China - H7N9 Human Isolates on Deposit at GISAID

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

We are grateful to the samplers, the depositing labs and the GISAID consortium for making the small batch of evaluation material available on 2013-03-31 during this zoonotic epidemic emergence of H7N9 that has the very unfortunate combination of a High Case Fatality Rate and Low clinical intervention effectiveness [GISAID Citations].

The H7N9 human cases show clinically and experimentally-confirmed Gain of Function traits on a minimum of 3 gene segments:

• Hemagglutinin 226L
• Neuraminidase aa69-73 stalk deletion (15 base)
• Polymerase Basic 2 627K

The H7N9 sequences are related at the polymorphism level to widely circulating human virus patterns including pH1N1, sH3N2 and to fatal human H5N1. Each component of the H7N9 human cases carries sub-segment genetics that have seen mammalian adaptation, including the external proteins, Hemagglutinin and Neuraminidase.

An up-to-date and comprehensive follow-up evaluation for each HA polymorphism found on the 3 human H7N9 sequences was provided Wednesday, 2013-04-03, demonstrating the Cross Serotype Homology details. The preliminary H7N9 Novelty Evaluation and Relationship Potential to pH1N1 with detailed Hemagglutinin amino-level polymorphism surfacing was made available for preview on 2013-03-31, formalised at midnight and is now being versioned.

Genetic specifics concerning animal origins and human / mammal adaption are under analysis. The full text of those intermediate reports are currently in pre-publication viewing status and are available at the following links. These compilations will be updated as labs release new sequences.

• GeneWurx Human Emergent H7N9 Cross Serotype Homology (External Genes)
• GeneWurx Human Emergent H7N9 Rare and Novel Hemagglutinin Antigens (External Genes)
• GeneWurx Human Emergent H7N9 ReAssortment Assessment (Internal Genes)

Additional sequences from early emergence fatal and recovered cases are critical to understanding the immune dynamics required for establishing a bulkhead toward the protection of public health.

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Human Adaptation

While multiple laboratories have investigated Avian Influenza models at amino acid position 186 (H3 numbering) and have found that variation toward Lysine and Asparagine on certain backgrounds acts as a co-effector toward increased infectivity of cell types in the human upper respiratory tract, the genetic record extends that potential with amino acid variations perhaps yet uncharacterised. The 2 most recent human H7N9 sequences carry a revision at aa186, HA 186V.

• ChinaAnhuiChuzhouCity1_E1_35F_2013_03_20_f
• ChinaShanghai2_E1_27M_2013_03_05_f

The Valine at this position is novel to H7N9, but is found within the wider H7 reservoir under 40 times and essentially in species considered as commercial poultry. The HA 186V is also found as wildtype in the H13 reservoir among serotypes often considered "dead-end" for avian host progression outside of gulls. Oddly enough, H13N2 has been documented in sea mammals and does carry the Valine in the instance under review. Additionally, the H13N2 positions 186, 187 and 188 correspond to these current H7N9 human sequences.

Perhaps H13 is not "dead-end" at all, but is some type of intermediate platform for preservation or movement between species groups. That speculation will not likely be answered in the near future, but we do have now HA 186V and two trailing amino values that correspond to this new H7N9 motif from an H13N2 sea mammal collection and the H7N9 novel motif of 188T wildtype + 189A revision matching the most commonly circulating pH1N1 subclade at 188T + 189A wildtype.

We may come to find that HA 186V on this background is an intermediate or a full co-effector of alpha 2,6 sialic binding. The combination of 186V / 226L on these H7N9 sequences may be found to parallel the 186K / 226L mutants evaluated on the H5N1 Gain of Function studies.

. . . . . . . . 195V [186V H7N7 Rare],
. . . . . . . . . . . . [H13N9 Avian wildtype],
. . . . . . . . . . . . [H13N2 Mammal wildtype],
. . . . . . . . . . . . [H5N1 Gain of Function Residue aa182:
. . . . . . . . . . . . . . . PubMed PMC2903244, 17108965]

The open-access, full-text Cross Serotype Homology Evaluation for the Human H7N9 Hemagglutinin segments was previously presented.

