What South Africa tells us about Omicron


By Dylan Barry, GCPPP staff, Johannesburg January 21st 2022

In less than two months, the Omicron variant of the coronavirus has spread rapidly from its early detection in South Africa and Botswana to become the world’s dominant strain of the virus—constituting more than 80% of cases in the United States, United Kingdom, and France, amongst others. Nevertheless, while Omicron continues to drive up staggering numbers of infections wherever it gains a foothold, in Southern Africa infections have plummeted as quickly as they first appeared and the same is now starting to happen in the UK. Despite only a quarter of its population having been fully vaccinated, the evidence from South Africa is that the Omicron variant is milder than its predecessors and produces fewer hospitalisations and deaths, even while infecting far greater numbers of people.

In this ANALYSIS—reported from the ground in South Africa—we summarise Omicron’s trajectory in the country, how the government’s response to Omicron differed from its response to previous coronavirus strains, and what lessons can be drawn from South Africa’s discovery of and response to Omicron. Next week, we will publish an article surveying what is known and not known about Omicron more broadly: its origins, severity, transmissibility, interaction with vaccines and variability.

The discovery and communication of Omicron (B.1.1.529)

Lesson number one concerns the benefit for a country and thereby the world of having a network of advanced medical laboratories and genetic sequencing capabilities, which in South Africa’s case shortened the time between the variant’s emergence and detection. The timeline was as follows:

  • November 4th, Alicia Vermeulen—a scientist at Lancet Laboratories in Pretoria, South Africa’s capital—spotted something strange in a single positive result from a batch of roughly 300 coronavirus tests processed at the laboratory that day. The test had failed to pick up on one of the three genes from SARS-Cov-2 targeted to confirm whether the virus is present in a biological sample—namely, the S-gene, which encodes for the virus’s spike proteins.
  • By November 11th, the laboratory was spotting such “S-gene dropouts” in greater numbers. Lancet began reviewing test results from its sister lab in Johannesburg and alerted the National Institute for Communicable Diseases (NICD)—run by the Department of Health—which began checking its own data from National Health Laboratory Service tests. There were only a few test results to go on as in the week to November 18th South Africa’s case numbers were close to a pandemic low, with fewer than 500 new infections per day. Nevertheless, within a few days, enough positive tests had come in to clarify that the number of results with S-gene dropout was rising slightly and that overall case positivity rates in Johannesburg and Pretoria had started to trend up too.
  • By November 19th, the NICD had confirmed from an initial analysis of the data that the virus genomes in the samples had diverged from known strains of the coronavirus.
  • On November 23rd, the NICD uploaded six complete genome sequences to GISAID—an open access repository of genome sequences for coronaviruses and influenza—and confirmed the news. There was a new strain of SARS-Cov-2.
  • In parallel, on November 22nd, a team at the Botswana-Harvard HIV Reference Laboratory (BHHRL) independently uploaded four near-identical genome sequences to the same platform, taken from positive test results reportedly from four visiting diplomats, whose origins have not been disclosed.
  • Back in South Africa, the new genome sequences were shared with the Network for Genomic Sequencing South Africa (NGS-SA), a network of scientists, laboratories and academic institutions established to respond rapidly to public health threats related to the COVID-19 pandemic. Alarmed by the number of mutations to the S-gene encoding for the spike proteins of the new variant, scientists there passed the information immediately to South Africa’s Department of Health and to the World Health Organisation.
  • On November 24th, the NGS-SA secured roughly one hundred randomly selected coronavirus samples taken at over thirty clinics in Gauteng—all with S-gene dropout. The samples were rapidly sequenced. Every one tested positive for the new variant. Within hours, the NGS-SA had briefed South Africa’s Minister of Health and Minister of Science on the discovery—followed by a briefing to President Cyril Ramaphosa. A press conference was held shortly thereafter.
  • On November 26th, the WHO gave the new variant its Greek name—Omicron. Press briefings and broadcasts had spread the news around the world.

Early spread and initial policy response

By the time of its announcement to the world, Omicron had already begun to spread rapidly. Nevertheless, the RSA government’s response to it was surprisingly subdued. This contrasted with some very drastic bans that were imposed on travel from Southern Africa to the United Kingdom (as early as November 26th) and other developed countries. Why?

The province of Gauteng had by late November begun to see serious exponential growth in COVID-19 cases—albeit from a very low baseline. Between November 19th and 26th, the daily rate of newly reported coronavirus infections rose from 509 to 2,174—and kept rising. The writer of this Analysis landed in Johannesburg on November 30th. That night newly reported cases in Gauteng doubled from 3,143 to 6,156. Moreover, although Omicron’s genome sequence had then only been confirmed in Gauteng, S-gene dropout was being picked up in all nine of South Africa’s provinces. Later genetic analysis of various local sub-strains of the new variant would show that Omicron had begun to spread to the other provinces—and two regions of neighbouring Botswana—from as early as late-October.

