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

Abstract

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.

Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters

“…During the last years, next generation sequencing has increasingly been used to study microbial populations in environmental samples, allowing the detection of several cultured and non-cultured microorganisms (Nooij et al, 2018; Osunmakinde et al, 2018). Nevertheless virus detection in environmental samples is challenging in metagenomics studies due to the high levels of (background) host and microbial DNA, high virus diversity in sewage, and the high rate of, potentially novel, unclassifiable sequences (Bibby and Peccia, 2013; Hjelmsø et al, 2017; Nooij et al, 2018).…”

“…Nevertheless virus detection in environmental samples is challenging in metagenomics studies due to the high levels of (background) host and microbial DNA, high virus diversity in sewage, and the high rate of, potentially novel, unclassifiable sequences (Bibby and Peccia, 2013; Hjelmsø et al, 2017; Nooij et al, 2018). In addition, low concentrations of NoV, the persistence of potential inhibitors that may prevent certain enzymatic reactions and the large diversity of other microorganisms present in the sample complicates the detection of NoV using metagenomic sequencing (Hata et al, 2017; Adriaenssens et al, 2018; Flaviani et al, 2018; Osunmakinde et al, 2018; Strubbia et al, 2019). Therefore, sequencing outcome is dependent on sample preparation, meaning that the relationship between sample concentration and the number of NoV reads may vary according to the method applied to concentrate and purify the nucleic acids (Hjelmsø et al, 2017; Fernandez-Cassi et al, 2018; Oechslin et al, 2018).…”

Profiling Bacterial Diversity and Potential Pathogens in Wastewater Treatment Plants Using High-Throughput Sequencing Analysis

“…Over the years, molecular technologies such as polymerase chain reaction (PCR) [4,25,26,27,28], quantitative real-time PCR (qPCR) [4,28,29,30], microarray [4,31], and other techniques have been widely used to target microbial species in environmental samples [8,30]. All of these molecular techniques have both strengths and weaknesses, but these approaches are always delegated to specifically target the identification of a pre-selected group of microbes or virulence genes [4,25,31,32]. The main limitation of these technologies is that they can only specifically detect certain pathogens, and cannot provide comprehensive insight into the potential pathogens in the environment.…”

Softwares para Gerenciamento Laboratorial: O uso da Tecnologia a Favor da Ciência e da Comunidade

“…O NGS baseado em abordagens metagenômicas são independentes do alvo e fornece identificação imparcial de informações comuns e inesperadas patógenos em uma determinada amostra (ZOU et al, 2017). É uma técnica de sequenciamento genômico que permite sequenciamento paralelo massivo de pequenos fragmentos de todo o material genético obtido de uma comunidade microbiana, que gera saída massiva de dados em apenas uma execução, através do uso de uma instrumentação de alto rendimento (OSUNMAKINDE et al, 2018). É uma abordagem promissora para o diagnóstico de doença infecciosa porque um abrangente espectro de causas potenciais virais, bacterianas, fúngicas e parasitárias pode ser identificada por ensaio único (WILSON et al, 2019).…”

“…Isto é seguido por fragmentação e ligação adequada do adaptador na plataforma desejada para a preparação da biblioteca e sequenciamento. A análise dos fragmentos e dados volumosos gerados a partir das diferentes plataformas de alto rendimento, é feita classificando e montando-as em contigs através de ferramentas de bioinformática, que geralmente é a tarefa mais desafiadora e tediosa ao realizar projetos de metagenômica (OSUNMAKINDE et al, 2018).…”