LCVD: Low-cost Cell-extract Viral Diagnostics

Lead Research Organisation: University of Cambridge
Department Name: Pathology

Abstract

Virus disease burden in South Africa
South Africa has one of the highest rates of HIV infection worldwide. For infected individuals, drug therapy depends on knowing their virus load (VL) that is, how much virus is in circulation. About 2.4 million HIV VL tests costing $25 to $40 each, were performed last year in SA but the test is still unavailable those without access to major health care centres. Human norovirus (HuNoV; "winter vomiting virus") is highly infectious and responsible for 90% of non-bacterial diarrheal disease and studies in sub-Saharan Africa suggest that a significant proportion of diarrhea-related deaths in children under 5 go unreported. Thus it is likely that HuNoV infection is an underestimated health threat in SA. Addressing both of these problems with low cost point-of care diagnostic tests would greatly improve diagnosis and treatment, reducing mortality and also the heavy economic burden these diseases.

Aims and goals of the proposal
Our ultimate aim is to co-develop methods to rapidly design and construct cost-effective point-of-care diagnostics for infectious disease agents responsible for high morbidity and mortality in South Africa and other low-income regions. We will target HIV virus load (VL) testing and human norovirus (HuNoV) diagnosis. Recently, biologically-based "biosensor" tests for Zika virus and Ebola virus have been developed that can be produced on paper strips. These tests have the potential to be very low cost because they use a soup or extract from cells to identify the virus. The "cell-free" extract can be spotted onto paper strips, which allows a type of "dipstick" biosensor test for the virus. We plan to refine this basic process by having a team of UK and SA researchers co-develop the cell-free biosensors for HIV and HuNoV. The co-development will both train SA researchers in method development but also allow the method to be taught to other researchers that can then apply the method to their own research. Hence, we aim to co-develop a sustainable technology for SA and other low-income areas. Our goals are:
1) to produce prototype low cost point-of-care diagnostic tests for HIV VL testing and HuNoV diagnosis
2) to use the co-development research process to generate a set of cell-free biosensor methods as a platform technology accessible to SA and other LMIC researcher and educators
3) to use the co-development research process to broadly train individual researchers (our research team) and teach the methods and train other researchers in SA. Our proposal is based on co-development of cell-free in vitro biosensor diagnostics using our research teamwork to drive innovation and integration of laboratories and personnel in the UK and South Africa.

Planned Impact

This project aims to produce prototype Point-of-Care cell-free paper based diagnostics for HIV Viral Load and Human Norovirus detection. The goal is to produce low-cost paper based sensors capable of accurately diagnosing HuNoV and reporting HIV viral load that have low equipment/infrastructure requirements such that they can be easily accessible and distributable in an LMIC setting.

Due to this, direct beneficiaries would include all LMIC's that would benefit from low-cost low-infrastructure compatible diagnostics for these two pathogens, and the list of these is fairly large, particularly in the African continent. This would benefit health organisations through lower costs, health professionals from faster turnaround and patients through increased accessibility.

The project includes extensive collaboration between UK and South African partners to both develop the prototype and build capacity locally in South Africa such that further biosensors can be developed in the future. The sensor being developed is essentially a platform technology that can be readily adapted to detection of other pathogens and environmental contaminants. This fact, combined with the knowledge transfer and infrastructural capacity enhancement coming from this project to the South African collaborators means that at the end of the granting period they will have the skills and equipment to develop further sensors suiting their needs in other areas.

Workshops and training events held by the team during the granting period will also serve to further disseminate the underlying principles of cell-free paper based biosensor technologies to the wider area. This will help engage the wider academic community in South Africa and other countries in the region and enhance their ability to further develop these technologies to suit their own needs.

The product development and capacity building resulting from this project will also mean that manufacture of the end product could take place in South Africa, providing high-skill jobs and potentially significant revenues which will serve to boost the local economy.