J Virol. 2010 July; 84(13): 6825?6833.
In Vitro Assessment of Attachment Pattern and Replication Efficiency of H5N1 Influenza A Viruses with Altered Receptor Specificity,
PubMed: PMC2903244
Salin Chutinimitkul, Debby van Riel, Vincent J. Munster, Judith M. A. van den Brand, Guus F. Rimmelzwaan, Thijs Kuiken, Albert D. M. E. Osterhaus, Ron A. M. Fouchier, and Emmie de Wit

Nature. 2006 Nov 16;444(7117):378-82.
Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors.
PubMed: 17108965
Yamada S, Suzuki Y, Suzuki T, Le MQ, Nidom CA, Sakai-Tagawa Y, Muramoto Y, Ito M, Kiso M, Horimoto T, Shinya K, Sawada T, Kiso M, Usui T, Murata T, Lin Y, Hay A, Haire LF, Stevens DJ, Russell RJ, Gamblin SJ, Skehel JJ, Kawaoka Y.

GISAID Citations

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Receptor Binding Site Transition
to Novel Value
Q226I

GISAID Citations

Fatal

HA Polymorphisms
GISAID 2013_04_05

. . . . ChinaHangzhou1_C1_38M_2013_03_24_f (
. . . . . . . . GISAID HA EPI440095
. . . . . . . . GISAID Isolate EPI_ISL_138977
. . . . . . . . 105 Polymorphisms (17 Amino and 88 Silent)
. . . . . . . . 11I,
. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235I [226I Human H3N2 Current wildtype],
. . . . . . . . . . . . [H3N2 commercial poultry
. . . . . . . . . . . . . . . . with HA 155, 156, 158, 159 VxX revisions
. . . . . . . . . . . . . . . . . . and G228S, known virulence marker],
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

NA Polymorphisms

. . . . ChinaHangzhou1_C1_38M_2013_03_24_f (
. . . . . . . . GISAID NA EPI440096
. . . . . . . . GISAID Isolate EPI_ISL_138977
. . . . . . . . 33 Polymorphisms (10 Amino and 23 Silent)
. . . . . . . . 16I [H5N1 Human Fatality China 2011],
. . . . . . . . . . . [H5N1 Human Cambodia 2005],
. . . . . . . . . . . [H5N1 Avian Rare (58) Scotland, Middle East and Asia]
. . . . . . . . . . . [pH1N1 Rare (35) Worldwide including Scotland and 1 US Low Reactor],
. . . . . . . . . . . [avH1N1farm],
. . . . . . . . 19A,
. . . . . . . . 40G,
. . . . . . . . 53T,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 335I,
. . . . . . . . 359A,
. . . . . . . . 401A)

HA 237S (H3 228S) and 255T (H3 246T) may be closer than we'd like to consider.

This HA 226I is novel to H7N9, but is found in avian H3N2 samples from commercial poultry species and in the most widely circulating human Influenza, H3N2, as the wildtype. Those HA sequences from the poultry bear sub-segment genomic homology to these human H7N9 fatalities, as well as homology to currently circulating human H3N2. The H7N9 HA varies at syn405I (ATc) from the current human cases.

At the NA segment, a synonymous revision occurs from the current set of human H7N9 cases, syn142R (cGA).

Though migratory birds have proven capable of carrying the HA 226I / 228S, the combination is known also in swine as recently as 2010 in North America and 2007 in Asia. avH3N2 is also on record with 226L / 228S in North America early in the last decade. The migratory birds sampled in South Dakota six years ago with 226I / 238S share downstream elements from aa228 up to 51 bases with currently circulating human H3N2 (Oceania, United States & Europe). HA 277N (H7N9 285N) is found in correlation on avian H3N2 segments that have variation at 226, including all 226I bearing segments. HA 138S (H7N9 146S) like our current index case, ChinaShanghai1_E1_87M_2013_02_26_f, is also located on the avian H3N2 segments bearing 226I.

