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UK: 607 confirmed fatalities due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Hospitals in Wales under siege as flu crisis deepens


HOSPITALS are facing a fortnight of intense pressure on staff and beds as the winter flu seasons reaches a peak in Wales.

Health board managers have already been forced to cancel operations in a bid to cope with winter pressures.

But two of Wales? largest health boards, which run the nation?s busiest hospitals, will take even more drastic action as demand for inpatient care continues to rise.

Morriston Hospital, in Swansea, which is also coping with a large norovirus outbreak, will convert part of a children?s ward into a general medical ward for sick adults.


http://www.walesonline.co.uk/news/w...r-siege-as-flu-crisis-deepens-91466-27951274/
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

20-year-old thought to be victim of H1N1 virus

A young mum is believed to have died of suspected swine flu at Bradford Royal Infirmary.

The woman, 20, is understood to have given birth in the last few weeks.

Bradford Teaching Hospitals NHS Foundation Trust, which runs BRI, would not comment on the grounds of patient confidentiality, but it is understood the woman died in the hospital?s intensive care unit on Thursday night.

It is believed the H1N1 swine flu virus is thought to be the cause of her death but tests are continuing to fully establish the circumstances.

Pregnant women are regarded as being at high risk from the virus and are in the core group of people being advised to get vaccinated.

http://www.thetelegraphandargus.co.uk/news/8779298.New_mum_dies_of__swine_flu__at_Bradford_hospital/
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Adults go to children's ward in hospital crisis (Wales)
By liz perkins health reporter

ADULT patients will be temporarily treated on a Swansea children's ward following the beds crisis sparked by norovirus and flu.

A lack of beds has led health bosses to take the unprecedented step at Morriston Hospital of opening up part of Ward M (paediatrics) for the next two weeks to men and women.

But Abertawe Bro Morgannwg University Health Board stressed adults and children would not be cared for on the same ward ? and that the measure was only temporary.

The Morriston site is under particular pressure ? as it is coping with a very high number of cases of flu and norovirus ? which has led to visiting being restricted at the hospital

...

continues at; http://www.thisissouthwales.co.uk/n...al-crisis/article-3078074-detail/article.html
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Rotherham swine flu death: fiancee tells of shock


The fiancee of a Rotherham man who died of swine flu has spoken of her shock at how rapidly her fit and healthy partner succumbed to the virus.

Dean Brown, 44, of East Herringthorpe, died on Wednesday, six days after being taken to Rotherham Hospital.

He is one of four people with swine flu to have died in Rotherham recently.

Asked if Mr Brown had any underlying health problems, his fiancee Sandra Kelsall said: "He didn't have anything. He was a fit man."


http://www.bbc.co.uk/news/uk-england-south-yorkshire-12142191
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Swine Flu crisis: Wythenshawe hospital on the front line of critical care


Four patients lie unconscious fighting for their lives as medics work around-the-clock to try to save them.

These are the human faces of the swine flu crisis ? people from all walks of life and backgrounds united by the H1N1 virus sweeping the country.

The sign on the door ? warning visitors they must wear gowns and masks ? is the first real indicator of the high stakes involved when treating some of the sickest swine flu victims in the country.

Here at Wythenshawe Hospital, medics are using specialist life support techniques to try to save the lives of swine flu victims in Greater Manchester for the first time. It is just one of five hospitals in the country equipped to treat seriously ill swine flu patients and is playing a vital role in dealing with the outbreak nationally.

Just three days ago, Keith Daglish, 43, was flown in an RAF helicopter from Durham to Wythenshawe in a last-ditch bid to save him.


...

http://menmedia.co.uk/manchestereve...e_hospital_on_the_front_line_of_critical_care
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Source: http://www.dailymail.co.uk/news/art...lu-virus-render-vaccine-useless.html?ITO=1490

Fears over mutating swine flu virus that could render vaccine useless

By Daily Mail Reporter
Last updated at 12:04 AM on 9th January 2011

A research team has hurriedly been re-formed to investigate whether the swine flu virus has started to mutate in a way that will render the vaccine ineffective.

Senior Government scientists have already discovered slight genetic mutations in the H1N1 virus.