Publications

10 25 50
 
Description Biomaker Africa Network (GCRF QR 2018-9 Pump Priming Fund)
Amount £80,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 01/2019 
End 08/2019
 
Description GCRF Pump-priming Fund
Amount £80,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 12/2018 
End 07/2019
 
Description Health effects of a large scale drinking water intervention on arsenic levels in Goalmari, Bangladesh
Amount £79,000 (GBP)
Funding ID RG100049 
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 02/2019 
End 07/2019
 
Description Synthetic Biology Strategic Research Initiative 2016-2019
Amount £165,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 10/2016 
End 09/2019
 
Title OpenMTA 
Description Introduction of a new MTA, the Open Material Transfer Agreement (OpenMTA), that relaxes restrictions on the redistribution and commercial use of biomaterials while maintaining aspects of standard MTAs that support widespread adoption (for example, incorporation into semiautomated administration systems). In developing the OpenMTA, our motivation was to realize a simple, standardized legal tool for sharing biological materials as broadly as possible without undue restrictions, while respecting the rights of creators and promoting safe practices and responsible research. Importantly, we wanted the tool to work within the practical realities of technology transfer and to be sufficiently flexible to accommodate the needs of many groups globally (for example, providing support for international transfers and compatibility with public and philanthropic funding policies). 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact We are seeing increasing adoption of this OpenMTA for public distribution of materials, now adopted by twenty academic reseach institutions, and a similar number of companies. Being adopted by Addgene as a major international partner. 
URL https://www.openplant.org/openmta/
 
Description Creating ultra-low-cost RNA sensors using in-house cell-free preparations 
Organisation Pontifical Catholic University of Chile
Country Chile 
Sector Academic/University 
PI Contribution We are optimizing drying protocols for cell-free systems (using a low-cost energy source) evaluating the stability of these samples after a shelf time and a transatlantic shipment. The outcome of this work will be directly used in our workshop 2020 at South Africa.
Collaborator Contribution They have designed toehold RNA sensors that can be programmed in house low-cost cell-free gene expression systems. We will use these results in our workshop 2020 at South Africa. Likewise, they will participate as speakers/ trainers in this workshop.
Impact A publication, "Ultra-low-cost RNA sensors using in-house cell-free preparations" (in preparation).
Start Year 2019
 
Description HIV and Hepatitis B Patient Sample Access in the UK 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution I and my research team will be contributing towards developing a Hepatitis B biosensor for use at the point of care. The Clinician involved (Professor Graham Cooke) is heavily involved with Hepatitis research in the UK and would profit from the development of a low cost diagnostic test.
Collaborator Contribution The Clinician is enabling our research team to access HIV viral load patient samples in the UK (and potentially Hepatitis B samples as well).
Impact None as of yet. We expect to begin testing patient samples by the end of the year.
Start Year 2018
 
Description Hepatitis B clinical sample access in South Africa 
Organisation National Institute for Communicable Diseases
Country South Africa 
Sector Public 
PI Contribution Our research team will be contributing towards the development of a low-cost, point-of-care (POC) test for Hepatitis B virus (HBV) detection and viral load quantification. The medical scientist with whom we have established a collaboration (Dr Nishi Prabdial-Sing) is the laboratory manager of the Hepatitis division at the National Institute for Communicable Diseases (NICD), South Africa. Dr Prabdial-Sing is also currently involved as a principal investigator in studies validating point-of-care tests for HBV and HCV viral load on patients attending the Liver clinic at Charlotte Maxeke hospital in Johannesburg.
Collaborator Contribution Dr Prabdial-Sing will provide our research team with Hepatitis B clinical samples in South Africa.
Impact None to date. We anticipate that clinical sample testing will begin by the end of the current year.
Start Year 2019
 
Description Hepatitis B clinical sample access in South Africa 
Organisation University of Pretoria
Country South Africa 
Sector Academic/University 
PI Contribution Our research team will be contributing towards the development of a low-cost, point-of-care (POC) test for Hepatitis B virus (HBV) detection and viral load quantification. The medical scientist with whom we have established a collaboration (Dr Nishi Prabdial-Sing) is the laboratory manager of the Hepatitis division at the National Institute for Communicable Diseases (NICD), South Africa. Dr Prabdial-Sing is also currently involved as a principal investigator in studies validating point-of-care tests for HBV and HCV viral load on patients attending the Liver clinic at Charlotte Maxeke hospital in Johannesburg.
Collaborator Contribution Dr Prabdial-Sing will provide our research team with Hepatitis B clinical samples in South Africa.
Impact None to date. We anticipate that clinical sample testing will begin by the end of the current year.
Start Year 2019
 
Description Riffyn 
Organisation Riffyn
Country United States 
Sector Private 
PI Contribution Introduction of Riffyn at Imperial College to training fellow researchers to use the software platform.
Collaborator Contribution Training of individuals to use the Riffyn software platform for experimental design, machine learning and data analysis. Continued support and advice on how to get the best out of the platform. Experimental and assay design advice.
Impact Training of Michael Crone in Oakland USA (January 2020) Training and introduction of Riffyn at Imperial and the London BioFoundry (Ongoing 2020)
Start Year 2020
 
