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John TJ, Dharmapalan D, Hirschhorn N. Intestinal mucosal immunity is unimportant for polio eradication: the failure of oral polio vaccination. Infect Dis (Lond) 2024; 56:669-677. [PMID: 38889538 DOI: 10.1080/23744235.2024.2367742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
AIMS To explore if intestinal immunity induced by infection with live viruses in the oral poliovirus vaccine (OPV) is essential, necessary or even helpful in interrupting transmission of wild poliovirus (WPV) for global polio eradication. METHODS We reviewed the biology of virus-host interactions in WPV infection and its alterations by OPV-induced immunity for direct evidence of the usefulness of intestinal immunity. We also explored indirect evidence by way of the effect of the inactivated poliovirus vaccine (IPV) on the biology and on transmission dynamics of WPV. RESULTS Immunity, systemic and intestinal, induced by infection with WPV or vaccine viruses, does not prevent re-infection with WPV or vaccine viruses respectively, when exposed. Such re-infected hosts shed virus in the throat and in faeces and are sources of further transmission. Immunity protects against polio paralysis-hence reinfection always remain asymptommatic and silent. CONCLUSION Vaccine virus-induced intestinal immunity is not necessary for polio eradication. The continued and intensive vaccination efforts using OPV under the assumption of its superiority over IPV have resulted in the well-known undesirable effects, namely vaccine associated paralytic polio and the emergence of de-attenuated circulating vaccine-derived polioviruses, in addition to the delay in completing global WPV eradication.
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Affiliation(s)
- T Jacob John
- Christian Medical College, Vellore, Tamil Nadu, India
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2
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Abeles SR, Kline A, Lee P. Climate change and resilience for antimicrobial stewardship and infection prevention. Curr Opin Infect Dis 2024; 37:270-276. [PMID: 38843434 DOI: 10.1097/qco.0000000000001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW This review covers recent research regarding the challenges posed by climate change within the areas of antimicrobial stewardship and infection prevention, and ways to build resiliency in these fields. RECENT FINDINGS Infectious disease patterns are changing as microbes adapt to climate change and changing environmental factors. Capacity for testing and treating infectious diseases is challenged by newly emerging diseases, which exacerbate challenges to antimicrobial stewardship and infection prevention.Antimicrobial resistance is accelerated due to environmental factors including air pollution, plastic pollution, and chemicals used in food systems, which are all impacted by climate change.Climate change places infection prevention practices at risk in many ways including from major weather events, increased risk of epidemics, and societal disruptions causing conditions that can overwhelm health systems. Researchers are building resilience by advancing rapid diagnostics and disease modeling, and identifying highly reliable versus low efficiency interventions. SUMMARY Climate change and associated major weather and socioeconomic events will place significant strain on healthcare facilities. Work being done to advance rapid diagnostics, build supply chain resilience, improve predictive disease modeling and surveillance, and identify high reliability versus low yield interventions will help build resiliency in antimicrobial stewardship and infection prevention for escalating challenges due to climate change.