As December began, new coronavirus infections started to spike in the provinces of the Western Cape—home to Cape Town, South Africa’s second-largest city—and KwaZulu-Natal, home to Durban, its third-largest city. That reflects the movement of people and goods between South Africa’s two biggest port cities and Johannesburg, its economic centre of gravity. Shortly thereafter, South Africa’s less populous (and more economically peripheral) provinces began to see new infections rise rapidly as well.

Yet following late-November meetings of the government’s National Coronavirus Command Council and of the president’s coordinating council and cabinet, the government decided not to impose stronger COVID-19 restrictions on the country. That decision was relayed by President Ramaphosa in a televised address. This still left in place a curfew from 24h00 to 04h00, restrictions on indoor and outdoor gatherings, and a mask mandate in public places—the breaking of which constitutes a criminal offence—but nevertheless, observers were surprised that the government chose not to do more, unlike with previous instances of sharply rising case numbers.

The contrasting approach to Omicron, explained Ramaphosa, represented a judgment that COVID-19 will remain a long-term challenge and that ways must be found to manage the virus while limiting disruptions to the economy. Ramaphosa also expressed confidence in the ability of higher rates of vaccination to help South Africa weather what would be its fourth wave of the coronavirus: as he spoke, just one-quarter of South Africa’s population had been fully vaccinated, well below levels in Botswana and Rwanda but still one of the leaders in sub-Saharan Africa.

The subtext, however, was that the government’s options had been severely constrained by the choices made abroad. The sudden travel bans imposed by the UK and others upended South Africa’s summer tourist season—a major source of foreign revenue. The Tourism Business Council of South Africa (TBCSA) estimated that the travel bans could lead to R25 billion (US$1.6 billion) in lost revenue, with more than 200,000 jobs supported by the industry placed at risk.

The prospect of intensifying the economic disruption of the new strain with further restrictions had become highly risky politically in a country with an unemployment rate (including discouraged workers) of 46.6 percent. The memory of the large-scale looting and civil unrest that had swept across the provinces of Gauteng and KwaZulu-Natal for nearly 10 days in July would have been fresh in the minds of politicians.

The reassuring role of acquired immunity

The second big lesson, which was communicated internationally early on by South African doctors but initially viewed sceptically abroad, is that while Omicron proved highly transmissible its effects have been less severe, even in a country with only 25% of people vaccinated. However, although hospitalisations and deaths have been less bad than in previous waves, they are taking longer to subside.

The rapid spread was in part expected, as South African scientists had immediately flagged the possibility that Omicron could be more transmissible than any previous variant due to its highly mutated spike proteins. During the first week of December, infections indeed infections rose rapidly across the country, led by Gauteng. Because South Africa’s testing capacity is more constrained than that in the developed world, raw case numbers give only an incomplete picture. Anecdotally, however, of the writer’s Johannesburg-based acquaintances, roughly half tested positive for COVID-19 in that week, and most of the rest began to self-isolate after a direct contact with someone who was COVID-19 positive. That is consistent with the estimated reproduction rate of the virus in that week, which peaked at 2.19 on December 3rd—almost twice as high as previous waves.

Scientists had also flagged the possibility that Omicron might have diverged enough from previous variants to evade existing immunity against the coronavirus, both from vaccination and previous infection. That was superficially borne out by Omicron’s rising caseload in Gauteng—the region of South Africa hardest hit by the coronavirus, especially the Delta variant. Serological testing had suggested that 60 to 80 percent of Gauteng residents had already been infected with the coronavirus before the emergence of Omicron. Plenty of breakthrough infections nevertheless did occur. The spread of Omicron through the author’s acquaintances was certainly notable for its prevalence among the young and fully vaccinated. Even so, it was also clear that the unvaccinated were significantly more likely to be hospitalised, showing that vaccination was still offering some protection from severe disease.

That young people appeared to make up a disproportionate proportion of Omicron cases was also consistent with reports from hospitals of greater numbers of children presenting with serious cases of COVID-19.. Nevertheless, overall rates of hospitalisation remained low relative to the number of infections—suggesting that Omicron was causing less serious disease than the Delta variant. The number of patients requiring intensive care and ventilation was also down compared to previous waves. These positive signs in key measures of COVID-19 severity translated into  even lower rates of COVID-19 mortality. That was a great relief in a country hard hit by the pandemic—with almost 300,000 lives estimated to have been lost to the coronavirus.