Company Name Colorifix Ltd. 
Description Colorifix has developed a new method to dye textiles where microbes are used to produce, deposit and fix pigments to fabric. The patent pending process can use engineered microbes NB: Although the company was registered in 2016, we did not gain significant funding until 2018. It is at this point where the LCVD award (and Open Plant) award had positive impact on my profile for investors. 
Year Established 2016 
Impact The patent pending process can use engineered microbes The method developed by Colorifix is sustainable and can be made into a circular economy. Importantly, the production of pigments are from engineered microbes that are produced using synthetic biology methods developed in the UK, supported by RCUK (BBSRC, EPSRC). These include DNA assembly methods, LOOP and BASIC. Importantly the company also has engaged with DNA foundries in London and in Norwich (Earlham Institute). From an environmental standpoint, compared to conventional methods based on petrochemical dyes and dyeing: No hazardous chemicals (no taxes or fines for use/disposal) No extraction of pigment (80% cost of fermented products) 90% reduction of water use 30% reduction in energy use <1% dye waste (3x better than industry standard) Combines two processes: lower carbon footprint
 
Description Bahir Dar Biomaker Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Biomaker Africa workshops were set up to get non-programmers up and running within a day or two. This is due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org
Year(s) Of Engagement Activity 2019
URL https://www.biomaker.org/visiting-workshops
 
Description Biomaker Challenge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The Biomaker Challenge calls on interdisciplinary teams to (i) build low-cost sensors and instruments for biology or (ii) develop some biological resource or outreach project. Over a number of years, the initiative has funded over 175 projects and involved hundreds of participants from a wide range of backgrounds. It has proved a great opportunity to learn new skills, collaborate with an interdisciplinary community and, in a short amount of time, develop tools and resources that are useful for real-world applications. Tools and resources developed during the Biomaker Challenge are openly documented and made freely available.
Year(s) Of Engagement Activity 2017,2018,2019,2020
URL https://www.biomaker.org/projectindex
 
Description Cafe Synthetique 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Café Synthetique is the monthly meetup for the Cambridge synthetic biology community with informal talks, discussion and pub snacks.
We meet monthly at the Panton Arms to share the latest developments in synthetic biology and related approaches and techniques. Speakers range from students and group leaders to industry professionals and entrepreneurs.
Year(s) Of Engagement Activity 2016,2017,2018,2019,2020
URL https://www.synbio.cam.ac.uk/events/cafe-synthetique/events/cafe-synthetique/past-cafe-synthetique
 
Description Cambridge SynBio Forums 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The SynBio Forums are sponsored by the University of Cambridge Synthetic Biology Interdisciplinary Research Centre, and feature prominent international speakers and excellent networking opportunities - they provide excellent opportunities to learn more about cutting edge synthetic biology.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019,2020
URL https://www.synbio.cam.ac.uk/events/forum
 
Description Cell-free Synthetic Biology workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Recent technical advances in the preparation of microbial cell-free extracts have given rise to a new class of highly efficient systems for gene expression that are cheap to deploy and have huge potential benefit for the provision of a wide variety of diagnostics, sensors, vaccines and research materials. Cell-free synthetic biology is thus a topic of growing interest to many groups in Cambridge and the Synthetic Biology IRC is pleased to share its programme of activities to promote and support interdisciplinary work in this space.
Year(s) Of Engagement Activity 2017,2018,2019,2020
URL https://www.synbio.cam.ac.uk/initiatives/cell-free-synthetic-biology
 
Description Guest speaker for CRISPR genome engineering workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact A small workshop was organised to teach participants about the use of CRISPR for genome engineering. I helped plan the workshop, provided technical advice and gave a guest presentation on the use of CRISPR systems for diagnostics.
Year(s) Of Engagement Activity 2020
URL https://www.meetup.com/Cambridge-Synthetic-Biology-Meetup/events/268612875/
 
