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Volume 28, Supplement—December 2022
SUPPLEMENT ISSUE
Surveillance

Comparison of COVID-19 Pandemic Waves in 10 Countries in Southern Africa, 2020–2021

Joshua Smith-SreenComments to Author , 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
Author affiliations: Public Health Institute/US Centers for Disease Control and Prevention Global Health Fellowship Program, Lilongwe, Malawi (J. Smith-Sreen, B. Miller); Malawi Centers for Disease Control and Prevention, Lilongwe (A.N. Kabaghe, E. Kim, N. Wadonda-Kabondo, A.F. Auld); Angola Centers for Disease Control and Prevention, Luanda, Angola (A. Frawley, S. Labuda); Angola Ministry of Health, Luanda (E. Manuel, H. Frietas); Public Health Institute of Malawi (PHIM), Lilongwe (A.C. Mwale); Botswana Centers for Disease Control and Prevention, Gaborone, Botswana (T. Segolodi, P. Harvey); Botswana Ministry of Health and Wellness, Gaborone (O. Seitio-Kgokgwe); Mozambique Centers for Disease Control and Prevention, Maputo, Mozambique (A.E. Vergara); Mozambique National Institute for Health, Maputo (A.E. Vergara, E.J. Gudo); Namibia Centers for Disease Control and Prevention, Windhoek, Namibia (E.J. Dziuban); Namibia Ministry of Health and Social Services, Windhoek (N. Shoopala); Zambia; Centers for Disease Control and Prevention, Lusaka, Zambia (J.Z. Hines, S. Agolory); Zambia National Public Health Institute (ZNPHI), Lusaka (M. Kapina, N. Sinyange); Zimbabwe Centers for Disease Control and Prevention, Harare, Zimbabwe (M. Melchior, K. Mirkovic); Zimbabwe Office of the President and Cabinet, Harare (A. Mahomva); US Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S. Modi, S.J. Salyer, C. McLean); Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia (S.J. Salyer, L.P. Riek); Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA (A.S. Azman); Lesotho Centers for Disease Control and Prevention, Maseru, Lesotho (F. Asiimwe); Eswatini Centers for Disease Control and Prevention, Lobamba, Swaziland (M. Adler, S. Mazibuko); Eswatini Ministry of Health, Lobamba (V. Okello); The Global Fund, Geneva, Switzerland (A.F. Auld)

Main Article

Table 4

Country-level genomic surveillance comparison across 3 COVID-19 pandemic waves for 10 countries in southern Africa, March 1, 2020–September 6, 2021*