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Affiliation(s)
- Shira R Abeles
- Division of Infectious Diseases and Global Public Health, Department of Medicine
| | - Ahnika Kline
- Associate Director, Clinical Microbiology Laboratory, Department of Pathology, University of California, San Diego
| | - Pamela Lee
- Division of Infectious Diseases, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
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3
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Nacov JA, Stemler J, Salmanton-García J, Cremer LM, Zeitlinger M, Mallon PWG, Pana ZD, Schmitt HJ, Cornely OA. Challenges in assessing the immunization status of adults in Germany-lessons from a population-based VACCELERATE survey on polio vaccination. Infection 2024; 52:1563-1574. [PMID: 38806974 PMCID: PMC11289296 DOI: 10.1007/s15010-024-02296-9] [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: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
Abstract
PURPOSE Considering the re-emergence of poliomyelitis (PM) in non-endemic regions, it becomes apparent that vaccine preventable diseases can rapidly develop epi- or even pandemic potential. Evaluation of the current vaccination status is required to inform patients, health care providers and policy makers about vaccination gaps. METHODS Between October 28 2022 and November 23 2022, 5,989 adults from the VACCELEREATE Volunteer Registry completed an electronic case report form on their previous PM vaccine doses including number, types/-valencies and the time of administration based on their vaccination records. A uni-/multivariable regression analysis was performed to assess associations in participant characteristics and immunization status. RESULTS Among German volunteers (n = 5,449), complete PM immunization schedule was found in 1,981 (36%) participants. Uncertain immunization, due to unknown previous PM vaccination (n = 313, 6%), number of doses (n = 497, 9%), types/-valencies (n = 1,233, 23%) or incoherent immunization schedule (n = 149, 3%) was found in 40% (n = 2,192). Out of 1,276 (23%) participants who reported an incomplete immunization schedule, 62 (1%) never received any PM vaccine. A total of 5,074 (93%) volunteers reported having been vaccinated at least once and 2,087 (38%) indicated that they received vaccination within the last ten years. Female sex, younger age, as well as availability of first vaccination record were characteristics significantly associated with complete immunization (p < 0.001). CONCLUSION Full PM immunization schedule was low and status frequently classified as uncertain due to lack of details on administered doses. There is an obviousneed for improved recording to enable long-term access to detailed vaccination history in the absence of a centralized immunization register.
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Affiliation(s)
- Julia A Nacov
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jannik Stemler
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jon Salmanton-García
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Louise M Cremer
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Patrick W G Mallon
- School of Medicine, University College Dublin, Centre for Experimental Pathogen Host Research, Dublin, Ireland
| | | | - Heinz-Josef Schmitt
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Oliver A Cornely
- Faculty of Medicine, Institute of Translational Research, University of CologneUniversity Hospital CologneCologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), Herderstr. 52-54, 50931, Cologne, Germany.
- Faculty of Medicine, Department I of Internal Medicine, Excellence Center for Medical Mycology (ECMM), University of Cologne, and University Hospital Cologne, Cologne, Germany.
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.
- Faculty of Medicine, University of Cologne, University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Köln), Cologne, Germany.
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4
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Walker DI, Witt J, Rostant W, Burton R, Davison V, Ditchburn J, Evens N, Godwin R, Heywood J, Lowther JA, Peters N, Porter J, Posen P, Wickens T, Wade MJ. Piloting wastewater-based surveillance of norovirus in England. WATER RESEARCH 2024; 263:122152. [PMID: 39096810 DOI: 10.1016/j.watres.2024.122152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/07/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024]
Abstract
Wastewater-based epidemiology (WBE) gained widespread use as a tool for supporting clinical disease surveillance during the COVID-19 pandemic. There is now significant interest in the continued development of WBE for other pathogens of clinical significance. In this study, approximately 3,200 samples of wastewater from across England, previously collected for quantification of SARS-CoV-2, were re-analysed for the quantification of norovirus genogroup I (GI) and II (GII). Overall, GI and GII were detected in 93% and 98% of samples respectively, and at least one of the genogroups was detected in 99% of samples. GI was found at significantly lower concentrations than GII, but the proportion of each genogroup varied over time, with GI becoming more prevalent than GII in some areas towards the end of the study period (May 2021 - March 2022). Using relative strength indices (RSI), it was possible to study the trends of each genogroup, and total norovirus over time. Increases in norovirus levels appeared to coincide with the removal of COVID-19 related lockdown restrictions within England. Local Moran's I analyses indicated several localised outbreaks of both GI and GII across England, notably the possible GI outbreak in the north of England in early 2022. Comparisons of national average norovirus concentrations in wastewater against concomitant norovirus reported case numbers showed a significant linear relationship. This highlights the potential for wastewater-based monitoring of norovirus as a valuable approach to support surveillance of norovirus in communities.
