'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 source for new variants'. science.org/doi/10.1126/sc…
Because the pandemic is very fast-moving, we are updating every week the results of our pan-African collaboration published in Science today at: genomics.africa/sars-cov-2-das…
SARS-CoV-2 variants in lineages in African countries
This is the work of 100s of authors from 122 African organizations, see the author list and please credit their work! See: Wilkinson et al. Science 2021 - science.org/doi/10.1126/sc…
Evolution of the C.1 lineage in South Africa with multiple Spike mutations - pre-print at: medrxiv.org/content/10.110… - In this tweet thread, I highlight this lineage (assigned as C.1.2), the potential impact of the mutations, and the likelihood that this become a variant of concern
The C.1.2 has 14 mutations in Spike, including three mutations at the Receptor Binding Motif, the Y449H, E484K, and N501Y - two of the mutations have been found in three of the four variants of concern (Alpha, Beta, and Gamma).
In relationship to decrease neutralization, in addition to the E484K, there are also deletions at position 144 and positions 242-243, the 144 deletions are also seen in the Alpha and the 242-243 in the Beta, which associates with a decrease neutralization of antibodies
Seems that the level4 restrictions in South Africa helped to control the third wave of #COVID19 - Reproductive number < 1 in the whole country and in most provinces.
The Western Cape and Eastern Cape seem to have peaked now, R =1
Gauteng #COVID19 cases are really in the downward path, R = 0.6
NGS-SA worked hard to increase sequencing in South Africa. We know now that the explosive #COVID19 third wave is dominatedd by the Delta variant.
In this tweet thread, we present recent data (sampled up to 24 June in many provinces in SA, including Gauteng) - Tweet 1/8
This graph shows the distribution of the variants over time in the different provinces. 2/8
The third wave in Gauteng was caused by the Delta variant, thanks to @nicd_sa and @krisp_news who worked day and night on the weekend to increase genomics surveillance in Gauteng.
Graph shows Black line = Daily cases (7-day average), Yellow = Beta, Green = Delta. Tweet 3/8
A Novel and Expanding SARS-CoV-2 Variant, B.1.1.318, dominates infections in Mauritius medrxiv.org/content/10.110…
Mauritius is an example of controlling #COVID19 in Africa, with 1,700 infections and only 18 deaths. However, one variant seems to have caused the great majority of all of the infections
Mauritius has stopped dozens of introductions of the Beta (501Y.V2/B.1.351) and Alpha (B.1.1.7) but the B.1.1.318, which has the 484K mutation (common to Beta) and the 681H mutation (common to Alpha) has caused all local transmitted cases.
In this online pre-print, we present a case of persistent SARS-CoV-2 infection with accelerated intra-host evolution in a patient with advanced HIV and antiretroviral treatment failure in South Africa.
SARS-CoV-2 RT-PCR was positive for 216 days (27 weeks). At all time-points between day 0 and day 216 there was a mean Ct ranging from 16.4 to 31.6. The patient had HIV drug resistance and was not responding to therapy.
Over 30 mutations accumulated over time, many of them changing aminoacids that are common of variants of concern.