Africa delayed genome sequencing during the first two years of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, with increased funding, more than 100,000 genomes from this continent have now been sequenced.
A new study summarizes the results of genetic surveillance so far, indicating how variants of virus concern may spread while indicating future directions for preparedness to respond.
Africa appears to have been relatively spared the high incidence and mortality during the ongoing pandemic, with nearly 11 million cases out of a total of 600 million deaths and a quarter of a million deaths among the more than 6.4 million deaths worldwide.
However, as the virus continued to change and mutate, new variants emerged that showed, in some cases, higher susceptibility to transmissibility and infection or virulence. Immune escape mutations have been identified in some variants, making them capable of increased prevalence even in previously vaccinated or infected populations. These were called variables of concern (VOC), and so far, there have been five of them – Alpha, Beta, Gamma, Delta and Omicron.
Of these, Beta and Omicron were first detected in Africa, although the other two also caused significant cases on this continent. In response to the increasing threat posed by the emergence of VOCs, samples were collected from multiple sites for sequencing. However, in April 2020, only 20 African countries had this capacity.
With global supply chains waning, these efforts stalled at the end of the year. After the first 10,000, analysis of some of the missing regions showed, in response, increased money was poured into building increased infrastructure and training staff in genetic monitoring.
The Africa CDC and the World Health Organization’s Africa Regional Office (or WHO AFRO) share responsibility for this, with the help of many other individuals and organizations. The result was that another 90,000 sequences were uploaded from April 2021 to March 2022.
To put this into perspective, less than 4,000 HIV and 12,000 influenza sequences have so far been uploaded, although they have been in Africa in alarming numbers for many years.
The current study published in Sciencesexplores the contribution of genetic sequencing to the scientific understanding of COVID-19 on this continent, and also introduces global public health measures through the ability to capture new variants early enough.
What did the study show?
The data illustrates multiple waves of infection, varying in size and period from country to country. After the first two waves, dominated by the B.1 and Alpha variants, the Delta and Omicron swept through Africa in dark succession.
Different strains predominated in different parts of Africa, such as C.36 and C.36.3, which caused 40% of infections in Egypt, versus B.1.160 strain in Tunisia. Either way, that gave way to a delta during the third wave.
In South Africa, the second wave was dominated by Beta rather than Alpha. Interestingly, although the C.1.2 variant showed signs of immune escape, it failed to produce a significant effect against the delta background.
Other strains that competed with Alpha included B.1.525 and A.23.1, which were eventually overtaken by the later emerging VOCs. Differences in lineage by region could be due to virus genes, human mobility, competition between circulating strains, and levels of immunity.
Delta has had the biggest impact, accounting for more than a third of all infections in Africa, according to several analysts. Beta causes about one in seven, and alpha is only about 4% overall. Omicron, which continues to spread, has caused more than a fifth of all infections, according to genetic sequencing.
In contrast to previous VOCs, Omicron became prominent against a background of high rates of infection and vaccination, with associated high levels of immunity. Besides its lower intrinsic virulence, Omicron resulted in lower mortality than other VOCs, corresponding to lower mortality in South Africa during this wave.
The first part of the epidemic resulted from strains belonging to the B.1 clade, or ancestral viruses, which were then replaced by the first group of VOCs from late 2020 onwards: Alpha and Beta, and then in 2021, Delta and Omicron. While alpha and beta spread mostly in distinct regions of Africa, delta and omicron infections dominated in Africa soon after their emergence.
The data come from a combination of epidemiological and genomic sequence data, along with information on the temporal and magnitude characteristics of these waves. However, some countries have tested only one in ten million populations, while others have tested more than 10,000 per ten million, indicating significantly heterogeneous testing rates.
Interestingly, countries with high testing rates have also reported higher case rates, but underreporting remains a reality, as is the case in the rest of the world. An increase in reporting has been achieved largely by the use of relatively inexpensive sequencing technology.
There is an urgent need to increase sequencing capacity, as 16 countries still lack domestic sequencing facilities while many others have limited capacity. Three major sequencing centres, and multiple regional sequencing centres, have been established to help consolidate resources in a few countries to maximize sequencing across the entire continent. These centers mostly helped sub-Saharan countries by handling the bulk of local sequencing efforts in some countries such as Angola and Namibia, but also collaborating with local sequencing efforts during waves.
Other facilities outside Africa have also been pressured into service to increase monitoring, particularly for countries in West and North Africa.
Ultimately, a combination of strategies from local sequencing, collaborative sharing of resources among African countries, and sequencing with academic collaborators outside the continent helped to close blind spots.. “
Even with low levels of sequencing, representative sampling over time helped maintain genetic surveillance and timely detection of variants, including Beta and Omicron. Moreover, the time taken is gradually reduced, for example, ~180 days to 50 days from October 2020 to one year thereafter.
This is preferred with local sequencing networks compared to regional or offshore installations, indicating the need to invest in the latter. The travel ban following the detection and reporting of beta and omicron VOCs shows how countries can be reluctant to report such data in the future. If sequencing could only be carried out outside the country, it would inevitably lead to a lack of monitoring in such cases.
Thus, encouraging local sequencing ability will help.”Generate regular and timely data for decision making at the local and regional levels. This will allow emerging variables to be detected early enough to allow time to interrupt their spread.
For example, Beta was discovered three months after its inception, but for Omicron, that was within five weeks. Furthermore, the WHO declared the latter to be VOCs within 72 hours of depositing their sequences into the database.
Sequencing efforts must be built, not only for SARS-CoV-2 but for new or reintroduced pathogens, including Ebola, measles and H1N1 influenza. According to the Africa CDC, more than 200 infectious disease outbreaks occur annually on this continent.
Combined with the current pandemic, continued investment in the capacity to diagnose and sequence these pathogens could serve the continent’s public health in the twenty-first century.. “