Potential for step-wise interchange exists.

[mixin]

Re: China - H7N9 Human Isolates on Deposit at GISAID

The Hangzhou Center for Disease Control and Prevention, has submitted a new case of the novel H7N9 strain to GISAID AI Digest and Helen Branswell

A/Hangzhou/1/2013

Submitting lab: Hangzhou Center for Disease Control and Prevention
Authors: Li,J;
Pan,JC;
Pu,XY;
Yu,XF;
Kou,Y;
Zhou,YY

In my alignment, Hangzhou nucleotides align with Shanghai/2/2013 and Anhui/1/2013; it has 2 unshared mutations in HA, 1 in NA and 2 in MP.

[Toaster2]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Has N158D with T318I, or H110Y with T160A been reported ? These were crucial mutations in H5N1 that conferred stability and transmissibility in the studies by Kawaoka and by Foucher respectively. Don't know what the H7N9 analogs of this would be though. Anyone ?

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Early analytic results demonstrate an influencer relationship on H7N9 from human H3N2. Historical signals during H3N2 species transition events correlate with the independent introductions into the H7 reservoir that created the Novel Hemagglutinin.

. . . . ChinaShanghai1_E1_87M_2013_02_26_f
. . . . . . . . GISAID HA EPI439486
. . . . . . . . GISAID Isolate EPI_ISL_138737

. . . . . . . . 146S [138S pH1N1 Rare (6)],
. . . . . . . . . . . . [H3N2 Human Rare (8)]
. . . . . . . . . . . . [zH1N1 Mammal (Mink 2012)],
. . . . . . . . . . . . [avH1N1farm],
. . . . . . . . . . . . [avH3N2 SouthDakota],
. . . . . . . . . . . . [H5N1 Human Fatality],
. . . . . . . . . . . . [H5N9 Commercial Poultry species],
. . . . . . . . . . . . [H6N1, H7N7, H9N2, H10N7]

• Ongoing Sequence Analysis - Open-Access, Full-Text
• GISAID Citation

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Potential H3 Involvement
in H7N9 Hemagglutinin Emergence

All emergent human H7N9 carries HA N307D (N299D) at a residue that is highly conserved as Asparagine within the H7 reservoir. The Aspartate (D) at aa299 demonstrates rare emergence at potential H3 host species transition events.

. . . . . . . . 307D [299D Canine H3N2],
. . . . . . . . . . . . [Human H3N2 Singular (US 2012)],
. . . . . . . . . . . . [Avian H3N8],

Is this apparent "thermocline", as suggested by the data, explicit in viral revision dynamics? Has H3 acted as a donor / influencer at the sub-segment level on an existing H7N9 Hemagglutinin to create this growing problem in humans?

• Ongoing Sequence Analysis - Open-Access, Full-Text
• GISAID Citation

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Potential H3 Involvement
in H7N9 Hemagglutinin Emergence

This 455 residue is highly conserved in H7 as Asparagine and is within a highly conserved region. The Aspartate revision located on all human H7N9 is also recently found as a polymorphism on Human H3N2, one in January 2013 that shows a mixed trace at residue 300 (co-infection potential).

. . . . . . . . 455D [446D H3N2 Human Rare (9), 2013 US with 128A & 300T mix wt, 2012-2, 2000-4, 1993-1, 1990-1],
. . . . . . . . . . . . [H7N3 Avian Commercial Poultry species],
. . . . . . . . . . . . [H7N2, H7N6 Avian Commercial Poultry species]

• Ongoing Sequence Analysis - Open-Access, Full-Text
• GISAID Citation

[sharon sanders]

Re: China - H7N9 Human Isolates on Deposit at GISAID

NS1 Thanks for all of the information! We have questions!


