A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa medrxiv.org/content/10.110…
By 5 May 2021, 14,504 SARS-CoV-2 genomes had been submitted to the GISAID database from 38 African countries and two overseas territories (Mayotte and Réunion) (Fig. 1A). Overall, this corresponds to approximately one sequence per ~300 reported cases.
Overall, the number of sequences correlates closely with the number of reported cases per country. lmost half of the sequences were from South Africa, consistent with it being responsible for almost half of the reported cases in Africa.
The countries/territories with the highest coverage of sequencing (defined as genomes per reported case) are Kenya (n=856, one sequence per ~203 cases), Mayotte (n=721; one sequence per ~21 cases), and Nigeria (n=660, one sequence per ~250 cases).
Half of all African genomes were deposited in the first ten weeks of 2021, suggesting intensified surveillance in the second wave following the detection of B.1.351/501Y.V2 and other variants
In total, we detected at least 730 viral introductions into African countries between February 2020 and February 2021, over half of which occurred before the end of May 2020.
Whilst the early phase of the pandemic was dominated by importations from outside Africa, predominantly from Europe.
There was then a shift in the dynamics, with an increasing number of importations from other African countries as the pandemic progressed.
South Africa, Kenya and Nigeria appear as major sources of importations into other African countries. Particularly striking is the southern African region, where South Africa is the source for a large proportion (~80%) of the importations to other countries in the region.
Africa has also contributed to the international spread of the virus with at least 356 exportation events from Africa to the rest of the world. Consistent with the source of importations, most exports were to Europe (41%), Asia (26%) and North America (14%).
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.
After its emergence in South Africa, B.1.351 became the most frequently detected SARS-CoV-2 lineage found in Africa. It was first sampled on 8 October 2020 in South Africa (13) and has since spread to 20 other African countries.
Although lineage A viruses were imported into several African countries, they only account for 1.3% of genomes sampled in Africa. Lineage A is the oldest SARS-CoV-2 lineage, representing the original Wuhan isolates of the virus from December 2019
there is evidence of an increasing prevalence of lineage A viruses in some African countries. In particular, A.23.1 emerged in East Africa and appears 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 - medrxiv.org/content/10.110…
n order to determine how some of the key SARS-CoV-2 variants are spreading within Africa, we performed phylogeographic analyses on the VOC B.1.351, the VOI B.1.525, and on two additional variants that emerged and that we designated as VOIs for this analysis (A.23.1 and C.1.1).
These African VOCs and VOIs have multiple mutations on Spike glycoprotein and molecular clock analysis of these four datasets provided strong evidence that these four lineages are evolving in a clocklike manner.
The B.1.525 is spreading widely in West Africa and C.1., which has originated in South Africa have added new Spike mutations are spreading north and east in the south of the continent
Conclusions: Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.
There are tons of people to thank! Over 30 countries, @GISAID, >100 organizations and many of the great funders in the world that believe that Africa can lead in their response to pandemics!
Paper open accessible at: medrxiv.org/content/10.110…

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More from @Tuliodna

13 May
Confirmed Detection of eight (8) more genomes B.1.617.2 and two (2) community transmission of B.1.1.7 in South Africa, By Network for Genomic Surveillance in South Africa (NGS-SA), 13 May 2021
The eight new cases of B.1.617.2 variant have been detected from KwaZulu-Natal province. More specifically, these were cases in crew members of a commercial vessel that arrived in Durban Port from India.
The cases were isolated on the vessel, and other crew members have been quarantined according to national COVID-19 case management guidelines. The individuals who tested positive for COVID-19 did not disembark in South Africa, with exception of one that was admitted to hospital
Read 9 tweets
9 May
Confirmed Detection of B.1.617.2 and B.1.1.7 in South Africa by NGS-SA

This report was sent to our Health Minister @DrZweliMkhize yesterday.

In this Twitter thread, we highlight the details and repercussion of the discovery to South Africa
In response to the continued emergence and spread of new variants around the world, the Network for Genomic Surveillance in South Africa (NGS-SA) recently intensified the monitoring of confirmed COVID-19 cases in recent arrivals to the country.
We can now confirm that today we detected four cases of the B.1.617.2 variant. The four cases have been detected from Gauteng (n=2) and KwaZulu-Natal (n=2) provinces and all have a history of recent arrivals from India.
Read 17 tweets
4 May
First genomic surveillance results from a traveler to India in South Africa. A patient at Tygerberg Hospital who tested positive for SARS-CoV-2 about 3 days after traveling to SA from India. This first genome is a 501Y.V2 (B.1.351) and not the B.1.617 described in India.
The 501Y.V2 (B.1.351) is the 3rd most common variant in India after the B.1.617 and the B.1.1.7. Below a graph from @trvrb showing the spread of the variants in India.
The 501Y.V2 (B.1.351) was firstly identified in South Africa by the network for genomic surveillance in South Africa (NGS-SA). It shows how variants can be introduced back and forth between countries.
Read 8 tweets
29 Mar
Today paper on neutralization of 501Y.V2 (B.1.351) - Show effective neutralization of other SARS-CoV-2 lineages by 501Y.V2 @nature


All start with a good cohort... We obtained convalescent plasma & sequenced the matching infecting virus of 1st & 2nd wave
A first wave variant lacking the 501Y.V2 RBD and NTD mutations (B.1.1.177) was outgrown from one participant infected in the first South African infection wave, and 501Y.V2 was outgrown from a participant at the beginning of the second wave.
A focus forming live virus neutralization assay (LVNA) was used to quantify neutralization.
Read 14 tweets
25 Mar
We just submitted a pre-print 'A novel variant of interest (VOI) of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.'

This VOI has 31 amino acids mutations. In Spike has 11 mutations and three deletions in the N-terminal domain Image
It has some key mutations, including the E484K, R346K and P681H. The R346K is the associated with resistance to class 3 RBD NAbs recently described by @jbloom_lab
There are also 5 substitutions and 3 deletions in the NTD antigenic supersite (Y144Δ, R246M, SYL247-249Δ and W258L)
It the most diverse A lineage sequencers ever described. It also worry us as it was found in three travelers from Tanzania in Angola. There is almost no data from COVID-19 in Tanzania. Image
Read 8 tweets
9 Mar
Finally out! Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein disq.us/t/3vewz4s

So many people to thank, thank you and thank you! @rjlessells @houzhou @Mittenavoig @MRCza @dsigovza

Great to see South African science advancing fast!
The paper starts by showing how the second wave in South Africa arise so quickly, which was completely unexpected as we were in the start of our summer.
It show how a new and unusual cluster emerged among the dozens of different lineages already circulating in South Africa.
Read 10 tweets

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