Africa lagged in genome sequencing in the course of the first two years of the coronavirus disease 2019 (COVID-19) pandemic, brought on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nevertheless, with increased funding, over 100,000 genomes have now been sequenced from this continent.

A latest study sums up the outcomes of genomic surveillance to this point, indicating how the variants of concern of the virus have spread while indicating future directions for response readiness.

Study: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Image Credit: Tartila/Shutterstock

Introduction

Africa gave the impression to be relatively spared of high cases and deaths in the course of the ongoing pandemic, with roughly 11 million cases out of a worldwide total of over 600 million and 1 / 4 of 1,000,000 deaths out of over 6.4 million deaths worldwide.

Nevertheless, because the virus continued to alter and mutate, latest variants emerged that showed, in some cases, higher transmissibility and infectivity or virulence. Immune escape mutations were identified in some variants, making them able to increased spread even amongst vaccinated or previously infected populations. These were called variants of concern (VOC), and to this point, there have been five of them – Alpha, Beta, Gamma, Delta, and Omicron.

Of those, Beta and Omicron were first detected in Africa, though the opposite two also caused significant cases on this continent. In response to the growing threat posed by the emergence of VOCs, samples were collected from multiple sites for sequencing. Nevertheless, in April 2020, only 20 African countries had this capability.

As global supply chains petered out, these efforts stopped towards the top of the 12 months. After the primary 10,000, an evaluation showed some missing areas, in response to which increased funds poured into the constructing of increased infrastructure and training staff for genomic surveillance.

Each the Africa Centers for Disease Control (Africa CDC) and the regional office of the WHO in Africa (or WHO AFRO) shared the responsibility for this, aided by many other individuals and organizations. The result was that one other 90,000 sequences were uploaded from April 2021 to March 2022.

To place this in perspective, lower than 4000 sequences of the human immunodeficiency virus (HIV) and 12,000 influenza sequences have been uploaded to this point, despite their presence in Africa in alarming numbers for a few years.  

The present study, published in Science, explores the contribution of genomic sequencing to the scientific understanding of COVID-19 on this continent and in addition introduces global public health measures via the power to select up latest variants early enough.

What did the study show?

The info demonstrates multiple waves of infection, different in scale and period from country to country. After the primary two waves, dominated by B.1 and Alpha variants, nevertheless, Delta and Omicron swept across Africa in grim succession.

Different strains predominated in various parts of Africa, equivalent to C.36 and C.36.3, which caused 40% of infections in Egypt, vs. B.1.160 lineage in Tunisia. In each cases, these gave approach to Delta in the course of the third wave.

In South Africa, Beta dominated the second wave as a substitute of Alpha. Interestingly, though the C.1.2 variant showed signs of immune escape, it didn’t make a big impact against the Delta background.

Other lineages that competed with Alpha included B.1.525 and A.23.1, which were finally outcompeted by later emerging VOCs. The differences in lineage by region might be as a result of virus genetics, human mobility, competition between co-circulating lineages, and immunity levels.

Delta caused the best impact, causing over a 3rd of all infections in Africa, in line with many analysts. Beta caused about one in seven, and Alpha only about 4% overall. Omicron, which continues to be spreading, caused over a fifth of all infections, as judged by genomic sequencing.

Unlike the sooner VOCs, Omicron became distinguished against a background of high infection and vaccination rates, with high associated immunity levels. Together with its lower intrinsic virulence, Omicron has led to fewer deaths than other VOCs, corresponding to the lower South African mortality rate during this wave.

The primary a part of the pandemic was brought on by strains belonging to the B.1 clade, or ancestral viruses, which were then replaced by the primary cluster of VOCs from late 2020 onwards: Alpha, Beta, after which, in 2021, Delta and Omicron. While Alpha and Beta circulated mostly in distinct regions of Africa, Delta and Omicron dominated infections in Africa starting soon after their emergence.

The info comes from combining epidemiologic data with genomic sequencing data, together with information on the temporal and size-related characteristics of those waves. Nevertheless, some countries have tested just one in ten million population, while others have tested over 10,000 per ten million, indicating grossly heterogeneous testing rates.

Interestingly, countries with high testing rates have reported higher case rates as well, but under-reporting continues to be a reality, as in the remainder of the world. Increased reporting was achieved largely by way of relatively inexpensive sequencing technology.

There’s an urgent need to extend sequencing capability, with 16 countries still lacking local sequencing facilities while many others have limited capability. Three premier sequencing centers, and multiple regional sequencing hubs, have been arrange to assist consolidate resources in just a few countries to maximise sequencing across the entire continent. These centers helped mostly sub-Saharan countries by handling the entire of the local sequencing efforts in some countries like Angola and Namibia, but additionally cooperating with local sequencing efforts during waves.

Other facilities outside Africa have also been pressed into service to extend surveillance, especially for West and North African countries.

Ultimately, a mixture of strategies from local sequencing, collaborative resource sharing amongst African countries and sequencing with academic collaborators outside the continent helped close surveillance blind spots.”

Even with low levels of sequencing, representative sampling over time has helped maintain genomic surveillance and detect variants in time, including Beta and Omicron. Furthermore, the turnaround time is being reduced progressively from, for example, ~180 days to 50 days from October 2020 to at least one 12 months later.

That is favored through the use of local sequencing networks in comparison with regional or external facilities, which indicates the necessity to speculate within the latter. The travel bans that followed the detection and reporting of the Beta and Omicron VOCs show how countries could hesitate to report such data in the longer term. If sequencing could be performed only outside the country, it will inevitably result in the absence of surveillance in such situations.

Thus, encouraging local sequencing capability will help “generate timely and regular data for local and regional decision making.” This might allow emerging variants to be detected early enough to permit time to interrupt their spread.

For instance, Beta was detected three months after its origin, but for Omicron, it was inside five weeks. Furthermore, the World Health Organization declared the latter a VOC inside 72 hours of depositing its sequence within the database.

 Sequencing efforts must be built up, not only for SARS-CoV-2 but other latest or re-introduced pathogens, including Ebola, measles, and H1N1 influenza. In accordance with Africa CDC, over 200 infectious disease outbreaks occur annually on this continent.

Beyond the present pandemic, continued investment in diagnostic and sequencing capability for these pathogens could serve the general public health of the continent well into the twenty first century.”