Then—as suddenly as it appeared—Omicron began to subside. In Gauteng, newly reported infections and new hospital admissions peaked on December 9th, declining sharply thereafter. Across South Africa, new infections peaked on December 17th. On December 30th, South Africa’s cabinet announced that it would be lifting the national curfew—the first time it has done so since the start of the pandemic. Although case numbers are still higher than they were in mid-October, just before Omicron emerged, South Africa has now returned to a state of (relative) normality.

Why South Africa was good at early-warnings, monitoring and surveillance

As we have seen, South Africa’s scientists, health officials and leaders set a stellar example in responding to the emergence of the new variant.

Despite the constraints it faces as a developing economy, South Africa has become a leader in SARS-CoV-2 early-warning, monitoring and surveillance. That is in significant part due to its experience managing a severe HIV/AIDS epidemic—the worst anywhere in the world, with 20.4% of South Africans currently living with the virus. As a consequence, early in the pandemic, the South African government and South Africa’s scientific community partnered to establish institutional structures for managing large-scale coronavirus testing, genomic sequencing and information sharing.

The most innovative of these are the NGS-SA (mentioned above) and the South African Medical Research Council’s (SAMRC) Wastewater Surveillance and Research Programme. Established in May 2020, the NGS-SA was designed to coordinate genomic surveillance in the country by connecting South Africa’s locally dispersed diagnostic laboratories with the major genomic laboratories at its higher education institutions—home to world class viral sequencing capabilities because of the HIV/AIDS epidemic. That includes private diagnostic laboratories, like Lancet Laboratories, and public ones—like those run by the NICD, a subsidiary of the Department of Health.

The NGS-SA monitors the spread and evolution of coronavirus variants in South Africa by randomly sequencing positive coronavirus samples and performing targeted sequencing in response to outbreaks. The NGS-SA publishes a weekly report of its findings and advises health officials on both local and national health policy measures. The clear lines of communication and established levels of trust between frontline diagnostic laboratories, the NGS-SA and government officials were vital in the early identification of Omicron and its immediate and transparent communication to the world.

Established in July 2020, the SAMRC’s Wastewater Surveillance and Research Programme is on the frontlineof South Africa’s SARS-CoV-2 early-warning capabilities. Every Monday, SAMRC technicians undertake sampling and analysis of wastewater from 72 wastewater treatment plants located in urban and rural areas around South Africa. The concentration of non-infectious SARS-CoV-2 RNA fragments in the wastewater of an area offers a window into the prevalence of SARS-CoV-2 in the community—often picking up outbreaks before case numbers start to rise appreciably.

That was certainly true of Omicron. The concentration of SARS-CoV-2 RNA fragments in wastewater from the region around Pretoria began to rise sharply from November 15th. That was several days before infections began to pick up. Those wastewater results—along with the first inklings of a rise in case numbers in and around Pretoria—were enough to persuade the NGS-SA, on November 19th, to shift resources in order to pre-emptively increase the rate of genomic sequencing in Gauteng. In retrospect, the move gave the NGS-SA a crucial head-start that accelerated the identification of Omicron.

What Omicron’s trajectory in South Africa means for others

The story of Omicron in South Africa is indicative in other ways too. The remarkable transmissibility of the new variant and its ability to evade pre-existing immunity has already been borne out in dramatic fashion across the globe, where new infections have soared to heights that would have been unimaginable just eight weeks ago.

Fortunately—consistent with the experience in South Africa—Omicron appears to be less likely to lead to severe disease, hospitalisation and death in other countries too. What South Africa lacked in terms of vaccinated immunity was made up by the high prevalence of immunity from prior infection in South Africa—with only 25 percent of the observed reduction in severity in the country due to the reduced virulence of Omicron itself. This is reassuring for highly vaccinated countries, but less so for any that lack both widespread acquired immunity or the vaccinated sort. Even a country such as China may have cause for concern, since fairly little virus has circulated among that vast population so far, and the Sinovac and Sinopharm activated-virus vaccines used there show considerably lower efficacy than the Pfizer, Moderna and AstraZeneca jabs used elsewhere.

In South Africa, Omicron cases declined rapidly after their peak in mid-December—an encouraging sign. However, while both new infections and new hospital admissions appeared to peak and then decline in lockstep, the story for other statistics is a little more mixed.

It is noteworthy that the number of patients admitted to intensive care and requiring ventilation in South Africa has continued to increase far further beyond the peak in cases than in previous waves. The same is true for newly reported deaths, which are still increasing in the country almost a full month since the peak in cases. That is unprecedented during the pandemic.

This means that celebrating the plateau and decline of Omicron case numbers may be premature. If the South African example is any indication, ICU admissions, ventilations and coronavirus deaths may continue to increase or stay high for many weeks after case numbers begin to decline—meaning that for overwhelmed hospitals, doctors and other healthcare workers may remain under great pressure for quite some time.

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