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Maree G, Els F, Naidoo Y, Naidoo L, Mahamuza P, Macheke M, Ndlovu N, Rachida S, Iwu-Jaja C, Taukobong S, Maposa S, O’Reilly K, Yousif M, McCarthy K. Wastewater surveillance overcomes socio-economic limitations of laboratory-based surveillance when monitoring disease transmission: The South African experience during the COVID-19 pandemic. PLoS One 2025; 20:e0311332. [PMID: 39999204 PMCID: PMC11856519 DOI: 10.1371/journal.pone.0311332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 01/22/2025] [Indexed: 02/27/2025] Open
Abstract
Wastewater and environmental surveillance has been promoted as a communicable disease surveillance tool because it overcomes inherent biases in laboratory-based communicable disease surveillance. Yet, little empirical evidence exists to support this notion, and it remains largely an intuitive, though highly plausible hypothesis. Our interdisciplinary study uses WES data to show evidence for underreporting of SARS-CoV-2 in the context of measurable and statistically significant associations between economic conditions and SARS-CoV-2 incidence and testing rates. We obtained geolocated, anonymised, laboratory-confirmed SARS-CoV-2 cases, wastewater SARS-CoV-2 viral load data and socio-demographic data for Gauteng Province, South Africa. We spatially located all data to create a single dataset for sewershed catchments served by two large wastewater treatment plants. We conducted epidemiological, persons infected and principal component analysis to explore the relationships between variables. Overall, we demonstrate the co-contributory influences of socio-economic indicators on access to SARS-CoV-2 testing and cumulative incidence, thus reflecting that apparent incidence rates mirror access to testing and socioeconomic considerations rather than true disease epidemiology. These analyses demonstrate how WES provides valuable information to contextualise and interpret laboratory-based epidemiological data. Whilst it is useful to have these associations established for SARS-CoV-2, the implications beyond SARS-CoV-2 are legion for two reasons, namely that biases inherent in clinical surveillance are broadly applicable across pathogens and all pathogens infecting humans will find their way into wastewater albeit in varying quantities. WES should be implemented to strengthen surveillance systems, especially where economic inequalities limit interpretability of conventional surveillance data.
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Affiliation(s)
- Gillian Maree
- Gauteng City-Region Observatory (GCRO), a Partnership of the University of Johannesburg, the University of the Witwatersrand, the Gauteng Provincial Government and Organised Local Government in Gauteng (SALGA), Johannesburg, Gauteng, South Africa
| | - Fiona Els
- Gauteng City-Region Observatory (GCRO), a Partnership of the University of Johannesburg, the University of the Witwatersrand, the Gauteng Provincial Government and Organised Local Government in Gauteng (SALGA), Johannesburg, Gauteng, South Africa
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Yashena Naidoo
- Gauteng City-Region Observatory (GCRO), a Partnership of the University of Johannesburg, the University of the Witwatersrand, the Gauteng Provincial Government and Organised Local Government in Gauteng (SALGA), Johannesburg, Gauteng, South Africa
| | - Laven Naidoo
- Gauteng City-Region Observatory (GCRO), a Partnership of the University of Johannesburg, the University of the Witwatersrand, the Gauteng Provincial Government and Organised Local Government in Gauteng (SALGA), Johannesburg, Gauteng, South Africa
| | - Phemelo Mahamuza
- Gauteng City-Region Observatory (GCRO), a Partnership of the University of Johannesburg, the University of the Witwatersrand, the Gauteng Provincial Government and Organised Local Government in Gauteng (SALGA), Johannesburg, Gauteng, South Africa
| | - Mokgaetji Macheke
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Nkosenhle Ndlovu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Said Rachida
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Chinwe Iwu-Jaja
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Setshaba Taukobong
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Sibonginkosi Maposa
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
| | - Kathleen O’Reilly
