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Kamga Njile D, Mugyia EA, Endegue-Zanga MC, Kfutwah JA, Djoumetio MD, Onana B, Diop OM, Njouom R, Sadeuh-Mba SA. Detection and genetic diversity of parechoviruses in children with acute flaccid paralysis in Cameroon. PLoS One 2024; 19:e0301771. [PMID: 38809876 PMCID: PMC11135751 DOI: 10.1371/journal.pone.0301771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/21/2024] [Indexed: 05/31/2024] Open
Abstract
Human Parechoviruses (HPeVs) have rarely been considered in the virological investigation of Acute Flacid Paralysis (AFP) cases in Africa, where enteric infections are very common. This study investigated the prevalence and genetic diversity of HPeV in 200 children aged ≤ 15 years with AFP in Cameroon from 2018 to 2019. HPeVs were detected in their faecal RNA using 5'-untranslated real-time RT-PCR. Detected HPeVs were typed by phylogenetic comparison with homologous sequences from homotypic reference strains. Overall, HPeV RNA was detected in 11.0% (22/200) of the 200 stool samples tested. Twelve HPeVs were successfully sequenced and reliably assigned to HPeV-A1, A4, A5, A10, A14, A15, A17 and A18 genotypes. Phylogenetic analyses revealed a high genetic variability among the studied HPeVs, as well as between the studied HPeVs and their previously reported counterparts from Cameroon in 2014. These findings suggest that different HPeV genotypes co-circulate in Cameroon without documented epidemics.
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Affiliation(s)
- Daniel Kamga Njile
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Faculty of Sciences, Department of Microbiology, University of Yaoundé 1, Yaounde, Cameroon
| | - Emmanuel Akongnwi Mugyia
- Faculty of Science, Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | | | | | | | - Boyomo Onana
- Faculty of Sciences, Department of Microbiology, University of Yaoundé 1, Yaounde, Cameroon
| | - Ousmane Madiagne Diop
- Global Polio Eradication Initiative (GPEI), World Health Organization, Geneva, Switzerland
| | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
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Armas F, Chandra F, Lee WL, Gu X, Chen H, Xiao A, Leifels M, Wuertz S, Alm EJ, Thompson J. Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era. ENVIRONMENT INTERNATIONAL 2023; 171:107718. [PMID: 36584425 PMCID: PMC9783150 DOI: 10.1016/j.envint.2022.107718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of a population's infections. In the past two years, WBS has proven to be crucial for managing the pandemic across different geographical regions. However, the changing context of the pandemic due to high levels of COVID-19 vaccination warrants a closer examination of its implication towards SARS-CoV-2 WBS. Two main questions were raised: 1) Does vaccination cause shedding of viral signatures without infection? 2) Does vaccination affect the relationship between wastewater and clinical data? To answer, we review historical reports of shedding from viral vaccines in use prior to the COVID-19 pandemic including for polio, rotavirus, influenza and measles infection and provide a perspective on the implications of different COVID-19 vaccination strategies with regard to the potential shedding of viral signatures into the sewershed. Additionally, we reviewed studies that looked into the relationship between wastewater and clinical data and how vaccination campaigns could have affected the relationship. Finally, analyzing wastewater and clinical data from the Netherlands, we observed changes in the relationship concomitant with increasing vaccination coverage and switches in dominant variants of concern. First, that no vaccine-derived shedding is expected from the current commercial pipeline of COVID-19 vaccines that may confound interpretation of WBS data. Secondly, that breakthrough infections from vaccinated individuals contribute significantly to wastewater signals and must be interpreted in light of the changing dynamics of shedding from new variants of concern.
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Affiliation(s)
- Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
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Liu P, Ibaraki M, VanTassell J, Geith K, Cavallo M, Kann R, Guo L, Moe CL. A sensitive, simple, and low-cost method for COVID-19 wastewater surveillance at an institutional level. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151047. [PMID: 34673061 PMCID: PMC8522675 DOI: 10.1016/j.scitotenv.2021.151047] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/16/2021] [Accepted: 10/13/2021] [Indexed: 05/08/2023]
Abstract
SARS-CoV-2 is a respiratory virus, but it is also detected in a significant proportion of fecal samples from COVID-19 cases. Recent studies have shown that wastewater surveillance can be a low-cost tool compared to massive diagnostic testing for tracking COVID-19 outbreaks in communities, but most studies have focused on sampling from wastewater treatment plants. Institutional level wastewater surveillance may serve well for early warning purposes because specific geographic areas/populations with emerging cases can be tracked and immediate action can be executed in the event of a positive wastewater signal. In this study, a novel Moore swab method was developed and used for wastewater surveillance of COVID-19 at an institutional level. Of the 442 swab samples tested, 148 (33.5%) swabs collected from the three campuses and two buildings were positive for SARS-CoV-2 RNA. Further study of the quarantine building with a known number of cases indicated that this method was sensitive enough to detect few cases in the building. In addition, comparison between grab samples and Moore swab samples from the hospital sewage line indicated that Moore swabs were more sensitive than grab samples and offer a simple, inexpensive method for obtaining a composite sample of virus in wastewater over a 24-48 h period. These results suggest that collection and analyses of Moore swabs for SARS-CoV-2 RNA detection is a sensitive, low-cost, and easy to use tool for COVID-19 surveillance that is useful for institutional settings and could be deployed in low-resource settings to identify emerging COVID-19 clusters in communities.
