20/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279088 A/CHRISTCHURCH/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279084 A/CHRISTCHURCH/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279082 A/CHRISTCHURCH/14/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279081 A/CHRISTCHURCH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279079 A/CHRISTCHURCH/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279078 A/CHRISTCHURCH/9/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279077 A/CHRISTCHURCH/4/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279076 A/CHRISTCHURCH/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279075 A/CHRISTCHURCH/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279072 A/BRISBANE/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279067 A/VICTORIA/514/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279024 A/VICTORIA/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278605 A/Christchurch/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278601 A/Christchurch/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI267752 A/New York/4662/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258582 A/California/VRDL93/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257724 A/Fujian-Licheng/SWL1658/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI245749 A/ENG/92900359/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI238325 A/Madagascar/9551/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI236485 A/ENG/93120033/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI231464 A/Massachusetts/32/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI213451 A/Singapore/ON1156/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI212510 A/Myanmar/JP101/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

gb|CY065051.1| Influenza A virus (A/New York/4662/2010(H1N1))... 28.2 1.2
gb|CY063115.1| Influenza A virus (A/California/VRDL93/2009(H1... 28.2 1.2
gb|CY049571.1| Influenza A virus (A/Singapore/ON1156/2009(H1N... 28.2 1.2
gb|GU014758.1| Influenza A virus (A/Myanmar/JP101/2009(H1N1))... 28.2 1.2

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PostPosted: Thu Oct 21, 2010 5:02 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 48101
Location: Pittsburgh, PA USA
C172T
EPI282642 A/San Salvador/WRAIR1109N/2009 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280338 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280335 A/Brisbane/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280317 A/Santiago/17389/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279232 A/DARWIN/36/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279214 A/CANBERRA/200/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279201 A/VICTORIA/817/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279186 A/DARWIN/47/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279168 A/PERTH/518/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279165 A/PERTH/504/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279158 A/CHRISTCHURCH/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279157 A/CHRISTCHURCH/6/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279135 A/WELLINGTON/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279132 A/WELLINGTON/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279118 A/WELLINGTON/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279101 A/BRISBANE/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279096 A/BRISBANE/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279095 A/BRISBANE/15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279094 A/CHRISTCHURCH/24/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279093 A/CHRISTCHURCH/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279090 A/CHRISTCHURCH/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279088 A/CHRISTCHURCH/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279084 A/CHRISTCHURCH/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279082 A/CHRISTCHURCH/14/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279081 A/CHRISTCHURCH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279079 A/CHRISTCHURCH/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279078 A/CHRISTCHURCH/9/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279077 A/CHRISTCHURCH/4/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279076 A/CHRISTCHURCH/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279075 A/CHRISTCHURCH/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279072 A/BRISBANE/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279069 A/BRISBANE/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279067 A/VICTORIA/514/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279058 A/VICTORIA/509/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279056 A/DARWIN/46/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279053 A/DARWIN/44/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279043 A/SINGAPORE/572/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279040 A/SINGAPORE/585/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279039 A/SINGAPORE/576/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279038 A/SINGAPORE/584/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279035 A/DARWIN/35/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279032 A/PERTH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279024 A/VICTORIA/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279015 A/DARWIN/29/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279012 A/DARWIN/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279009 A/DARWIN/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279006 A/DARWIN/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279003 A/DARWIN/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279000 A/DARWIN/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278844 A/Alabama/06/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278605 A/Christchurch/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278603 A/Christchurch/8/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278601 A/Christchurch/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278599 A/Victoria/502/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278595 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278594 A/Brisbane/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278580 A/Norway/445/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272697 A/Qingdao/1215/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272049 A/VICTORIA/800/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271772 A/Singapore/SS004/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271770 A/Singapore/SS003/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271323 A/Brussels/INS243/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263409 A/Singapore/GP2362/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI259407 A/New York/INS150/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI258280 A/Henan/18/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257045 A/Nagasaki/HA-10-22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI255237 A/Ghana/N12981/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI254502 A/Bilthoven/4360903104/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI254469 A/Bilthoven/4310901550/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247168 A/Alabama/08/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247058 A/Delhi/NIV3704/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI243896 A/Kansas/01/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI240365 A/Michigan/27/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI229812 A/Sweden/19/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI224016 A/Texas/45122886/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI223896 A/Texas/45072128/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI223880 A/Texas/45071344/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI212841 A/New York/3651/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI211691 A/Tajikstan/1aSV/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI211689 A/Tajikstan/1SV/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Thu Oct 21, 2010 5:05 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 48101
Location: Pittsburgh, PA USA
G360A
EPI282759 A/Mexico City/WRAIR1786T/2009 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI282743 A/Mexico City/WRAIR1779T/2009 (A/H1N1) segment 4 (HA) 52.8 0.00000
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280338 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280335 A/Brisbane/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280317 A/Santiago/17389/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279232 A/DARWIN/36/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279217 A/GRAFTON/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279214 A/CANBERRA/200/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279201 A/VICTORIA/817/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279186 A/DARWIN/47/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279168 A/PERTH/518/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279165 A/PERTH/504/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279158 A/CHRISTCHURCH/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279157 A/CHRISTCHURCH/6/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279135 A/WELLINGTON/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279132 A/WELLINGTON/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279118 A/WELLINGTON/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279101 A/BRISBANE/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279096 A/BRISBANE/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279095 A/BRISBANE/15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279094 A/CHRISTCHURCH/24/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279093 A/CHRISTCHURCH/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279090 A/CHRISTCHURCH/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279088 A/CHRISTCHURCH/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279084 A/CHRISTCHURCH/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279082 A/CHRISTCHURCH/14/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279081 A/CHRISTCHURCH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279079 A/CHRISTCHURCH/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279078 A/CHRISTCHURCH/9/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279077 A/CHRISTCHURCH/4/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279076 A/CHRISTCHURCH/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279075 A/CHRISTCHURCH/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279072 A/BRISBANE/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279069 A/BRISBANE/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279067 A/VICTORIA/514/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279058 A/VICTORIA/509/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279056 A/DARWIN/46/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279053 A/DARWIN/44/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279043 A/SINGAPORE/572/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279040 A/SINGAPORE/585/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279039 A/SINGAPORE/576/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279038 A/SINGAPORE/584/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279035 A/DARWIN/35/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279032 A/PERTH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279024 A/VICTORIA/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279015 A/DARWIN/29/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279012 A/DARWIN/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279009 A/DARWIN/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279006 A/DARWIN/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279003 A/DARWIN/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279000 A/DARWIN/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278844 A/Alabama/06/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278605 A/Christchurch/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278601 A/Christchurch/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278599 A/Victoria/502/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278595 A/Brisbane/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278594 A/Brisbane/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278580 A/Norway/445/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI277985 A/Mexico City/WR1762T/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276585 A/ENG/888/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276576 A/ENG/95260539/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276559 A/ENG/1049/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276534 A/ENG/94840810/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276507 A/ENG/868/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276482 A/ENG/849/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276313 A/ENG/716/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272049 A/VICTORIA/800/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271772 A/Singapore/SS004/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI271770 A/Singapore/SS003/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI263409 A/Singapore/GP2362/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257692 A/Jiangxi-Donghu/SWL15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257420 A/Jiangsu-Canglang/SWL1616/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI255102 A/swine/Thailand/CU-RA29/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI247058 A/Delhi/NIV3704/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI232249 A/Moldova/G-140/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI216727 A/Barbados/280/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI214538 A/Wisconsin/629-D01606/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI213127 A/Norway/2010/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

