Volume 28, Supplement—December 2022
SUPPLEMENT ISSUE
Surveillance
Comparison of COVID-19 Pandemic Waves in 10 Countries in Southern Africa, 2020–2021
, Bridget Miller, Alinune N. Kabaghe, Evelyn Kim, Nellie Wadonda-Kabondo, Alean Frawley, Sarah Labuda, Eusébio Manuel, Helga Frietas, Anne C. Mwale, Tebogo Segolodi, Pauline Harvey, Onalenna Seitio-Kgokgwe, Alfredo E. Vergara, Eduardo S. Gudo, Eric J. Dziuban, Naemi Shoopala, Jonas Z. Hines, Simon Agolory, Muzala Kapina, Nyambe Sinyange, Michael Melchior, Kelsey Mirkovic, Agnes Mahomva, Surbhi Modhi, Stephanie Salyer, Andrew S. Azman, Catherine McLean, Lul P. Riek, Fred Asiimwe, Michelle Adler, Sikhatele Mazibuko, Velephi Okello, and Andrew F. Auld
Table 3
Overall genomic surveillance comparison across 3 COVID-19 pandemic waves for 10 countries in southern Africa, March 1, 2020–September 6, 2021*
| Measure | Before wave 2 start | After wave 2 start, before wave 3 start | After wave 3 start | Overall |
|---|---|---|---|---|
| Total no. (%) specimens,† |
5,543 (23.8) |
7,660 (32.9) |
10,103 (43.3) |
23,306 (100) |
| Originating country, no. (%) | ||||
| Angola | 615 (11.1) | 264 (3.4) | 20 (0.2) | 899 (3.9) |
| Botswana | 83 (1.5) | 216 (2.8) | 799 (7.9) | 1098 (4.7) |
| Eswatini | 11 (0.2) | 77 (1.0) | 34 (0.3) | 122 (0.5) |
| Lesotho | 2 (<0.1) | 16 (0.2) | 0 | 18 (0.1) |
| Malawi | 16 (0.3) | 391 (5.1) | 104 (1.0) | 511 (2.2) |
| Mozambique | 126 (2.3) | 388 (5.1) | 66 (0.7) | 580 (2.5) |
| Namibia | 19 (0.3) | 196 (2.6) | 48 (0.5) | 263 (1.1) |
| South Africa | 4,013 (72.4) | 5,601 (73.1) | 8,850 (87.6) | 18,464 (79.2) |
| Zambia | 426 (7.7) | 182 (2.4) | 84 (0.8) | 692 (3.0) |
| Zimbabwe |
232 (4.2) |
329 (4.3) |
98 (1.0) |
659 (2.8) |
| Submitting country, no. (%) | ||||
| Botswana | 83 (1.5) | 216 (2.8) | 799 (7.9) | 1,098 (4.7) |
| Germany‡ | 1 (<0.1) | 64 (0.8) | 47 (0.5) | 112 (0.5) |
| Malawi | 14 (0.3) | 8 (0.1) | 38 (0.4) | 60 (0.3) |
| South Africa | 4,794 (86.5) | 6,910 (90.2) | 9,135 (90.4) | 20,839 (89.4) |
| Spain‡ | 13 (0.2) | 117 (1.5) | 0 | 130 (0.6) |
| United Kingdom‡ | 210 (3.8) | 189 (2.5) | 0 | 399 (1.7) |
| United States‡ | 0 | 12 (0.2) | 0 | 12 (0.1) |
| Zambia |
426 (7.7) |
144 (1.9) |
84 (0.8) |
654 (2.8) |
| Patient sex, no. (%) | ||||
| F | 2,951 (53.2) | 4,053 (52.9) | 5,695 (56.4) | 12,699 (54.5) |
| M | 2,132 (38.5) | 3,274 (42.7) | 4,044 (40.0) | 9,450 (40.5) |
| Unknown |
460 (8.3) |
333 (4.3) |
364 (3.6) |
1,157 (5.0) |
| Patient age, y, median (IQR) |
37 (27–50) |
37 (25–52) |
39 (27–54) |
38 (26–52) |
| Genomic surveillance coverage,† median (IQR) |
1.55 (0.66–2.79) |
3.76 (2.68–4.56) |
3.98 (3.37–4.58) |
3.48 (2.70–4.44) |
| Detected SARS-CoV-2 variants, no. (%)§ | ||||
| Alpha, B.1.1.7 + Q.x | 33 (0.6) | 158 (2.1) | 168 (1.7) | 359 (1.5) |
| Beta, B.1.351 + B.1.351.x | 749 (13.7) | 6,176 (80.6) | 1,493 (14.8) | 8,418 (36.2) |
| Delta, B.1.617.2 + AY.x | 0 | 129 (1.7) | 7,454 (73.8) | 7,583 (32.6) |
| Gamma, P.1 + P.1.x | 1 (<0.1) | 0 | 1 (<0.1) | 2 (<0.1) |
| Variant of interest | 0 | 1 (<0.1) | 0 | 1 (<0.1) |
| Variant under monitoring | 9 (0.2) | 37 (0.5) | 174 (1.7) | 220 (0.9) |
| Former variant of interest | 2 (<0.1) | 1 (<0.1) | 1 (<0.1) | 4 (<0.1) |
| Lineages with no WHO label | 4,673 (85.3) | 1,155 (15.1) | 812 (8.0) | 6,640 (28.6) |
| January 2020 strain | 14 (0.3) | 3 (<0.1) | 0 | 17 (0.1) |
*Source: GISAID (https://www.gisaid.org), accessed 2021 Sep 20. IQR, interquartile range; World Health Organization. †Genomic surveillance coverage was defined as the number of reported cases per million per sample sequenced. A country with a higher number of reported cases per million per sample sequenced has lower genomic surveillance coverage than a country with a lower number of reported cases per million per sample sequenced. ‡Germany submitted sequences for specimens collected in Mozambique (n = 1), Namibia (n = 73), Zambia (n = 38). Spain submitted sequences for specimens collected in Mozambique (n = 130). UK submitted sequences for specimens collected in Zimbabwe (n = 401). The United States submitted sequences for specimens collected in South Africa (n = 12). §Specimens were classified using labels defined by the World Health Organization (Appendix Table 2).