- Centre for Mathematical Modelling of Infectious Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mukhlid Yousif
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- Department of Virology, School of Pathology, University of Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Kerrigan McCarthy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, Gauteng, South Africa
- School of Public Health, University of Witwatersrand, Johannesburg, Gauteng, South Africa
- Department of Virology, School of Pathology, University of Witwatersrand, Johannesburg, Gauteng, South Africa
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Grassly NC, Shaw AG, Owusu M. Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges. THE LANCET. MICROBE 2025; 6:100939. [PMID: 39222653 DOI: 10.1016/j.lanmic.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 09/04/2024]
Abstract
Wastewater surveillance holds great promise as a sensitive method to detect spillover of zoonotic infections and early pandemic emergence, thereby informing risk mitigation and public health response. Known viruses with pandemic potential are shed in human stool or urine, or both, and the experiences with SARS-CoV-2, monkeypox virus, and Zika virus highlight the feasibility of community-based wastewater surveillance for pandemic viruses that have different transmission routes. We reviewed human shedding and wastewater surveillance data for prototype viruses representing viral families of concern to estimate the likely sensitivity of wastewater surveillance compared with that of clinical surveillance. We examined how data on wastewater surveillance detection, together with viral genetic sequences and animal faecal biomarkers, could be used to identify spillover infections or early human transmission and adaptation. The opportunities and challenges associated with global wastewater surveillance for the prevention of pandemics are described in this Personal View, focusing on low-income and middle-income countries, where the risk of pandemic emergence is the highest. We propose a research and public health agenda to ensure an equitable and sustainable solution to these challenges.
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Affiliation(s)
- Nicholas C Grassly
- Department of Infectious Disease Epidemiology & MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Alexander G Shaw
- Department of Infectious Disease Epidemiology & MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Michael Owusu
- Department of Medical Diagnostics, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Thompson KM, Badizadegan K. Review of Poliovirus Transmission and Economic Modeling to Support Global Polio Eradication: 2020-2024. Pathogens 2024; 13:435. [PMID: 38921733 PMCID: PMC11206708 DOI: 10.3390/pathogens13060435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/27/2024] Open
Abstract
Continued investment in the development and application of mathematical models of poliovirus transmission, economics, and risks leads to their use in support of polio endgame strategy development and risk management policies. This study complements an earlier review covering the period 2000-2019 and discusses the evolution of studies published since 2020 by modeling groups supported by the Global Polio Eradication Initiative (GPEI) partners and others. We systematically review modeling papers published in English in peer-reviewed journals from 2020-2024.25 that focus on poliovirus transmission and health economic analyses. In spite of the long-anticipated end of poliovirus transmission and the GPEI sunset, which would lead to the end of its support for modeling, we find that the number of modeling groups supported by GPEI partners doubled and the rate of their publications increased. Modeling continued to play a role in supporting GPEI and national/regional policies, but changes in polio eradication governance, decentralized management and decision-making, and increased heterogeneity in modeling approaches and findings decreased the overall impact of modeling results. Meanwhile, the failure of the 2016 globally coordinated cessation of type 2 oral poliovirus vaccine use for preventive immunization and the introduction of new poliovirus vaccines and formulation, increased the complexity and uncertainty of poliovirus transmission and economic models and policy recommendations during this time.
