niman

Podcast on WHO presser and comments on 7% Tamiflu resistance (R292K) http://recombinomics.co/thedrnimanshow/2017/03/030117.mp3

The release of HPAI sequences (at GISAID) from birds or people linked to Guangdong, China has raised concerns. Currently four human sequences have been made public and all four have the same poly-basic cleavage site in H7 and the Tamiflu resistance marker in N9, R292K. This is in marked contrast to seven avian HPAI sequences and over 60 recent human LPAI H7N9 sequences, all of which are Tamiflu sensitive. This linkage between the resistance and human HPAI sequences was actively ignored at the recent WHO presser, even though the vast majority of the above sequences were generated by the WHO regional influenza center in Beijing, who was one of the two presenters at the presser. The presser noted that 7% of recent human sequences were Tamiflu resistant, but failed to note that 7% of the human sequences were HPAI and the frequency was the same as Tamiflu resistance because 100% of the human HPAI sequences had R282K and 0% of the LPAI H7N9 had this change (even though both populations were treated with Tamiflu). Although the presser was actively covered in subsequent media reports, the dramatic correlation between Tamiflu resistance and human HPAI was not cited, raising serious transparency concerns.

Comments on cluster confusion http://recombinomics.co/thedrnimanshow/2017/02/022717.mp3

Comments on cluster confusion http://recombinomics.co/thedrnimanshow/2017/02/022717.mp3

Taiwanese man dies of H7N9 Kaohsiung businessman visited China in January By Matthew Strong,Taiwan News, Staff Writer 2017/02/28 15:50 (By Central News Agency) TAIPEI (Taiwan News) – A 69-year-old businessman who worked in China became the second person in Taiwan to die of the H7N9 avian flu, officials said Tuesday. Of five known cases, a foreign citizen first died, making the businessman from Kaohsiung the first Taiwanese national to fall victim to the bird flu. The man was working in the city of Yangjiang in China’s province of Guangdong last January 23 when he felt a fever and decided to return to Taiwan two days later to seek treatment. He was diagnosed with a flu, but on January 29, his fever turned more serious and he suffered breathing difficulties, leading to the hospital treating him as a case of pneumonia. On February 1, he began a stay in hospital, after which he was only diagnosed with H7N9 following a second battery of tests. The conclusion led to his transfer to an intensive care unit. Because existing drugs did not seem to work in his case, the Centers for Disease Control applied for the importation of a new type of drug from Japan. Nevertheless, the patient’s condition continued to deteriorate, and during the evening of February 27 he died of multiple organ failure, the CDC announced Tuesday. The businessman had a history of high blood pressure and was over the age of 60, two of several factors making him more vulnerable to the impact of H7N9, officials said. The CDC cautioned visitors to China to stay away from poultry markets and to only eat thoroughly cooked poultry products. http://www.taiwannews.com.tw/en/news/3105094

Map Update https://www.google.com/maps/d/edit?hl=en&hl=en&authuser=0&authuser=0&mid=18hzYEnr0cRj2MpRMciJAN_b2e6s&ll=24.783676813171994%2C121.16203306953128&z=8

