Covid-19: Africa scrambles to increase genomic testing capacity as variants spread

Covid-19: Africa scrambles to increase genomic testing capacity as variants spread African countries are struggling to bolster genomic sequencing as SARS-CoV-2 variants spread on the continent, reports Abdullahi Tsanni As the world entered 2021, the covid-19 pandemic began a new phase, one dominated by worries over emerging variants. But the way of detecting these threats has not been standardised—even in the UK, where genomic sequencing is relatively frequent, only 5-10% of covid-19 positive cases were being sequenced at the start of the year.1 The spotlight on sequencing has highlighted inequalities in global capacity. Many countries in Africa do not perform sequencing themselves, and those that do only do so on a small scale. Genomic sequencing requires expertise, machinery, software, reagents, and funding. Over the past year, as African countries grappled with scaling up basic testing capacity for covid-19, it hasn’t been a high priority. But as variants such as B.1.351—first identified in South Africa and which now accounts for some 90% of the country’s covid-19 cases—led to growing concern, there are worries that the lack of sequencing capacity will leave the continent unable to spot and stop variant outbreaks before they fuel a new wave of infections. Nigeria, the continent’s most populous country, has sequenced and shared 0.03% of its reported covid-19 cases (versus, at the time of writing, nearly 2% for the US, 42% for Singapore, and 48% for … The BMJ

As the world entered 2021, the covid-19 pandemic began a new phase, one dominated by worries over emerging variants. But the way of detecting these threats has not been standardised—even in the UK, where genomic sequencing is relatively frequent, only 5-10% of covid-19 positive cases were being sequenced at the start of the year.1

The spotlight on sequencing has highlighted inequalities in global capacity. Many countries in Africa do not perform sequencing themselves, and those that do only do so on a small scale. Genomic sequencing requires expertise, machinery, software, reagents, and funding. Over the past year, as African countries grappled with scaling up basic testing capacity for covid-19, it hasn’t been a high priority. ...

“Genomic sequencing is crucial at this point to understand circulating strains and their impact on vaccine efficacy, disease transmission, and severity,” says Christian Happi, director of the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) in Ede, south west Nigeria. “We need to keep sequencing so that we can see exactly how the virus is mutating and spreading.”

ACEGID is a reference laboratory for the joint World Health Organization and Africa Centres for Disease Control and Prevention (Africa CDC) Covid-19 Genomic Sequencing Network. Happi’s team sequenced the first coronavirus samples in sub-Saharan Africa within 72 hours of diagnosis and identified two new variants—B.1.5.2.5, first found in Nigeria, and B.1.1.7, first identified in the UK.3

Chikwe Ihekweazu, director general of NCDC, says sequencing has a key role as Nigeria begins vaccination—in March it received 3.9 million doses of the Oxford AstraZeneca vaccine from the Covax initiative. “If the effectiveness of vaccines is affected by the evolution of new variants, we have to be able to detect them. Genomic sequencing, linked to good surveillance data, is one way of doing this,” he says. This is especially important in large countries like Nigeria, which sees a lot of movement between regions as well as a high influx of travellers from other countries. ...

There are no SARS-CoV-2 sequences available for about 40% of African countries in GISAID, the global online database of viral sequences. According to the media outlet Devex, South Africa leads the continent with the number of sequences of SARS-CoV-2 contributed—nearly 4000 samples—but has only sequenced about 0.3% of its positive cases.4 ...