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Fang L, Chen M, Zhu S, Zhang W, Yan D, Li X, Huang S, Li C, Guo X, Zeng H, Ke B, Li H, Xu W, Ke C, Deng X, Zhang Y, Zheng H. A comparative study on environmental surveillance of enterovirus: Using a two-phase separation method and a filtration method with a mixed cellulose ester (MCE) membrane. BIOSAFETY AND HEALTH 2023; 5:174-180. [PMID: 40078513 PMCID: PMC11894982 DOI: 10.1016/j.bsheal.2023.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 03/14/2025] Open
Abstract
This study aimed to compare the sensitivity of two-phase separation and the filtration method using a mixed cellulose ester (MCE) membrane to detect enteroviruses in sewage samples. From December 2015 to July 2016, four domestic sewage samples (1 L/sample) were collected monthly from the Guangzhou Liede Sewage Treatment Plant, and each sewage sample was divided into two aliquots (500 mL). The sewage sample was concentrated using the two-phase separation and the filtration method using an MCE membrane, and the treated solutions were inoculated into cells for enterovirus isolation. Polymerase chain reaction amplification, VP1 sequencing, and enterovirus molecular typing were performed on the positive isolates. The detection rates of poliovirus (PV) and non-polio enterovirus (NPEV) obtained using the filtration method using an MCE membrane were higher than those using the two-phase separation method. McNemar's test showed that the detection rates of PV, NPEV, type 1 Sabin-like (SL1), type 2 Sabin-like (SL2), and type 3 Sabin-like (SL3) strain were not statistically significant (P > 0.05). In Guangdong Province, China, the detection rates for PV and NPEV were 53.13% and 62.50% (20/32), respectively. Twenty-seven PVs were isolated, three highly variable strains of the type 1 vaccine, with seven nucleotide substitutions in the VP1 region, compared with the type 1 Sabin strains. Eighty-seven strains of NPEV were isolated and nine serotypes were identified, among which coxsackievirus B3 (CVB3), echovirus 6(E6), and echovirus 11(E11) were the dominant strains. The filtration method using an MCE membrane is more sensitive than two-phase separation and can be used as a robust, sensitive, and cost-effective method to isolate enteroviruses from sewage.
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Affiliation(s)
- Ling Fang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Meizhong Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wei Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaolei Li
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shufen Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Caixia Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Xue Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Hui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, China
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Tushabe P, Bwogi J, Eliku JP, Aine F, Birungi M, Gaizi J, Nakabazzi L, Kabaliisa T, Turyahabwe I, Namuwulya P, Nanteza MB, Bukenya H, Kanyesigye C, Katushabe E, Ampeire I, Kisakye A, Bakamutumaho B, Byabamazima CR. Environmental surveillance detects circulating vaccine-derived poliovirus type 2 that was undetected by acute flaccid paralysis surveillance in 2021 in Uganda. Arch Virol 2023; 168:140. [PMID: 37059887 PMCID: PMC10104764 DOI: 10.1007/s00705-023-05759-w] [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: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The success of the global polio eradication initiative is threatened by the genetic instability of the oral polio vaccine, which can result in the emergence of pathogenic vaccine-derived polioviruses following prolonged replication in the guts of individuals with primary immune deficiencies or in communities with low vaccination coverage. Through environmental surveillance, circulating vaccine-derived poliovirus type 2 was detected in Uganda in the absence of detection by acute flaccid paralysis (AFP) surveillance. This underscores the sensitivity of environmental surveillance and emphasizes its usefulness in supplementing AFP surveillance for poliovirus infections in the race towards global polio eradication.
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Affiliation(s)
- Phionah Tushabe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Josephine Bwogi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - James Peter Eliku
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francis Aine
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Molly Birungi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Gaizi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Lucy Nakabazzi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Theopista Kabaliisa
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Irene Turyahabwe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Prossy Namuwulya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Mary Bridget Nanteza
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Bukenya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Edson Katushabe
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | | | - Annet Kisakye
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | - Barnabas Bakamutumaho
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles R Byabamazima
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
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6
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Gwinji PT, Musuka G, Murewanhema G, Moyo P, Moyo E, Dzinamarira T. The re-emergence of wild poliovirus type 1 in Africa and the role of environmental surveillance in interrupting poliovirus transmission. IJID REGIONS 2022; 5:180-182. [PMID: 36471795 PMCID: PMC9718956 DOI: 10.1016/j.ijregi.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Although there has been a global reduction in wild poliovirus (WPV) type 1 cases, Africa has experienced a re-emergence of the disease. This article discusses the re-emergence of WPV in Africa, the transmission and pathogenesis of WPV, and the role of environmental surveillance and other strategies used to interrupt all WPV transmission in the region permanently.
