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
 
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
 
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 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 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