From another member:

For those of us that are not genetic specialists, can someone provide a simplified status of the H7N9 virus as we understand it today?

Is it a reassortment between two avian viruses, and if so when did it occur?

If not, is it some kind of human reassortment?

Have we identified one or more natural reservoirs?

Should we be worried about asymptomatic wild birds transporting the virus?

Of the unique genetic markers, what are the implications?

Ease of transmission?

Increased human virulence?

Increased antiviral resistance?

and anything else that might be important.

[JJackson]

Re: China - H7N9 Human Isolates on Deposit at GISAID

For those of us that are not genetic specialists, can someone provide a simplified status of the H7N9 virus as we understand it today?

Absolutely not a genetics expert but I have been trying to address some of these questions in the H7N9 - Discussion thread. This is a personal assessment based on very little data and much of it is likely to turn out to be wrong with the benefit of hind-site so caveat emptor.

Is it a reassortment between two avian viruses, and if so when did it occur?

Yes there seems to have been more than one reassortment event. Certainly the H & N have come from one source and the rest from a different lineage. The main event is estimated to have occurred in mid to late 2011 but see posts #48 & 50 in the linked thread.

If not, is it some kind of human reassortment?

My guess is not. There are mammalian markers but, at present, I think these have been picked up by the birds and have made this avian strain better mammalian adapted - hence the spate of zoonotic infections.

Have we identified one or more natural reservoirs?

No. This is the problem at present, why this rash of human infections and no apparent H2H? This should be becoming clear by now. The OIE is now getting reports and they are mainly chickens and some pigeon but this may be more to do with where they are concentrating their testing. My guess is asymptomatic chickens but would like to see more testing in the pig farming regions - especially those responsible for the floating carcases.

Should we be worried about asymptomatic wild birds transporting the virus?

Yes. The best match for the internal segments come from a Bramling (in the Finch family) which was sampled last year in Beijing. The problem with wild birds is, being wild, they do not tend to have the types of close contacts with humans to make them a good primary infection source. They are, however, very useful to the virus as a genetic reservoir.

Of the unique genetic markers, what are the implications?

This is a bit of a Catch22. There are mammalian markers but if there were not then there probably would not be any Zoonotic infections. This could be due to the reservoir being in an intermediate mammalian host or may just be that an avian strain is causing human infections because it happened to have picked up some mammalian traits (which should make it less fit in its natural bird hosts). I am leaning to the later explanation at present which might be good. If the strain is not fit enough to compete with other avian viruses then it may just fade out or mutate back to a better avian fit (no longer able to infect mammals). With the proviso it does not get established in a mammalian host before it does so.

Ease of transmission?

No idea. Without knowing the animal host or how many milder cases underlie those tested because they ended up in ICU this is an unknown. The relative lack of cases among the close contacts (currently 500+) and HCW suggest poor H2H but that then begs the question what did infect them?

Increased human virulence?

In the absence of H2H we are collateral damage to a virus that is alien. The, apparent, high virulence is probably just due to poor immune response to a totally new Ha & Na pairing. It may also be an artefact of testing to date and, as with H1N1(2009), evaporate once we have a better handle on the number of undetected milder cases.

Increased antiviral resistance?

The markers for antiviral resistance are missing so the current version is probably fairly susceptible. I have not seen any testing data or treatment outcome data and there are questions about just how much they help anyway. Roche have just agreed to release the Tamiflu clinical trials data (at very long last) to the Cochrane Collaboration so we may get a slightly clearer picture once it is analysed.

and anything else that might be important.

I would dearly like to see sentinel flu lab data for "Type A - unsubtyped" returns. When samples are RT-PCR tested it is against supplied primers one of which tests for a match against conserved areas on the 'M' RNA strand which is common to all type A flus. If it passes this test then it is checked for a match against seasonal flu markers, which it would fail. If there have been other human H7N9 infection in the general ILI background then they should show up as a spike in the "Type A - unsubtyped" returns. This is important data we are missing and, if the samples have been retained, a prime candidate for retesting once the H7N9 primers have been sent out to the labs in the sentinel system (of which I believe there are about 600).

