Approaching COVID-19 with epidemiological genomic surveillance and the sustainability of biodiversity informatics in Africa

Abstract

COVID-19 is an acute respiratory illness caused by Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2). The first case was reported in Africa on February 14, 2020 and has surged to 11 million as of July 2022, with 43% and 30% of cases in Southern and Northern Africa. Current epidemiological data demonstrate heterogeneity in transmission and patient outcomes in Africa. However, the burden of infectious diseases such as malaria creates a significant burden on public health resources that are dedicated to COVID-19 surveillance, testing, and vaccination access. Several control measures, such as the SHEF2 model, encompassed Africa's most effective preventive measure. With the help of international collaborations and partnerships, Africa's pandemic preparedness employs effective risk-management strategies to monitor patients at home and build the financial capacity and human resources needed to combat COVID-19 transmission. However, the lack of safe sanitation and inaccessible drinking water, coupled with the financial consequences of lockdowns, makes it challenging to prevent the transmission and contraction of COVID-19. The overwhelming burden on contact tracers due to an already strained healthcare system will hurt epidemiological tracing and swift counter-measures. With the rise in variants, African countries must adopt genomic surveillance and prioritize funding for biodiversity informatics.

Keywords: Africa; COVID variants; COVID-19 pandemic; SARS-CoV-2 infection; biodiversity; bioinformatics; genomic surveillance; phylogenetics.

Figure 1

The process and outcomes of epidemiological genome surveillance from a SARS‐CoV‐2 infected patient and large‐scale databases from CDC Africa utilizing biodiversity informatics. (Original imaging created with biorender.com by H. H.). SARS‐CoV‐2, Severe Acute Respiratory Syndrome‐Coronavirus 2.