Beyond Xpert: The fastfollowers and the NAAT pipeline

Transcription

1 Beyond Xpert: The fastfollowers and the NAAT pipeline David Boyle PATH 7 th July 2014 Adv. TB Dx Course McGill University Montreal

2 The Emerging TB Dx technology Landscapes Annual or semi-annual reviews focusing on the status of the TB Dx pipeline Peer reviewed articles: specific focus on technologies, performance parameters and placement Slide 2

3 The current WHO TB Dx pipeline

4 The Fast Follower NAATs What we want to see Choice More robust tech Cheaper Perf. As good or better than current tools A selection of Tools that meet varied market needs COMPETITION! Slide 4

5 The Fast Followers What we currently see Xpert MTB/RIF endorsed in Manual NAAT still pending Further STAG review, Q4 2014/Q1 15) MTBDRsl 2013 MDRTBplus v2.0? Fast Followers = Emerging TB Dx technologies Slide 5

6 The Current TB Landscape Slide 6 UNITAID 2014 TB Dx pipeline

7 Point of care (or point of treatment?) Slide 7 Source: World Health Organization. Diagnostics for tuberculosis: Global demand and market potential (2006).

8 The UNITAID 2014 Pipeline 1. All NAAT platforms were considered for TB Dx and MDR/XDR, not just ones described for use in peripheral settings 2. Screened NIH funding to developers/academic groups 3. Reached out to over 190 companies or research groups (67 companies, 182 products) Slide 8 4. We asked them to complete a basic questionnaire

9 Questionnaire Components 1. Intended Use 2. Primary market(s) 3. Price 4. Performance 5. Operational Characteristics 6. Regulatory Approval And Manufacturing Information Slide 9

10 NAAT Products Identified Companies Products Setting Lab TB Dx MDR/XDR Integrated Partially integrated Open Reference Intermediate Peripheral Companies Products Setting Lab TB Dx MDR/XDR Integrated Partially integrated Open Reference Intermediate Peripheral Slide 10

11 NAAT at the Upper Laboratory Levels Larger laboratories often get ignored : High throughput and/or high complexity tests can be performed TB Dx and MDR/XDR screening is needed Improved Dx and analysis Sample prep automated Cost effective at scale Existing platforms used in USA and beyond Slide 11

12 Existing High Throughput TB Dx Tools Genprobe (USA) Amplified Mycobacterium Tuberculosis Direct (AMTD) assay, US FDA (1995), semi-automated, batch processing TMA amplification. 50 tests/5.5. hrs. BD (USA) ProbeTec ET Direct TB, semi-automated, SDA, 150 tests/day Roche (Switzerland), COBAS TaqMan MTB, real time PCR, internal control flags, UNG to prevent test contamination, bar coding for tracking. Automated systems. 44 tests/3 hrs. Abbott m2000, real time PCR 94 samples in 5 hrs. Slide 12

13 Platform Agnostic Technologies. Many laboratories have real time PCR capability BUT many TB assays described as technology dependent CapitalBio Corp., Qiagen, Zeesan (all China) and Seegene (Korea) have developed CE-IVD marked TB assays that are less platform specific Mycobacteria Real-time PCR, 36 tests /4 hours caretb-rt PCR kit, 90 tests/6 hours Seegene Anyplex II MTB/MDR/XDR Dual priming oligo (DPO), Tagging Oligonucleotide Cleavage Extension (TOCE) and Real Amplicon Detection (READ) Slide 13

14 Seegene Products Anyplex II MTB/MDR/XDR Detection Key features 1. Simultaneous Screening of MTB infection and drug resistance 2. Direct and positive based detection of drug R mutations 27 MDR and 13 XDR 3. Real time PCR sensitivity and specificity (DPO/TOCE) Anyplex II MTB/NTM/MDR-TB Detection Key features 1. Simultaneous determination of MTB and NTM 2. For MTB, add an additional 40 minutes for MDR 3. Direct and positive based detection of drug R mutations 21 MDR 4. Real time PCR sensitivity and specificity (DPO/READ) Comparatively rapid (90 tests/6 hours) and platform agnostic Slide 14