Rescue 27 days first Taiwanese people dyed H7N9 died -A + A On the Yahoo! Kimo | the Yahoo Kimo (Breaking News) - February 28, 2017 2:25 PM share it recommend A Taiwanese businessmen to work in mainland China, diagnosed in early February infected H7N9 avian influenza, after 27 days of hospitalization, the condition continued to deteriorate last night due to multiple organ failure died, is the case of 5 cases of H7N9 case 2 died, is the first Taiwanese. Deputy Director of the Hospital Authority, Mr Lo Yijun (pictured). (Central News Agency) Weifu Ministry of Health announced in early February a 69-year-old Kaohsiung Taiwan businessmen, January 23 to work in Yangjiang City, Guangdong Province, China, due to fever, chills, 2 days after returning to medical treatment, test the new influenza A Negative, 29 start fever, cough with sputum, respiratory asthma and other symptoms, once again medical diagnosis of suspected pneumonia, February 1 hospitalized disease once again informed of a new type of influenza, the second only to detect H7N9 positive, then admitted to the intensive care unit treatment The Subsequently, the Department of Health found that Taiwan-infected H7N9 influenza virus mutation, the existing influenza, fluole and other antiviral drugs with drug resistance, so the project to apply for a new Japanese antiviral drugs for patients to use. The Deputy Director of the Hospital for Disease Control, Dr Lo Yijun, said today that the patient was treated by an intensive care unit and an infectious disease specialist, who continued to use antiviral drugs, respirators, leaf capsules, hemodialysis and other treatments. Failure, died on the evening of February 27, is 5 cases of domestic diagnosis of H7N9 influenza cases, the first two cases of death, but also the first Taiwanese people. Luo Yijun said that patients with age over 60 years of age, plus a history of hypertension, severe pneumonia, persistent high oxygen demand, resistance to influenza, etc., these are known in the medical literature and H7N9 death associated with high risk factors , Even if the medical team to make every effort to treat, still unfortunately died. Luo Yijun pointed out that the recent H7N9 cases in mainland China continued to increase, since October last year, 461 cases of H7N9 flu cases, the largest in Jiangsu Province, 128 cases, followed by Zhejiang Province, 79 cases, 52 cases of Guangdong Province, Anhui Province, 50 cases, Poultry, live poultry market exposure history, and another 1/3 no bird contact history, more than 50 years of age for the community, the mortality rate of nearly 4 percent. The KPC reiterates that the Chinese mainland is still at the peak of the H7N9 flu, both local and businessmen who are planning to travel to the region, should be vigilant to implement personal hygiene measures such as handwashing to avoid contact with birds and poultry market. The Commission reminds that eating chickens, ducks, geese and eggs are cooked to avoid infection. If you have any symptoms such as fever and cough, you should take the initiative to inform the airline personnel and the airport port quarantine personnel. If you have any of the above symptoms, you should go to the ward for medical treatment. The relevant information can be found on the website of the UNDCP (http: /www.cdc.gov.tw), or call the Free Epidemic Prevention Line 1922 (or 0800-001922).

A Taiwanese businessmen to work in mainland China, diagnosed in early February infected H7N9 avian influenza, after 27 days of hospitalization, the condition continued to deteriorate last night due to multiple organ failure died, https://tw.news.yahoo.com/搶救27天-首名台籍人士染h7n9病逝-062517780.html

A 57-year-old male with symptom onset on 5 January 2017. The case is still hospitalized and in critical condition as of 22 February 2017. He was reported to have had poultry exposure. http://www.who.int/csr/don/27-february-2017-ah7n9-china/en/

Isolate name: A/Guangdong/17SF006/2017 Isolate ID: EPI_ISL_249308 Passage details/history: E1 Type: A / H7N9 Lineage: Sample information Collection date: 2017-01-12 Host Human Additional host information: Zip code: Patient status: Last vaccinated: In-vivo pathogenicity test: Location: China Additional location information: Guangdong Patient age: 57 Year(s) Gender: Male Outbreak: Treatment: Specimen source: Institute information Originating lab: Sample ID given by the sample provider: Address: Submitting lab: WHO Chinese National Influenza Center Sample ID given by the submitting laboratory: Authors: Address: WHO Chinese National Influenza Center Virology Institute, Chinese CDC 155 Changbai Road, Changping District, Beijing 102206 China Publication Publication In vivo antiviral resistance Phenotype Genotype Unspecified Antiviral resistance tested by experimental procedures Adamantanes: Unknown Oseltamivir: Unknown Zanamivir: Unknown Peramivir: Unknown Other: Unknown Additional information Antigenic characterization: Note: Sequence segment identifier length accession # INSDC Sequence PB2 A/Guangdong/17SF006/2017-PB2 2280 EPI919596 PB1 A/Guangdong/17SF006/2017-PB1 2274 EPI919597 PA A/Guangdong/17SF006/2017-PA 2151 EPI919595 HA A/Guangdong/17SF006/2017-HA 1695 EPI919599 NP A/Guangdong/17SF006/2017-NP 1497 EPI919592 NA A/Guangdong/17SF006/2017-NA 1398 EPI919598 MP A/Guangdong/17SF006/2017-MP 982 EPI919594 NS A/Guangdong/17SF006/2017-NS 838 EPI919593 Submitter information Submitter: Yang, Lei Submission Date: 2017-02-20 Last modifier: Yang, Lei Last modified: 2017-02-21 Address: WHO Chinese National Influenza Center Virology Institute, Chinese CDC 155 Changbai Road, Changping District, Beijing 102206 China