Description International workshop on viral diagnostics development - South Africa 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We ran a free, 3-day workshop dedicated to practical and theoretical training in the use of cell-free synthetic biology technologies, paper-based microfluidic techniques and open-source electronics and detection systems for low-cost viral diagnostics (LCVD) applications. The workshop consisted of several modules focusing on: Diagnostic needs in South Africa, Application of the diagnostics life cycle, ASSURED criteria for diagnostic tests, Scaling up, Regulation and intellectual property, Practical training in cell-free synthetic biology and low-cost electronics. The workshop involved early- and mid-career academics, government and industry representatives and entrepreneurs in the diagnostics field.
Year(s) Of Engagement Activity 2019
URL https://www.lcvd.org/
 
Description Kumasi Biomaker Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Cambridge Biomaker organisers headed to Ghana to run a two-day workshop at Kumasi Hive, an entrepreneurship and innovation hub and one of the implementing arms of the Biomaker initiative. Twenty participants gathered in Kumasi for an accelerated course in programming hardware for low-cost, open-source bioinstrumentation. Half of the participants had worked with the Biomaker system before, and together with the new participants, further developed their projects by learning to program a customisable touchscreen interface for their existing hardware. The fast-paced, energetic training sessions were broken up by project presentations from the teams, talks from researchers from Cambridge and the nearby Kwame Nkrumah University of Science and Technology.
Year(s) Of Engagement Activity 2019
URL https://www.biomaker.org/news/2019/8/29/biomaker-in-ghana-conversations-from-a-2-day-workshop-with-i...
 
Description Open Technology Week 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Open Technology Week showcases and celebrates open source technologies in research and education developed across Cambridge and beyond. This multi-day event includes lectures, demos and workshops that explore examples of open technologies and their implications, featuring projects by Biomaker Challenge teams as well as makers in the community.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
URL https://www.synbio.cam.ac.uk/initiatives/Open_Technology_Week/
 
Description Pretoria Biomaker Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Biomaker Africa workshops were set up to get non-programmers up and running within a day or two. This is due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org.
Year(s) Of Engagement Activity 2019
URL https://www.biomaker.org/visiting-workshops
 
Description Seminars at University of Cape Town 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Drs Jenny Molloy and Lalitha Sundaram were invited to give a seminar at the University of Cape Town's Research Contracts & Innovation division. Approximately 35 people attended the event; the audience was composed of researchers involved in intellectual property, innovation, and biotechnology.
Dr Molloy's talk was entitled "Open Intellectual Property as a Strategy for Innovation in the Bioeconomy" and Dr Sundaram's "Innovations in biotech: getting the regulation right". Both talks sparked discussions among the audience, on the state of regulatory frameworks in South Africa and on current practices surrounding intellectual property.

A number of contacts were made, notably with industrial actors in the plant biotech space as well as with biosafety analysts in South Africa.
Year(s) Of Engagement Activity 2019
 
Description Sequencing workshop in Ghana 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact We ran a sequencing workshop for scientists studying pathogens. This workshop provided hands on training in nanopore sequencing to ~20 scientists from over the African continent.
Year(s) Of Engagement Activity 2018
 
Description Smart Imaging Sandpit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Workshop to introduce the use of AI techniques, image processing and low-cost hardware for real world applications in low resource settings - co-organised by the Synthetic Biology IRC, Sensors SRN and Global Challenges SRI at the University of Cambridge, with support from BITRI Botswana, Royal College of Arts and Mathworks. The workshop led to 5 projects being conceived and funded, and competetive pitches.
Year(s) Of Engagement Activity 2019
URL https://www.gci.cam.ac.uk/events/cgc-co-creation-events/smart-imaging-development-sandpit-and-seed-f...
 
Description Xalapa Biomaker Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This Biomaker workshop was run at the University of Veracruz, Xalapa, Mexico, and designed to get non-programmers up and running within a day or two. This was due to use of the no-code programming environment XOD, which can be used to introduce biologists to hands-on physical computing. This proves to be a great way of promoting co-creation in interdisciplinary teams - where both the engineers and the biologists can communicate properly! (https://www.hackster.io/jim-haseloff/biomaker-starter-kit-xod-023e8b). In addition, we've doubled down on the use of the 4D Systems touchscreens with XOD and the Biomaker Starter kits, to allow code-free communication between Arduino devices and the touchscreens, with their ViSi-Genie interfaces. We've built better tutorial materials to kick-start this (e.g. https://www.hackster.io/jim-haseloff/biomaker-tutorial-4-programming-the-4ds-touchscreen-3b2006). Details of the 2-day workshops and associated open resources can be found at https://www.biomaker.org
Year(s) Of Engagement Activity 2019
URL https://www.biomaker.org/visiting-workshops