Country and collection period No. samples† (% total) In-country submissions (% samples) Submitting country 
(% samples) Genomic surveillance coverage,† 
median (IQR) Patient sex 
(% samples) Patient age, y, median (IQR) SARS-CoV-2 variants detected (% samples)
Angola‡
Before wk 2 start 615 (68.4) 0 South Africa (100.0) 0.98 (0.85–1.02) M (55.9); 
F (43.4); 
Unk (0.7) 35.00 (21.25–47.00) Alpha (5.2); Beta (31.1); Gamma (0.2); VUM (1.5); former VOI (0.3); other lineages (61.8)
After wk 2 start 264 (29.4) 0 South Africa (100.0) 2.71 (2.58–3.93) M (61.0); 
F (38.6); 
Unk (0.4) 35.00 (24.00–45.00) Alpha (40.5); Beta (25.4); Delta (4.2); VOI (0.4); VUM (10.6); other lineages (18.9)
After wk 3 start 20 (2.2) 0 South Africa (100.0) 58.02 (58.02–58.63) M (25.0); 
F (75.0) 25.50 (7.75–34.75) Alpha (5.0); Beta (10.0); Delta (85.0)
Overall
 899 (100.0)
 0
 South Africa (100.0)
 1.02 (0.94–2.53)
 M (56.7); 
F (42.7); 
Unk (0.6)
 35.00 (22.00–46.00)
 Alpha (15.6); Beta (28.9); Delta (3.1); Gamma (0.1); VOI (0.1); VUM (4.1); former VOI (0.2); other lineages (47.8)
Botswana
Before wk 2 start 83 (7.6) 83 (100.0) Botswana (100.0) 48.22 (16.00–65.23) F (49.4); 
M (31.3); 
Unk (19.3) 37.00 (25.50–44.00) Beta (15.7); other lineages (84.3)
After wk 2 start, before wk 3 start 216 (19.7) 216 (100.0) Botswana (100.0) 49.83 (37.96–67.59) F (54.2); 
M (45.8) 35.00 (26.00–44.00) Beta (85.6); Delta (1.4); other lineages (12.0); January 2020 strain (0.9)
After wk 3 start 799 (72.8) 799 (100.0) Botswana (100.0) 37.30 (32.09–74.33) F (52.7); 
M (46.9); 
Unk (0.4) 29.00 (15.00–41.00) Beta (19.6); Delta (67.5); VUM (0.1); other lineages (12.8);
Overall
 1,098 (100.0)
 1,098 (100.0)
 Botswana (100.0)
 39.36 (33.02–71.40)
 F (52.7); 
M (45.5); 
Unk (1.7)
 31.00 (17.00–42.00)
 Beta (32.3); Delta (49.4); VUM (0.1); other lineages (18.0); January 2020 strain (0.2)
Eswatini
Before wk 2 start 11 (9.0) 0 South Africa (100.0) 483.33 (471.89–483.33) F (63.6); 
M (36.4) 41.00 (24.50–49.00) Beta (63.6); other lineages (36.4)
After wk 2 start, before wk 3 start 77 (63.1) 0 South Africa (100.0) 211.40 (191.60–211.40) M (51.9); 
F (48.1) 35.00 (25.00–44.00) Beta (24.7); Delta (67.5); VUM (3.9); other lineages (3.9)
After wk 3 start 34 (27.9) 0 South Africa (100.0) 493.27 (489.76–493.27) M (58.8); 
F (41.2) 35.50 (28.50–42.50) Beta (5.9); Delta (82.4); VUM (11.8)
Overall
 33 (100.0)
 0
 South Africa (100.0)
 211.40 (210.67–486.35)
 M (52.5); 
F (47.5)
 35.00 (25.25–44.00)
 Beta (23.0); Delta (65.6); VUM (5.7); other lineages (5.7)
Lesotho
Before wk 2 start 2 (11.1) 0 South Africa (100.0) 482.50 (479.55–485.45) F (50.0); 
M (50.0) 25.00 (18.00–32.00) Other lineages (100.0)
After wk 2 start, before wk 3 start 16 (88.9) 0 South Africa (100.0) 193.79 (92.81–203.15) F (56.2); 
M (43.8) 47.00 (41.50–59.25) Beta (87.5); Other lineages (12.5)
After wk 3 start NA NA NA NA NA NA NA
Overall
 18 (100.0)
 0
 South Africa (100.0)
 203.15 (115.71–203.15)
 F (55.6); 
M (44.4)
 44.50 (39.25–55.75)
 Beta (77.8); other lineages (22.2)
Malawi
Before wk 2 start 16 (3.1) 14 (87.5) Malawi (87.5); 
South Africa (12.5) 17.71 (12.97–18.36) F (12.5); 
Unk (87.5) 30.00 (29.50–30.50) Alpha (6.2); Beta (6.2); other lineages (87.5)
After wk 2 start, before wk 3 start 391 (76.5) 8 (2.0) South Africa (98.0); Malawi (2.0) 2.71 (2.09–4.25) M (60.1);
 F (37.3); 
Unk (2.6) 36.00 (26.00–46.00) Alpha (1.0); Beta (83.6); Delta (6.6); other lineages (8.7)
After wk 3 start 104 (20.4) 38 (36.5) South Africa (63.5); Malawi (36.5) 17.09 (17.02–19.45) Unk (40.4); 
M (37.5); 
F (22.1) 37.00 (28.00–48.00) Beta (4.8); Delta (84.6); c (10.6)
Overall
 511 (100.0)
 60 (11.7)
 South Africa (88.3); Malawi (11.7)
 4.14 (2.26–4.45)
 M (53.6); 
F (33.5); 
Unk (12.9)
 36.00 (26.00–46.75)
 Alpha (1.0); Beta (65.2); Delta (22.3); other lineages (11.5)
Mozambique
Before wk 2 start 126 (21.7) 0 South Africa (88.9); Spain (10.3); 
Germany (0.8) 3.28 (2.41–3.76) M (55.6); 
F (44.4) 35.50 (29.00–46.25) Beta (31.7); other lineages (68.3)
After wk 2 start, before wk 3 start 388 (66.9) 0 South Africa (69.8); Spain (30.2) 3.46 (2.00–5.10) F (52.1); 
M (46.9); 
Unk (1.0) 33.00 (23.00–43.00) Alpha (0.3); Beta (76.0); other lineages (23.7)
After wk 3 start 66 (11.4) 0 South Africa (100.0) 40.63 (39.15–43.29) M (59.1); 
F (40.9) 32.00 (24.00–45.00) Delta (100.0)