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Affiliation(s)
- Phanuel Tawanda Gwinji
- Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Godfrey Musuka
- International Initiative for Impact Evaluation, Harare, Zimbabwe
| | - Grant Murewanhema
- Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Perseverance Moyo
- Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Enos Moyo
- Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
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7
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Kilaru P, Hill D, Anderson K, Collins MB, Green H, Kmush BL, Larsen DA. Wastewater Surveillance for Infectious Disease: A Systematic Review. Am J Epidemiol 2022; 192:305-322. [PMID: 36227259 PMCID: PMC9620728 DOI: 10.1093/aje/kwac175] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 02/07/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to be a valuable source of information regarding SARS-CoV-2 transmission and coronavirus disease 2019 (COVID-19) cases. Although the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens that have been surveilled through wastewater. Herein we identify the infectious diseases that have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as were themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and nonpolio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did, the value reported varied by study. Wastewater surveillance should be considered as a potential public health tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.
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Affiliation(s)
- Pruthvi Kilaru
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Des Moines University College of Osteopathic Medicine, Des Moines, Iowa, United States
| | - Dustin Hill
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States
| | - Kathryn Anderson
- Department of Medicine, State University of New York Upstate Medical University, Syracuse, New York, United States
| | - Mary B Collins
- Department of Environmental Studies, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Hyatt Green
- Department of Environmental Biology, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Brittany L Kmush
- Department of Public Health, Syracuse University, Syracuse, New York, United States
| | - David A Larsen
- Correspondence to Dr. Dave Larsen, Department of Public Health, Syracuse University, 430C White Hall, Syracuse, NY 13244 ()
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Brouwer AF, Eisenberg MC, Shulman LM, Famulare M, Koopman JS, Kroiss SJ, Hindiyeh M, Manor Y, Grotto I, Eisenberg JNS. The role of time-varying viral shedding in modelling environmental surveillance for public health: revisiting the 2013 poliovirus outbreak in Israel. J R Soc Interface 2022; 19:20220006. [PMID: 35582812 PMCID: PMC9114981 DOI: 10.1098/rsif.2022.0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/06/2022] [Indexed: 12/17/2022] Open
Abstract
Environmental pathogen surveillance is a sensitive tool that can detect early-stage outbreaks, and it is being used to track poliovirus and other pathogens. However, interpretation of longitudinal environmental surveillance signals is difficult because the relationship between infection incidence and viral load in wastewater depends on time-varying shedding intensity. We developed a mathematical model of time-varying poliovirus shedding intensity consistent with expert opinion across a range of immunization states. Incorporating this shedding model into an infectious disease transmission model, we analysed quantitative, polymerase chain reaction data from seven sites during the 2013 Israeli poliovirus outbreak. Compared to a constant shedding model, our time-varying shedding model estimated a slower peak (four weeks later), with more of the population reached by a vaccination campaign before infection and a lower cumulative incidence. We also estimated the population shed virus for an average of 29 days (95% CI 28-31), longer than expert opinion had suggested for a population that was purported to have received three or more inactivated polio vaccine (IPV) doses. One explanation is that IPV may not substantially affect shedding duration. Using realistic models of time-varying shedding coupled with longitudinal environmental surveillance may improve our understanding of outbreak dynamics of poliovirus, SARS-CoV-2, or other pathogens.