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Affiliation(s)
- David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK.
| | - Jessica Witt
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Wayne Rostant
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Robert Burton
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Vicki Davison
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jackie Ditchburn
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Nicholas Evens
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Reg Godwin
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jane Heywood
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Nancy Peters
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jonathan Porter
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Paulette Posen
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Tyler Wickens
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Matthew J Wade
- Data Analytics & Surveillance Group, UK Health Security Agency, 10 South Colonnade, London, UK
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Bleotu C, Matei L, Dragu LD, Necula LG, Pitica IM, Chivu-Economescu M, Diaconu CC. Viruses in Wastewater-A Concern for Public Health and the Environment. Microorganisms 2024; 12:1430. [PMID: 39065197 PMCID: PMC11278728 DOI: 10.3390/microorganisms12071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/26/2024] Open
Abstract
Wastewater monitoring provides essential information about water quality and the degree of contamination. Monitoring these waters helps identify and manage risks to public health, prevent the spread of disease, and protect the environment. Standardizing the appropriate and most accurate methods for the isolation and identification of viruses in wastewater is necessary. This review aims to present the major classes of viruses in wastewater, as well as the methods of concentration, isolation, and identification of viruses in wastewater to assess public health risks and implement corrective measures to prevent and control viral infections. Last but not least, we propose to evaluate the current strategies in wastewater treatment as well as new alternative methods of water disinfection.
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Affiliation(s)
- Coralia Bleotu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
- Research Institute of the University of Bucharest (ICUB), University of Bucharest, 060023 Bucharest, Romania
- The Academy of Romanian Scientist, 050711 Bucharest, Romania
| | - Lilia Matei
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Laura Denisa Dragu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Laura Georgiana Necula
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Ioana Madalina Pitica
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Mihaela Chivu-Economescu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
| | - Carmen Cristina Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (C.B.); (L.M.); (L.D.D.); (L.G.N.); (I.M.P.); (C.C.D.)
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6
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Alathari S, Joseph A, Bolaños LM, Studholme DJ, Jeffries AR, Appenteng P, Duodu KA, Sawyerr EB, Paley R, Tyler CR, Temperton B. In field use of water samples for genomic surveillance of infectious spleen and kidney necrosis virus (ISKNV) infecting tilapia fish in Lake Volta, Ghana. PeerJ 2024; 12:e17605. [PMID: 39011377 PMCID: PMC11248997 DOI: 10.7717/peerj.17605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/30/2024] [Indexed: 07/17/2024] Open
Abstract
Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapid in situ monitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission. Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the "lab in a suitcase" approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities.
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Affiliation(s)
- Shayma Alathari
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Andrew Joseph
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Luis M Bolaños
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - David J Studholme
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Aaron R Jeffries
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Patrick Appenteng
- Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Accra, Ghana
| | - Kwaku A Duodu
- Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Accra, Ghana
| | - Eric B Sawyerr
- Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Accra, Ghana
| | - Richard Paley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Charles R Tyler
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- University of Exeter, Sustainable Aquaculture Futures Centre, Exeter, United Kingdom
| | - Ben Temperton
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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Singh R, Ryu J, Hyoung Lee W, Kang JH, Park S, Kim K. Wastewater-borne viruses and bacteria, surveillance and biosensors at the interface of academia and field deployment. Crit Rev Biotechnol 2024:1-21. [PMID: 38973015 DOI: 10.1080/07388551.2024.2354709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/28/2024] [Indexed: 07/09/2024]
Abstract
Wastewater is a complex, but an ideal, matrix for disease monitoring and surveillance as it represents the entire load of enteric pathogens from a local catchment area. It captures both clinical and community disease burdens. Global interest in wastewater surveillance has been growing rapidly for infectious diseases monitoring and for providing an early warning of potential outbreaks. Although molecular detection methods show high sensitivity and specificity in pathogen monitoring from wastewater, they are strongly limited by challenges, including expensive laboratory settings and prolonged sample processing and analysis. Alternatively, biosensors exhibit a wide range of practical utility in real-time monitoring of biological and chemical markers. However, field deployment of biosensors is primarily challenged by prolonged sample processing and pathogen concentration steps due to complex wastewater matrices. This review summarizes the role of wastewater surveillance and provides an overview of infectious viral and bacterial pathogens with cutting-edge technologies for their detection. It emphasizes the practical utility of biosensors in pathogen monitoring and the major bottlenecks for wastewater surveillance of pathogens, and overcoming approaches to field deployment of biosensors for real-time pathogen detection. Furthermore, the promising potential of novel machine learning algorithms to resolve uncertainties in wastewater data is discussed.
