Beyond Xpert: The fast-followers and the NAAT pipeline

David BoylePATHdboyle@path.org

7th July 2014 Adv. TB Dx CourseMcGill UniversityMontreal

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

The current WHO TB Dx pipeline

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

The Fast Followers…What we currently see

Xpert MTB/RIF endorsed in 2010

2013 Manual NAAT still pendingFurther STAG review, Q4 2014/Q1 15)2015

2013 MTBDRsl2013 MDRTBplus v2.0?

Fast Followers = Emerging TB Dx technologiesSlide 5

The Current TB Landscape

UNITAID 2014 TB Dx pipelineSlide 6

Point of care (or point of treatment?)

Source: World Health Organization. Diagnostics for tuberculosis: Global demand and market potential (2006).

Slide 7

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)

4. We asked them to complete a basic questionnaireSlide 8

Questionnaire Components

1. Intended Use2. Primary market(s)3. Price4. Performance5. Operational Characteristics6. Regulatory Approval And Manufacturing

Information

Slide 9

NAAT Products IdentifiedCompaniesProducts

3292

Setting Lab TB Dx MDR/XDR Integrated Partially integrated

Open

Reference 18 6 3 3 10 5

Intermediate 63 18 15 9 25 29

Peripheral 11 3 1 1 6 5

CompaniesProducts

1228

Setting Lab TB Dx MDR/XDR Integrated Partially integrated

Open

Reference 1 1 0 0 1 0

Intermediate 10 7 3 7 0 3

Peripheral 17 6 6 15 3 0

Slide 10

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 neededImproved Dx and analysisSample prep automatedCost effective at scale

Existing platforms used in USA and beyondSlide 11

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

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 hourscareTB-RT PCR kit, 90 tests/6 hoursSeegene Anyplex II™ MTB/MDR/XDRDual priming oligo (DPO), Tagging Oligonucleotide Cleavage Extension (TOCE) and Real Amplicon Detection (READ)

Slide 13

Seegene ProductsAnyplex II™ MTB/MDR/XDR Detection

Key features1. Simultaneous Screening of MTB infection and drug resistance2. Direct and positive based detection of drugR mutations

27 MDR and 13 XDR3. Real time PCR sensitivity and specificity (DPO/TOCE)

Anyplex II™ MTB/NTM/MDR-TB DetectionKey features1. Simultaneous determination of MTB and NTM2. For MTB, add an additional 40 minutes for MDR3. Direct and positive based detection of drugR mutations

21 MDR4. Real time PCR sensitivity and specificity (DPO/READ)

Comparatively rapid (90 tests/6 hours) and platform ‘agnostic’Slide 14

NAAT based tools for MDR/XDR TB

Source: Barnard et al., 2009 AJRCC

Line Probe Assays: Hybridization assays for MTB, MDR and XDR

AID (Germany) 3 products*Fuji Rebio (Belgium) 2 productsHain Lifescience (Germany) 5 products*Nipro (Japan) 4 productsVircell (Spain) 2 productsYD Diagnostics (R. Korea) 5 products*

*Offer hyb. stations and scanners

Slide 15

Microarrays for TB Dx/MDR/XDRScreening of wider numbers of genetic markersSeveral platforms exist with TB Dx/MDR testsPartially integratedAkonni, AutoGenomics, CapitalBio and Veredus48 tests per 6.5 hrs.10-15 tests per 8 hrs.$80k - 240K…

Slide 16

Xpert MTB/RIF Refresher

2 min 15 min 1 min <2 hrs.Adapted from Scott, 2010

Bufferchambers

PCR tube

Syringebarrel

Cartridgebase

Cap

Cartridgebody

Gasket

Valvebody

Nested PCR/real time PCR6 color detection5 color probe determination

TB (rpoB)RifR (rpoB)

Automated result scoringReaction waste stored in cartridgeHIV VL in developmentNew MDR assay in development

Source: Niemz and Boyle, 2012Slide 17

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

The First Wave of Emerging Technologies for LRS

Four technologies are currently in evaluationMost developed privately via Dx start ups:

1. *Epistem – Genedrive M.tb iD2. FIND/Eiken – Loopamp MTBC3. *Molbio - Truelab™ M.tb4. *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