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Affiliation(s)
- Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Lester M. Shulman
- Central Virology Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - James S. Koopman
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Musa Hindiyeh
- Central Virology Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Yossi Manor
- Central Virology Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Itamar Grotto
- Ministry of Health, Jerusalem, Israel
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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9
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Kalkowska DA, Pallansch MA, Cochi SL, Thompson KM. Modeling Poliovirus Surveillance and Immunization Campaign Quality Monitoring Costs for Pakistan and Afghanistan for 2019-2023. Open Forum Infect Dis 2021; 8:ofab264. [PMID: 34295942 DOI: 10.1093/ofid/ofab264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background The Global Polio Eradication Initiative (GPEI) Strategic Plan for 2019-2023 includes commitments to monitor the quality of immunization campaigns using lot quality assurance sampling surveys (LQAS) and to support poliovirus surveillance in Pakistan and Afghanistan. Methods We analyzed LQAS and poliovirus surveillance data between 2016 and 2020, which included both acute flaccid paralysis (AFP) case-based detection and the continued expansion of environmental surveillance (ES). Using updated estimates for unit costs, we explore the costs of different options for future poliovirus monitoring and surveillance for Pakistan and Afghanistan. Results The relative value of the information provided by campaign quality monitoring and surveillance remains uncertain and depends on the design, implementation, and performance of the systems. Prospective immunization campaign quality monitoring (through LQAS) and poliovirus surveillance will require tens of millions of dollars each year for the foreseeable future for Pakistan and Afghanistan. Conclusions LQAS campaign monitoring as currently implemented in Pakistan and Afghanistan provides limited and potentially misleading information about immunization quality. AFP surveillance in Pakistan and Afghanistan provides the most reliable evidence of transmission, whereas ES provides valuable supplementary information about the extent of transmission in the catchment areas represented at the time of sample collection.
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Affiliation(s)
| | - Mark A Pallansch
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Stephen L Cochi
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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10
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Kalkowska DA, Pallansch MA, Cochi SL, Thompson KM. Updated characterization of poliovirus transmission in Pakistan and Afghanistan and the impacts of different outbreak response vaccine options. J Infect Dis 2021; 224:1529-1538. [PMID: 33885734 PMCID: PMC8083227 DOI: 10.1093/infdis/jiab160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Background Pakistan and Afghanistan remain the only reservoirs of wild poliovirus transmission. Prior modeling suggested that before the COVID-19 pandemic, plans to stop the transmission of serotype 1 wild poliovirus (WPV1) and persistent serotype 2 circulating vaccine-derived poliovirus (cVDPV2) did not appear on track to succeed. Methods We updated an existing poliovirus transmission and Sabin-strain oral poliovirus vaccine (OPV) evolution model for Pakistan and Afghanistan to characterize the impacts of immunization disruptions and restrictions on human interactions (i.e., population mixing) due to the COVID-19 pandemic. We also consider different options for responding to outbreaks and for preventive supplementary immunization activities (SIAs). Results The modeling suggests that with some resumption of activities in the fall of 2020 to respond to cVDPV2 outbreaks and full resumption on January 1, 2021 of all polio immunization activities to pre-COVID-19 levels, Pakistan and Afghanistan would remain off-track for stopping all transmission through 2023 without improvements in quality. Conclusions Using trivalent OPV (tOPV) for SIAs instead of serotype 2 monovalent OPV (mOPV2) offers substantial benefits for ending the transmission of both WPV1 and cVDPV2, because tOPV increases population immunity for both serotypes 1 and 2 while requiring fewer SIA rounds, when effectively delivered in transmission areas.