My attention span is limited and my eyes glaze over after about three paragraphs. That is probably all I and most other FT readers can digest at one time.

Thanks in advance.

[Laidback Al]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Thanks for the comments, JJackson.

[sharon sanders]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Also thanks JJackson.

Please see this:

80% of Flu Cases in Shenzhen are H1N1 Swine Flu Sicknesses - How much of remaining 20% is un-subtyped A? - April 7

[JJackson]

Re: China - H7N9 Human Isolates on Deposit at GISAID

Sharon
That link had already caught my eye but following it back to source, and its links, did not get me to any data or its source.

[sharon sanders]

Re: China - H7N9 Human Isolates on Deposit at GISAID

The source is a news conference yesterday conducted to inform the public that 80% of the flu cases in the area test positive for H1N1pdm09. The news conference was really about H7N9 and the preparations being made by the Shenzhen CDC. Here is a lengthy article about the press conference:

Shenzhen found that more than 80% of the influenza case of H1N1 high-risk the crowd Jiangzai detection
News - China network news.china.com.cn　　time: 2013-04-07　　

Shenzhen Luohu District 518, Zhongzhen Buiding, Luofang Road, a district of the roof of households raising pigeons, wild sparrows from time to time, ran into the cage.
　　The Shenzhen CDC held a news briefing yesterday, Detailed seasonal flu (H1N1) H 7 N 9 avian influenza difference, and revealed in Shenzhen H 7 N 9 cases of bird flu infection yet found, members of the public not to panic. City Communicable Disease Prevention Branch main Renxie Xu said, the seasonal flu, including the type of influenza A H1N1, influenza A H3N2 and influenza B, influenza H 1N 1 influenza accounted for 80% or more, the recent influenza detection data in previous years, was essentially flat over the same period, the public can take general preventive measures for influenza, and influenza vaccination. At present, Shenzhen has set up a human infection of H7N9 avian influenza prevention and control of the Group of Experts, the head of the Third People's Hospital of Shenzhen Zhoubo Ping, Shenzhen People's Hospital, vice president Qiu Chen, City of Hospitals has been designated a special ward to deal with possible The emergence of the epidemic.
　　Shenzhen found a case of H1N1 flu more than 80%
　　Previously, the investigation confirmed cases of Influenza A H1N1 influenza cases in Shenzhen City Hospital, Peking University Shenzhen Hospital treatment. "Last night has detected cases of unexplained pneumonia is completed, not influenza A (H1N1) to exclude H 7N 9 avian influenza virus infection. Yesterday morning City Communicable Disease Prevention Branch main Renxie Xu, introduction, people are very concerned Shenzhen found that the H1N1 flu, in fact, the flu is no stranger has seasonal flu, flu found in Shenzhen now more than 80% of the H1N1.
　　"We are generally referred to as Influenza A (H1N1) to a stream, the current can be cured, if there is no basis of disease, generally will not be severe." Said Xie Xu, has expanded the scope of testing related to unexplained fever, unexplained pneumonia cases would be the first a time detection investigation.
　　March of each year is the rise of Shenzhen influenza incidence intensity. Xie Xu said, these days detected three cases of H1N1, deserve attention, but do not tense, unless their own basis of disease, otherwise you can quickly cure. Recently to pay more attention to high-risk populations such as the elderly, children, the chronically ill, once sick, the small number of patients, there may be complications (such as viral pneumonia, central nervous system infections, etc.) lead to serious consequences, influenza vaccination remains the prevention of influenza effective means. They have contact with schools, hospitals and other departments, pandemic flu illness will make recommendations, such as the suspension of classes, to avoid a large-scale infection.
　　The Shenzhen hospital emergency requisition 15 negative pressure rooms
　　Xie Xu introduced, is more concerned about the H7N9 avian flu, and they are to strengthen communication with the animal health sector, concerned about the health status of poultry operators, personnel engaged in the poultry business, processing for high-risk groups need more attention to prevention. Mainly census for high-risk groups, the general health follow-up every year in March and September sampling and testing of serum twice, mainly to see whether H 5N 1 avian influenza infection.
　　"This year, the first sample has been completed, but was unable to detect H 7N 9 avian flu, we are ready to re-detect again." Xie Xu said that they would soon be part of the high-risk groups for review. Feeding, trafficking and processing of poultry personnel flu-like symptoms such as fever, cough, need to go to the hospital for examination and treatment as soon as possible, do not forget the narrative condition with a history of contact with animals, etc. to your doctor, there is help doctors accurately determine the cause.
