In recent years, laboratories on the continent have ramped up genomic sequencing capabilities, offering in-country analyses rather than outsourcing the job.
Three days after the confirmation of Nigeria’s first COVID-19 case, the genome sequencing results of the SARS-CoV-2 specimen were announced on March 1. The sputum samples, taken from an Italian consultant who entered Nigeria through Lagos on February 27 before traveling to the neighboring Ogun State, were analyzed at the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer University. They became the first analysis of SARS-CoV-2 in Africa, signaling the continent’s contribution to the growing global body of evidence to understand the virus’s behavior outside China.
“We have moved from being spectators to contributors and players in the field of infectious disease genomics,” Christian Happi, ACEGID director in Ede, Nigeria, who led the sequencing effort, tells The Scientist.
Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries.—Chikwe Ihekweazu, Nigeria Centre for Disease Control
Nigeria’s demonstration of rapid sequencing during a health emergency shows that African countries have capacities to monitor the progression of an infectious disease outbreak in real time to understand transmission patterns, says Chikwe Ihekweazu, the director general of the Nigeria Centre for Disease Control based in Abuja.
Africa’s ability to sequence its own COVID-19 cases demonstrates that countries in the region have invested in diagnostic capabilities, says Ihekweazu. “Whether the tool is used for disease outbreaks or routine surveillance, we now have the capacity to perform in-country sequencing, which has traditionally been done through collaborations with laboratories outside the countries,” he tells The Scientist.
The Africa Center for Disease Control (CDC) is encouraging countries that have the ability to sequence their own samples to do so, while those that cannot should send their samples to institutions such as ACEGID, Sofonias Kifle Tessema, the head of the genomic sequencing program at Africa CDC, tells The Scientist.
Africa CDC says 4,871 total COVID-19 cases have been reported in 46 African countries with a total of 152 deaths and 340 recoveries as of March 30. ACEGID has enough expertise and equipment to sequence all confirmed cases from Africa so far, but would need more reagents and additional staff to support bigger outbreaks, says Happi. Each sequencing costs about $600 US.
The center got its first equipment and staff in January 2014 from a World Bank investment of $8 million US that was part of a $165 million package for 19 higher education institutions specializing in STEM initiatives in eight West African nations.
The need to enable Africa to contribute to the genomics revolution, and to reduce the knowledge and economic gaps between the rest of the world and Africa, prompted this investment, Happi says. “I wanted to use genomics technologies and to address health problems in Africa, especially infectious disease and facilitate outbreak response,” he says.
Long before the coronavirus epidemic struck, in 2014, ACEGID sequencing gave the first accurate diagnosis of the Ebola virus in Nigeria.
The ability to conduct genomic sequencing locally will contribute to the global fight against COVID-19, says Denis Chopera, the program executive manager of the Sub-Saharan African Network for TB/HIV Research Excellence at the Africa Research Institute (SANTHE) in KwaZulu-Natal in South Africa. “Viruses can easily change form to adapt to the environment and evade recognition by the immune system and drugs so it is crucial to understand all these aspects of this virus,” says Chopera. “Remember, it is a new virus and very little is known about it,” he adds. SANTHE has the expertise and resources for sequencing, but is not actively working on coronavirus samples as all laboratory tests are being conducted by the South Africa’s National Institute for Communicable Diseases.
The World Health Organization has been supporting African governments with early detection by providing thousands of COVID-19 testing kits to countries, training dozens of health workers, and strengthening surveillance in communities, resulting in 46 countries being able test for COVID-19. So far, the number of cases in Africa is dwarfed by those on other continents.
The initial cases detected in Africa were from travelers coming from countries with widespread outbreaks. “The Nigeria virus is similar to the viruses recently circulating in Europe, which is consistent with the travel history of the COVID-19 patient,” Ihekweazu says of the first case.
“I do not think that the sequence can tell us why there are few cases in Africa at this point as it is highly likely that the climate in Africa is the reason. However, we will know whether the virus is changing to adapt to the climate, which is a possibility and this could result in more cases on the African continent,” Chopera tells The Scientist.
Ihekweazu says a number of different factors can be contributing to the limited number of cases detected, and sequencing will provide evidence to show if SARS-CoV-2 is changing, if it’s acquired during hospitalization, and if importations from other countries are still causing outbreaks or if community transmission is driving numbers upward.
For Akebe Luther King Abia, a Cameroonian environmental microbiologist at the University of KwaZulu-Natal in South Africa, the biggest contribution African scientists can bring are their experiences with previous outbreaks such as Ebola. After the first SARS-CoV outbreak of 2003, scientists within the continent started looking for other members of the coronavirus family in bats and developing methods to detect them, for instance. Medical personnel were trained and health infrastructure was improved to handle future emergencies. Following the previous SARS and Ebola outbreaks, Nigeria created the Nigerian Center for Disease Control and established a network of laboratories within the country for rapid identification of cases.
“It is no doubt that most countries on the continent do not have sophisticated equipment, but the fact that they have been exposed to numerous diseases outbreaks has made most of them to be ready with what they have,” Abia tells The Scientist.