15 NAAT based tools for MDR/XDR TB Line Probe Assays: Hybridization assays for MTB, MDR and XDR AID (Germany) 3 products* Fuji Rebio (Belgium) 2 products Hain Lifescience (Germany) 5 products* Nipro (Japan) 4 products Vircell (Spain) 2 products YD Diagnostics (R. Korea) 5 products* *Offer hyb. stations and scanners Slide 15 Source: Barnard et al., 2009 AJRCC

16 Microarrays for TB Dx/MDR/XDR Screening of wider numbers of genetic markers Several platforms exist with TB Dx/MDR tests Partially integrated Akonni, AutoGenomics, CapitalBio and Veredus 48 tests per 6.5 hrs tests per 8 hrs. $80k - 240K Slide 16

17 Xpert MTB/RIF Refresher 2 min 15 min 1 min <2 hrs. Adapted from Scott, 2010 Buffer chambers PCR tube Slide 17 Source: Niemz and Boyle, 2012 Syringe barrel Cartridge base Gasket Valve body Cartridge body Cap Nested PCR/real time PCR 6 color detection 5 color probe determination TB (rpob) Rif R (rpob) Automated result scoring Reaction waste stored in cartridge HIV VL in development New MDR assay in development

18 Not all Microscopy Cenrters are Equal Source: TB Alert Source: PATH Although both are functional areas there s fundamental differences: Space, staff, and infrastructure all affect ability to perform NAAT What NAATs are available to meet all peripheral settings? Slide 18

19 The First Wave of Emerging Technologies for LRS Four technologies are currently in evaluation Most developed privately via Dx start ups: 1. *Epistem Genedrive M.tb id 2. FIND/Eiken Loopamp MTBC 3. *Molbio - Truelab M.tb 4. *Ustar - NATeasy TB All positioned to compete with Xpert based on cost and simplified technology * Development efforts focused on entry to private or local markets Slide 19

20 Epistem Genedrive M.tb id Epistem Manchester, UK based company Rapid detection of MTB and Rif R via a novel approaches to sample prep, and real time PCR Slide 20 Novel paper based Extraction device 3 reaction amplification Cartridge Lyophilized reagents High quality plastics Single unit Battery powered device Novel engineering reduces power needs Real time PCR with high res melt curve analysis

21 Epistem Genedrive M.tb id Process flow 10 min 1 min 45 min Add sputum to lysis cartridge Dry for 10 minutes Punch out 3 paper discs Add to 3 reaction chambers with 20 µl water Insert cartridge into device, press start button CE-IVD marked, DCGI India Distributors in place for Asia (Xcelris) Manufacturers in place (US and China) Limited peer reviewed evidence Slide 21

22 FIND/Eiken Loopamp MTBC 1. PDP between FIND and Eiken Chemical Corp (Japan) 2. Open platform 3. Loop mediated amplification (LAMP) assay for TB 4. Isothermal amplification, simplified yet rapid and sensitive test 5. Manual, minimally instrumented sample preparation, batch capable Source: UNITAID TB Dx pipeline semi annual report 2012 Slide 22

23 FIND/Eiken Loopamp MTBC Simple, minimally instrumented sample preparation, batch capable, 6 samples ~ 1 hr Slide 23

24 FIND/Eiken Loopamp MTBC Current status: CE-IVD marked 1. Technology performance described: Mitarai et al Large China eval in Dossier of test data presented to Expert review group 20 th April, evaluation studies (rural or simple urban microscopy centers) performed in 4 countries a) while the LAMP technology has potential as a rapid TB diagnostic tool the body of evidence presented to the Group was insufficient to make a recommendation either in favor of, or against the use of TB-LAMP as a replacement test for AFB microscopy. 3. A further 14 independent studies are complete (>7,000 tests) 4. The Expert Group review in Q4 2014/Q Slide 24