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Affiliation(s)
- Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
| | - Makoto Ibaraki
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Jamie VanTassell
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kelly Geith
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Matthew Cavallo
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Rebecca Kann
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Lizheng Guo
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
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Alleman MM, Coulliette-Salmond AD, Wilnique P, Belgasmi-Wright H, Sayyad L, Wong K, Gue E, Barrais R, Rey-Benito G, Burns CC, Vega E. Environmental Surveillance for Polioviruses in Haïti (2017-2019): The Dynamic Process for the Establishment and Monitoring of Sampling Sites. Viruses 2021; 13:v13030505. [PMID: 33803868 PMCID: PMC8003210 DOI: 10.3390/v13030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Haïti is at risk for wild poliovirus (WPV) importation and circulation, as well as vaccine-derived poliovirus (VDPV) emergence. Environmental surveillance (ES) for polioviruses was established in Port au Prince and Gonaïves in 2016. During 2017–2019, initial ES sites were re-evaluated, and ES was expanded into Cap Haïtien and Saint Marc. Wastewater samples and data on weather, hour of collection, and sample temperature and pH were collected every 4 weeks during March 2017–December 2019 (272 sampling events) from 21 sites in Cap Haïtien, Gonaïves, Port au Prince, and Saint Marc. Samples were processed for the detection of polio and non-polio enteroviruses using the two-phase and “Concentration and Filter Elution” methodologies. Polioviruses were serotyped and underwent intra-typic characterization. No WPV or VDPVs were isolated. Sabin-like polioviruses (oral vaccine strain) of serotypes 1 and 3 were sporadically detected. Five of six (83%), one of six (17%), five of six (83%), and two of three (67%) sites evaluated in Cap Haïtien, Gonaïves, Port au Prince, and Saint Marc, respectively, had enterovirus isolation from >50% of sampling events; these results and considerations, such as watershed population size and overlap, influence of sea water, and excessive particulates in samples, were factors in site retention or termination. The evaluation of 21 ES sampling sites in four Haïtian cities led to the termination of 11 sites. Every-four-weekly sampling continues at the remaining 10 sites across the four cities as a core Global Polio Eradication Initiative activity.
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Affiliation(s)
- Mary M. Alleman
- Polio Eradication Branch, Centers for Disease Control and Prevention, Global Immunization Division, Atlanta, GA 30329, USA
- Correspondence: ; Tel.: +1-404-639-8703
| | - Angela D. Coulliette-Salmond
- Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA 30329, USA; (A.D.C.-S.); (C.C.B.); (E.V.)
- United States Public Health Service, Rockville, MD 20852, USA
| | - Pierre Wilnique
- Laboratory and Research, Division of Epidemiology, Ministère de la Santé Publique et de la Population (Ministry of Public Health and Population (MSPP)), Port au Prince HT6110, Haiti; (P.W.); (R.B.)
| | | | | | - Kimberly Wong
- IHRC, Inc., Atlanta, GA 30346, USA; (H.B.-W.); (K.W.)
- Cherokee Nation Assurance, Catoosa, OK 74015, USA;
| | - Edmund Gue
- Pan American Health Organization, World Health Organization, Region of the Americas, Port au Prince HT6110, Haiti;
| | - Robert Barrais
- Laboratory and Research, Division of Epidemiology, Ministère de la Santé Publique et de la Population (Ministry of Public Health and Population (MSPP)), Port au Prince HT6110, Haiti; (P.W.); (R.B.)
| | - Gloria Rey-Benito
- Pan American Health Organization, World Health Organization, Washington, DC 20037, USA;
| | - Cara C. Burns
- Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA 30329, USA; (A.D.C.-S.); (C.C.B.); (E.V.)
| | - Everardo Vega
- Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA 30329, USA; (A.D.C.-S.); (C.C.B.); (E.V.)
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Hamisu AW, Blake IM, Sume G, Braka F, Jimoh A, Dahiru H, Bonos M, Dankoli R, Mamuda Bello A, Yusuf KM, Lawal NM, Ahmed F, Aliyu Z, John D, Nwachukwu TE, Ayeni MF, Gumede-Moeletsi N, Veltsos P, Giri S, Praharaj I, Metilda A, Bandyopadhyay A, Diop OM, Grassly NC. Characterizing Environmental Surveillance Sites in Nigeria and Their Sensitivity to Detect Poliovirus and Other Enteroviruses. J Infect Dis 2020; 225:1377-1386. [PMID: 32415775 PMCID: PMC9016446 DOI: 10.1093/infdis/jiaa175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/08/2020] [Indexed: 01/02/2023] Open
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 nonpolio 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 were matched to 1345 samples with an average enterovirus prevalence among sites of 68% (range, 9%-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.
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Affiliation(s)
| | - Isobel M Blake
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Gerald Sume
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Fiona Braka
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Abdullateef Jimoh
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Habu Dahiru
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Mohammed Bonos
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Raymond Dankoli
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Ahmed Mamuda Bello
- World Health Organization Nigeria, Abuja, Federal Capital Territory (FCT), Nigeria
| | - Kabir M Yusuf
- National Primary Health Care Development Agency, Garki, Abuja, FCT, Nigeria
| | - Namadi M Lawal
- National Primary Health Care Development Agency, Garki, Abuja, FCT, Nigeria
| | - Fatimah Ahmed
- Public Health Development, Garki, Abuja, FCT, Nigeria
| | - Zainab Aliyu
- National Primary Health Care Development Agency, Garki, Abuja, FCT, Nigeria
| | - Doris John
- Public Health Development, Garki, Abuja, FCT, Nigeria
| | | | | | - Nicksy Gumede-Moeletsi
- World Health Organization Regional Office for Africa, Cité du Djoué, Brazzaville, Republic of Congo
| | | | - Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ira Praharaj
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Angeline Metilda
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Ousmane M Diop
- World Health Organization Headquarters, Geneva, Switzerland
| | - Nicholas C Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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