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Affiliation(s)
- Rajendra Singh
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
| | - Jaewon Ryu
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
| | - Woo Hyoung Lee
- Department of Civil, Environmental, and Construction Engineering, University of Central FL, Orlando, FL, USA
| | - Joo-Hyon Kang
- Department of Civil and Environmental Engineering, Dongguk University-Seoul, Seoul, South Korea
| | - Sanghwa Park
- Bacteria Research Team, Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju-si, South Korea
| | - Keugtae Kim
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
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8
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Cottrell S, Moore C. Emerging and Re-Emerging Enterovirus Infections: The Known Unknowns. Pediatr Infect Dis J 2024:00006454-990000000-00941. [PMID: 38986004 DOI: 10.1097/inf.0000000000004472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Affiliation(s)
- Simon Cottrell
- From the Communicable Disease Surveillance Centre and Vaccine Preventable Disease Programme, Public Health Wales, Cardiff, United Kingdom
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, United Kingdom
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Toro L, de Valk H, Zanetti L, Huot C, Tarantola A, Fournet N, Moulin L, Atoui A, Gassilloud B, Mouly D, Jourdain F. Pathogen prioritisation for wastewater surveillance ahead of the Paris 2024 Olympic and Paralympic Games, France. Euro Surveill 2024; 29. [PMID: 38994605 PMCID: PMC11241851 DOI: 10.2807/1560-7917.es.2024.29.28.2400231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
BackgroundWastewater surveillance is an effective approach to monitor population health, as exemplified by its role throughout the COVID-19 pandemic.AimThis study explores the possibility of extending wastewater surveillance to the Paris 2024 Olympic and Paralympic Games, focusing on identifying priority pathogen targets that are relevant and feasible to monitor in wastewater for these events.MethodsA list of 60 pathogens of interest for general public health surveillance for the Games was compiled. Each pathogen was evaluated against three inclusion criteria: (A) analytical feasibility; (B) relevance, i.e. with regards to the specificities of the event and the characteristics of the pathogen; and (C) added value to inform public health decision-making. Analytical feasibility was assessed through evidence from peer-reviewed publications demonstrating the detectability of pathogens in sewage, refining the initial list to 25 pathogens. Criteria B and C were evaluated via expert opinion using the Delphi method. The panel consisting of some 30 experts proposed five additional pathogens meeting criterion A, totalling 30 pathogens assessed throughout the three-round iterative questionnaire. Pathogens failing to reach 70% group consensus threshold underwent further deliberation by a subgroup of experts.ResultsSix priority targets suitable for wastewater surveillance during the Games were successfully identified: poliovirus, influenza A virus, influenza B virus, mpox virus, SARS-CoV-2 and measles virus.ConclusionThis study introduced a model framework for identifying context-specific wastewater surveillance targets for a mass gathering. Successful implementation of a wastewater surveillance plan for Paris 2024 could incentivise similar monitoring efforts for other mass gatherings globally.