Epistem Genedrive M.tb iDEpistem – Manchester, UK based companyRapid detection of MTB and RifR via a novel approaches to sampleprep, and real time PCR

Novel paper based Extraction device

3 reaction amplificationCartridgeLyophilized reagentsHigh quality plastics

Single unit Battery powered deviceNovel engineering reduces power needsReal time PCR with high res melt curve analysis

Slide 20

Epistem Genedrive M.tb iDProcess flow

Add sputum to lysis cartridgeDry for 10 minutesPunch out 3 paper discs

Add to 3 reaction chambers with 20 µL water

Insert cartridge intodevice, press startbutton

10 min 1 min 45 min

CE-IVD marked, DCGI IndiaDistributors in place for Asia (Xcelris)Manufacturers in place (US and China)Limited peer reviewed evidence

Slide 21

FIND/Eiken – Loopamp MTBC

Source: UNITAID TB Dx pipeline semi annual report 2012

1. PDP between FIND and Eiken Chemical Corp (Japan)2. ‘Open’ platform3. Loop mediated amplification (LAMP) assay for TB4. Isothermal amplification , simplified yet rapid and sensitive test5. Manual, minimally instrumented sample preparation, batch

capable

Slide 22

FIND/Eiken – Loopamp MTBCSimple, minimally instrumented sample preparation, batch capable, 6 samples ~ 1 hr

Slide 23

FIND/Eiken – Loopamp MTBCCurrent status: CE-IVD marked

1. Technology performance described: Mitarai et al. 20112. Large China eval in 20133. Dossier of test data presented to Expert review group 20th

April, 2012. 11 evaluation studies (rural or simple urban microscopy centers) performed in 4 countriesa) “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/Q1 2015

Slide 24

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, DCGSuite of kits, tools and equipment (all battery powered and 2 wireless enabled)

Molbio - Truelab™ M.tb

6 µL

Slide 25

Molbio - Truelab™ M.tbUnique aspects to core technologyDisposable chip based PCR reactor‘Hot block’ on chipLyophilized reagentsUnique reaction sealing upon heating

Single module instrumentAndroid controller Upload all test data Download Rx instruction GPS Data storage

Slide 26

Molbio - Truelab™ M.tb

An example of data output – TB positive

Source: UNITAID TB Dx pipeline: semi annual updateSlide 27

Ustar - NATeasy TBUstar Biotechnologies – Hangzhou, ChinaRapid detection of MTB via cross isothermal priming amplification (CPA)No dedicated instrumentationCE-IVD marked kit requiring hot block, pipettor and centrifugeCFDA approvedSyringe based extraction tool in evaluation

Slide 28

Ustar - NATeasy TB

Unique aspects to core technologyGlassified CPA reagentsDisposable and sealed immunochromatographic stripNo instrumentation of significant cost

Slide 29

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# 2009Genedrive PCR N Y Y 1 Y MC 2013Loopamp LAMP N Y N 1 N MC 2012Truelab PCR N Y Y 1 N MC 2013EasyNAT 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 dependentthan the Xpert# The GeneXpert was designed for use in laboratoriesNone of these emerging assays are fully integratedNone of these assays are (yet) WHO endorsed

Slide 30

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

Emerging Integrated Platforms for Use in LRS

Wave 80 (USA) EOSCAPE

Slide 32

EOSCAPE Processor

Slide 33

Core Components and Instrumentation

Slide 34

Insilixa HYDRAFully-integrated, hand-held, and highly-multiplexed genotyping platform for POC diagnostics

Targeted performance for TB testing:

1. <1hr 4. +250 SNPs 2. Fully-integrated 5. Test cost comparable to Xpert® 3. Hand-held 6. Instrument cost < $1000

Slide from G. Skoolnik, Stanford

Slide 35

NWGHF Integrated TB Device

Funded via QuidelCustom designed collection cupMTB cells lysed at 95 ˚CExogenous controlSingle module instrumentOn board control controllerBattery poweredProduct marketed to LRS

Upload all test and QM data Data storage

Slide 36

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• Innovative technology = greater robustness, lower costSlide 37

THANK YOU!!!

1. UNITAID – Funding2. The technology developers – Info 3. Madhu Pai

Gabe Bienczycki: PATH Slide 38