Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa

Abstract

Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.

Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry

“…Complex techniques are used in the case of viruses to potentiate the coding ability of genomes due to the small size of the genome [146]. Bioinformatics, in collaboration with genomics, has provided a significant amount of information to understand the pathogenetic mechanisms as well as the spread of anti-microbial resistance to the immune responses of host cells in infectious diseases [147]. The size of the genetic sequence of novel severe acute respiratory syndrome 2 (SARS-CoV-2) has been reported to vary from 29.8 to 29.9 kb, with sequence variation as compared to the human coronaviruses, such as SARS and Middle East Respiratory Syndrome (MERS), recognized earlier [148].…”

Immune Responses to the Sexual Stages of Plasmodium falciparum Parasites

“…These methods are relatively fast and high throughput, leading to the identification of a plethora of essential genes or antigens through comparative analyses (139, 141–143). The implications of omics in the fight against infectious disease was recently reviewed by Bah et al (144). But this would be strengthened by the concomitant ability to cultivate the sequenced lines and generate sexual stages from them for phenotypic studies.…”

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

“…Improvement in laboratory protocols to increase yields of otherwise trace amounts of DNA has at the same time led to studies that can total hundreds of ancient individuals ( Olalde et al, 2018 ; Mathieson et al, 2018 ), spanning single ( Bos et al, 2011 ) to thousands of organisms ( Warinner et al, 2014 ). These differences of disciplines have led to a heterogeneous landscape in terms of the types of analyses undertaken, and their computational resource requirements ( Tastan Bishop et al, 2015 ; Bah et al, 2018 ). Taking into consideration the unequal distribution of resources (and infrastructure such as internet connection), easy-to-deploy, streamlined and efficient pipelines can help increase accessibility to high-quality analyses.…”