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Affiliation(s)
- Laila Toro
- Santé publique France (French National Public Health Agency), Montpellier, France
| | - Henriette de Valk
- Santé publique France (French National Public Health Agency), Saint-Maurice, France
| | - Laura Zanetti
- Santé publique France (French National Public Health Agency), Saint-Maurice, France
| | - Caroline Huot
- Institut national de santé publique du Québec, Québec, Canada
| | - Arnaud Tarantola
- Santé publique France (French National Public Health Agency), Saint-Denis, France
| | - Nelly Fournet
- Santé publique France (French National Public Health Agency), Saint-Denis, France
| | | | - Ali Atoui
- ANSES Nancy Laboratory for Hydrology, Nancy, France
| | | | - Damien Mouly
- Santé publique France (French National Public Health Agency), Toulouse, France
| | - Frédéric Jourdain
- Santé publique France (French National Public Health Agency), Montpellier, France
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10
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Mullish BH, Merrick B, Quraishi MN, Bak A, Green CA, Moore DJ, Porter RJ, Elumogo NT, Segal JP, Sharma N, Marsh B, Kontkowski G, Manzoor SE, Hart AL, Settle C, Keller JJ, Hawkey P, Iqbal TH, Goldenberg SD, Williams HRT. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut 2024; 73:1052-1075. [PMID: 38609165 DOI: 10.1136/gutjnl-2023-331550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/03/2024] [Indexed: 04/14/2024]
Abstract
The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.
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Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - Mohammed Nabil Quraishi
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Aggie Bak
- Healthcare Infection Society, London, UK
| | - Christopher A Green
- Department of Infectious Diseases & Tropical Medicine, University Hospitals NHS Foundation Trust, Birmingham Heartlands Hospital, Birmingham, UK
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
| | - David J Moore
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Robert J Porter
- Department of Microbiology, Royal Devon and Exeter Hospitals, Barrack Road, UK
| | - Ngozi T Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Jonathan P Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Naveen Sharma
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Belinda Marsh
- Lay representative for FMT Working Party, Healthcare Infection Society, London, UK
| | - Graziella Kontkowski
- Lay representative for FMT Working Party, Healthcare Infection Society, London, UK
- C.diff support, London, UK
| | - Susan E Manzoor
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
| | - Ailsa L Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Department of Gastroenterology and Inflammatory Bowel Disease Unit, St Mark's Hospital and Academic Institute, Middlesex, UK
| | | | - Josbert J Keller
- Department of Gastroenterology, Haaglanden Medisch Centrum, The Hague, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Hawkey
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Public Health Laboratory, Faculty of Medicine, University of Birmingham, Birmingham, UK
| | - Tariq H Iqbal
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - Horace R T Williams
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
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11
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Bandyopadhyay AS, Burke RM, Hawes KM. Polio Eradication: Status, Struggles and Strategies. Pediatr Infect Dis J 2024; 43:e207-e211. [PMID: 38564755 DOI: 10.1097/inf.0000000000004330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Affiliation(s)
- Ananda S Bandyopadhyay
- From the Polio, Global Development, Bill & Melinda Gates Foundation, Seattle, Washington
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12
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Mullish BH, Merrick B, Quraishi MN, Bak A, Green CA, Moore DJ, Porter RJ, Elumogo NT, Segal JP, Sharma N, Marsh B, Kontkowski G, Manzoor SE, Hart AL, Settle C, Keller JJ, Hawkey P, Iqbal TH, Goldenberg SD, Williams HRT. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. J Hosp Infect 2024; 148:189-219. [PMID: 38609760 DOI: 10.1016/j.jhin.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.
