A TReND in Africa collaboration
Open RT
testing for africa
One of the key actions to limit the socio-economic and health impacts of COVID-19 is widespread testing followed by rapid track and trace strategies but traditional testing often incurs in delays of several days and relies on expensive equipment
Point of care diagnostic (POC) tests overcome this limitation, but for African countries, bottlenecks in the global supply chain of reagents are still a challenge.
We have developed an open source SARSCoV-2 POC test2 that can be locally manufactured in African countries and we aim at establishing its use as a diagnostic tool in two African countries, in view of its future widespread use across the continent.
Covid tests for all
To be effective, testing needs to be affordable, rapid and widely available. That is why early in the pandemic, the World Health Organisation put as number one priority to mobilise research for rapid point of care diagnostics (POC) at the community level.
Unlike conventional reverse transcription, quantitative polymerase chain reaction (RT-qPCR) tests, which take around 5 hours to complete and require expensive equipment, POC tests can detect viral RNA often without specialised equipment in just ~30 minutes.
This project aim to help validate a locally-manufacturable POC viral RNA test that has been developed by the teams in Vienna (Vienna-LAMP). This test frees local users from international supply chains and represents a low cost, highly reliable and fast alternative for SARS-CoV-2 diagnostics.
The Vienna-LAMP test is based on reverse transcription and loop mediated isothermal amplification4 (RT-LAMP) using open-source enzymes2. At its simplest, it consists of dried reagents for an optimised RT-LAMP reaction to which saliva in a quick extract buffer is added prior to incubation for ~30 min at 63°C (Figure 1).
Positive results return a colour change that can be observed by eye or in a lab setting with a plate reader for highthroughput read-out. Importantly, in addition to its value to diagnose SARS-CoV-2, the same test format can be easily modified (exchange of the primers) to diagnose other (RNA based) infectious diseases.
VIENNA BIOCENTER RT LAMP TEAM
Early on in the pandemic, a multidisciplinary group of researchers got together to figure out how they can help in responding to the current situation. Establishing robust alternative means of testing was the top priority, and from this effort, the RT-LAMP project at the VBC came to be. Over the months, a sensitive and specific molecular test for covid-19 was developed in Vienna, gained recognition of regulatory bodies, and uptake in diverse testing setups. Since then, the team has also put together an open-access series of protocols on how to produce enzymes and reagents for LAMP testing. The team is making their progress public via the website rtlamp.org which includes detailed information on the implementation of LAMP tests.
COVID SITUATION IN AUSTRIA
The current pandemic has hit Austria hard, with over half a million confirmed cases and over 9000 casualties of the pandemic being recorded in March 2021. Testing is done primarily through the use of point-of-care antigen tests and PCR. The niche in the middle of these tests is supplemented by LAMP tests developed, produced, and popularized at the VBC. LAMP easier and cheaper alternative to PCR tests while being much more sensitive than antigen tests, ideal for testing companies, small labs, and collectives. Austria is on track to vaccinate its population by end of 2021, but testing remains a crucial way to combat the pandemic and save lives in the state of vaccine supply shortage.
ROLE IN PROJECT
The people at Vienna BioCenter are the providers of key knowledge on the implementation and development of LAMP. They give advice and help steer the project. The VBC team ships out freeze-dried LAMP reagents to our partner sites in Africa.
AFRICAN PARTNERS
By now, we all know that one of the key actions to limit the socio-economic and health impacts of COVID-19 is widespread testing followed by rapid track and trace strategies, but for African countries, bottlenecks in the global supply chain of reagents are still a challenge.
Traditional testing often incurs delays of several days and relies on expensive equipment. Because of this, we have developed an open-source SARS-CoV-2 POC test2 that can be locally manufactured in African countries.
We aim at establishing its use as a diagnostic tool with our partners in Ghana and Cameroon. Once that is done, we will invest in making its use widespread across the continent in the next months.
