Unseen Ideas #3: Ebola gene sequencing – Seeing the bigger pictureOn September 1, 2019 by Raul Dinwiddie
In 2013 in a small village in Guinea, a two-year-old boy died – he had caught Ebola. It triggered an epidemic that tore through West Africa. The virus spread easily, from person to person, through villages and across borders. From Guinea to Sierra Leone – countries that have suffered from years of civil war – quarantine caused riots and hospitals overcrowded. Treatment centres were built, but if your family went in they rarely came out. Anyone who escaped died at home, spreading the disease further. A virus that is this deadly and contagious in a country with fragile medical infrastructure was devastating. In this chaos taking samples was hard enough, no one could see the bigger picture. Foreign aid was slow but in Cambridge, in the UK, Ian Goodfellow refused to stand by and watch. But the people he spoke to didn’t want his help because he wasn’t a doctor. After many months, Ian finally got support from Public Health England. In Autumn 2014, Ian left his family behind to travel to Makeni. It was a hotspot for transmission, and at the centre of the epidemic. “I arrived in Makeni in December 2014, with a 20-person team We moved tonnes of equipment by hand in 35-degree heat. In two weeks we’d built one of the first diagnostic laboratories in Sierra Leone on a scrubland building site. Soon we were diagnosing samples – up to 100 every day – from all over Sierra Leone. But to stop an epidemic like this diagnosis alone is not enough, you need to monitor viral transmission and evolution as fast as possible, and to track the evolution of a virus you first need its genetic sequence. In a modern laboratory sequencing whole genomes in 24 hours has only just become realistic. In a tent, during an epidemic, it was unprecedented. But with help from the Wellcome Trust and Thermo Fisher we brought a gene sequencer to Makeni. It meant we could produce whole viral genome sequences within 24 hours, and trace where new cases of Ebola may have come from. Using this information, the virus could be contained for good. By early 2016, just over one year after I’d arrived in Sierra Leone, the World Health Organization declared the Ebola virus epidemic over. “When I worked with Ian at the treatment centre, he promised he’d donate his equipment once the epidemic was over. Now he lives here at Uni Mak where I am based, Ian and his team train us in the latest techniques to sequence viruses, and track emerging infectious diseases as soon as possible. They come back often to look at schools, to teach children about how diseases like Ebola, cholera and malaria spread. Last year a new case of Ebola appeared, but Ian did not need to be here. My colleagues and I were able to find the genetic sequence of the virus in just 48 hours. Whatever happens next, because of Ian, Sierra Leone is ready.