They are checking whether this is causing some people to be more severely affected, although there is no evidence at this stage to suggest the changes would stop the vaccine working or prevent the anti-viral drug Tamiflu from being effective...
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

I have made copies of some of the genetic oriented posts to this thread:

UK Genetic Evaluation thread


If I have missed any posts on this thread that need to be copied over, please private message me.

Thank you!
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Shiloh said:
Source: http://www.dailymail.co.uk/news/art...lu-virus-render-vaccine-useless.html?ITO=1490

Fears over mutating swine flu virus that could render vaccine useless

By Daily Mail Reporter
Last updated at 12:04 AM on 9th January 2011

A research team has hurriedly been re-formed to investigate whether the swine flu virus has started to mutate in a way that will render the vaccine ineffective.

Senior Government scientists have already discovered slight genetic mutations in the H1N1 virus.

They are checking whether this is causing some people to be more severely affected, although there is no evidence at this stage to suggest the changes would stop the vaccine working or prevent the anti-viral drug Tamiflu from being effective...
Click to expand...

From last week Eurosurveillance report: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19760

(...)

Virological investigations

Influenza A(H1N1)2009 isolates characterised to date, in samples from the community, hospitalised patients and fatal cases, are antigenically homogeneous and similar to the A(H1N1)2009 virus included in the 2010/11 seasonal influenza vaccine, A/California/7/2009.
Click to expand...

Only minor genetic drift has been noted in influenza A(H1N1)2009 viruses circulating in 2010 compared with the earliest isolates in April 2009, and this observed genetic diversity has been consistent with expected patterns of virus evolution (...).
Click to expand...

Phylogenetic analysis shows that HA sequences from nine fatal and four severe cases in the UK in 2010 were interspersed with sequences from mild cases in 2010 from the UK and elsewhere.
Click to expand...

All UK 2010 viruses cluster in two main branches, characterised by either E374K with additional mutations in minor subclusters such as D97N, S185T, S451N and N125D, some of which have been recently described [10], or by A134T and S183P, with additional substitutions such as N441K, R509M and V527I.
Click to expand...

Almost all viruses from winter 2010 analysed to date from fatal and non-fatal cases had 222D in the HA gene (39/41).
Click to expand...

Preliminary analyses from a limited number of whole genome sequences including some from fatal cases, indicate that these are consistent with observations from seasonal influenza and from the first and second waves of the recent pandemic: so far no unique mutations have been associated with severe or fatal cases of influenza A(H1N1)2009, but further comprehensive analysis is required.

(...)

Between October and December 2010, antiviral resistance monitoring was undertaken on 156 community and 159 hospital isolates.

Six cases of oseltamivir resistance associated with the H275Y mutation in the neuraminidase (NA) gene have been detected.
Click to expand...

Only one of these cases has had known exposure to oseltamivir, Two of them have been identified from community surveillance of uncomplicated infections, three cases have been detected before treatment in individuals hospitalised with underlying risk factors, and the sixth case has been detected after oseltamivir treatment in a hospitalised individual.

(...)


-
------
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Almost all viruses from winter 2010 analysed to date from fatal and non-fatal cases had 222D in the HA gene (39/41).
Click to expand...

Just so no one gets confused; D222 is non-mutated. There were only 2 cases found with D222G.

From the phylo tree, they were:
England/4880378/2010 December
England/4940476/2010 December

Both appear on the E374K branch
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Flu strikes 16,000 NHS staff
By Nick Owens 9/01/2011

EXCLUSIVE

More than 16,000 doctors, nurses and NHS workers were off with flu-related illnesses yesterday in a staff crisis that is costing the NHS ?12million a week.

...

Anne Bellenie, 51, told how her "gentle giant" husband Ade, 47, had died in Sunderland on New Year's Eve just weeks after their first wedding anniversary.

And sufferer Katy Savage, 21, from Biddulph, Staffs, is in urgent need of a lung transplant since contracting the virus four months ago.



