niman Posted February 27, 2017 Report Share Posted February 27, 2017 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. Link to comment Share on other sites More sharing options...
niman Posted February 27, 2017 Author Report Share Posted February 27, 2017 Guangdong Qingyuan 57 M Under investigation 17/01/2017 http://www.chp.gov.hk/files/pdf/2017_avian_influenza_report_vol13_wk03.pdf Link to comment Share on other sites More sharing options...
niman Posted February 27, 2017 Author Report Share Posted February 27, 2017 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 Link to comment Share on other sites More sharing options...
niman Posted February 27, 2017 Author Report Share Posted February 27, 2017 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 Link to comment Share on other sites More sharing options...
niman Posted February 27, 2017 Author Report Share Posted February 27, 2017 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 Link to comment Share on other sites More sharing options...
niman Posted February 27, 2017 Author Report Share Posted February 27, 2017 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/ Link to comment Share on other sites More sharing options...
niman Posted February 28, 2017 Author Report Share Posted February 28, 2017 Comments on cluster confusion http://recombinomics.co/thedrnimanshow/2017/02/022717.mp3 Link to comment Share on other sites More sharing options...
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