In Africa, more sequencing is needed to better monitor variants
The rapid spread of the Omicron variant, first identified in South Africa and Botswana, once again raises the question of variant surveillance.
Alpha Kabinet Keita, University of Montpellier; Dramane Kania and Richard Njouom, Pasteur Center of Cameroon
Alpha Keita, a virologist at IRD and deputy director of Cerfig (Guinea’s Center for Research and Training in Infectious Diseases), Dramane Kania, a pharmacist and virologist at the Muraz Center of the National Institute of Public Health in Burkina Faso, and Richard Njouom, Head of the Virology Department at the Pasteur Center of Cameroon in Yaoundé, provide an update on the COVID-19 epidemic in Africa and discuss the challenges related to sequencing.
The Conversation: What is the current status of the pandemic in Africa? What do we know about the spread of the virus today?
Dramane Kania: When we compare the situation on the African continent to that on other continents, the impact of the pandemic appears to be less severe: the number of reported cases is lower, as is the number of deaths.
However, we should not jump to conclusions: these figures are likely misleading, and in reality, the spread of the virus is certainly more widespread than these numbers suggest. This discrepancy can be explained by issues specific to the African continent: in many countries, diagnostic capacity is limited and data is lacking, even though projects like APHRO-COV and other initiatives have helped strengthen diagnostic capacity in several countries. Furthermore, a large portion of the population is not necessarily accustomed to seeking care from healthcare facilities when facing health issues. For these reasons, the actual number of COVID-19 cases is almost certainly underestimated.
This hypothesis is supported by the fact that, in countries with greater resources where diagnosis can therefore be performed more routinely (such as South Africa or the Maghreb countries), the number of reported cases is higher. In West Africa, by contrast, the existence of underreporting has been confirmed by seroprevalence studies, which detect antibodies produced following infection with the virus. These studies have shown that in some areas, more than half of the population has been exposed to SARS-CoV-2 in recent months.
Alpha Keita: As of January 2, there were more than 9.5 million cases and nearly 230,000 deaths in Africa. This is less than on other continents, but there are significant disparities from one country to another: most of the recorded deaths occur in countries with the most effective healthcare systems, which are capable of accurately collecting data related to the pandemic. This supports the hypothesis that cases are underreported.
As part of the Ariacov project, which supported Africa’s response to the coronavirus pandemic, we conducted a serological study in Guinea using samples collected from the population of the capital, Conakry. This work, which consisted of three surveys conducted a few months apart, revealed that by December 2020, 17% of Conakry’s population had been exposed to the virus. By late February–early March, that figure had risen to over 30% of the population. By June–July, it had reached nearly 50%.
These results clearly indicate that the number of cases is underestimated. The number of deaths is also underestimated, as only those occurring in hospitals and centers affiliated with the university hospital are counted. Ultimately, while the pandemic certainly did not result in the mass casualties that were anticipated, it is important to understand that the numbers of cases and deaths have been underestimated.
Richard Njouom: In Cameroon, the situation regarding the COVID-19 pandemic is the same as in other sub-Saharan African countries: the number of confirmed cases of SARS-CoV-2 infection is low, as is the number of deaths attributed to the virus, likely due to underreporting.
To better understand the impact of the COVID-19 pandemic and monitor the spread of SARS-CoV-2 across the African continent, we launched a collaborative research program called REPAIR in the spring of 2020, in partnership with all African member institutes of the Pasteur Network. This work spans various fields: the development and performance evaluation of diagnostic tests (at the Pasteur Center in Cameroon, we have developed an easy-to-use colorimetric test, currently being evaluated in the field and at other institutes in the Pasteur Network), molecular epidemiological studies of the virus, mathematical modeling of its spread… SARS-CoV-2 seroprevalence surveys have also been conducted among several “sentinel” populations, such as healthcare workers and blood donors.
TC: Could the circulation of SARS-CoV-2 contribute to the emergence of variants?
DK: What the theory tells us is that, indeed, the more a virus circulates, the greater the risk of variants emerging. This is because when a virus replicates within an infected cell, it copies its genetic material countless times. In doing so, it can make errors—mutations. Some of these mutations are harmful, and the viruses carrying them die out; others are repaired; still others persist.
The key question is whether these changes occurring in the genome (which is, in a sense, the “blueprint for viral particles,” ed.) will result in changes to the virus’s structure, and if so, what the consequences will be: will they alter its transmissibility? Its virulence? Other characteristics?
To detect this, a robust monitoring or surveillance system is needed, one that relies heavily on sequencing capabilities. Unfortunately, in Africa, most laboratories lack the necessary technical capabilities. In most cases, we are limited to diagnostic tests, which merely detect the presence of the virus or confirm its absence.
