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

Abstract

We used publicly available data to describe epidemiology, genomic surveillance, and public health and social measures from the first 3 COVID-19 pandemic waves in southern Africa during April 6, 2020-September 19, 2021. South Africa detected regional waves on average 7.2 weeks before other countries. Average testing volume 244 tests/million/day) increased across waves and was highest in upper-middle-income countries. Across the 3 waves, average reported regional incidence increased (17.4, 51.9, 123.3 cases/1 million population/day), as did positivity of diagnostic tests (8.8%, 12.2%, 14.5%); mortality (0.3, 1.5, 2.7 deaths/1 million populaiton/day); and case-fatality ratios (1.9%, 2.1%, 2.5%). Beta variant (B.1.351) drove the second wave and Delta (B.1.617.2) the third. Stringent implementation of safety measures declined across waves. As of September 19, 2021, completed vaccination coverage remained low (8.1% of total population). Our findings highlight opportunities for strengthening surveillance, health systems, and access to realistically available therapeutics, and scaling up risk-based vaccination.

Keywords: Africa; COVID-19; COVID-19 testing; SARS-CoV-2; comparative studies; coronavirus disease; respiratory infections; severe acute respiratory disease coronavirus 2; southern Africa; viruses.

Figure 1

Reported 7-day average of new COVID-19 cases per 1 million population across 10 countries in southern Africa, March 5, 2020–September 17, 2021. Source: Our World in Data (https://www.ourworldindataorg), accessed 2021 Sep 20.

Figure 2

Reported 7-day average new COVID-19 cases (A) and deaths (B) per 1 million persons across pandemic waves in 10 countries in southern Africa, March 5, 2020–September 19, 2021. Colored lines indicate designated wave periods, dashed lines indicate periods between waves. We used differing y-axis scales in this figure to better visualize the wave patterns in each individual country. See Appendix Figure 2 for the same figure placed on corresponding y-axis scales to compare wave magnitudes across countries. Source: Our World in Data (https://www.ourworldindataorg), accessed 2021 Sep 20.

Figure 4

Counts of SARS-CoV-2 variants (World Health Organization classifications) in 10 countries in southern Africa, March 1, 2020–September 6, 2021. Definitions of variants are in Appendix Table. We used differing y-axis scales used in this figure to better visualize genomic sampling patterns in each individual country. See Appendix Figure 3 for the same figure placed on corresponding y-axis scales to compare wave magnitudes across countries. Source: GISAID (https://www.gisaid.org), accessed 2021 Sep 20.

Figure 3

Percentage of SARS-CoV-2 variants among specimens submitted to GISAID in southern Africa, March 1, 2020–September 6, 2021. Definitions of variants are in Appendix Table 2. Source: GISAID (https://www.gisaid.org), accessed 2021 Sep 20.

Figure 5

Comparison of public health and social measure stringency and 7-day average new COVID-19 cases per million across 3 COVID-19 pandemic waves in 10 countries in southern Africa, April 6, 2020–July 17, 2021. Source: GISAID (https://www.gisaid.org), accessed 2021 Sep 20.