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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

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 ha...

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Autores principales: Osunmakinde, Cecilia Oluseyi, Selvarajan, Ramganesh, Sibanda, Timothy, Mamba, Bhekie B, Msagati, Titus A.M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115975/
https://www.ncbi.nlm.nih.gov/pubmed/30110939
http://dx.doi.org/10.3390/v10080429
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author Osunmakinde, Cecilia Oluseyi
Selvarajan, Ramganesh
Sibanda, Timothy
Mamba, Bhekie B
Msagati, Titus A.M
author_facet Osunmakinde, Cecilia Oluseyi
Selvarajan, Ramganesh
Sibanda, Timothy
Mamba, Bhekie B
Msagati, Titus A.M
author_sort Osunmakinde, Cecilia Oluseyi
collection PubMed
description 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.
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spelling pubmed-61159752018-08-31 Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes Osunmakinde, Cecilia Oluseyi Selvarajan, Ramganesh Sibanda, Timothy Mamba, Bhekie B Msagati, Titus A.M Viruses Review 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. MDPI 2018-08-14 /pmc/articles/PMC6115975/ /pubmed/30110939 http://dx.doi.org/10.3390/v10080429 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Osunmakinde, Cecilia Oluseyi
Selvarajan, Ramganesh
Sibanda, Timothy
Mamba, Bhekie B
Msagati, Titus A.M
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title_full Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title_fullStr Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title_full_unstemmed Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title_short Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
title_sort overview of trends in the application of metagenomic techniques in the analysis of human enteric viral diversity in africa’s environmental regimes
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115975/
https://www.ncbi.nlm.nih.gov/pubmed/30110939
http://dx.doi.org/10.3390/v10080429
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