　　The person in charge of the city guard appointed, at the HA, Shenzhen has been set up as head of Municipal Third People's Hospital Zhoubo Ping, Qiu Chen, vice president of the Municipal People's Hospital, City Hospital, vice president YANG Da-guo, City Children's Hospital Vice Dean Man fly ball to the deputy head of the people infected with H 7N 9 avian flu clinical expert medical treatment, a total of 25 people, covered by the Department of Respiratory and Critical Care Medicine, Department of Infectious Diseases, Chinese medicine, neurology, pediatrics, nephrology, radiology , nursing and other areas of the city most experts, the majority of the members experienced when SARS and the stream of anti-treatment, bear the guidance of the city's people infected with H 7N 9 avian flu medical treatment, consultation, and training.
　　Shenzhen People's Hospital, vice president, said Qiu Chen, currently under the process, the body fluid samples of patients with unexplained fever CDC identified as H7N9, H7N9 avian influenza medical treatment clinical expert group will end their "Frontline" collective patients most professional rescue and treatment services. Experience of Shanghai, Anhui, H7N9 avian influenza found that the sooner, the earlier the treatment, the greater the chances of survival in patients, and therefore the most enhanced early warning, to notify the CDC by the hospital in the fastest time, with the fastest time to determine The specimen is H7N9, race against time to save the patient.
　　In order to cope with the possible emergence of H7N9 avian flu, the Third People's Hospital in Shenzhen has opened a special ward.
　　Shenzhen, 15 negative pressure rooms in the hospital, emergency requisition of the ward as a fight against the H 7N 9 avian flu dedicated dean Zhou Boping revealed. Negative pressure wards a total of 30 beds, the hospital has adequate reserve of the the Tamiflu treatment drugs and the N 95 masks, isolation clothing and other protective equipment.
　　The rooftop pigeon neighborhood flustered?
　　View of recent Influenza multiple, pigeons samples were found to carry the H7N9 avian influenza virus, members of the public to see the pigeons flustered. Yesterday, public rebellion, said Jing Xuan, 518, Zhongzhen Buiding, Luofang Road, Luohu District, Garden 7 8 floor rooftop owners enclosed illegal construction pigeon house, keep pigeons.
　　Yesterday afternoon, the South is a reporter on the scene saw the roof the rooftop door locked, about dozens of pigeons, pigeon houses has windowsill for pigeons sitting-site, there are a lot of sparrows flew into pigeon holes, open space inside or snatch . Community Security introduced the household is not at home, the Dovecote not illegally built, had not received the residents complained. Luohu city management supervision that will be sent to the scene view, if illegal breeding will be dealt with according to law.
　　The many pharmacies Banlangen stock
　　Jiangsu Provincial Health Department opened the prevention of the H7N9 avian flu prescription taking Banlangen other traditional Chinese medicine, it is recommended that high-risk groups. Suddenly, over the public panic buying Radix, Shenzhen is no exception. The Southern Reporter visited a number of pharmacies Nepstar consistent Tongrentang found Banlangen granules has been out of stock for two days.
　　Sold out of stock, coincided Qingming small holiday, do not know when to make the arrival. "Lotus Village, consistent pharmacy sales staff said, these days in addition to Banlangen granules, the selling disposable masks, oral anti-viral. The the Tongrentang the Longgang auspicious store sales staff also said the store usually sell boxes of Banlangen granules daily, and these days daily sales climbed to a hundred boxes, the price has not changed.
　　Leung Chun-ying, Hong Kong Chief Executive:
　　Stopping or treating SARS supplies enough people do not need to go to snap up
　　Hong Kong has 38 million surgical masks, N95 masks, 14 million, 18 million Tamiflu drugs, 1,400 isolation beds ... yesterday, ready to depart departure of the Chief Executive of Hong Kong to participate in the Boao Forum for Asia in Hainan Leung Chun-ying, at the Hong Kong International Airport through the media to the people of Hong Kong will pay close attention to the development of the H7N9 outbreak, follow-up and co-ordination of various government departments fight the epidemic prevention work. Enough epidemic prevention, the fight against SARS supplies for the Hong Kong health care workers in the epidemic peak period of 3 months, no need to rush to buy.
　　Hong Kong in addition to infrared temperature detection method will deploy more Auxiliary Medical Service, Civil Aid Service and health surveillance assistants the mobile detector spot checks at various ports immigrants temperature. Live poultry at all levels of the supply chain are also other relevant departments to strengthen their routine inspections. Ko Wing-man, Hong Kong Secretary for Food and Health, to remind the people of Hong Kong, "there should be psychologically prepared, no one could have anticipated occurring and infected. No chilled poultry and egg imports of East China found H7N9 virus in poultry in Hong Kong, will be suspended with immediate the live poultry entrance, partial or comprehensive culling, to take a series of measures such as the suspension and large cleaning.