25 Molbio - Truelab M.tb Molbio India, a collaboration between Bigtec (Bangalore) and Tulip Group (Goa) Rapid detection of MTB and via a novel chip based real time PCR, CE-IVD marked, DCG Suite of kits, tools and equipment (all battery powered and 2 wireless enabled) 6 µl Slide 25

26 Molbio - Truelab M.tb Unique aspects to core technology Disposable chip based PCR reactor Hot block on chip Lyophilized reagents Unique reaction sealing upon heating Single module instrument Android controller Upload all test data Download Rx instruction GPS Data storage Slide 26

27 Molbio - Truelab M.tb An example of data output TB positive Source: UNITAID TB Dx pipeline: semi annual update Slide 27

28 Ustar - NATeasy TB Ustar Biotechnologies Hangzhou, China Rapid detection of MTB via cross isothermal priming amplification (CPA) No dedicated instrumentation CE-IVD marked kit requiring hot block, pipettor and centrifuge CFDA approved Syringe based extraction tool in evaluation Slide 28

29 Ustar - NATeasy TB Unique aspects to core technology Glassified CPA reagents Disposable and sealed immunochromatographic strip No instrumentation of significant cost Slide 29

30 A Basic Comparison of Emerging Tests to Xpert Test Amplification Fully Integrated Dedicated Instrument M/plex (IAC) TAT (hrs) MDR Intended Setting* Market Release MTB/RIF PCR Y Y Y 2 Y MC # 2009 Genedrive PCR N Y Y 1 Y MC 2013 Loopamp LAMP N Y N 1 N MC 2012 Truelab PCR N Y Y 1 N MC 2013 EasyNAT CPA N N Y 2 N MC 2013 * While all assays are intended for use in the periphery, these technologies claim to be less infrastructure dependent than the Xpert # The GeneXpert was designed for use in laboratories None of these emerging assays are fully integrated None of these assays are (yet) WHO endorsed Slide 30

31 The Next Wave(s) Fully Integrated platforms for NAAT with TB Dx/DR assay potential All are direct competitors to Xpert Alere q, Enigma ML, Great Basin Inc., icubate +, Insilixa, NanoBioSys Inc., NWGHF, QuantuMDx, and Wave 80 + icubate market a RUO TB product Slide 31

32 Emerging Integrated Platforms for Use in LRS Wave 80 (USA) EOSCAPE Slide 32

33 Slide 33 EOSCAPE Processor

34 Slide 34 Core Components and Instrumentation

35 Insilixa HYDRA Fully-integrated, hand-held, and highly-multiplexed genotyping platform for POC diagnostics Slide from G. Skoolnik, Stanford Slide 35 Targeted performance for TB testing: 1. <1hr SNPs 2. Fully-integrated 5. Test cost comparable to Xpert 3. Hand-held 6. Instrument cost < $1000

36 NWGHF Integrated TB Device Funded via Quidel Custom designed collection cup MTB cells lysed at 95 C Exogenous control Single module instrument On board control controller Battery powered Product marketed to LRS Upload all test and QM data Data storage Slide 36

37 Summary The first wave of emerging technologies will meet their targeted markets (e.g. India, China, Asian subcontinent) Only the Loopamp tools has been evaluated at scale Reagent costs are (more) competitive re Cepheid Lower cost instrumentation Increased costs for user training and continual evaluation (QA and QC) There are new waves of technology being developed Greater degrees of integration Broader range of targets Increased sample volume Specifically designed for LRS markets Slide 37 Innovative technology = greater robustness, lower cost

38 THANK YOU!!! 1. UNITAID Funding 2. The technology developers Info 3. Madhu Pai Slide 38 Gabe Bienczycki: PATH