Beyond Xpert: fast-followers and NAAT pipeline

David Boyle

Program for Appropriate Technology for Health (PATH)

July 8th, 2013 Advanced TB DX Research McGill University Montreal

The Emerging TB Dx technology Landscapes

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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

Current TB Dx pipeline from the WHO

The Fast Followers…What we want to see

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• Choice

• More robust tech

• Cheaper

• Perf. good or better

• Tools to meet varied

market needs

COMPETITION!

The Fast Followers…What we currently see

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Xpert MTB/RIF endorsed in 2010

2013 Manual NAAT still pending

Further STAG review, 2014

2013 MTBDRsl ‘endorsed’

Fast Followers = Emerging TB Dx technologies

Point of care (or point of treatment?)

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

The UNITAID 2013 Pipeline

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1. Screened NIH funding to developers

2. Reached out to over 190 companies or research groups

3. We asked them to complete a basic questionnaire

4. All NAAT platforms were considered for TB Dx and MDR/XDR, not just ones described for use in peripheral settings

Questionnaire Components

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1. Intended Use 2. Price 3. Performance 4. Operational Characteristics 5. Regulatory Approval And Manufacturing

Information

Technologies Identified and Assessed

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Commercial 17

Setting Lab TB Dx MDR/XDR Integrated Partially integrated

Reference 14 8 6/4 0 14

Peripheral 5 5 2/0 1 4

Development 10

Setting Lab TB Dx MDR/XDR Integrated Partially integrated

Reference 5 5 4 1 4

Peripheral 5 5 3 4 1

NAAT at the Upper Laboratory Levels

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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

Existing High Throughput TB Dx Tools

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Amplified Mycobacterium Tuberculosis Direct (AMTD) assay Hologic Genprobe (USA), US FDA approved since 1995, semi-automated, batch processing TMA amplification. 50 tests/5.5. hrs. ProbeTec ET Direct TB, Becton Dickinson (USA), 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.

Platform Agnostic Technologies.

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Many laboratories have real time PCR capability BUT many TB assays described as technology dependent.

CapitalBio Corp. (China) and Seegene (Korea) have developed CE-IVD marked TB assays that are less platform specific.

Mycobacteria Real-time PCR, 36 tests /4 hours

Seegene Anyplex II™ MTB/MDR/XDR

Dual priming oligo (DPO), Tagging Oligonucleotide Cleavage Extension (TOCE) and Real Amplicon Detection (READ)

Seegene Products

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Anyplex II™ MTB/MDR/XDR Detection Key features

1. Simultaneous Screening of MTB infection and drug resistance 2. Direct and positive based detection of drugR 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 drugR mutations 21 MDR 4. Real time PCR sensitivity and specificity (DPO/READ)

Comparatively rapid (90 tests/6 hours)

NAAT based tools for MDR/XDR TB

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Source: Barnard et al., 2009 AJRCC

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

Hain Lifescience (Germany) GenoType® MDRTBplus v1.0 (v2.0) (MTB/RIF/INH)

GenoType® MDRTBsl (KAN/CAP/FQ/ETH/STR) Automated sample prep and hybridization

Nipro (Japan) NTM/MDR-TB INH PZA FQ Manual sample prep and hybridization

Innogenetics (Belgium) INNO-LiPA Rif.TB - discontinued

Microarrays for MDR/XDR

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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.

10-15 tests per 8 hrs.

$80k - 240K…

Xpert MTB/RIF Refresher

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

Buffer chambers

PCR tube

Syringe barrel

Cartridge base

Cap

Cartridge body

Gasket

Valve body

Nested PCR/real time PCR

6 color detection

5 color probe determination

TB (rpoB)

RifR (rpoB)

Automated result scoring

Reaction waste stored in cartridge

HIV VL in development

New MDR assay in development

Source: Niemz and Boyle, 2012

Not all Microscopy Clinics are Equal…

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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 tools are available to meet all peripheral setting?

The First Wave of Emerging Technologies for LRS

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Four technologies are currently in late stage development and/or 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

Epistem Genedrive M.tb iD

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Epistem – Manchester, UK based company

Rapid detection of MTB and RifR via a novel approaches to sample

prep, and real time PCR

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

Epistem Genedrive M.tb iD

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Process flow

Add sputum to lysis cartridge

Dry for 10 minutes

Punch out 3 paper discs

Add to 3 reaction

chambers with

20 mL water

Insert cartridge into

device, press start

button

10 min 1 min 45 min

No peer reviewed data (yet)

CE-IVD marked

Distributors in place (Xcelris and BD)

Manufacturer of Genedrive in place

FIND/Eiken – Loopamp MTBC

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PDP between FIND and Eiken Chemical Corp (Japan).

Loop mediated amplification (LAMP) assay for TB

Isothermal amplification , simplified yet rapid and sensitive test

Source: UNITAID TB Dx pipeline semi annual report 2012

Simple, minimally instrumented sample preparation, batch capable

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FIND/Eiken – Loopamp MTBC

Simple, minimally instrumented sample preparation, batch capable, 6 samples ~ 1 hr.

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FIND/Eiken – Loopamp MTBC

Current status:

1. Technology performance described: Mitarai et al. 2011

2. Dossier of test data presented to Expert review group 20th April, 2012 a) 11 evaluation studies (rural or simple urban microscopy centers)

performed in 3 countries

b) “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 10 ‘independent’ studies are underway

4. Further publications and release of the Expert review report are anticipated in 2013

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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

Suite of kits, tools and equipment (all battery powered and wireless)

Molbio - Truelab™ M.tb

Molbio - Truelab™ M.tb

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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

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Molbio - Truelab™ M.tb

An example of data output – TB positive

Source: UNITAID TB Dx pipeline: semi annual update

Ustar - NATeasy TB

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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

Syringe based extraction tool in evaluation

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Ustar - NATeasy TB

Unique aspects to core technology

Glassified CPA reagents

Disposable and sealed immunochromatographic strip

No instrumentation of significant cost

CFDA submission underway

A Basic Comparison of Emerging Tests to Xpert

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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 2009

* While all assays are intended for use in the periphery,

these technologies claim to be less infrastructure dependent

than the Xpert

None of these emerging assays are fully integrated

None of these assays are WHO endorsed

The Next Wave(s)

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Fully Integrated platforms for NAAT with TB Dx assay potential

All are competitors to the GeneXpert

Abbott (m2000)*, Alere q*, BD (BD MAX), Biocartis Apollo*, Biofire Dx (Idaho Technologies), Enigma ML*, iCubate+*, iQuum (LIAT), Nanosphere* (Verigene), NWGHF, Wave 80*

+ iCubate market a RUO TB product

* These groups have TB products in development

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

EOSCAPE Processor

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Core Components and Instrumentation

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NWGHF Integrated TB Device

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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

Summary

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• The first wave of emerging technologies will meet only their targeted markets (e.g. India, China, Indian subcontinent)

• Only the Loopamp tool has been evaluated elsewhere

• Reagent costs are competitive with Cepheid

• Increased costs for user training and continual evaluation (QA and QC)

There are new waves of technology being developed

• Greater degrees of integration

• Wider range of targets

• Improved sample collection

• Designed for LRS markets

THANK YOU!

Slide 36

1. UNITAID

2. The technology developers

3. Madhu