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South Africa Study Shows Power of Genomic Surveillance Amid COVID-19 Pandemic

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COVID-19 testing in South Africa
Credit: iStock/Thomas Faull

Considerable research is underway around the world to monitor the spread of new variants of SARS-CoV-2, the coronavirus that causes COVID-19. That includes the variant B.1.351 (also known as 501Y.V2), which emerged in South Africa towards the end of 2020 [1, 2]. Public health officials in South Africa have been busy tracing the spread of this genomic variant and others across their country. And a new analysis of such data reveals that dozens of distinct coronavirus variants were already circulating in South Africa well before the appearance of B.1.351.

A study of more than 1,300 near-whole genome sequences of SARS-CoV-2, published recently in the journal Nature Medicine, shows there were in fact at least 42 SARS-CoV-2 variants spreading in South Africa within the pandemic’s first six months in that country [3]. Among them were 16 variants that had never before been described. Most of the single-letter changes carried by these variants didn’t change the virus in important ways and didn’t rise to significant frequency. But the findings come as another critical reminder of the value of genomic surveillance to track the spread of SARS-CoV-2 to identify any potentially worrisome new variants and to inform measures to get this devastating pandemic under control.

SARS-CoV-2 was first detected in South Africa on March 5, 2020, in a traveler returning from Italy. By November 2020, despite considerable efforts to slow the spread, more than 785,000 people in South Africa were infected, accounting for about half of all reported COVID-19 cases on the African continent.

Recognizing the importance of genomic surveillance, researchers led by Houriiyah Tegally and Tulio de Oliveira, University of KwaZulu-Natal, Durban, South Africa, wasted no time in producing 1,365 near-complete SARS-CoV-2 genomes by mid-September, near the end of the coronavirus’s first peak in the country. Those samples had been collected in hundreds of clinics over the course of the pandemic in eight of South Africa’s nine provinces, offering a broad picture of the spread and emergence of new variants across the country.

The data revealed three main variants, dubbed B.1.1.54, B.1.1.56, and C.1, that were responsible for 42 percent of all the infections in South Africa’s first wave. Of the 16 newly described variants, most carried single-letter changes that haven’t been identified in other countries.

The majority of changes were what scientists refer to as “synonymous,” meaning that they don’t change the structure or function of any of the virus’s essential proteins. The exception is the newly identified C.1, which includes 16 single-letter changes compared to the original sequence from Wuhan, China. One of those 16 changes swaps a single amino acid for another on SARS-CoV-2’s spike protein. That’s notable because the spike protein is a key target of antibodies and also is essential to the virus’s ability to infect human cells.

In fact, four of the most prevalent variants in South Africa all carry this same mutation. The researchers also saw three other changes that would alter the spike protein in different ways, although the significance of these for viral spread and our efforts to stop it isn’t yet clear.

Importantly, the data show that the bulk of introductions to South Africa happened early on, before lockdown and travel restrictions were implemented in late March. Subsequently, much of the spread within South Africa stemmed from hospital outbreaks. For example, an outbreak of the C.1 variant in the North West Province in April ultimately led this variant to become the most geographically widespread in South Africa by the end of August. Meanwhile, an earlier identified South African-specific variant, B.1.106, first identified in April, vanished altogether after outbreaks were controlled in KwaZulu-Natal Province, where the researchers reside.

Genomic surveillance has remarkable power for understanding the evolution of SARS-CoV-2 and tracking the dynamics of its transmission. Tegally and de Oliveira’s team notes that this type of intensive genomic surveillance now can be used on a large scale across Africa and around the world to identify new variants of SARS-CoV-2 and to develop timely measures to control the spread of the virus. They’re now working with the African CDC to expand genomic surveillance across Africa [4].

Such genomic surveillance was crucial in the subsequent identification of the B.1.351 variant in South Africa that we’ve been hearing so much about, with its potential to evade our current treatments and vaccines. By picking up on such concerning mutations early through genomic surveillance and understanding how the virus is spreading over time and space, the hope is we’ll be better informed and more adept in our efforts to get this pandemic under control.


[1] Emerging SARS-CoV-2 variants. Centers for Disease Control and Prevention.

[2] Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Bhiman J, Williamson C, de Oliveira T, et al. medRxiv 2020 Dec 22.

[3] Sixteen novel lineages of SARS-CoV-2 in South Africa. Tegally H, Wilkinson E, Lessells RJ, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman JN, von Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Glass AJ, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Petruccione F, Sigal A, Gazy I, Hardie D, Hsiao NY, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenço J, Alcantara LCJ, de Oliveira T. Nat Med. 2021 Feb 2.

[4] Accelerating genomics-based surveillance for COVID-19 response in Africa. Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN.Lancet Microbe. 2020 Aug 18.


COVID-19 Research (NIH)

Houriiyah Tegally (University of KwaZulu-Natal, Durban, South Africa)

Tulio de Oliveira (University of KwaZulu-Natal)

Global Effort to End AIDS Would Save Millions of Lives

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Prevent HIV AIDS

Scanning electromicrograph of an HIV-infected T cell/NIAID

Almost 37 million people around the world are now infected with human immunodeficiency virus (HIV), the virus that causes AIDS [1]. But many don’t know they are infected or lack access to medical care. Even though major strides have been made in treating the infection, less than half receive antiretroviral therapy (ART) that could prevent full-blown AIDS and reduce the likelihood of the virus being transmitted to other people. Now, a new report restores hope that an end to this very serious public health challenge could be within reach—but that will require a major boost in commitment and resources.

The study conducted by an NIH-funded research team evaluated the costs and expected life-saving returns associated with ambitious goals for HIV testing and treatment, the so-called 90-90-90 program, issued by the Joint United Nations Programme on HIV/AIDS (UNAIDS) in 2014 [2]. The new analysis, based on HIV disease progression and treatment data in South Africa, finds that those goals, though expensive to implement, can be achieved cost-effectively, potentially containing the AIDS epidemic and saving many millions of lives around the globe.

Creative Minds: Harnessing Technologies to Study Air Pollution’s Health Risks

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Perry Hystad

Perry Hystad
Credit: Hannah O’Leary, Oregon State University

After college, Perry Hystad took a trip to India and, while touring several large cities, noticed the vast clouds of exhaust from vehicles, smoke from factories, and soot from biomass-burning cook stoves. As he watched the rapid urban expansion all around him, Hystad remembers thinking: What effect does breathing such pollution day in and day out have upon these people’s health?

This question stuck with Hystad, and he soon developed a profound interest in environmental health. In 2013, Hystad completed his Ph.D. in his native Canada, studying the environmental risk factors for lung cancer [1, 2, 3]. Now, with the support of an NIH Director’s Early Independence Award, Hystad has launched his own lab at Oregon State University, Corvallis, to investigate further the health impacts of air pollution, which one recent analysis indicates may contribute to as many as several million deaths worldwide each year [4].