Characterizing environmental surveillance sites in Nigeria and their sensitivity to detect poliovirus and other enteroviruses
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Accepted version
Author(s)
Type
Journal Article
Abstract
Background
Environmental surveillance (ES) for poliovirus is increasingly important for polio eradication, often detecting circulating virus before paralytic cases are reported. The sensitivity of ES depends on appropriate selection of sampling sites, which is difficult in low-income countries with informal sewage networks.
Methods
We measured ES site and sample characteristics in Nigeria during June 2018 - May 2019, including sewage physicochemical properties using a water-quality probe, flow volume, catchment population and local facilities such as hospitals, schools and transit hubs. We used mixed-effects logistic regression and machine-learning (random forests) to investigate their association with enterovirus isolation (poliovirus and non-polio enteroviruses) as an indicator of surveillance sensitivity.
Results
Four quarterly visits were made to 78 ES sites in 21 states of Nigeria, and ES site characteristic data matched to 1,345 samples with an average enterovirus prevalence among sites of 68% (range 9% to 100%). A larger estimated catchment population, high total dissolved solids and higher pH were associated with enterovirus detection. A random forests model predicted ‘good’ sites (enterovirus prevalence >70%) from measured site characteristics with out-of-sample sensitivity and specificity of 75%.
Conclusions
Simple measurement of sewage properties and catchment population estimation could improve ES site selection and increase surveillance sensitivity.
Environmental surveillance (ES) for poliovirus is increasingly important for polio eradication, often detecting circulating virus before paralytic cases are reported. The sensitivity of ES depends on appropriate selection of sampling sites, which is difficult in low-income countries with informal sewage networks.
Methods
We measured ES site and sample characteristics in Nigeria during June 2018 - May 2019, including sewage physicochemical properties using a water-quality probe, flow volume, catchment population and local facilities such as hospitals, schools and transit hubs. We used mixed-effects logistic regression and machine-learning (random forests) to investigate their association with enterovirus isolation (poliovirus and non-polio enteroviruses) as an indicator of surveillance sensitivity.
Results
Four quarterly visits were made to 78 ES sites in 21 states of Nigeria, and ES site characteristic data matched to 1,345 samples with an average enterovirus prevalence among sites of 68% (range 9% to 100%). A larger estimated catchment population, high total dissolved solids and higher pH were associated with enterovirus detection. A random forests model predicted ‘good’ sites (enterovirus prevalence >70%) from measured site characteristics with out-of-sample sensitivity and specificity of 75%.
Conclusions
Simple measurement of sewage properties and catchment population estimation could improve ES site selection and increase surveillance sensitivity.
Date Issued
2020-04-09
Date Acceptance
2020-04-06
Citation
The Journal of Infectious Diseases, 2020, 225 (8)
ISSN
0022-1899
Publisher
Oxford University Press (OUP)
Journal / Book Title
The Journal of Infectious Diseases
Volume
225
Issue
8
Copyright Statement
© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Sponsor
Bill & Melinda Gates Foundation
Medical Research Council (MRC)
Identifier
https://academic.oup.com/jid/article/doi/10.1093/infdis/jiaa175/5818305
Grant Number
OPP1171890
MR/R015600/1
Subjects
Science & Technology
Life Sciences & Biomedicine
Immunology
Infectious Diseases
Microbiology
environmental
eradication
poliovirus
sewage
surveillance
ERADICATION
PROGRESS
environmental
eradication
poliovirus
sewage
surveillance
Microbiology
06 Biological Sciences
11 Medical and Health Sciences
Publication Status
Published
Date Publish Online
2020-04-09