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Affiliation(s)
| | - Mark A Pallansch
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen L Cochi
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kimberly M Thompson
- Kid Risk, Inc., Orlando, FL, USA
- Please address correspondence to: Dr. Kimberly Thompson, Kid Risk, Inc., 7512 Dr. Phillips Blvd. #50-523, Orlando, FL 32819, 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: 1.3] [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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Hamouda M, Mustafa F, Maraqa M, Rizvi T, Aly Hassan A. Wastewater surveillance for SARS-CoV-2: Lessons learnt from recent studies to define future applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143493. [PMID: 33190883 PMCID: PMC7648500 DOI: 10.1016/j.scitotenv.2020.143493] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 05/02/2023]
Abstract
Wastewater-based epidemiology (WBE) is successful in the detection of the spread of SARS-CoV-2. This review examines the methods used and results of recent studies on the quantification of SARS-CoV-2 in wastewater. WBE becomes essential, especially with virus transmission path uncertainty, limitations on the number of clinical tests that could be conducted, and a relatively long period for infected people to show symptoms. Wastewater surveillance was used to show the effect of lockdown on the virus spread. A WBE framework tailored for SARS-CoV-2 that incorporates lessons learnt from the reviewed studies was developed. Results of the review helped outline challenges facing the detection of SARS-CoV-2 in wastewater samples. A comparison between the various studies with regards to sample concentration and virus quantification was conducted. Five different primers sets were used for qPCR quantification; however, due to limited data availability, there is no consensus on the most sensitive primer. Correlating the slope of the relationship between the number of gene copies vs. the cumulative number of infections normalized to the total population served with the average new cases, suggests that qPCR results could help estimating the number of new infections. The correlation is improved when a lag period was introduced to account for asymptomatic infections. Based on lessons learnt from recent studies, it is recommended that future applications should consider the following: 1) ensuring occupational safety in managing sewage collection and processing, 2) evaluating the effectiveness of greywater disinfection, 3) measuring viral RNA decay due to biological and chemical activities during collection and treatment, 4) assessing the effectiveness of digital PCR, and 5) conducting large scale international studies that follow standardized protocols.
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Affiliation(s)
- Mohamed Hamouda
- Civil and Environmental Engineering and the National Water Center, United Arab Emirates University, P.O. Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, Abu Dhabi, United Arab Emirates.
| | - Munjed Maraqa
- Civil and Environmental Engineering and the National Water Center, United Arab Emirates University, P.O. Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
| | - Tahir Rizvi
- Department of Microbiology & Immunology, College of Medicine & Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, Abu Dhabi, United Arab Emirates.
| | - Ashraf Aly Hassan
- Civil and Environmental Engineering and the National Water Center, United Arab Emirates University, P.O. Box 15551, Al Ain, Abu Dhabi, United Arab Emirates; Civil and Environmental Engineering, University of Nebraska Lincoln, 900 N 16th St., Lincoln, NE 68588-0531, USA.
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13
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Investigation Report of cVDPV2 Outbreak in Bokh Woreda of Dollo Zone, Somali Regional State, Ethiopia. Case Rep Infect Dis 2020; 2020:6917313. [PMID: 32908734 PMCID: PMC7471813 DOI: 10.1155/2020/6917313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/27/2020] [Accepted: 08/20/2020] [Indexed: 11/29/2022] Open
Abstract
Background Poliovirus isolates detected in persons or in the environment can fall into three major categories: wild, Sabin and Sabin-like, or vaccine-derived. Detection of wild or vaccine-derived poliovirus may constitute an emergency, which can be categorized as an event that can lead to an outbreak, depending on characteristics of the isolate and the context in which it appears. The aim of the study was investigation report of cVDPV2 outbreak in Bokh woreda of Dollo Zone, Somali regional state, Ethiopia. Methods A team of experts drawn from different organizations was deployed to Bokh woreda to make detailed field investigation from May 25 to June 17, 2019. By using standard World Health Organization polio outbreak investigation checklist, document review of surveillance, immunization, and clinical data related to the case was made. Key informant's interview was made to health professionals, managers, parents of case, woreda and kebele leaders, religious leaders, and HEWs related to acute flaccid paralysis outbreak. Result The notified AFP case was a 39-month-old female from Angalo kebele of Bokh woreda, Dollo Zone. On 19th May 2019, the patient developed high grade fever and was taken to Angalo Health Post on 20th May 2019. As per the examination by a health extension worker, the child had high grade fever and neck stiffness with preliminary diagnosis of meningitis for which ceftriaxone injection was prescribed. Contact sample was taken from three children on 28th May 2019 and 29th May 2019 and was sent to Addis Ababa National Polio Laboratory. All contact stool samples were found to be positive for poliovirus type 2 and referred for sequencing in National Institute of Communicable Diseases (NICD), South Africa, the Regional Polio Reference Laboratory. Conclusion and Recommendation. The clinical presentation of the cases is compatible with poliovirus infection, improving the quality and coverage of supplementary polio immunization activities through proper planning; strict supervision and follow-up can reduce the occurrence of acute flaccid paralysis.