Read more: http://www.mirror.co.uk/news/top-st...-000-nhs-staff-115875-22836958/#ixzz1AXVOkfb6
 
225G Only in 2 Sequences from Severe UK Wave

225G Only in 2 Sequences from Severe UK Wave

The UK Health Protection Agency released a group of 37 sequences at GISAID dated 2010-01-05 that appeared sometime after that date. Some of the sequences in this deposit also appear on the Figure 3 Phylogenetic Tree from the HPA Eurosurveilance paper requested to be cited as:
<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p>
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
Date of submission: 31 December 2010

The science community expected a full deposit to back the paper, but not all sequences noted on the phylogenetic table were in place at GISAIS as of this 2nd deposit.

The recent GISAID deposit added 4 of the fatalities noted on the phylogenetic tree to the 4 fatalities previously released on 2010-12-20. The previously released sequences were not marked at GISAID with a fatality notation, but now have been notated as "Deceased" as of yesterday. Oddly enough, on the 2010-01-05 deposit, none of the sequences notated as fatal on the phylogenetic tree were marked as to outcome at GISAID?

None of the sequences at the GISAID database that correspond to notated fatalities on the Eurosurveillance paper carry the severity marker of HA 225G.

225G is found on identical HA sequences noted as 2 severe cases.




  • UKEngland4880378_2010_12
  • UKEngland4940476_2010_12
The two sequences fall on a 100N, 188T, syn338G, 377K with 454N background. Appended to that background is a silent 179L previously found in US military sequences and as a regional marker in an alternate coding. A silent 448L completes the 225G sequences and is demonstrated in at least one fatal case, including in Russia.

. . . . UKEngland4940476_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg) [Regional Marker 2009 (tTA)]
. . . . . . . . . . . . . . . . . . . . [TexasAF2588_2009_10_04,
. . . . . . . . . . . . . . . . . . . . TexasJMS404_2010_01_08],
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [Yakutsk_EAV_2009_11_18,
. . . . . . . . . . . . . . . Yaroslavl_CHMV_2009_11_10_f with 224K & 225G mix],
. . . . . . . . 454N)

. . . . UKEngland4880378_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L,
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L,
. . . . . . . . 454N)
 
Last edited:
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Didier Raoult et G. CORNAGLIA dans la revue ESCMID, http://onlinelibrary.wiley.com/doi/10.1111/j.1469-0691.2010.03455.x/pdf

Sometimes They Come Back - The return of Influenza
(G. CORNAGLIA, D. RAOULT)

snip

The question of a resumption of emergency vaccination therefore arises, and we
consider it a priority for Public Health in Europe. We strongly believe that promotion of
the vaccine should be improved and that information should be promptly organised and
structured far better than it was one year ago. Noteworthy, all influenza A H1N1 (2009)
viruses characterised to date, in samples from the community, hospitalised patients and
fatal cases in the United Kingdom, are antigenically homogeneous and similar to the
vaccine virus A/California/7/2009 [3].

In 2009-10, poor communication led people not trusting in scientists and Public
Health officers, let alone politicians, and many did not get vaccinated. The apparent lack
of serious consequences reinforced the people?s belief that vaccine was not needed
(and, according to many, even harmful). Now the actual consequences of nonvaccination,
i.e. the return of influenza striking a non-immune population, risk to ignite a
new ?flu emergency?, and the question arises whether people will be finally convinced or
will retain their anti-vaccine attitude. This time, the consequences might well pass the
visibility threshold and show that the dramatic forecasts of 2009-10 were only wrong as
for their timing.
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

New delivery of swine flu vaccine on Monday



SUPPLIES of the pandemic swine flu jab will be sent to GP surgeries in Cardiff and the Vale on Glamorgan on Monday, the Echo has learned.
The move comes as NHS stocks of the seasonal flu vaccine, which protects against three different types of the flu virus, including swine flu, are running low across the region.
GPs have been given permission to start using the swine flu jab Pandemrix to meet the surge in demand from patients for protection.
Dr Sharon Hopkins, director of health at Cardiff and Vale University Health Board, said: “The seasonal flu stocks are running low and we have agreed to release the H1N1 vaccine.