WACCBIP
WACCBIP’s COVID-19 research has generally covered two broad areas of research: viral evolution & seroprevalence. The Centre’s viral evolution research has involved two rounds of SARS-CoV-2 genome sequencing and real-time tracking of viral substitutions within the country. Two seroprevalence surveys have also been completed, compiling demographic data on persons exposed to the virus and collecting blood samples for immunological analysis.
Viral Evolution: WACCBIP harnessed its advanced computing capacity and bioinformatics expertise, and its modern next-generation sequencing facilities to produce timely context-relevant research on the strains of COVID-19 in circulation in Ghana.
Using both Illumina and Oxford Nanopore sequencing platforms, the WACCBIP team continues to track and compare changes in the genome of the virus to understand the origins and behavior of various strains as they evolve over time. The large volumes of data drawn from the genomes of the virus are subjected to bioinformatics analyses, which help make sense of clusters of information about the nature of specific strains.
So far, WACCBIP has sequenced about 500 genomes and identified many circulating variants including most of the variants of concern that have been reported globally. Results from both rounds of sequencing have been submitted to the Global Initiative on Sharing All Influenza Data (GISAID) database and are available on the Nextstrain platform.
Based on their sequence data, the WACCBIP team has also helped influence public health policy on COVID-19 safety and control. The team has contributed policy briefs and advised the government of Ghana in matters concerning the spread and evolution of SARS-CoV-2 in Ghana.
The data has also been shared with the larger scientific community in a peer-reviewed paper and has been explained extensively to non-scientific audiences through several media engagements led by WACCBIP scientists and the Centre’s Communication & Public Engagement function.
Seroprevalence: WACCBIP’s SARS-CoV-2 seroprevalence research focuses on estimating, using serological analysis, the level of COVID-19 exposure among priority populations in major cities in Ghana, with the aim of providing important data on the spread and prevalence of the disease to guide the management of COVID-19.
The first phase of the study was conducted over a two-month period in public places including municipal markets and lorry stations, shopping malls, and COVID-19 testing centers, and other research institutions/health centers in and around Ghana’s capital, Accra. Overall, a prevalence rate of around 20 percent was detected from a random sample of 1,305 consenting individuals who participated in the study. Using a pre-validated antibody rapid diagnostic test (RDT), the scientists were able to determine exposure to SARS-CoV-2, by detecting COVID-19 antibodies in blood samples taken from the participants.
The prevalence rate of about 20 percent in Accra translated to an estimate of about 1.2 million people who had been exposed at some point to the virus. The study had important implications for public health strategy, as the available data were based only on symptomatic cases and travelers, based on PCR testing across the country.
The second phase, conducted between December 2020 and February 2021, extended beyond the Greater Accra Region to Akropong-Akuapem in the Eastern Region, and parts of the Central Region of Ghana. More than 1000 people participated in the second phase. The team is currently working on analyzing the data collected during the second phase.
CRESAR
Description of CRESAR
CRESAR was created in 2000 from a triple partnership between John Hopkins Cameroon program, the Centres for Disease Control and Prevention (CDC- Atlanta- USA) and the French institute for research on development. It is a reference centre for research and biomedical diagnosis for the Cameroonian Defence force. Its vision is to be a leader in research and biomedical diagnosis.
Mission
It is intended to conduct research and biomedical diagnosis for the benefit of the defence forces, their families and Cameroon as a Whole. It is committed to health-oriented research’ surveillance of zoonosis, emerging and re-emerging infections such as the Human Influenza, HIV virus and Malaria and the development of a collaborative network on early detection of human and animal epidemics and pandemics in Cameroon.
COVID 19-TESTING SITUATION AT CRESAR, YAOUNDE, CAMEROON
The first confirmed case of Covid-19 was detected in Cameroon in March 2020. According to figures from the Ministry of Public Health (MINSANTE) March 2021, 35714 new cases have been confirmed, of which 551 died and 32594 have recovered. In response to this health threat, MINSANTE has put in place the 3T strategy; Trace- Test-Treat. Screening is done with the aid of rapid diagnostic tests (RDT) and in case of positivity, confirmation is obtained by the polymerase chain reaction test (PCR). The Military Heath Research Center (CRESAR) located in Yaoundé, is carrying out research and biomedical testing of COVID-19 for the benefit of the Defence forces, their families as well as other populations. It is one of the reference-approved laboratories for the molecular diagnosis of COVID-19. With the advent of new cases and an increase in the number of infections, there is a high demand for SARS CoV-2 testing. PCR is time-consuming and requires highly trained personnel for its realisation. Hence, a comparable test that is faster, easier to use and does not require a sophisticated technical platform could help promote and ameliorate COVID-19 prevention and surveillance through active testing.