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Affiliation(s)
- B H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - B Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK
| | - M N Quraishi
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - A Bak
- Healthcare Infection Society, London, UK
| | - C A Green
- Department of Infectious Diseases & Tropical Medicine, University Hospitals NHS Foundation Trust, Birmingham Heartlands Hospital, Birmingham, UK; School of Chemical Engineering, University of Birmingham, Birmingham, UK
| | - D J Moore
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - R J Porter
- Department of Microbiology, Royal Devon and Exeter Hospitals, Barrack Road, UK
| | - N T Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; Norfolk and Norwich University Hospital, Norwich, UK
| | - J P Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - N Sharma
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - B Marsh
- Lay Representative for FMT Working Party, Healthcare Infection Society, London, UK
| | - G Kontkowski
- Lay Representative for FMT Working Party, Healthcare Infection Society, London, UK; C.diff support, London, UK
| | - S E Manzoor
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK
| | - A L Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Department of Gastroenterology and Inflammatory Bowel Disease Unit, St Mark's Hospital and Academic Institute, Middlesex, UK
| | - C Settle
- South Tyneside and Sunderland NHS Foundation Trust, South Shields, UK
| | - J J Keller
- Department of Gastroenterology, Haaglanden Medisch Centrum, The Hague, The Netherlands; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - P Hawkey
- Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Public Health Laboratory, Faculty of Medicine, University of Birmingham, Birmingham, UK
| | - T H Iqbal
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, London, UK
| | - S D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College London, London, UK.
| | - H R T Williams
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK; Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK.
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13
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Spatz S, Afonso CL. Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases. Vet Sci 2024; 11:239. [PMID: 38921986 PMCID: PMC11209166 DOI: 10.3390/vetsci11060239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology's operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the "core" of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through "implementation research" by a consortium of interested institutions working on common samples.
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Affiliation(s)
- Stephen Spatz
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA;
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14
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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] [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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15
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Cárdenas-Calle M, Patiño L, Pernia B, Erazo R, Muñoz C, Valencia-Avellan M, Lozada M, Regato-Arrata M, Barrera M, Aquino S, Fuentes S, Duque J, Velázquez-Araque L, Carpio B, Méndez-Roman C, Calle C, Cárdenas G, Guizado-Herrera D, Tello CL, Bravo-Basantes V, Francis J, Uyaguari M. Detection of thermotolerant coliforms and SARS-CoV-2 RNA in sewage and recreational waters in the Ecuadorian coast: A call for improving water quality regulation. PLoS One 2024; 19:e0302000. [PMID: 38709720 PMCID: PMC11073733 DOI: 10.1371/journal.pone.0302000] [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: 12/22/2023] [Accepted: 03/26/2024] [Indexed: 05/08/2024] Open
Abstract
Wastewater surveillance represents an alternative approach to regulating contamination and the early detection of infectious agents and outbreaks of diseases of public health importance. This study evaluated domestic wastewater effects on recreational waters in estuarine and seawater bodies in Guayas and Santa Elena provinces in Ecuador, South America. Fecal indicator bacteria (thermotolerant coliforms) served as key indicators for evaluation. Physical, chemical, and microbiological quality markers following the Ecuadorian environmental quality standard and the discharge of effluents to the water resource were analyzed. Samples were collected from 44 coastal sites and 2 oxidation lagoons during the dry and rainy seasons of 2020 and 2021, respectively. SARS-CoV-2 RNA was detected in samples with higher E. coli concentrations using reverse transcription quantitative PCR to detect the genes N and ORF1ab. All samples analyzed for SARS-CoV-2 showed Ct ˂ 40 for at least one gene. Four samples showed at least 20 genome copies of gene N per reaction. These were at an artisanal fishing port, an estuarine area (Palmar), a recreational bay, and an oxidation lagoon. A moderate correlation was found between SARS-CoV-2 RNA, thermotolerant coliform and E. coli (p-value ≤ 0.0037), and a strong and positive correlation between thermotolerant coliform and E. coli. (p-value ≤ 0.00001), highlighting the utility of these established parameters as a proxy of the virus. Significant differences were found in the concentrations of thermotolerant coliforms between seasons (p-value = 0.016) and sites (p-value = 0.005). The highest levels of coliforms were found in the dry season (63000 MPN/100 mL) in Anconcito and during the rainy season (14000 MPN/100 mL) at Esterillo in Playas County. It is recommended that the decentralized autonomous governments of the surveyed provinces in Ecuador implement urgent corrective actions and establish medium-term mechanisms to minimize a potential contamination route. Additional parameters must be included in the monitoring, such as Enterococcus and intestinal parasites, due to their public health implications. In the oxidation lagoons, maintenance actions must be carried out, including the dissolution of sediments, an increase in water retention times, and in situ treatment of the sludge, to improve the system's performance.
