covid-19

Continued Emergence and Evolution of Omicron in South Africa

: Communications; COVID-19; 06 May 2024; Hits: 21169

Abstract

South Africaâs fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern. We have now identified two new lineages, BA.4 and BA.5. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del, L452R, F486V and the wild type amino acid at Q493. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure with the TaqPathâ¢ COVID-19 qPCR assay. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa from the first week of April 2022 onwards. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.07 - 0.09) and 0.12 (95% CI: 0.09 - 0.15) per day respectively over BA.2 in South Africa. Read more!

Context-specific emergence and spread of SARS-CoV-2 lineages

: Communications; COVID-19; 06 May 2022; Hits: 21625

CERI & KRISP Talks: Context-specific emergence and spread of SARS-CoV-2 lineages. Read more!

South Africa’s latest surge is a possible preview of the pandemic’s next chapter

: Communications; COVID-19; 06 May 2022; Hits: 11821

Coronavirus cases are surging again in South Africa, and public health experts are monitoring the situation, eager to know what’s driving the spike, what it says about immunity from previous infections and what its implications are globally. Read more!

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

: Communications; COVID-19; 06 May 2022; Hits: 12228

Abstract

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. Read more!

Are new Omicron subvariants a threat?

: Communications; COVID-19; 06 May 2022; Hits: 17592

In South Africa, a network of researchers are studying whether new lineages BA.4 and BA.5 escape immunity from COVID-19 vaccines and prior infections. Read more!

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