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Thompson KM, Kalkowska DA. Review of poliovirus modeling performed from 2000 to 2019 to support global polio eradication. Expert Rev Vaccines 2020; 19:661-686. [PMID: 32741232 PMCID: PMC7497282 DOI: 10.1080/14760584.2020.1791093] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/22/2020] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Over the last 20 years (2000-2019) the partners of the Global Polio Eradication Initiative (GPEI) invested in the development and application of mathematical models of poliovirus transmission as well as economics, policy, and risk analyses of polio endgame risk management options, including policies related to poliovirus vaccine use during the polio endgame. AREAS COVERED This review provides a historical record of the polio studies published by the three modeling groups that primarily performed the bulk of this work. This review also systematically evaluates the polio transmission and health economic modeling papers published in English in peer-reviewed journals from 2000 to 2019, highlights differences in approaches and methods, shows the geographic coverage of the transmission modeling performed, identified common themes, and discusses instances of similar or conflicting insights or recommendations. EXPERT OPINION Polio modeling performed during the last 20 years substantially impacted polio vaccine choices, immunization policies, and the polio eradication pathway. As the polio endgame continues, national preferences for polio vaccine formulations and immunization strategies will likely continue to change. Future modeling will likely provide important insights about their cost-effectiveness and their relative benefits with respect to controlling polio and potentially achieving and maintaining eradication.
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Jorgensen D, Pons-Salort M, Shaw AG, Grassly NC. The role of genetic sequencing and analysis in the polio eradication programme. Virus Evol 2020; 6:veaa040. [PMID: 32782825 PMCID: PMC7409915 DOI: 10.1093/ve/veaa040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to the Global Polio Eradication Initiative has grown with the increasing incidence of vaccine-derived poliovirus (VDPV) infections in Africa specifically (470 reported cases in 2019), and globally, alongside persistent transmission of serotype 1 wild-type poliovirus in Pakistan and Afghanistan (197 reported cases in 2019). Adapting what has been learned about the virus genetics and evolution to address these threats has been a major focus of recent work. Here, we review how phylogenetic and phylogeographic methods have been used to trace the spread of wild-type polioviruses and identify the likely origins of VDPVs. We highlight the analysis methods and sequencing technology currently used and the potential for new technologies to speed up poliovirus detection and the interpretation of genetic data. At a pivotal point in the eradication campaign with the threat of anti-vaccine sentiment and donor and public fatigue, innovation is critical to maintain drive and overcome the last remaining circulating virus.
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Affiliation(s)
- David Jorgensen
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Margarita Pons-Salort
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Alexander G Shaw
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Nicholas C Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
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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: 19] [Impact Index Per Article: 3.8] [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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Kalkowska DA, Duintjer Tebbens RJ, Thompson KM. Environmental Surveillance System Characteristics and Impacts on Confidence About No Undetected Serotype 1 Wild Poliovirus Circulation. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2019; 39:414-425. [PMID: 30239023 PMCID: PMC7857156 DOI: 10.1111/risa.13193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Surveillance for poliovirus during the polio endgame remains uncertain. Building on prior modeling of the potential for undetected poliovirus transmission for conditions like those in Pakistan and Afghanistan, we use a hypothetical model to explore several key characteristics of the poliovirus environmental surveillance (ES) system (e.g., number and quality of sites, catchment sizes, and sampling frequency) and characterize their impacts on the time required to reach high (i.e., 95%) confidence about no circulation (CNC95%) following the last detected case of serotype 1 wild poliovirus. The nature and quality of the existing and future acute flaccid paralysis (AFP) surveillance and ES system significantly impact the estimated CNC95% for places like Pakistan and Afghanistan. The analysis illustrates the tradeoffs between number of sites, sampling frequency, and catchments sizes, and suggests diminishing returns of increasing these three factors beyond a point that depends on site quality and the location of sites. Limitations in data quality and the hypothetical nature of the model reduce the ability to assess the extent to which actual ES systems offer benefits that exceed their costs. Thus, although poliovirus ES may help to reduce the time required to reach high confidence about the absence of undetected circulation, the effect strongly depends on the ability to establish effective ES sites in high-risk areas. The costs and benefits of ES require further analysis.