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PostPosted: Thu Oct 21, 2010 5:09 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 48101
Location: Pittsburgh, PA USA
V251A
EPI283494 A/Peru/FLE1118/2009 (A/H1) segment 4 (HA) 52.8 0.00000
EPI280344 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280341 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI280317 A/Santiago/17389/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279201 A/VICTORIA/817/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279158 A/CHRISTCHURCH/7/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279157 A/CHRISTCHURCH/6/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279135 A/WELLINGTON/21/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279132 A/WELLINGTON/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279118 A/WELLINGTON/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279096 A/BRISBANE/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279095 A/BRISBANE/15/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279094 A/CHRISTCHURCH/24/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279093 A/CHRISTCHURCH/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279090 A/CHRISTCHURCH/22/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279088 A/CHRISTCHURCH/19/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279084 A/CHRISTCHURCH/17/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279082 A/CHRISTCHURCH/14/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279081 A/CHRISTCHURCH/12/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279079 A/CHRISTCHURCH/10/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279078 A/CHRISTCHURCH/9/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279077 A/CHRISTCHURCH/4/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279076 A/CHRISTCHURCH/3/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279075 A/CHRISTCHURCH/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279072 A/BRISBANE/23/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279067 A/VICTORIA/514/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI279024 A/VICTORIA/5/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278607 A/Christchurch/16/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278605 A/Christchurch/2/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278603 A/Christchurch/8/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI278601 A/Christchurch/13/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI276540 A/SC/84/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI272597 A/AOMORI/18/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI267808 A/New York/7480/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI257680 A/Ningxia-Xixia/SWL116/2010 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI245724 A/GIBRALTAR/SB164/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI244281 A/WAKAYAMA/291/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI236499 A/ENG/93200035/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI236497 A/GIBRALTAR/SB160/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI233088 A/MALAYSIA/233/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000
EPI219274 A/Wisconsin/629-S0435/2009 (A/H1N1 swl) segment 4 (HA) 52.8 0.00000

gb|CY045124.1| Influenza A virus (A/Peru/FLE1118/2009(H1)) se... 28.2 1.2
gb|CY065107.1| Influenza A virus (A/New York/7480/2010(H1N1))... 28.2 1.2
gb|CY051471.1| Influenza A virus (A/Wisconsin/629-S0435/2009(... 28.2 1.2

