Science of sequencing: the African researchers keeping pace with new Covid variants
The discovery of Omicron has shone a light on the work of South African scientists
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In October 2020, South African scientist Tulio de Oliveira and his team, sequencing coronavirus samples at their lab in the eastern coastal city of Durban, were the first to detect the Beta variant, or B.1.351.
“We immediately informed our Ministry of Health and our President Cyril Ramaphosa when we discovered the Beta variant in South Africa very early in our second wave (of Covid-19 infections),” said Professor de Oliveira, a bioinformatician who has become a familiar face on South African TV during the pandemic.
Within a day, new legislation was drafted, putting the country into a stricter level of lockdown. “It took less than 48 hours of knowing about the new variant to do that,” he said.
De Oliveira is the director of KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) and the Centre for Epidemic Response and Innovation (CERI), part of a network of scientific institutions in South Africa established in June 2020 to ensure the public health system had access to the best possible scientific data about the SARS-CoV-2 virus.
In the last week, De Oliveira’s name has again been splashed across international media, this time because of the discovery of the Omicron variant.
As part of the Network for Genomic Surveillance in South Africa, a collaboration of laboratories, scientists and academic institutions, De Oliveira reported that a new variant with a “constellation of mutations” had been identified in samples sequenced in South Africa’s Gauteng province, which is experiencing a surge of Covid-19 cases.
Omicron has already spread across the world. Scientists are urgently working to determine how transmissible and deadly it is, and whether it may be able to evade the protections of current vaccines.
The work of De Oliveira and his colleagues has highlighted the critical importance of genomic surveillance in identifying variants quickly, tracking their transmission around the globe and helping authorities to make quick public health decisions.
In Africa, there are over 500 scientists working in 30 countries involved in sequencing, according to the South Africa-based Human Heredity and Health in Africa (H3Africa) initiative, which aims to create and support a pan-continental network of laboratories conducting research in genomic sciences.
But the continent lags far behind the rest of the world when it comes to sequencing, said Dr Matshidiso Moeti, WHO Regional Director for Africa. “Only 1 per cent of over 3 million Covid-19 sequences conducted worldwide occur in Africa,” she said in September.
“Countries must step up surveillance because without genomic information, variants can spread undetected. You can’t fix what you don’t measure.”
Variants of concern
Like all viruses, SARS-CoV-2, mutates as it spreads. Some mutations do not change the virus very much, but some may make it more contagious, or affect the performance of vaccines or how serious the disease is.
When scientists note that a mutation has genetic changes that could predict faster transmissibility or increased virulence, the WHO designates it a variant of interest.
There are several variants of interest circulating around the globe, the WHO has identified Lamda (first detected in Peru) and Mu (first detected in Colombia); while the Africa CDC is monitoring B.1.525 (first sampled in the UK) and A.23.1 (first detected in East Africa).
A variant of interest becomes a variant of concern when the mutations make it more contagious or make the disease more transmissible and decrease the effectiveness of public health measures to control the virus – for instance, if the variant does not respond to vaccines. On November 26, the WHO designated Omicron, or B.1.1.52, a variant of concern, extending a list that already includes Beta and Delta.
Disease surveillance
Genomic sequencing is not new to Africa and is already well established for other viruses. “The African continent is dealing with in excess of a hundred diseases per year,” said Dr Alan Christoffels, the director of the South African National Bioinformatics Institute, one of four specialised genomics and bioinformatic centres in Africa.
