The West African Centre for Cell Biology for Infectious Pathogens (WACCBIP), from December 11-15, hosted 21 scientists from 13 countries in a training workshop on novel advanced technologies for real-time surveillance and epidemiological tracking of virus outbreaks.
The workshop was organised by the Tackling Infections to Benefit Africa (TIBA) Partnership and the ARTIC network, a Wellcome Trust-funded project led by world-leading scientists to provide a system for real-time genomic epidemiology of virus outbreaks.
“This workshop is about building local capacity to respond to infectious disease events using a combination of DNA sequencing and computational analysis,” said Prof. Jennifer Gardy, who holds the Canada Research Chair in Public Health Genomics at the University of British Columbia. “We're hoping that, by the end of the workshop, the participants, each of whom are familiar with parts of the process””[some with] the laboratory part; [others with] the computational part””[will] have a better understanding [of the entire process], from start to finish, how you would use this approach to investigate a disease outbreak.”
Facilitators from the ARTIC network team delivered hands-on virus genome sequencing training using the novel Oxford Nanopore MinION technology. The MinION is a fast, portable, and robust real-time device for DNA and RNA sequencing. The course team, drawn from some of the world's leading universities, was composed of world-leaders in nanopore sequencing of pathogens, molecular epidemiology of infectious disease and the use of pathogen genomes for public health. Key experts included Andrew Rambaut, Professor of Molecular Evolution at the University of Edinburgh; Ian Goodfellow, Professor of Virology from the University of Cambridge; and Nicholas Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham. The team aimed to train participating scientists to understand applications of the technology for acquiring epidemiological information that could be crucial for disease outbreak response.
“It's a very new paradigm for responding to infectious disease events but it's a very powerful one and a very easy one to use no matter where you are in the world,” Dr. Gardy said. “In the past, a lot of this technology””the computational work””was limited to only a small number of academic labs usually in places like North America [and] Western Europe but we want to see this technology used everywhere. We want to see it used by the people who are on the frontlines of disease response.”
On the opening day of the workshop, participants were guided through some principles of safe sample handling, extraction of viral nucleic acid and subsequent testing by real-time PCR. Participants were subsequently led in the preparation of sequencing libraries and loading of sequencing libraries onto the MinION sequencer. On days three and four, most of the lab work focused on running the MinION sequencer, monitoring the output, diagnosing problems and assembling genome sequences. Participants, on the final day, learnt to interpret the results, make actionable epidemiological inferences, and conduct broader phylogenetic and phylodynamic analyses.
Prof. Gordon Awandare, Director of WACCBIP, said that the Centre was honoured to host the workshop, which, according to him, was very important for the African fight against viral epidemics such as Ebola. He said it was fitting that the workshop, one of the first of its kind in Africa, would be hosted in the first University of the first sub-Saharan African country to have achieved independence, which was a mark of Ghana's drive for excellence.
“We were the first country in sub-Saharan Africa to achieve independence, which shows our drive to take initiative and excel on our own terms,” Prof. Awandare said. “It is in that spirit of excellence that the Centre was established, and that same drive has made it one of the leading research and training institutions on the continent.”
Prof. Awandare encouraged participants to become ambassadors of WACCBIP and carry out the message of excellence the Centre is continually working to achieve. He said that WACCBIP was always open to receive more financial and human resource support, reiterating the need for collaboration across the continent to solve its pertinent healthcare challenges.
Participants were generally pleased with the wealth of knowledge they gained particularly in the ways in which they will be able to adapt the technologies to their own contexts.
“So far, it has been exciting,” said Dr. George Githinji, a postdoctoral research fellow at the KEMRI-Wellcome Trust Institute in Kenya. “I am a computational biologist and I'm in the lab learning how to sequence and apply these technologies to understand the details of viral transmissions on different scales.”
He was eager for similar workshops to be held in other parts of the continent to ensure that African scientists can stem out virus outbreaks such as Ebola as soon as they are discovered without relying too heavily on scientists from other parts of the world.
“I think we now have the technology and set-up that can facilitate Africans taking control of their [own] situation,” Dr. Githinji said. “What I would have liked to see, although it's very technical [and] very scientific, is for policymakers to jump in and take advantage of these technologies [towards] joint African efforts to control virus epidemics.”
The five-day workshop was sponsored by the National Institute for Health Research (NIHR) in the United Kingdom, the Fogarty International Center at the National Institutes of Health (NIH) in the United States of America, the Wellcome Trust, and WACCBIP.