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Kroiss SJ, Ahmadzai M, Ahmed J, Alam MM, Chabot-Couture G, Famulare M, Mahamud A, McCarthy KA, Mercer LD, Muhammad S, Safdar RM, Sharif S, Shaukat S, Shukla H, Lyons H. Assessing the sensitivity of the polio environmental surveillance system. PLoS One 2018; 13:e0208336. [PMID: 30592720 PMCID: PMC6310268 DOI: 10.1371/journal.pone.0208336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/15/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The polio environmental surveillance (ES) system has been an incredible tool for advancing polio eradication efforts because of its ability to highlight the spatial and temporal extent of poliovirus circulation. While ES often outperforms, or is more sensitive than AFP surveillance, the sensitivity of the ES system has not been well characterized. Fundamental uncertainty of ES site sensitivity makes it difficult to interpret results from ES, particularly negative results. METHODS AND FINDINGS To study ES sensitivity, we used data from Afghanistan and Pakistan to examine the probability that each ES site detected the Sabin 1, 2, or 3 components of the oral polio vaccine (OPV) as a function of virus prevalence within the same district (estimated from AFP data). Accounting for virus prevalence is essential for estimating site sensitivity because Sabin detection rates should vary with prevalence-high immediately after supplemental immunization activities (SIAs), but low in subsequent months. We found that most ES sites in Pakistan and Afghanistan are highly sensitive for detecting poliovirus relative to AFP surveillance in the same districts. For example, even when Sabin poliovirus is at low prevalence of ~0.5-3% in AFP surveillance, most ES sites have ~34-50% probability of detecting Sabin. However, there was considerable variation in ES site sensitivity and we flagged several sites for re-evaluation based on low sensitivity rankings and low wild polio virus detection rates. In these areas, adding new sites or modifying collection methods in current sites could improve sensitivity of environmental surveillance. CONCLUSIONS Relating ES detections to virus prevalence significantly improved our ability to evaluate site sensitivity compared to evaluations based solely on ES detection rates. To extend our approach to new sites and regions, we provide a preliminary framework for relating ES and AFP detection rates, and descriptions of how detection rates might relate to SIAs and natural seasonality.
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Affiliation(s)
- Steve J. Kroiss
- Institute for Disease Modeling, Bellevue, WA, United States of America
| | - Maiwand Ahmadzai
- National Emergency Operations Centre for Polio Eradication, Kabul, Afghanistan
| | - Jamal Ahmed
- World Health Organization, Geneva, Switzerland
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
- World Health Organization, Islamabad, Pakistan
| | | | - Michael Famulare
- Institute for Disease Modeling, Bellevue, WA, United States of America
| | - Abdirahman Mahamud
- World Health Organization, Islamabad, Pakistan
- National Emergency Operations Centre for Polio Eradication, Islamabad, Pakistan
| | - Kevin A. McCarthy
- Institute for Disease Modeling, Bellevue, WA, United States of America
| | - Laina D. Mercer
- Institute for Disease Modeling, Bellevue, WA, United States of America
| | - Salman Muhammad
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Rana M. Safdar
- National Emergency Operations Centre for Polio Eradication, Islamabad, Pakistan
| | - Salmaan Sharif
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
- World Health Organization, Islamabad, Pakistan
| | - Shahzad Shaukat
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
- World Health Organization, Islamabad, Pakistan
| | - Hemant Shukla
- National Emergency Operations Centre for Polio Eradication, Kabul, Afghanistan
| | - Hil Lyons
- Institute for Disease Modeling, Bellevue, WA, United States of America
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