zhttp://news.china.com.cn/live/2013-04/07/content_19394237.htm

[NS1]

Re: China - H7N9 Human Isolates on Deposit at GISAID

GISAID Citations

Shanghai Wet Market Surveillance
2013-04-07

Deposited by Harbin Veterinary Research Institute at GISAID on 2013-04-07.

The human adaption Q226I from H3N2 found on the latest human case on file, ChinaHangzhou1_C1_38M_2013_03_24_f, is NOT manifested in the avian and environmental samples from the Shanghai markets. The HA 252I rising on the pgnChinaShanghaiS1069_2013_04_02 is a SNP off the wildtype HA 243I (ATA) of H5N1 (H3 numbering). The H5 sequences that carry the exact codon from this H7N9 pigeon (ATc) display a remarkable host range though the revision only occurs in 111 isolates of over 5,000 on file.

H5 HA 243I-bearing sequences have infected at least 7 different bird species and 3 mammal species. The most recent finding is in a 2011 Cambodian human with previous findings in a tiger, 2 raccoon dog isolates and another Cambodian human. Across all gene segments, the constellation of polymorphisms in this H7N9 emergence is proving to be knowledgeable about mammals.

Numbering on the following polymorphism lists is absolute (no offset), but the antigenic center of the HA can be managed to H3 numbering with a -9, e.g. 235L becomes 226L. Synonymous changes have been removed from the lists pending verification.