Isolate name: A/Guangdong/17SF006/2017 Isolate ID: EPI_ISL_249308 Passage details/history: E1 Type: A / H7N9 Lineage: Sample information Collection date: 2017-01-07 Host Human Additional host information: Zip code: Patient status: Last vaccinated: In-vivo pathogenicity test: Location: China Additional location information: Guangdong Patient age: 56 Year(s) Gender: Male Outbreak: Treatment: Specimen source: Institute information Originating lab: Sample ID given by the sample provider: Address: Submitting lab: WHO Chinese National Influenza Center Sample ID given by the submitting laboratory: Authors: Address: WHO Chinese National Influenza Center Virology Institute, Chinese CDC 155 Changbai Road, Changping District, Beijing 102206 China Publication Publication In vivo antiviral resistance Phenotype Genotype Unspecified Antiviral resistance tested by experimental procedures Adamantanes: Unknown Oseltamivir: Unknown Zanamivir: Unknown Peramivir: Unknown Other: Unknown Additional information Antigenic characterization: Note: Sequence segment identifier length accession # INSDC Sequence PB2 A/Guangdong/17SF006/2017-PB2 2280 EPI919596 PB1 A/Guangdong/17SF006/2017-PB1 2274 EPI919597 PA A/Guangdong/17SF006/2017-PA 2151 EPI919595 HA A/Guangdong/17SF006/2017-HA 1695 EPI919599 NP A/Guangdong/17SF006/2017-NP 1497 EPI919592 NA A/Guangdong/17SF006/2017-NA 1398 EPI919598 MP A/Guangdong/17SF006/2017-MP 982 EPI919594 NS A/Guangdong/17SF006/2017-NS 838 EPI919593 Submitter information Submitter: Yang, Lei Submission Date: 2017-02-20 Last modifier: Yang, Lei Last modified: 2017-02-20 Address: WHO Chinese National Influenza Center Virology Institute, Chinese CDC 155 Changbai Road, Changping District, Beijing 102206 China

Isolate name: A/Qingyuan/GIRD1/2017 Isolate ID: EPI_ISL_249102 Passage details/history: Type: A / H7N9 Lineage: Sample information Collection date: 2017-01-14 Host Human Additional host information: Zip code: Patient status: Deceased Last vaccinated: In-vivo pathogenicity test: Location: China / Guangdong Province Additional location information: Patient age: 56 Year(s) Gender: Male Outbreak: Sporadic Treatment: Treatment by Oseltamivir Specimen source: Tracheal Institute information Originating lab: State Key Laboratory of Reipiratory Disease (Guangzhou Medical University) Sample ID given by the sample provider: Address: State Key Laboratory of Reipiratory Disease (Guangzhou Medical University) 195, Dongfengxi Road, Yuexiu District, Guangzhou, Guangdong Province, China, Guangzhou China Submitting lab: guangzhou institute of respiratory disease Sample ID given by the submitting laboratory: Authors: Wenda Guan,PhD; Wenjun Song,PhD; Jianfeng He,MD; Changwen Ke,MD; Zifeng Yang,PhD; Haibo Zhou,MD; Qinhan Lin,MD; Yonghui Zhang,MD; Nanshan Zhong,MD Address: guangzhou institute of respiratory disease 1 kangda road, guangzhou China Publication Publication In vivo antiviral resistance Phenotype Genotype Unspecified Antiviral resistance tested by experimental procedures Adamantanes: Unknown Oseltamivir: Unknown Zanamivir: Unknown Peramivir: Unknown Other: Unknown Additional information Antigenic characterization: Note: Sequence segment identifier length accession # INSDC Sequence PB2 A/Qingyuan/GIRD1/2017 2341 EPI918730 PB1 A/Qingyuan/GIRD1/2017 2341 EPI918732 PA A/Qingyuan/GIRD1/2017 2233 EPI918734 HA A/Qingyuan/GIRD1/2017 1744 EPI918736 NP A/Qingyuan/GIRD1/2017 1565 EPI918737 NA A/Qingyuan/GIRD1/2017 1444 EPI918738 MP A/Qingyuan/GIRD1/2017 1027 EPI918739 NS A/Qingyuan/GIRD1/2017 890 EPI918740 Submitter information Submitter: guan, wenda Submission Date: 2017-02-19 Last modifier: guan, wenda Last modified: 2017-02-19 Address: guangzhou institute of respiratory disease 1 kangda road, guangzhou China