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PostPosted: Thu Oct 21, 2010 5:34 pm 
Online

Joined: Wed Aug 19, 2009 10:42 am
Posts: 48101
Location: Pittsburgh, PA USA
Commentary

http://www.recombinomics.com/News/10211 ... _2010.html

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PostPosted: Thu Oct 21, 2010 6:24 pm 
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Joined: Fri Jan 08, 2010 3:22 pm
Posts: 5184
Location: East of London
http://www.cidrap.umn.edu/cidrap/conten ... riant.html

CIDRAP's article,

Study: 2009 H1N1 variant gained a foothold in three countries

Quote:
Lisa Schnirring Staff Writer

Oct 21, 2010 (CIDRAP News) – Laboratory experts from Australia and Singapore have identified changes in the 2009 H1N1 flu virus that they say don't seem to make the vaccine less effective but bear watching.

Researchers first identified the genetic variants in April 2010 in Singapore, where they became more common, spreading to New Zealand and Australia during their winter flu seasons.

The group described its findings in today's issue of Eurosurveillance. Other experts contacted by CIDRAP News said the findings are not surprising.

Over the past several months, global health officials have said the circulating 2009 H1N1 strains are a good match with the ones included in the latest seasonal flu vaccines for both hemispheres. The authors wrote that earlier genetic variants, D222G and E391K, have not predominated in a country or region like the new variations have.

They found that 2009 H1N1 viruses isolated this year from Singapore, New Zealand, and Australia showed the E391K change in the hemagglutinin protein, a further change in the HA (N142D), along with changes in the neuraminidase (NA) protein, M15I and N189S. Viruses with the changes became predominant in Singapore by the middle of 2010 and were found in New Zealand in July and August.

So far viruses with the HA changes have been detected only sporadically in other areas, such as Guam. Viruses with both the HA and NA changes have so far not been reported in any Northern Hemisphere countries.

In Australia and Singapore, the variant 2009 H1N1 viruses were associated with several vaccine breakthroughs (infections that occur in spite of vaccination) in teens and adults who received the 2009 H1N1 vaccine, as well as in a number of fatal cases.

However, the researchers said that without complete patient records they can't compare the breakthrough frequency of the variant and nonvariant strains. Also, a comprehensive review of patient record would reveal possible confounding factors, such as age and immune status.

When the investigators used hemagglutination inhibition (HI) assays to assess antigenic variation with the variant virus, they found no differences between it and reference and vaccine viruses. When they tested the variant against a small human serum panel, they found some reduction in HI titers with postvaccination sera, but, when considering both HI analyses, they said the findings suggest no major antigenic differences with the variant viruses in this stage of their evolution.

"It remains to be seen whether this variant will continue to predominate for the rest of the influenza season in Oceania and in other parts of the southern hemisphere and then spread to the northern hemisphere or merely die out," the group wrote.

Though the findings don't appear to represent a significant antigenic change, they might signal the start of a drift in the 2009 H1N1 virus that may require a vaccine update sooner than expected, they concluded.

Vincent Racaniello, PhD, a virologist at Columbia University who writes Virology Blog, told CIDRAP News that the findings aren't surprising: The virus is drifting genetically, but the amino acid changes haven't yet affected the antigenic structure of the virus.

He said the findings don't signal the start of antigenic drift, and there are no specific properties associated with the changes the researchers observed.

The data included in the study reflect a small fraction of the thousands of virus specimens World Health Organization (WHO) laboratories collect and study as they assess antigenic drift and whether a drifted strain is likely to spread in populations, Racaniello said.

Nancy Cox, MD, director of the Influenza Division at the US Centers for Disease Control and Prevention (CDC), told CIDRAP News that the data in the study are not new to the CDC. She said they came out of WHO collaborating centers and were reviewed over the summer and at the end of September when WHO experts made their recommendations for the Southern Hemisphere's 2011 flu season.

She added that the CDC constantly monitors circulating flu viruses for both genetic and antigenic changes.


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