Overall
 478 (100.0)
 0
 South Africa (77.4); Spain (22.4); 
Germany (0.2)
 3.55 (2.10–5.13)
 F (51.2); 
M (48.1); 
Unk (0.7)
 34.00 (24.00–43.00)
 Alpha (0.2); Beta (57.8); Delta (11.4); other lineages (30.7)
Namibia
Before wk 2 start 19 (7.2) 0 South Africa (100.0) 263.12 (191.37–263.12) F (57.9); 
M (42.1) 30.00 (25.50–36.00) Other lineages (100.0)
After wk 2 start, before wk 3 start 196 (74.5) 0 South Africa (86.7); Germany (13.3) 76.60 (76.60–76.60) F (60.7); 
M (39.3) 31.00 (18.00–43.00) Alpha (1.5); Beta (55.1); other lineages (43.4)
After wk 3 start 48 (18.3) 0 Germany (97.9); 
South Africa (2.1) 724.01 (724.01–957.56) F (62.5); 
M (37.5) 46.50 (32.00–62.75) Beta (4.2); Delta (93.8); other lineages (2.1)
Overall
 263 (100.0%)
 0
 South Africa (72.2); Germany (27.8)
 76.60 (76.60–153.58)
 F (60.8); 
M (39.2)
 32.00 (19.00–47.00)
 Alpha (1.1); Beta (41.8); Delta (17.1); other lineages (39.9)
South Africa
Before wk 2 start 4,013 (21.7) 4,013 (100.0) South Africa (100.0) 2.15 (0.70–2.83) F (56.6); 
M (33.7); 
Unk (9.7) 37.00 (27.00–51.00) Beta (11.4); other lineages (88.5); January 2020 strain (0.1)
After wk 2 start, before wk 3 start 5,601 (30.3) 5,589 (99.8) South Africa (99.8); USA (0.2) 3.66 (2.71–4.51) F (55.1); 
M (39.6); 
Unk (5.3) 39.00 (26.00–55.00) Alpha (0.7); Beta (84.2); Delta (0.7); VUM (0.1); former VOI (0.0); other lineages (14.3)
After wk 3 start 8,850 (47.9) 8,850 (100.0) South Africa (100.0) 3.85 (3.31–4.33) F (57,6); 
M (39.4); 
Unk (3.0) 41.00 (28.00–55.00) Alpha (1.9); Beta (15.0); Delta (73.4); Gamma (0.0); VUM (1.9); former VOI (0.0); other lineages (7.9)
Overall
 18,464 (100.0)
 18,452 (99.9)
 South Africa (99.9); USA (0.1)
 3.42 (2.84–4.28)
 F (56.6); 
M (38.2); 
Unk (5.1)
 39.00 (27.00–54.00)
 Alpha (1.1); Beta (35.2); Delta (35.4); Gamma (0.0); VUM (0.9); former VOI (0.0); other lineages (27.3)
Zambia
Before wk 2 start 426 (61.6) 426 (100.0) Zimbabwe (100.0) 0.56 (0.23–0.79) F (37.8); 
M (54.0); 
Unk (8.2) 39.00 (31.00–48.00) Other variant (99.1); January 2020 strain (0.9)
After wk 2 start, before wk 3 start 182 (26.3) 144 (79.1) Zimbabwe (79.1); 
Germany (20.9) 14.80 (6.82–19.88) F (40.7); 
M (47.8); 
Unk (11.5) 32.00 (22.00–43.00) Alpha (1.1); Beta (88.5); VUM (0.5); other lineages (9.3); January 2020 strain (0.5)
After wk 3 start 84 (12.1) 84 (100.0) Zimbabwe (100.0) 59.11 (59.11–59.11) F (39.3); 
M (57.1); 
Unk (3.6) 15.50 (14.25–17.00) Delta (97.6); other lineages (2.4)
Overall
 692 (100.0)
 654 (94.5)
 Zimbabwe (94.5); 
Germany (5.5)
 0.89 (0.42–15.49)
 F (38.7); 
M (52.7); 
Unk (8.5)
 35.00 (23.00–46.00)
 Alpha (0.3); Beta (23.3); Delta (11.8); VUM (0.1); other lineages (63.7); January 2020 strain (0.7)
Zimbabwe
Before wk 2 start 232 (35.2) 0 UK (91.4); South Africa (8.6) 0.80 (0.06–3.39) F (57.8); 
M (41.4); 
Unk (0.9) 34.50 (27.00–44.75) Beta (20.4); other lineages (77.0); January 2020 strain (2.6)
After wk 2 start, before wk 3 start 329 (49.9) 0 UK (57.4); South Africa (42.6) 3.76 (2.74–4.89) M (51.1); 
F (48.9) 38.00 (30.00–49.00) Beta (86.3); other lineages (13.7)
After wk 3 start 98 (14.9) 0 South Africa (100.0) 53.33 (45.82–66.19) Unk (55.1); 
F (22.4); 
M (22.4) 36.00 (29.50–46.00) Beta (1.0); Delta (98.0); VUM (1.0)
Overall 659 (100.0) 0 UK (60.8); South Africa (39.2) 3.47 (2.65–5.62) F (48.1); 
M (43.4); 
Unk (8.5) 37.00 (29.00–48.00) Beta (50.5); Delta (14.6); VUM (0.9); other lineages (33.8); January 2020 strain (0.2)

*Source: GISAID (https://www.gisaid.org), accessed September 2021 Sep 20. IQR, interquartile range; NA, not applicable because Lesotho had no sequences submitted after the start of the third wave; VOI, variant of interest; VUM, variants under monitoring; Unk, unknown. †Genomic surveillance coverage is defined as the number of reported cases per sample sequenced. As such, a country with a higher number of reported cases per sample sequenced has lower genomic surveillance coverage than a country with a lower number of reported cases per sample sequences. ‡Angola was currently experiencing their third wave at the time of this analysis (September 19, 2021).

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Page created: July 12, 2022
Page updated: December 11, 2022
Page reviewed: December 11, 2022
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