CRID
MBOALAB
MboaLab is an open and collaborative space located in Yaoundé, Cameroon. Mboalab was founded in 2018 by Dr. Thomas Mboa, It is a laboratory for social innovation and community education and mediation at the service of the community.
Aim and missions
The aim of MboaLab is to catalyze sustainable local development and improve people’s living conditions through open science.
To this end, the main missions of Mboalab are as follows:
- provide community and lifelong education for the population, as well as formal education for the younger generations;
- serve as a platform for exchanges on issues related to local context;
- mediate between local communities and academia;
- propose solutions that meet the needs of communities, using local knowledge and open digital technologies;
- raise public awareness of environmental issues;
- facilitate access to basic health care.
Mboalab Biotech and its role in the achievement of our mission.
Mboalab Biotech is a node of the Open Bioeconomy Lab hosted in MboaLab space. Established in 2018, the lab currently runs a number of projects amongst which is the open enzyme manufacturing project. At its core, the work in Mboalab Biotech is focused on making biotechnology research and tools more accessible to labs around the world through scientific research and development and local production of reagents. The laboratory is committed to the development of open educational resources as well as simple and cost-effective protocols that can be applied in resource-limited settings. Contributing to scientific research projects targeting local health issues, Mboalab Biotech also provides internship placements and training to scientists and students from local universities to equip them with Molecular Biology and DIY-Biology skills, necessary for carrier development.
Since 2019, by partnering with the UK based not for profit Beneficial Bio Ltd, Mboalab biotech operates as a biomanufacturing and research unit focusing on
1. Local production of enzymes and reagents: to solve the challenge with reagents access for Cameroonian scientists and provide Labs, Academic, and Research Institutions with a better way to procure appropriate research tools and services quickly, at a fair price, and with the specialized local support they need.
2. Capacity building for young scientists to develop researchers who can apply state-of-the-art biotechnology to achieve sustainable development goals within their own context and build enterprises that will generate employment.
Team and role in the RT- Lamp Project
Mboalab’s role in the RT-Lamp project as (Production partner) is to focus on local expression of the protein, Enzyme production, functionality testing, and working on the QA/QC framework that will be put in place during the project. The core Mboalab team members that were mobilized on the projects are:
- Minette Shalo – Researcher – MboaLab
- Stephane Fadanka – Research Manager – MboaLab
- Nadine Mowoh – Quality Manager – MboaLab
For more information:
meet the team
Prof. Gordon Awandare, WACCBIP, University of Ghana, Ghana
Lt. Colonel Julius Nwobegahay, Military Health Research Center (CRESAR), Cameroon
Stephane Fandanka, MboaLab, Cameroon
Prof. Charles Wondji, Liverpool School of Tropical Medicine, UK and Centre for Research and Infectious Diseases (CRID), Cameroon
Dr. Thomas Auer, Center for Integrative Genomics, University of Lausanne, Switzerland
Dr., Jenny Molloy, Department of Chemical Engineering and Biotechnology, University of Cambridge, UK
Dr., Julius Brennecke, Institute of Molecular Biotechnology Vienna, Austria
.
Dr. Lucia Prieto-Godino, The Francis Crick Institute, England
Dr., Andrea Pauli, Institute of Molecular Pathology Vienna, Austria.
Prof. Dr. Jochen Wittbrodt, Center for Organismal Studies, University of Heidelberg, Germany
Partner Universities
Kindly sponsored by Volkswagen Stiftung
Get in touch
Send us an email if you would like to get more information about this project or want your institution to join this project.