While it is sometimes possible to sequence the genomes of viruses from samples that test positive, this can only be done on an ad hoc basis, and sometimes only 3 or 4 months after the samples were collected. The capacity for real-time monitoring of variants is severely lacking; for this reason, our understanding of the evolution of the epidemic and the actual number of variants circulating on the continent is certainly distorted.
Countries capable of implementing this type of surveillance detect more variants, which likely explains in part why South Africa has identified at least two variants of concern within its borders since the start of the pandemic. This allowed authorities to alert the international community very early on. As proof of the importance of sequencing, at the Muraz Center in Bobo Dioulasso—a partner of ANRS | Emerging Infectious Diseases—we were able to detect two cases of infection with the Omicron variant in mid-December, meaning it is also circulating in Burkina Faso.
TC: In practical terms, how is variant surveillance conducted?
AK: It essentially depends on countries’ ability to sequence circulating viruses. Currently, when we look at contributions to databases where researchers upload the sequences they’ve obtained (such as the GISAID platform, for example), we see that Africa’s participation is very limited. Guinea, for example, has submitted only 311 genomes to GISAID since January 10, 2020.
(During the same period, South Africa filed nearly 25,000, France 16,000, the United Kingdom nearly 1.5 million, and the United States 1.9 million. China filed 1,299, Ed.)
To improve the situation, the Afroscreen project was launched. Funded by the French Development Agency (AFD) and coordinated by ANRS | Emerging Infectious Diseases, in collaboration with the Pasteur Institute and IRD, the project has enabled us, in particular in Guinea, to routinely screen samples over the past two months.
This approach involves screening samples that have tested positive for mutation profiles corresponding to known variants listed by the World Health Organization (WHO). This screening is conducted on samples taken from patients hospitalized at one of the capital’s three major healthcare centers, from individuals who come in for testing on their own initiative, or from travelers. Results are available within a few hours, enabling real-time monitoring.
As effective as it may be, screening nevertheless has its limitations, since it focuses on already known variants (variants of interest or variants of concern), whose mutations have already been identified. The mutation profiles of unclassified variants are all listed as “wild-type,” which provides no additional information and does not allow for comprehensive monitoring of emerging variants.
Only whole-genome sequencing can provide a detailed analysis of the mutations that may arise in new variants and determine whether they are cause for concern, whether there is reason to fear that they might make the virus more transmissible, or enable it to evade immunity—whether natural or vaccine-induced—and so on.
It is therefore necessary to strengthen these capabilities in as many countries as possible (in particular to enable comparisons of data across countries), which is also the purpose of the Afroscreen network.
RN: Sequencing is indeed essential for studying the spread of SARS-CoV-2 over time and space and for tracking the emergence of dangerous variants. In Cameroon, we have been able to strengthen our capabilities, both in terms of equipment and staff training. As a result, we were able to establish genomic surveillance as early as January 2021, which resulted in the sequencing of 116 complete genomes. The results confirmed the circulation of the Alpha, Beta, Delta, and Gamma variants in the country. We hope that the Afroscreen network will enable us to significantly expand this effort.
Another benefit of being part of a network of this size, which brings together 13 African countries, is the sharing of knowledge and data. By publishing the results in the open-access GISAID database, it will be possible to track and better understand the spread of the virus in the region.
TC: Regarding vaccination, what is the current status on the continent?
DK: Many countries initially faced difficulties in securing the vaccine. To address this issue, various initiatives have been launched. Beyond this question of accessibility—which is certainly essential—a second problem arises: that of public acceptance, as people generally lack the scientific information needed to answer their questions. Fake news, on the other hand, is widely shared on social media and fuels people’s mistrust of vaccination. At present, it seems that only citizens who are required to travel are willing to get vaccinated… Reversing this trend is another challenge.
RN: In Cameroon, the vaccination campaign is significantly behind schedule: only 1.1% of the target population has been fully vaccinated. People are wary of the vaccines available in the country. One of the challenges is therefore to convince people of the value of vaccines. This vaccination lag observed in Africa makes it all the more important to strengthen surveillance of variants through sequencing. If we can determine which variants are circulating in which areas, it would be easier for health authorities to decide on targeted vaccination campaigns, which are more effective in containing the epidemic.
Alpha Kabinet Keita, Microbiologist, Researcher at the TransVIHMI Unit (University of Montpellier, IRD, INSERM), Deputy Director of CERFIG, University of Montpellier; Dramane Kania, Pharmacist-Virologist, MURAZ Center (Bobo-Dioulasso, Burkina Faso) – National Institute of Public Health; and Richard Njouom, Head of the Virology Department at the Pasteur Center of Cameroon, Pasteur Center of Cameroon
This article is republished from The Conversation under a Creative Commons license. Readthe original article.