“There will be a mixture of seasonal and H1N1 flu vaccine available – where there is no seasonal flu vaccine available you will get your jab with the H1N1 Pandemrix vaccine.
“This only protects against the swine flu strain but given that this is the virus that’s causing slightly more flu, we believe its worthwhile for those in the at-risk groups to have it.”


​
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Widow grieves after swine flu kills husband


SWINE flu has claimed the life of a Wearside father.

Ade Bellenie had recently celebrated his first wedding anniversary,.

The death of the 47-year-old, of Fulwell, Sunderland, has left his family, including wife Anne, 51, devastated.

In a cruel twist of fate, the same registrar who married them also issued his death certificate.

Mr Bellenie was taken ill on December 27 when his oxygen levels and blood pressure dropped.

Just a day later he was rushed into intensive care where medics discovered he had swine flu.

As thousands were getting ready to ring in 2011, the father-of-four died in hospital.

His widow Anne told how her husband had appeared perfectly healthy before falling ill.

Mr Bellenie was being treated for pneumonia before the doctors found it was swine flu.

http://www.sunderlandecho.com/news/local/widow_grieves_after_swine_flu_kills_husband_1_2915439
 
Re: UK Genetic Evaluation thread

Re: UK Genetic Evaluation thread

I ran all the HA nucleotides of the UK sequences with gs's program and then grouped them together in a way that looked right. Keep in mind that I'm no scientist. Maybe someone else will see different clades; please feel free to offer opinions.

The severe and fatal cases are marked; notice that about half of them appear on clade B.

Clade A: 451,598,658,1408,1464
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,G1403A,C1408T,C1464T(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,G1403A,C1408T,C1464T(4)

G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T879C,C1098T,A1172G,G1266A,C1408T,C1464T,A1568G,G1577T,G1630A(4)
G451A,T598C,T658A,T858C,T879C,C1098T,A1172G,G1266A,C1408T,C1464T,A1568G,G1577T,G1630A
G451A,T598C,G605A,T658A,A1172G,A1213G,G1266A,C1408T,C1464T,G1577T,G1630A(4)
G451A,T598C,G610T,T658A,A1172G,G1266A,C1408T,C1464T,G1577T,G1630A(4) F

G451A,G531A,T598C,T658A,C921T,A1131G,C1408T,C1464T(4)

Clade B: 340,658,1056,1171,1403,1408
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T1653C(4)
G340A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,T1653C(4)
G340A,G605C,T658A,T680C,T1056C,G1171A,G1403A,C1408T,T1653C(4) F
G340A,G605C,C612T,T658A,T1056C,G1171A,G1403A,C1408T,T1653C(4)

G340A,A579G,G605C,T658A,C704T,T1056C,G1171A,A1386G,G1403A,C1408T(4)
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403A,C1408T(4) S
G340A,A579G,G605C,T658A,T1056C,G1171A,A1386G,G1403A,C1408T(4) S
G340A,A579G,G605C,A611G,T658A,T1056C,G1171A,A1386G,G1403A,C1408T(4) F
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G,G1403A,C1408T(4) S
G340A,A579G,G605C,T658A,A716G,T1056C,G1171A,A1386G,G1403A,C1408T(4) S

Clade C: 40,207,605,658,1056,1171,1403,1408,1629
A40G,G207A,G302T,C573A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,G1629T(4)
A40G,G207A,G515R,G605C,T658A,C816T,T1056C,G1171A,G1396A,G1403A,C1408T,G1629T(4)
A40G,G340A,A579G,G605C,T658A,C672T,T1056C,G1171A,A1386G,G1403A,C1408T,G1624A(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A,C1408T,G1473A,G1629T(4)
A40G,G207A,G605C,T658A,G832A,T1056C,G1171A,G1403A,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,G1005A,T1056C,G1171A,G1403A,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,G1629T(4) F
A40G,G207A,G605C,T658A,T1056C,G1171A,C1182T,G1403A,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T834A,T1056C,G1171A,G1403A,C1408T,G1629T(4)
A40G,G207A,G605C,T658A,T1056C,G1171A,G1403A,C1408T,A1435G,G1629T(4) (? F/S)