Guangdong Qingyuan 57 M Under investigation 17/01/2017 http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk03.pdf

The status of the HPAI H7N9 case(s)/cluster in Qingyuan remains confused. CHP initially reported a case (57M) in Qingyaun, Guangdong province as "under investigation. On Feb 19 the Guangdong (GD) CDC released a full H7N9 sequence from Qingyuan that was HPAI (poly-basic cleavage site) with Tamiflu resistance (R292K) and PB2 mammalian adaptation (E627K). The collection date was Jan 14 from a fatal case (56M) which was similar to the above CHP case. On Feb 20 WHO (Beijing) release a full sequence which was vitually identical to the above sequence.Segments were identical (H7,MP,NP,NS), had a single difference (N9,PB2,PA) or 2 differences (PB1) suggesting the sequence was from the same case (which Beijing said was also 56M collected a week earlier (Jan 7). However,the next day WHO modified teh collection date (to Jan 12) and changed age from 56 to 57 (which matched the CHP data). Today WHO issued an update on HPAI cases and cited a 57M case who was symptomatic on Jan 5 and was in critical condition (as of Feb 22). Thus, it is unclear if the two closely related sequences are from one case with an age and status discrepancy (56 or 57) and (dead in January or critical in February) or are from two individuals at the same location (Qinyuan) collected within days of each other,and virtually identical,signaling a cluster.

Disease outbreak news 27 February 2017 On 18 February 2017, the National Health and Family Planning Commission of China (NHFPC) reported to WHO the results of genetic sequencing on virus isolates from two previously reported cases of human infection with avian influenza A(H7N9) virus from Guangdong province. Changes at the cleavage site of the HA gene suggestive of being highly pathogenic to poultry was confirmed by the Chinese National Influenza Centre of the Chinese Centre for Disease Control and Prevention (China CDC). Details of the cases The two cases were reported through International Health Regulations (IHR) notification on 19 January 2017. A 43-year-old female with symptom onset on 29 December 2016. The case recovered. She had poultry exposure but also cared for her sister who was hospitalized with avian influenza A(H7N9). This was reported as a family cluster. A 57-year-old male with symptom onset on 5 January 2017. The case is still hospitalized and in critical condition as of 22 February 2017. He was reported to have had poultry exposure. Investigation revealed exposure to sick and dead poultry. None of the 105 close contacts of these two cases developed symptoms during the two weeks of medical observation. To date, there is no evidence of changes in pathogenicity to and transmissibility among humans. Public health response Considering the new developments in H7N9 genetic sequence, the Chinese government is implementing additional measures in Guangdong province on top of current existing measures: Closure of markets for cleaning. Emergency monitoring of poultry markets and flocks. Culling of flocks if the strain is confirmed in them. WHO risk assessment This is the first report of avian influenza A(H7N9) virus, since its emergence in 2013, having genetic sequences that are suggestive of evolving from a low pathogenic into a highly pathogenic avian virus. Similar changes at the cleavage site of the HA gene were also found in genetic sequence data uploaded in Global Initiative on Sharing Avian Influenza Data (GISAID) of a virus from a recent human case reported by Taiwan, China earlier to WHO on 4 February 2017 with travel history to Guangdong. In addition the Ministry of Agriculture China reported to World Organisation for Animal Health (OIE) on 21 February 2017 that genetic sequences of virus samples from live poultry markets in Guangdong also showed changes consistent with highly pathogenic avian influenza viruses. So far the above genetic changes have been found in viruses from human, poultry and environmental samples from Guangdong or with travel history to Guangdong province. In addition the genetic sequences from the two human cases from Guangdong and the case reported by Taiwan, China showed amino acid substitutions associated with neuraminidase inhibitor antiviral drug resistance. It was reported that the three patients received antiviral treatment before samples were taken. So far there is no evidence of change of epidemiological patterns of avian influenza A(H7N9) infection in humans. There is no evidence that a change in the virus from low pathogenic to high pathogenic avian influenza virus has an impact on the pathogenicity or transmissibility in humans. Overall the likelihood of further community level spread remains low. WHO is closely monitoring the impact of these viruses on public health through its Global Influenza Surveillance and Research System (GISRS) network, and its effect on animal health through collaboration with Food and Agriculture Organization of the United Nations (FAO) and OIE, and will update public health risk assessment accordingly. A change in the virus from low pathogenicity to highly pathogenicity in poultry may have implications on surveillance and control strategies at the animal sector. WHO advice WHO advises that travellers to countries with known outbreaks of avian influenza should avoid, if possible, poultry farms, contact with animals in live poultry markets, entering areas where poultry may be slaughtered, or contact with any surfaces that appear to be contaminated with faeces from poultry or other animals. Travellers should also wash their hands often with soap and water, and follow good food safety and good food hygiene practices. WHO does not advise special screening at points of entry with regard to this event, nor does it currently recommend any travel or trade restrictions. As always, a diagnosis of infection with an avian influenza virus should be considered in individuals who develop severe acute respiratory symptoms while travelling in or soon after returning from an area where avian influenza is a concern. WHO encourages countries to continue strengthening influenza surveillance, including surveillance for severe acute respiratory infections (SARI) and influenza-like illness (ILI) and to carefully review any unusual patterns, ensure reporting of human infections under the IHR 2005, and continue national health preparedness actions. http://www.who.int/csr/don/27-february-2017-ah7n9-china/en/

