Results Updated – 7 March 2022
(Figures updated from Wilkinson et al. Science 2021).
SARS-CoV-2 variants in lineages in African countries
| Variant | Alternative names | Lineage/sub-lineages | Total confirmed (Sequences in GISAID) | Sequences submitted in past 30 days | Sequences sampled in past 30 days | Date of first sequence | Date of last sequence | No. Days since last sampling |
|---|---|---|---|---|---|---|---|---|
| Alpha | VOC-2020-12-01 | B.1.1.7, AZ.X | 3605 | 394 | 1 | 2020-08-02 | 2022-02-16 | 19 |
| Beta | VOC-2020-12-02 | B.1.351, B1.351.X | 11957 | 237 | 0 | 2020-05-27 | 2022-02-02 | 34 |
| Delta | VOC-2021-03-02 | B.1.617.2, AY.X | 33598 | 1776 | 2 | 2020-03-29 | 2022-02-21 | 14 |
| Omicron | VOC-2021-11-26 | B.1.1.529, BA.X | 16775 | 7901 | 611 | 2021-11-09 | 2022-02-24 | 11 |
| A.23.1 | NA | A.23.1 | 420 | 12 | 0 | 2020-03-23 | 2021-08-22 | 197 |
| B.1.1.318 | VUM-2021-06-04 | B.1.1.318 | 1311 | 230 | 0 | 2021-01-06 | 2021-03-02 | 370 |
| C.1 | NA | C.1 | 427 | 0 | 0 | 2020-04-12 | 2021-09-17 | 171 |
| C.1.2 | VUM-2021-09-01 | C.1.2 | 295 | 9 | 0 | 2021-05-11 | 2022-01-17 | 49 |
| C.36.3 | VUM-2021-06-16 | C.36.3 | 458 | 18 | 0 | 2020-04-02 | 2022-01-18 | 48 |
| Eta | VUM-2021-02-03 | B.1.525 | 2069 | 403 | 0 | 2020-03-28 | 2021-12-01 | 96 |
| For more information on each variant, click the variant name in the table. (Table updated 7 March) |
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
We also want to acknowledge and apologize to the Angola Ministry of Health (Dr. Silvia Lutucuta and Dr. Joana Moraes) and the Malawi Minister of Health (Dr. Benson Chilima, Dr. Bernard Mvula, and Moses Chitenje) who due to a mistake were not listed among the 309 authors of the Science paper.
Key resources and publications describing the genomics activities in Africa:
- Africa CDC Pathogen Genomics Initiative (Africa PGI) dashboard
- Accelerating genomics-based surveillance for COVID-19 response in Africa. Tessema et al Lancet Microbe 2020
- Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Inzaule et al. Lancet Infectious Diseases 2020
- A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Wilkinson et al. Science 2021