Scientists carrying out genomic surveillance analysis of Sars-CoV-2 in Africa are warning that the continent could become a breeding ground for new Coronavirus variants.
Their grim warning, they say, is based on detected increases in the number of exportation events from Africa to the rest of the world between December 2020 and March 2021.
“We describe the emergence and spread of a number of key Sars-CoV-2 variants in Africa, and highlight how the spread of B.1.351 (Beta) (501Y.V2) and other variants contributed to the more severe second wave of the pandemic in many countries,” says a new report titled “A year of genomic surveillance reveals how the Sars-CoV-2 pandemic unfolded in Africa’.”
Analysis of Sars-CoV-2 genomic data from 33 African countries and two overseas territories to help characterise the dynamics of the pandemic in Africa, also shows that though early introductions were predominantly from Europe, as the pandemic has progressed there was increasing spread between African countries. In total, the researchers say they detected at least 757 (95 percent) viral introductions into African countries between the start of 2020 and February 2021, over half of which occurred before the end of May 2020.
As air travel came to an almost complete halt in March/April 2020, the numbers of detectable viral imports into Africa decreased and the pandemic entered a phase that was characterised in sub-Saharan Africa by sustained low levels of within-country movements and occasional international viral movements between neighbouring countries, presumably via road and rail links. Though some border posts between countries were closed during the initial lockdown period, others remained open to allow trade to continue.
“The rapid, unimpeded spread of B.1.351 into these countries suggests that current land-border controls that are intended to curb the international spread of the virus are ineffective. Perhaps targeted testing of cross-border travellers, genotyping of positive cases and the focused tracking of frequent cross-border travellers such as long-distance truckers, would more effectively contain the spread of future VOCs and VOIs that emerge within this region,” says the researchers.
First sampled on October 8, 2020 in South Africa (analysis suggests that it emerged earlier, around August 2020), B.1.351 became the most frequently detected Sars-CoV-2 lineage found in Africa. This was introduced multiple times to African countries and has been detected in all but one of the countries included in this analysis. It is defined by 10 mutations in the spike protein.
By November 2020, the variant had spread into neighbouring Botswana and Mozambique and by December 2020 it had reached Zambia and Mayotte. Within the first three months of 2021, further exports from South Africa into Botswana, Zimbabwe, Mozambique and Zambia occurred. By March 2021, B.1.351 had become the dominant lineage within most Southern African countries as well as the overseas territories of Mayotte and Réunion.
The scientists’ reconstruction also demonstrates movement of B.1.351 into East and Central Africa directly from southern Africa. Analysis of a wider sample of B.1.351 isolates demonstrates the spread of the lineage into West Africa. A patient from West Africa had a known travel history to Europe so it is possible the patient acquired the infection while in Europe or in transit and not from other African sources.
According to a reconstruction by this study, B.1.525, first sampled and initially believed to have originated in the United Kingdom in mid-December 2020, originated in Nigeria in November 2020. Since then, it has spread throughout much of Nigeria and neighbouring Ghana. Given sparse sampling from other neighbouring countries within West and Central Africa, the extent of its spread in the region is not clear, according to the researchers. Beyond Africa, it has spread to Europe and the US.
A.23.1, another virus of interest, was first detected in a Ugandan prison in Amuru in July 2020, from where the lineage was transmitted to Kitgum prison, possibly facilitated by the transfer of prisoners. Subsequently, it spilled into the general population and spread to Kampala, adding other mutations along the way. It has since spread regionally into neighbouring Rwanda and Kenya and has now also reached South Africa and Botswana in the south and Ghana in the west.
“However, our reconstruction of A.23.1 suggests that the introduction into Ghana may have occurred via Europe, whereas the introductions into southern Africa likely occurred directly from East Africa. This is consistent with epidemiological data suggesting that the case detected in South Africa was a contact of an individual who had recently travelled to Kenya,” says the report.
Another variant of interest, C.1, emerged in Johannesburg and spread within South Africa during the first wave in March 2020 during a cluster outbreak prior to the first wave of the epidemic. It spread to Zambia (June-July, 2020) and Mozambique (July-August 2020), it mutated to C.1.1, seemingly in Mozambique around mid-September 2020. There, it became the most prevalent C.1.1. lineage until the introduction of B.1.351, which has dominated the epidemic since.
The B.1.1.7, variant of concern, first sampled in Kent, England in September 2020, has also increased in prevalence in several (11) African countries. The study suggests that this lineage was introduced into Africa on at least 16 occasions between November 2020 and February 2021 with evidence of local transmission in Nigeria and Ghana.
Yet the scientists say the introductions identified are just a tip of the iceberg. They also say although Africa accounts for a relatively low proportion of reported cases and deaths, the numbers have been distorted by low sampling numbers and blind-spots.
Throughout the Covid-19 pandemic, the researchers note, “emerging data from seroprevalence surveys and autopsy studies in some African countries suggests that the true number of infections and deaths may be higher than reported.”
South Africa, Kenya and Nigeria appear as major sources of importations into other African countries.
“Although this is likely to be influenced by these three countries having the greatest number of deposited sequences. Particularly striking is the southern African region, where South Africa is the source for a large proportion (about 80 percent) of the importations to other countries in the region. The North African region demonstrates a different pattern to the rest of the continent, with more viral introductions from Europe and Asia (particularly the Middle East) than from other African countries,” said the report.
Even more interesting is findings that Africa has also contributed to the international spread of the virus with at least 324 exportation events from Africa to the rest of the world detected in the researchers’ dataset.
An increase in the number of exportation events occurred between December 2020 and March 2021, which coincided with the second wave of infections in Africa and with some relaxations of travel restrictions around the world.
“Slow rollout of vaccines in most African countries creates an environment in which the virus can replicate and evolve: this will almost certainly produce additional variants of concern, any of which could derail the global fight against Covid-19,” said the report.
Lead scientist, Eduan Wilkinson, from the University of Stellenbosch, South Africa, says “If the pandemic is not controlled in Africa, we may see the production of vaccine escape variants that may profoundly affect the population in Africa and across the world.”
But while the early phase of the pandemic was dominated by importations from outside Africa, predominantly from Europe, there was a shift in the dynamics, with increasing intra-African importations as the pandemic progressed.
Although lineage A viruses were imported into several African countries, they only account for 1.3% of genomes sampled in Africa. Despite lineage A viruses initially causing many localised clustered outbreaks, they were later largely replaced by lineage B viruses as the pandemic evolved. This is possibly due to the increased transmissibility of B lineage viruses by virtue of the mutation in spike. However, there is evidence of an increasing prevalence of lineage.
‘A’ viruses in some African countries (11), in particular, A.23.1, emerged in East Africa and appear to be increasing rapidly in prevalence in Uganda and Rwanda. Furthermore, a highly divergent variant from lineage A was recently identified in Angola from individuals arriving from Tanzania.