Viral diversity and abundance in polluted waters in Kampala, Uganda

O’Brien, Evan; Nakyazze, Joyce; Wu, Huiyun; Kiwanuka, Noah; Cunningham, William E.; Kaneene, John B.; Xagoraraki, Irene

doi:10.1016/j.watres.2017.09.063

Cited by 53 publications

(40 citation statements)

References 54 publications

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“…Watershed modeling would therefore become an integral component of the wastewater-based epidemiology methodology for rural locations. In a study performed by Xagoraraki's research group, preliminary investigation into the wastewater epidemiology methodology was conducted [132]. Samples were collected from a wastewater treatment plant and surrounding surface waters in Kampala, Uganda.…”

Section: Sampling In Urban and Rural Locationsmentioning

confidence: 99%

“…The first of these studies, conducted with samples from both Michigan and France, detected a comparatively high number of metagenomic hits for human herpesviruses and also detected human parvovirus and human polyomavirus in wastewater effluents [37]. Their other study, conducted in Uganda, detected human astroviruses, papillomaviruses, as well as a BLAST (Basic Local Alignment Search Tool) hit for Ebola virus [132]. While more research is still required to attain more robust genomic information and comparison databases, metagenomic methods can still be a useful tool for the identification of potential viruses that can then be monitored with qPCR methods.…”

Section: Quantification Of Virusesmentioning

confidence: 99%

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Wastewater-Based Epidemiology for Early Detection of Viral Outbreaks

Xagoraraki

O’Brien

2019

Women in Engineering and Science

Self Cite

157

133

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The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.

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Section: Sampling In Urban and Rural Locationsmentioning

confidence: 99%

Section: Quantification Of Virusesmentioning

confidence: 99%

Wastewater-Based Epidemiology for Early Detection of Viral Outbreaks

Xagoraraki

O’Brien

2019

Women in Engineering and Science

Self Cite

157

133

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“…Up till now, only few studies have been published on viruses of groundwater (Eydal and Jägevall, 2009;Kyle and Eydal, 2008;Pan et al, 2017;Smith et al, 2013) and, to our knowledge, no metagenomic study of viral diversity in this environment has been reported. Moreover, there have only been limited studies of viral diversity and viral roles in polluted waters (Marie and Lin, 2017;O'Brien et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Analysis of viral and bacterial communities in groundwater associated with contaminated land

Costeira

Doherty

Allen

et al. 2019

Science of The Total Environment

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Bacteriophages are considered to be key entities of various environments  Groundwater microbial communities were studied using molecular biology approaches  Phage and bacterial diversities were correlated with contamination and pH  Viruses of degraders were identified and phage-bacterial associations described  A total environmental community approach provides valuable insights towards bioremediation 2

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“…Studies on viral metagenomic have revealed that a lot of the generated sequences are not similar or matching to known viruses, hence the need for viral metagenomic analysis in the virology field [ 171 , 177 ]. Specifically, viral metagenomics has provided the detection of viral species presumed to be a potential threat to human health [ 130 , 178 ], means for virus discovery [ 179 ], and the characterization of the viral population [ 171 , 180 ]. Figure 4 A, B provide an overview of the number of research articles on metagenomic studies on human virome in diverse parts of the world.…”

Section: Conventional Methods For the Identification Of Hev In Envmentioning

confidence: 99%

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

Osunmakinde

Selvarajan

Sibanda

et al. 2018

Viruses

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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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Viral diversity and abundance in polluted waters in Kampala, Uganda

Cited by 53 publications

References 54 publications

Wastewater-Based Epidemiology for Early Detection of Viral Outbreaks

Wastewater-Based Epidemiology for Early Detection of Viral Outbreaks

Analysis of viral and bacterial communities in groundwater associated with contaminated land

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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