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Innovative Medicines & Omics Open source bioinformatics tools in Africa

monitor viral mutations in real-time, revealing the virus’s
adaptive capabilities and the emergence of potentially
more virulent strains. 44,45 Genetic analyses helped map
out transmission routes, enabling authorities to trace
the origins and progression of outbreaks accurately. In
addition, insights from genomic data directly influenced
public health responses, optimizing contact tracing,
isolation, and quarantine protocols. 46
A mutation in the glycoprotein gene GP-A82V emerged
as particularly concerning due to its association with
increased transmissibility. This discovery helped prioritize
containment efforts in high-risk regions and shaped
targeted interventions.
3.2.2. COVID-19 genomic surveillance (South Africa)

South Africa’s robust genomic surveillance, powered by
platforms like Global Initiative on Sharing All Influenza Data
(GISAID) and Nextstrain, has been pivotal in monitoring
Figure 3. A pictorial summary of molecular docking. The figure depicts the evolution and spread of SARS-CoV-2. Sequencing viral
the methodological approach used by scientists to analyze the bonds genomes from local cases enabled the early detection of
involved. variants of concern, such as the Beta variant B.1.351. 47

(BWA) for aligning sequencing reads, the study identified Genomic surveillance has been a game changer,
specific single nucleotide polymorphisms within the particularly with the early detection of the Beta variant.
HBB gene influencing hemoglobin structure and disease This variant, characterized by increased transmissibility
severity. These findings have improved genetic counseling and immune evasion, posed a serious challenge. Its early
services and enabled the development of personalized identification through advanced sequencing technologies
treatment strategies, such as targeted hydroxyurea therapy allowed South African health authorities to take action
and improved blood transfusion protocols in high- quickly. 48
prevalence regions. 41 The discovery of the Beta variant was not just a scientific
achievement; it had real-world consequences. Prompt
3.1.2. Crop improvement (Genomic selection)
identification led to targeted lockdowns and accelerated
The case study included was on drought-resistant maize vaccination campaigns. These data-driven interventions
in Kenya. It was reported that the authors utilized helped mitigate a potentially catastrophic surge. It shows
bioinformatics platforms such as Bioconductor and Galaxy how science directly influences policy and saves lives. 47
to analyze the genomes of drought-tolerant maize strains. Genomic data also paved the way for better vaccine
The study identified key genes, such as ZmDREB2A and strategies. Understanding the Beta variant’s impact on
ZmNAC111, that regulate the plant’s response to water vaccine efficacy guided developers to tweak existing
stress. These genes have been integrated into marker- formulations. Proactive detection and response helped

assisted breeding programs, resulting in the development of safeguard populations by tailoring interventions. Without
maize varieties that thrive in drought-prone environments, this foresight, the situation could have been chaotic. 47
thereby enhancing food security in Kenya’s semi-arid
regions. 42 For example, early detection of the Beta variant led to
rapid development and deployment of vaccines designed
3.2. Infectious disease research to target its structure. This proactive approach reduced the

3.2.1. Ebola virus surveillance (West Africa) variant’s impact on South Africa’s population. It may not
have been perfect, but it was effective and protected lives.
During the devastating 2014 – 2016 Ebola outbreak in
West Africa, tools like Nextstrain played a critical role in 3.3. Phylogenetic analysis in disease tracking
real-time viral surveillance. By sequencing genomes from
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infected individuals, researchers could meticulously track 3.3.1. Phylogenetic tree construction for Ebola
the virus’s evolution and transmission patterns. Real-time In 2014, an Ebola outbreak occurred across West Africa.
evolution tracking using Nextstrain enabled researchers to Gire et al. used Bayesian evolutionary analysis sampling
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Volume 2 Issue 2 (2025) 55 doi: 10.36922/imo.8111