Odd Ones
C148T,G340A,A424G,A566G,T658A,G684A,C870T,T927C,G1171A,A1230G,G1326A,C1408T,A1536G(4)
T216C,G340A,A424G,G435A,T658A,C672T,G1171A,C1408T(4) F
T243C,G340A,A424G,C473T,T658A,G713A,A747G,G1171A,C1408T,C1627A(4) F
C172T,G360A,A424G,T519A,T658A,G1171A,C1408T(4)
G154A,G207A,G605C,T658A,T1056C,G1171A,C1383A,G1403A,C1408T,G1524K,G1629T(4)
T17C,G565A,T658A,A973G,G1171A,T1197C,G1395A,C1404T,C1408T,G1524A,A1651G(4) F
G396A,G451A,G531A,T598C,T658A,A795G,C921T,A1131G,G1407A,C1408T,C1464T,A1553G,A1579G(4)
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T(4)

By areas
1 Coventry
4 Newcastle-upon-tyne
3 Oxford
1 Durham
2 Leeds
1 Manchester
4 Birmingham
1 Leicester
1 York
1 Cambridge (Fatal)
6 London
2 Nottingham
3 Whitechapel (2 Fatal)
1 Middlesex
1 North Yorkshire

8 Severe/fatal with no locations given
1 Possible severe/fatal no location
 
Hyper-Zoonoses in the UK Matching World Circulation Reservoir

Hyper-Zoonoses in the UK Matching World Circulation Reservoir

UK Genetic Evaluation thread Response #27 from mixin

mixin produced data output today concerning the recent deposit of UK sequences. The original evaluation is on the genetic evaluation thread. We've provided a link, but if a moderator would prefer to instantiate the post prior to this response, we'd be pleased.

==

Thank you for evaluating these sequences, mixin.

Bear in mind that a program is most useful when the heuristics and assumptions are fully externalised. We are not in receipt of those information points, so our comments here will be given as one in the dark. We've attempted to gain this required insight in the past without success.

From your narrative and the block of output, we can ascertain that the program did some level of data organisation (unstated) and that you then re-arranged parts of the output based on some secondary heuristics.

Does each line represent one sequence and the nucleotide changes on that sequence? Does the program have a method to effectively label those lines with the sequence names (at the beginning and end)? Does any possibility exist to manage ambiguity codes? Does any possibility exist to notate the amino acid positions in parentheses next to the nucleotide positions [e.g. G451A (137T), T1056C (syn338G), et al] or to provide a separate report notated by amino acid position with silent changes differentiated?

Per line, could we see an automated count of the SNPs (silent and non-syn) and have highlighted the SNPs matching the selected sub-clade standards:

Clade A: 451,598,658,1408,1464
G451A,T598C,T658A,T933C,T1020C,T1191C,G1206A,C1245T,T1374G,C1408T,C1464T[x SNPs, x Silent, x Non-syn] (4)

An output format of .csv would increase ease of visualisation if the changes are properly aligned per dataset. Input into a spreadsheet allows additional automated analyses. Output designed for insertion / update into a relational database is even more useful.

Also note that the sequence deposit does not directly match the Ellis Figure 3 Phylogenetic Tree. So overall count and category counts are very dependent on identifying the individual sequence / sample name.

==

At any rate, the output and the post-processing organisation appears to demonstrate that the selected sub-clades demonstrate a lower CFR than the "Odd Ones"? The odd ones, we suggest, are the sequences that do not pattern onto the major groupings using the unstated parameters and hueristics of the program?

If this statement is true concerning the method of selecting the "Odd Ones", then we may conclude that this category has a CFR of 37.5% (3 of 8) as opposed to much lower death rates on the selected larger groups? In fact, the largest suggested sub-clade has the lowest CFR signalling that transmission v. severity are two different concerns with the current circulating reservoir combinations in the UK.

CFR by Suggested Sub-Clade

37.5% - Odd Ones (3 of 8)
20.0% - Clade B (2 of 10)
20.0% - Clade C (1 or 2 of 10)
08.3% - Clade A (1 of 12)

A higher death rate among unpatterned sequences may potentially signal that the hyper-morphic phase has re-initiated. Our analyses indicate that many of the novel and rare changes incoming to PF11 at this time also exist in animal reservoirs that have been previously related to human infection. Small changes in human influenza matching animal genetics are known to create significant changes in severity levels and viral behaviour.

