JMIR Publications

ABSTRACT

Background:

This study updates the COVID-19 pandemic surveillance in SSA we first conducted in 2020 by providing two additional years of data for the region.

Objective:

First, we aim to measure whether there was an expansion or contraction in the pandemic in SSA when the World Health Organization (WHO) declared the end of the public health emergency for the COVID-19 pandemic on May 5, 2023. Second, we use dynamic and genomic surveillance methods to describe the history of the pandemic in the region and situate the window of the WHO declaration within the broader history. Third, we aim to provide historical context for the course of the pandemic in Sub-Saharan Africa.

Methods:

In addition to updates of traditional surveillance data and dynamic panel estimates from the original study Post et al. (2021), this study used data on sequenced SARS-CoV-2 variants from the Global Initiative on Sharing All Influenza Data (GISAID) to identify the appearance and duration of variants of concern. We used Nextclade nomenclature to collect clade designations from sequences and Pangolin nomenclature for lineage designations of SARS-CoV-2. Finally, we conducted a one-sided t-test for whether regional weekly speed was greater than an outbreak threshold of ten. We ran the test iteratively with six months of data across the sample period.

Results:

Speed for the region remained well below the outbreak threshold before and after the WHO declaration. Acceleration and jerk were also low and stable. The 7-day persistence coefficient remained somewhat large (1.106) and statistically significant. However, both shift parameters for the weeks around the WHO declaration were negative, meaning the clustering effect of new COVID-19 cases had become smaller recently. From November 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling t-test of speed equal to ten was entirely insignificant for the entire sample period.

Conclusions:

While COVID-19 continues to circulate in Sub-Saharan Africa, the region as whole never reached outbreak status, and the transmission rate remained below one case per week per 100K population for well over one year ahead of the WHO declaration. COVID-19 is endemic in the region and no longer reaches the threshold of the pandemic definition. Both standard and enhanced surveillance metrics confirm that the pandemic had ended by the time of the WHO declaration.