Gambia Invests in Genome Sequencing to Reduce Chances of COVID-19 Mutations

BANJUL, The Gambia — The global fight to contain the novel coronavirus has received a boost in the past few months with mass production of vaccines in several countries. Access to those vaccines for poorer countries, however, is very limited as richer countries are making mass purchases to protect their populations

“COVAX can only reach 20% of the African population by 2021,” the World Health Organization said in a tweet on March 13, referring to the WHO-led global initiative to provide countries equitable access to vaccines. “More needs to be done for vaccine equity because no one is safe until everyone is safe.”

Gambia, the smallest country in mainland Africa, has so far received about 46,000 doses, enough to vaccinate just 1.9% of its 2.3 million population — a figure roughly equal to the country’s public service workforce. Without timely and adequate access to vaccines, health care leaders here are recognizing the need to invest in genome sequencing of COVID-19 to detect new variants if they occur as the virus continues to spread.

“The more people the virus infects, the opportunity it has to mutate, and perhaps to a more aggressive strain,” says Abdul Karim Sesay , a genomics lab manager at the Medical Research Council at the London School of Hygiene and Tropical Medicine in Serekunda, Gambia’s largest city.

“There is a possibility that we could have a more aggressive strain in the country.” Sesay and his team work in collaboration with Gambia’s National Public Health Laboratory with support from the West Africa Health Organization (WAHO) and the U.N.’s WHO.

Genome sequencing, the process of determining the DNA sequence of an organism’s genome, helps scientists track mutations of the virus. It is an expensive but necessary venture for poorer countries; the limited access to vaccines amid a rising number of infections means African countries will need to invest in genome sequencing to understand the scale of the spread of COVID-19, says Sesay.

The country has uploaded 430 sequenced genomes on the global database compiled by GISAID, the global science initiative that provides open access to genomic data of influenza viruses such as COVID-19. By the beginning of March, Gambia had sequenced 1,000 genomes, or 20% of its positive samples, Sesay says.

By last December, the data from the GISAID initiative ranked the West African country sixth in the world for percentage of positive COVID-19 samples sequenced, according to The Washington Post.

Informing Treatment and Quarantine Protocols

In January, Gambia detected its first two cases of the highly infectious coronavirus strain from the United Kingdom, one of three known highly infectious COVID-19 variants in the world.

Though Gambia is doing well with slightly more than 5,400 confirmed cases and more than 160 deaths since March of 2020, the country’s health care infrastructure is sparse. This makes it crucial to detect any infectious variants of COVID-19 early to properly contain it.

Sequencing positive COVID-19 samples is crucial in informing treatment and quarantine protocols in the country, says Dr. Mustapha Bittaye, the country’s director of health services.

“If you have a very transmissible one, the management is different… If you are infected with a U.K. strain, if you do not have two negative tests after treatment, we don’t release you,” he says.

Equally important, according to Bittaye, is determining what vaccines to buy. “If the vaccine we are using is not very effective against a particular strain, we will have a big decision to make.”

Gambia’s COVID-19 treatment response is led by Dr. Abubacarr Jagne, a kidney specialist. Mutations of the virus, especially if it is more infectious, have clinical and epidemiological implications. When the country detected the U.K. variant of SARS-CoV-2 in January among a family, Jagne’s team had to quickly quarantine the entire family and test each one for infections.

“Genome sequencing is very important because very early enough we knew what variants we had … and we do that better than most countries,” Jagne says.

Decentralizing Genome Sequencing in the Region

In September of last year, the African Center for Disease Control joined WHO officials in urging African countries to strengthen their genome sequencing capacity.

The organizations launched 12 labs across the continent to improve the capacity of countries to do genome sequencing of COVID-19. In February, up to about 7,891 sequences were produced in the region, says the WHO.

“The emergence of new, more contagious SARS-CoV-2 variants is reinforcing the need to step up genomic surveillance,” the WHO stated in its Feb. 25 news release.

Despite some improvement, Sesay is concerned about the limited capacity in the region to do sequencing. He is currently supporting work to strengthen labs in Guinea Bissau, Mali and Burkina Faso to do sequencing.

During the early days of the outbreak, Gambia had very effective lockdown measures, sending all incoming travelers to hotels. At that time, there were no community transmissions and borders were closed. But now, the airspace is opened and so is the porous border with neighboring Senegal.

Sesays says without adequate measures outside Gambia’s borders, his country’s success in genome sequencing of the virus may not mean much in the fight against it.

“We need sequencing in all African countries to know what is going on around other countries in Africa,” he says. “We can control what is happening at Gambia’s airport but we do not control what happened at our porous borders.”

This story has been supported by the Solutions Journalism Network, a nonprofit organization dedicated to rigorous and compelling reporting about responses to social problems.

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