Hyper-morphism (high change rate) with a significant percentage of animal-matched intake equates to a present hyper-zoonotic set of strains.

This hypothesis appears to agree with your data . . . if we are guessing correctly at the underlying parameters.
 
Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

UK Genetic Evaluation thread response #30 from gsgs

GSGS responded to the genetics thread at the prior link. The original evaluation is on the genetic evaluation thread. We've provided a link, but if a moderator would prefer to instantiate the post prior to this response, we'd be pleased.

==

gsgs said:
I just found this thread.
When will the sequences be published so we can
verify and discuss it freely ?
Click to expand...

According to the narrative, these sequences have apparently been
processed through a program of your authorship?

Earlier attempts to assign differences in virulence to
different substrains had failed.
Remember Argentina last year, Ukraine, early Mexico.
Click to expand...

Clear indications of severity markers and Vaccine Escape domains are available as are indications of drug resistance.

A complete statistic with the proportion of deaths in the
published (or GISAID) substrains would be useful, though.
Click to expand...

Some outdated material has been produced and analysed to little effect due to scarcity and unreliable parameters.

calculating % of deaths (or ICU) per mutation is straight forward,
then assign the sums of the values to each virus
then calculate the average for each month and chart
it over time, per country,continent
Click to expand...

Such small point factors are unreliable for many reasons, but, most importantly, due to various synergies among combinations of polymorphisms, some that produce little net effect and others that produce multiplicative effect. The record is observable on these matters.

Calculations based on selected combinations of polymorphisms chosen by frequency / absence on a background among other factors may provide comparisons that feedback to the choice of SNPs to include on that calculation. Due to sparsity of data and clinical meta-data, the calculations must be iterated and interpreted with a high level of earnestness and objectivity.

it has been speculated that more middle-age people are infected
this season vs. more children last season.
And the children die less often from ***, more are immune now,
and that that allone could explain the increased number of deaths.

Do we have UK-deaths by age 2009/10 vs. 2010/11 ?
Click to expand...

The data have been produced by HPA and provided in spreadsheet format. Transparency and timely reporting is not occurring, nor do we expect valid data in the near term.

GeneWurx_UK_ICU_Categories_v1.xls

Virologically it's remarkable that these substrains are new,
they emerged from early Cancun viruses, presumably in Asia
and have nothing in common with the strains circulating
in USA,Europe last season.

These mutations do not occur e.g. in my list of 28 substrains
from Nov.2010
Click to expand...


Though novelty and divergency is now the norm in the UK reservoir, one of the strains that was previously found in a robust form during the late Australia winter season is easily trackable.

Emergence began in late 2009 in the United States of the most frequent background and continued via domaining during the early part of 2010 and the summer in the Northern Hemisphere, translating well into the winter in the Southern Hemisphere.

GeneWurx analyses show a pattern of emergence throughout the world of this particular currently low CFR strain. What will happen next may be more predictable should sequences be provided in a timely fashion in conjunction with mild, severe and fatal cases.

GeneWurx_UK_December_Emerging_Genetics_v3.xls
 
UK Severe Wave Sequences Show No Fatalities with 225G

UK Severe Wave Sequences Show No Fatalities with 225G

UK Severe Wave Sequences Show No Fatalities with 225G

The UK Health Protection Agency released a group of 37 sequences at GISAID dated 2010-01-05 that appeared sometime after that date. Some of the sequences in this deposit also appear on the Figure 3 Phylogenetic Tree from the HPA Eurosurveilance paper requested to be cited as:

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
Date of submission: 31 December 2010

The science community expected a full deposit to back the paper, but not all sequences noted on the phylogenetic table were in place at GISAID as of this 2nd deposit.

The recent GISAID deposit added 4 of the fatalities noted on the Ellis Figure3 <SUP>1</SUP> phylogenetic tree to the 4 fatalities previously released on 2010-12-20. The previously released sequences were not marked at GISAID with a fatality notation, but now have been notated as "Deceased" as of yesterday. Oddly enough, on the 2010-01-05 deposit, none of the sequences notated as fatal on the phylogenetic tree were marked as to outcome at GISAID? This dys-synchronicity and cycling of outcome data is less than optimal for worldwide communication.