Isolate name:A/Guangdong/17SF003/2016 Isolate ID:EPI_ISL_249309 Passage details/history:E1 Type:A / H7N9 Lineage:Sample informationCollection date:2016-12-29 HostHuman Additional host information:Zip code:Patient status:Last vaccinated:In-vivo pathogenicity test:Location:China Additional location information:Guangdong Patient age:43 Year(s) Gender:Female Outbreak:Treatment:Specimen source:Institute informationOriginating lab:Sample ID given by the sample provider:Address:Submitting lab:WHO Chinese National Influenza CenterSample ID given by the submitting laboratory:Authors:Address:WHO Chinese National Influenza CenterVirology Institute, Chinese CDC155 Changbai Road, Changping District, Beijing 102206ChinaPublicationPublicationIn vivo antiviral resistancePhenotypeGenotypeUnspecifiedAntiviral resistance tested by experimental proceduresAdamantanes:Unknown Oseltamivir:Unknown Zanamivir:Unknown Peramivir:Unknown Other:Unknown Additional informationAntigenic characterization:Note:Sequencesegment identifier length accession # INSDC SequencePB2A/Guangdong/17SF003/2016-PB22280EPI919604PB1A/Guangdong/17SF003/2016-PB12274EPI919605PAA/Guangdong/17SF003/2016-PA2151EPI919603HAA/Guangdong/17SF003/2016-HA1695EPI919607NPA/Guangdong/17SF003/2016-NP1497EPI919600NAA/Guangdong/17SF003/2016-NA1398EPI919606MPA/Guangdong/17SF003/2016-MP982EPI919602NSA/Guangdong/17SF003/2016-NS838EPI919601Submitter informationSubmitter:Yang, Lei Submission Date:2017-02-20 Last modifier:Yang, Lei Last modified:2017-02-20 Address:WHO Chinese National Influenza CenterVirology Institute, Chinese CDC155 Changbai Road, Changping District, Beijing 102206China

Guangdong Zhaoqing 43 F Pneumonia 17/01/2017 http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk03.pdf

Guangdong Zhaoqing 45 F Fatal 05/01/2017 http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk01.pdf

A 45-year-old female (previously reported on 9 January) from Sihui city, Guangdong province. She had symptom onset on 17 December 2016, and died on 24 December 2016. She was exposed to poultry. Another case was a 43-year-old female from Guangzhou city, Guangdong province. She had symptom onset on 30 December 2016 and was admitted to hospital on the same day. She is the sister of the 45-year old female described above. She took care of her hospitalized sister but also had exposure to poultry. At the time of reporting, she was suffering from pneumonia. http://www.who.int/csr/don/20-february-2017-ah7n9-china/en/

WHO has reported a cluster involving sisters (45F & 43F) who were reported by CHP as being in Zhaoqing (likely hospitalization location). Index case has died, while sister discharged. Sequence from sister was HPAI and Tamiflu resistance (but did not have E627K).