HA Polymorphisms

. . . . pgnChinaShanghaiS1069_2013_04_02 (
. . . . . . . . GISAID HA EPI440701
. . . . . . . . GISAID Isolate EPI_ISL_138985
. . . . . . . . 105 Polymorphisms (18 Amino and 87 Silent)
. . . . . . . . 11I,
. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235L,
. . . . . . . . 252I [243I],
. . . . . . . . . . . .[H3N2 Human Rare (4):
. . . . . . . . . . . . . . . . . 2012-12-27 USNavy with UltraAmbiguity,
. . . . . . . . . . . . . . . . . 2009 Hong Kong,
. . . . . . . . . . . . . . . . . 2008 Florida,
. . . . . . . . . . . . . . . . . 2005 USNavy Distant-to-Relative],
. . . . . . . . . . . .[H7N7 Avian Rare (13), 2004-2006, 2008, 2009],
. . . . . . . . . . . .[H7N1 Avian Rare (4), 2000, 2004, 2008, 2009 including
. . . . . . . . . . . . . . . . . non-gallinaceous commercial avian,
. . . . . . . . . . . . . . . . . Ostrich 2000 Pneumo- & Neuro-Tropic to Mice with PB2 627K],
. . . . . . . . . . . .[H7N8 Avian Singular],
. . . . . . . . . . . .[H7N3 Avian Rare (6), 2006, 2007],
. . . . . . . . . . . .[H7N2 Avian Rare (2), 2006, 2007],
. . . . . . . . . . . .[H5N1 Mammals (Human, Tiger, Raccoon Dog)],
. . . . . . . . . . . .[H5N1 Avian (7 Species)],
. . . . . . . . . . . .[H5N2 Mexico commercial avian (gallinaceous), 1994, 1995],
. . . . . . . . . . . .[H5N3 Hong Kong commercial avian (anser), 1976],
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

. . . . envChinaShanghaiS1088_2013_04_03 (
. . . . . . . . GISAID HA EPI440693
. . . . . . . . GISAID Isolate EPI_ISL_138984
. . . . . . . . 105 Polymorphisms (17 Amino and 88 Silent)
. . . . . . . . 11I,
. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235L,
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

. . . . ckChinaShanghaiS1053_2013_04_03 (
. . . . . . . . GISAID HA EPI440685
. . . . . . . . GISAID Isolate EPI_ISL_138983
. . . . . . . . 107 Polymorphisms (17 Amino and 90 Silent)
. . . . . . . . 11I,
. . . . . . . . 130A,
. . . . . . . . 183S,
. . . . . . . . 188V,
. . . . . . . . 195V,
. . . . . . . . 198A,
. . . . . . . . 211V,
. . . . . . . . 217N,
. . . . . . . . 235L,
. . . . . . . . 285N,
. . . . . . . . 307D,
. . . . . . . . 321R,
. . . . . . . . 410N,
. . . . . . . . 427I,
. . . . . . . . 455D,
. . . . . . . . 462K,
. . . . . . . . 541V)

NA Polymorphisms

. . . . pgnChinaShanghaiS1069_2013_04_02 (
. . . . . . . . GISAID NA EPI440700
. . . . . . . . GISAID Isolate EPI_ISL_138985
. . . . . . . . 33 Polymorphisms (10 Amino and 23 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 40G,
. . . . . . . . 53T,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 335I,
. . . . . . . . 359A,
. . . . . . . . 401A)

. . . . envChinaShanghaiS1088_2013_04_03 (
. . . . . . . . GISAID NA EPI440692
. . . . . . . . GISAID Isolate EPI_ISL_138984
. . . . . . . . 32 Polymorphisms (12 Amino and 20 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 53T,
. . . . . . . . 57V,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 305V,
. . . . . . . . 335I,
. . . . . . . . 350I,
. . . . . . . . 359A,
. . . . . . . . 401A)

. . . . ckChinaShanghaiS1053_2013_04_03 (
. . . . . . . . GISAID NA EPI440684
. . . . . . . . GISAID Isolate EPI_ISL_138983
. . . . . . . . 34 Polymorphisms (14 Amino and 20 Silent)
. . . . . . . . 16I,
. . . . . . . . 19A,
. . . . . . . . 38R,
. . . . . . . . 53T,
. . . . . . . . 57V,
. . . . . . . . 81T,
. . . . . . . . 84N,
. . . . . . . . 112S,
. . . . . . . . 269Y,
. . . . . . . . 305V,
. . . . . . . . 335I,
. . . . . . . . 350I,
. . . . . . . . 359A,
. . . . . . . . 401A)