None of the sequences at the GISAID database that correspond to notated fatalities on the Eurosurveillance paper carry the severity marker of HA 225G.

225G is found on identical HA sequences noted as 2 severe cases.

  • UKEngland4940476_2010_12
  • UKEngland4880378_2010_12
. . . . UKEngland4940476_2010_12 (
. . . . . . . . 100N,
. . . . . . . . syn179L (CTg) [Regional Marker 2009 (tTA)]
. . . . . . . . . . . . . . . . . . . . [TexasAF2588_2009_10_04,
. . . . . . . . . . . . . . . . . . . . TexasJMS404_2010_01_08],
. . . . . . . . 188T,
. . . . . . . . 225G,
. . . . . . . . syn338G,
. . . . . . . . 377K,
. . . . . . . . syn448L [Regional Marker 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)

With 8 fatalities noted on the tree and none of them coming from cases manifesting an HA 225G severity marker, we must ask for more data while looking elsewhere for causality. The common theme in recent UK and other geographies is hyper-zoonosis creating divergency. Animal reservoirs (H3N8, H5N1, H7N7) carry change values matching the recent intake into the pH1N1 circulation. Data suggests that this human disease is rapidly diversifying by accumulating genetic information from multiple animal reservoirs.

For example, the 377G that is emergent in 2009 Human H5N1 from Dakahlia, Egypt is also emergent in England and Iran in the Pandemic H1N1 reservoir. A recent fatal case from England, UKEngland4500186_2010_11_f, carries the same coding for 377G combined with a 190Y that is found elsewhere in 2010 Malmoe, Sweden pH1N1 and in Avian H6N1.

The HPA Ellis Figure3 <SUP>1</SUP> phylogenetic tree did not notate the 377G branch though 5 English sequences, including this fatal one, appear on the chart carrying the H5N1 Human adaptation.


  • UKEngland83_2010_10
  • UKEngland87_2010_10
  • UKEngland5500192_2010_10
  • UKEngland119_2010_11
  • UKEngland4500186_2010_11_f
GeneWurx has annotated the Ellis Figure3 <SUP>1</SUP> phylogenetic tree with green boxes next to the four fatal GISAID 2010-12-20 deposited sequences and has proposed polymorphism notations on various unmarked branches in an attempt to provide clarity.

UK_2010_Phylo_ELLIS_Fig3new_4_GISAID_Notated_2011_01_08.JPG

Is the Hydra Effect providing Immune Escape capacity for this circulating viral reservoir? Has an accelerant been insinuated into the reservoir?

In many locales around the United Kingdom, half of the ICU beds are occupied by Influenza patients. Only 1 of 12 ICU beds was occupied by an Influenza patient at the peak of last year's pandemic. 100% of the ECMO capacity (heart/lung machine) has been utilised for more than 2 weeks. Hospitals have moved to "Black Alert" status. Ireland has set new records for the number of ER (Casualty, A&E) patients left on gurneys due to room capacity problems.

Do these facts move the HPA to quickly derive plausible causality and workable next steps?

Usable data streams with matched clinicals to the sequences are the primary inputs required to investigate and validate causality. An explanation is deserved from the HPA on their removal of this valuable data from the science community?


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
 
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Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Re: UK: Reports of Approximately 57 Deaths and 800+ Patients in intensive care (50 deaths confirmed by HPA as for Jan. 06 2011) due to influenza

Just a question. Can anyone give a short and comprehensive response to these questions ? I see a huge amount of data and analyses and have lost the overview:

The changes in aa 188 and 186: As I understand these are in about half of teh UK sequences. Are they expected to be linked to the severity and vaccine escape ?

D225G: only present in 2 of the sequences ?

H275Y: Tamiflu resitance - I saw somewhere that this is getting fixed in this years H1n1. Is this correct ?

In other words: Are the novel sequences as alarming as for example suggested by HenryN or is there "no cause for concern" ?

Thanks !
 
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