Over the last few weeks, the B.1.1.529 variant of COVID-19, known as the omicron variant, has been the subject of many concerns by the global health community. Though experts are still trying to determine the impact of this new variant, the discovery has highlighted the genomic surveillance capabilities of South Africa — where scientists first discovered the beta variant in 2020 and were involved in the detection of the omicron variant.
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Genomic sequencing is the process of reading the genetic material of pathogens, which enables public health specialists to track their evolution, identify mutations, and develop tailored vaccines and treatments.
In early November, laboratory technicians in Pretoria noticed a missing gene in the genome profile of the virus while testing for COVID-19. Though at the time they were unaware of what this change meant, their discovery triggered further analysis which eventually led to the discovery of the new variant.
Dr. Anne von Gottberg, a professor and clinical microbiologist at the Centre for Respiratory Diseases and Meningitis at the National Institute for Communicable Diseases in South Africa, said the timeline for the upload of the information on the new variant happened almost at the same time that scientists in Botswana also uploaded their sequencing data.
“So it was thanks to Botswana that we knew that the sequences actually mean something and that it wasn't an error and that we needed to investigate this quickly and to work together with other partners both regionally — in the continent — and then work globally,” von Gottberg said.
The country’s genomic sequencing capabilities heavily rely on the Network for Genomic Surveillance in South Africa, known as NGS-SA, which is a network of laboratories, scientists, and academic institutions that have joined forces to ensure the public health responses to COVID-19 in South Africa have access to the best possible scientific data.
The initiative was launched in June 2020 when five of the South African National Health Laboratory Services’ largest laboratories and their associated academic institutions in Bloemfontein, Cape Town, Durban, Johannesburg, and Tygerberg were awarded a grant by the South African government. The network has since expanded to include private diagnostic laboratories and other academic institutions within South Africa and beyond.
Beyond South Africa, NGS-SA is also an integral part of the Africa Pathogen Genomics Initiative, which is led by the World Health Organization and the Africa Centres for Disease Control and Prevention and connects the continent’s genomic sequencing laboratories. Launched in September 2020, the network of 12 laboratories has reinforced genome sequencing of the virus. This has resulted in a significant advancement of genomic surveillance on the continent, which has since recorded a fivefold increase in the number of genomes sequenced.
So far South Africa has published 24,000 COVID-19 genomic sequences — accounting for over 41% of total genomic sequences from Africa. Kenya — which has the second-highest number of sequences in the continent — has published just over 5,000.
While South Africa leads with the highest number of COVID-19 sequences in Africa, it has only sequenced about 0.8% of its confirmed cases. In comparison, the United States, the global sequencing leader, has submitted over 1.7 million sequences representing nearly 4% of its positive cases while Iceland has published sequences for 54% of its cases.
Von Gottberg said the country uses a random sampling approach and is trying to maintain ongoing surveillance that is representative of the geographic spread in all South African provinces. Though she noted that this approach has proven to be reliable, she said there is still a need to improve the efficiency by reducing the turnaround time from sample collection to sharing sequences.
“Omicron has been identified through sequencing in at least five of our provinces that have sequencing data and we think the other provinces were just not identifying it yet because they don't have specimens that have been sequenced for those provinces,” she said.
“What we need to do going forward is to have a coordinated approach for managing the variants, because we know that there will be another variant for sure.”
— Dr. John Nkengasong, director, Africa Centres for Disease Control and PreventionPeter van Heusden, a bioinformatician at the South African National Bioinformatics Institute, said there is also a need to improve the continental network by ensuring all countries have adequate capacity in order to get a “truer picture” of the state of the pandemic across the continent.
“The other national genomic surveillance systems are not functioning effectively. Poor national government financial and infrastructural support are responsible for the underutilization of the facilities,” Oyewale Tomori, a Nigerian professor of virology, said.
According to von Gottberg, South Africa — which has the most confirmed cases of the omicron variant globally — is also leading with globally relevant knowledge for reinfection and vaccine efficacy.
She said out of 249 genomic sequences that were published by the NGS-SA network in November, 183 were omicron, which represented nearly 75% of all cases — suggesting the variant is driving the pandemic in South Africa. While sequencing data is still trickling in, the country is using a testing database for both its PCR and antigen-based testing to monitor tests that come in, for cases of reinfection.
If an individual that had previously tested positive has another positive test within 90 days, then this is described as reinfection.
She said reinfections were limited during the beta and delta waves showing that the initial infection provided some form of protection on the individual against reinfection. But this is not the case for the omicron variant as there have been numerous reinfections suggesting previous infections did not provide protection.
While the global community is fixated on vaccine efficacy against omicron, von Gottberg said what is more concerning is the population’s greater susceptibility considering previous infection used to protect against delta but not against omicron.
“With omicron, that doesn't seem to be the case. We believe that vaccines will still, however, protect against severe disease because we've seen the increase in protection using vaccines,” she said.
Despite the headway, scientists in the country said instead of being applauded, their transparency has resulted in the stigmatization of southern African countries. In an article published in The Lancet, seven South African scientists criticized the travel bans initiated in response to the discovery, which they said: “could be damaging to the health response, economy, and freedom of movement.”
Countries such as the United Kingdom, Israel, and the U.S initiated travel restrictions for travelers from southern Africa soon after the discovery of the variant.
“South Africa and other southern African countries have been stigmatised and will pay a heavy economic and societal price for sharing information,” the scientists wrote. “This situation puts countries such as South Africa in a difficult position, and potentially threatens future willingness to share information and weakens global solidarity.”
They added that the most concerning COVID-19 variants for a highly vaccinated population would likely arise in a high transmission environment where there are high levels of vaccine coverage, such as the U.K., France, or Italy.
Dr. Michael Marks, associate professor at London School of Hygiene & Tropical Medicine’s department of clinical Research, said though the genomic sequencing expertise in South Africa played an important role in detecting omicron, the variant might have originated elsewhere, especially places with subpar genomic surveillance capabilities. Adding that the travel restrictions send a signal to countries that “if you have good genomic surveillance you may be punished for reporting new variants.”
“We don’t actually know that Omicron ‘emerged’ in Botswana or South Africa — just that it was first detected by sequencing there. It could have emerged in a different place with less good genomic surveillance for example (which might well still be in Africa but not one of the countries targeted by travel bans),” he said.
Dr. John Nkengasong, director at Africa CDC, said the surveillance system in South Africa should be recognized and appreciated for the transparency and the timeliness of sharing the information and called for solidarity.
“If everyone around the world was doing that, we would be in a very good place. I mean, very, very good place,” he said. “What we need to do going forward is to have a coordinated approach for managing the variants, because we know that there will be another variant for sure.”