TY  - JOUR
AU  - Lundberg, Alexander L
AU  - Soetikno, Alan G
AU  - Wu, Scott A
AU  - Ozer, Egon A
AU  - Welch, Sarah B
AU  - Mason, Maryann
AU  - Murphy, Robert L
AU  - Hawkins, Claudia
AU  - Liu, Yingxuan
AU  - Moss, Charles B
AU  - Havey, Robert J
AU  - Achenbach, Chad J
AU  - Post, Lori A
PY  - 2024
DA  - 2024/10/23
TI  - Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in Sub-Saharan Africa: Longitudinal Trend Analysis
JO  - JMIR Public Health Surveill
SP  - e53409
VL  - 10
KW  - SARS-CoV-2
KW  - COVID-19
KW  - sub-Saharan Africa
KW  - pandemic
KW  - surveillance
KW  - public health
KW  - COVID-19 transmission
KW  - speed
KW  - acceleration
KW  - deceleration
KW  - jerk
KW  - dynamic panel
KW  - generalized method of moments
KW  - Arellano-Bond
AB  - Background: This study updates the initial COVID-19 pandemic surveillance in sub-Saharan Africa (SSA) from 2020 by providing 2 additional years of data for the region. Objective: First, we aimed to measure whether there was an expansion or contraction in the pandemic in SSA when the World Health Organization (WHO) declared an end to the public health emergency for the COVID-19 pandemic on May 5, 2023. Second, we used 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 aimed to provide historical context for the course of the pandemic in SSA. Methods: In addition to updates of traditional surveillance data and dynamic panel estimates from the original study by 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 used Pangolin nomenclature for lineage designations of SARS-CoV-2. Finally, we conducted a 1-sided t-test to assess whether regional weekly speed was greater than an outbreak threshold of 10. We ran the test iteratively with a rolling 6-month window 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 (1.11) 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 recently smaller. From November 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling t-test of speed equal to 10 was insignificant for the entire sample period. Conclusions: While COVID-19 continues to circulate in SSA, the region never reached outbreak status, and the weekly transmission rate remained below 1 case per 100,000 population for well over 1 year ahead of the WHO declaration. COVID-19 is endemic in the region and no longer reaches the threshold for its classification as a pandemic. Both standard and enhanced surveillance metrics confirm that the pandemic ended in SSA by the time the WHO made its declaration. 
SN  - 2369-2960
UR  - https://publichealth.jmir.org/2024/1/e53409
UR  - https://doi.org/10.2196/53409
UR  - http://www.ncbi.nlm.nih.gov/pubmed/39013111
DO  - 10.2196/53409
ID  - info:doi/10.2196/53409
ER  -