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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

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Nanotechnology and Water Sustainability Research Unit, College of Science, Engineering and Technology, University of South Africa-Science Campus, Florida 1710, South Africa
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Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa-Science Campus, Florida 1710, South Africa
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Author to whom correspondence should be addressed.
Viruses 2018, 10(8), 429; https://doi.org/10.3390/v10080429
Received: 1 July 2018 / Revised: 3 August 2018 / Accepted: 10 August 2018 / Published: 14 August 2018
(This article belongs to the Section Animal Viruses)
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address. View Full-Text
Keywords: metagenomics; enteric viruses; viral diversity; virus identification metagenomics; enteric viruses; viral diversity; virus identification
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Osunmakinde, C.O.; Selvarajan, R.; Sibanda, T.; Mamba, B.B.; Msagati, T.A. Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes. Viruses 2018, 10, 429.

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