Cancel Preloader

Variant hunters: the scientists tracking Covid’s every move

The institute’s serene, leafy grounds and raised walkways are a picture of calm. 

Aside from the odd researcher in a white lab coat hurrying between meetings, there is almost nothing to suggest that the scattering of modernist buildings lie at the heart of East Africa’s fight against the pandemic. 

But inside a series of world-class laboratories at the joint Kenya Medical Research Institute (Kemri) and Wellcome Trust Research Programme in the coastal town of Kilifi, more than a hundred researchers pore over countless vials and flasks on the hunt for dangerous new coronavirus variants. 

Since the pandemic began, they have genetically sequenced more than 2,000 biohazardous Sars-Cov-2 samples from across Kenya and from as far afield as Sudan, Somalia, Ethiopia and the Seychelles.  

Without this, the country would be flying blind, says Professor Isabella Oyier, head of Biosciences at the Kemri-Wellcome.

The state-of-the-art facility pivoted sharply to Covid research in early 2020
The state-of-the-art facility pivoted sharply to Covid research in early 2020 CREDIT: Kang-Chun Cheng/The Telegraph

“[Genetic sequencing] essentially tells you what the make-up of the virus is. It’s like a sentence: what are the letters that make up the sentence? The reason that’s important is that if any of those letters change you begin to see these variants,” says Professor Oyier.

“We need to look out for the other variant that is about to pop up. I’m hoping it doesn’t. But just based on the data we know the virus is still changing,” she adds.  

Some 750 miles away in Entebbe, on the banks of Lake Victoria, a much smaller two-person team at the Uganda Virus Research Institute’s Medical Research Council unit (UVRI / MRC) are also toiling away to keep track of the virus’s every move, sequencing roughly 40 Sars-Cov-2 genomes a week.  

In the last few months the vast majority of samples are the highly contagious delta variant, which first emerged in India late last year and has since wrought havoc the world over.

Members of George Githinji's team prepare Covid samples for genomic sequencing
Members of George Githinji’s team prepare Covid samples for genomic sequencing CREDIT: Kang-Chun Cheng/The Telegraph

But back in October, as Daniel Bugembe Lule and Dr My Phan analysed samples from prison outbreaks in northern Uganda, the duo noticed something different; slight shifts in the spike protein the virus uses to latch onto and enter human cells. 

“We checked everything, over and over, to be absolutely sure that we’d identified something new,” says Dr Phan. “When it was completely confirmed, I just felt like all the years of sitting in school, passing difficult exams, had finally paid off. This is exactly what we’d been trained for.” 

The strain, known as A.23.1, has since been detected in at least 26 different countries, though it is not yet designated as either a variant of ‘interest’ or ‘concern’ by the World Health Organization. 

But its discovery has helped to shine a light on the virus’ evolution in Africa, a region that lags behind the rest of the world when it comes to genetic surveillance – just one per cent of some three million Sars-Cov-2 sequences conducted globally come from the continent. 

Kemri and the UVRI are part of a cohort of path-breaking research centres working to change that paradigm and generate the data needed to guide African leaders through both this pandemic, and the next one. 

Pipetting samples in preparation for genomic sequencing
Pipetting samples in preparation for genomic sequencing CREDIT: Kang-Chun Cheng/The Telegraph

Last week, that effort received a boost with the creation of the Centre for Epidemic Response and Innovation (Ceri) in South Africa, which is already the continent’s major surveillance hub. 

The initiative – a collaboration between organisations including the South African Medical Research Council and the University of KwaZulu-Natal – will be the “largest genomics facility on the African continent” and will dramatically expand sequencing capability, according to its founding director, Professor Tulio de Oliveira.

It is one of many initiatives launched in the last six months to create a “global immune system” to prevent a repeat of the Covid crisis. 

In May, the UK announced a collaboration with the WHO and Wellcome to develop a “global pandemic radar”. The UN health agency has also launched a Hub for Pandemic and Epidemic Intelligence in Berlin this month to harness data tools including artificial intelligence and quantum computing, and put them “to practical use on the ground all over the world”. 

Lab assistants in the Epidemiology department
Lab assistants in the Epidemiology department CREDIT: Kang-Chun Cheng/The Telegraph

Dr Divya Shah, Epidemics Research Lead at Wellcome – which has invested $4.5m in Kemri and UVRI – says such initiatives are a “step in the right direction” to combat the startling holes in our defences laid bare by the pandemic. 

“Covid-19 has exposed the urgent need to reinforce our local, national, and international disease surveillance systems,” she says. “If we fail to do so, then we risk being caught off guard by new and dangerous pathogens with pandemic potential.”

But any successful attempt to eradicate blind spots, Dr Shah adds, must build a surveillance system that “is locally owned and internationally networked”. 

“This means equipping and supporting researchers with local knowledge of health systems to sequence viruses, while international structures are assembled that can rapidly collect, monitor, and distribute these insights,” she says.

There are also less obvious challenges to overcome, says Dr Phan. It may sound dull and technical, but chief among them is procurement. 

The world renowned health research unit works in partnership with the Wellcome Trust and University of Oxford
The world renowned health research unit works in partnership with the Wellcome Trust and University of Oxford CREDIT: Kang-Chun Cheng/The Telegraph

During the pandemic UVRI struggled to get hold of many of the critical supplies needed to analyse Sars-Cov-2 genomes, including reagents and enzymes. Orders were also more expensive, as the small lab was unable to buy at the same bulk scale as European or American counterparts.

Border checks and transportation delays added a further layer of complexity – because most raw materials are made in the West, they took weeks or months to arrive. Flow cells, a core element of sequencing apparatus, usually made it to UVRI just five to six weeks before they expired. 

“The people are here, the human resources are here, and the staff are really excited to learn and embark on new projects,” says Dr Phan. “We are ready for the next pandemic or the next virus, but the things that are not ready are procurement, logistics and the supply chain.”

Back in Kilifi, where life has finally settled down into a relatively steady rhythm, researchers at the Kemri-Wellcome institute are reflecting on a frantic 18 months – and planning for the future. 

The team that works under George Githinji in developing computational methods for processing large-scale genomic data
The team that works under George Githinji in developing computational methods for processing large-scale genomic data CREDIT: Kang-Chun Cheng/The Telegraph

“Initially we would dress like we were going to the moon,” jokes Jennifer Musyoki, project manager for Biosciences, harking back to the early days of the pandemic. “We would wash our hands like you were trying to remove them. I would then go home and gargle salt.”

On a more serious note, adds Prof Oyier, the critical work done by African experts has helped shatter old stereotypes about the continent and laid the groundwork to take on persistent killers including malaria, HIV and tuberculosis. 

“The narrative [in the West about Africa being helpless in the face of the pandemic] is disappointing, you kind of need to live here to know what we’re capable of,” says Prof Oyier.

“I think one of the lessons from the pandemic which was great for Africa… was having a facility, such as this one, and technical expertise in place [so] we could respond.”

“Of course, we want to see ourselves grow,” adds Dr Phan in Entebbe, describing the MRC Uganda unit and Kemri labs as a sequencing hub for East Africa. “I think we really have the skills to push this forward, it seems like there’s lots of space for us to develop. We’re still in our infancy – watch this space.”

Source Credits: Variant hunters: the scientists tracking Covid’s every move (

Leave A Comment

Your email address will not be published. Required fields are marked *