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Affiliation(s)
- Maritza Cárdenas-Calle
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Leandro Patiño
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | - Beatriz Pernia
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Faculty of Natural Sciences, Natural Resources Research Institute, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Roberto Erazo
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Labcestta, Guayaquil, Guayas, Ecuador
| | - Carlos Muñoz
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Magaly Valencia-Avellan
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Facultad del Mar y Medio Ambiente, Universidad del Pacífico, Guayaquil, Guayas, Ecuador
| | - Mariana Lozada
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Environmental Microbiology Laboratory, Institute of Biology of Marine Organisms, CONICET, Puerto Madryn, Chubut, Argentina
| | - Mary Regato-Arrata
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, National Reference Center for Exanthematous, Gastroenteric and Vector-borne Viruses, Guayaquil, Guayas, Ecuador
| | - Miguel Barrera
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Segundo Aquino
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Stefania Fuentes
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Javier Duque
- Interinstitutional Network for the Study of Aquatic Ecosystems of Ecuador, Guayaquil, Guayas, Ecuador
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Luis Velázquez-Araque
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
| | - Bertha Carpio
- Dirección del Medio Ambiente, Gobierno Provincial de Santa Elena, Santa Elena, Ecuador
| | - Carlos Méndez-Roman
- Área Nacional de Recreación Playas Villamil, Ministerio de Ambiente Agua y Transición Ecológica, Playas, Ecuador
| | - Carlos Calle
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - Guillermo Cárdenas
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
| | - David Guizado-Herrera
- Faculty of Chemical Engineering, University of Guayaquil, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | - Clara Lucía Tello
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- National Institute for Public Health Research–INSPI- Dr. Leopoldo Izquieta Pérez, Technical Direction of Research, Development and Innovation, Guayaquil, Guayas, Ecuador
| | | | - Jhannelle Francis
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Miguel Uyaguari
- Ambiente Sociedad & Empresa Research Group, University of Guayaquil, Guayaquil, Guayas, Ecuador
- Fundación Bioelit, Guayaquil, Guayas, Ecuador
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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16
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Miles SJ, Harrington C, Sun H, Deas A, Oberste MS, Nix WA, Vega E, Gerloff N. Validation of improved automated nucleic acid extraction methods for direct detection of polioviruses for global polio eradication. J Virol Methods 2024; 326:114914. [PMID: 38458353 DOI: 10.1016/j.jviromet.2024.114914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Polioviruses (PV), the main causative agent of acute flaccid paralysis (AFP), are positive-sense single-stranded RNA viruses of the family Picornaviridae. As we approach polio eradication, accurate and timely detection of poliovirus in stool from AFP cases becomes vital to success for the eradication efforts. Direct detection of PV from clinical diagnostic samples using nucleic acid (NA) extraction and real-time reverse transcriptase polymerase chain reaction (rRT-PCR) instead of the current standard method of virus isolation in culture, eliminates the long turn-around time to diagnosis and the need for high viral titer amplification in laboratories. An essential component of direct detection of PV from AFP surveillance samples is the efficient extraction of NA. Potential supply chain issues and lack of vendor presence in certain areas of the world necessitates the validation of multiple NA extraction methods. Using retrospective PV-positive surveillance samples (n=104), two extraction kits were compared to the previously validated Zymo Research Quick-RNA™ Viral Kit. The Roche High Pure Viral RNA Kit, a column-based manual extraction method, and the MagMaX™ Pathogen RNA/DNA kit used in the automated Kingfisher Flex system were both non-inferior to the Zymo kit, with similar rates of PV detection in pivotal rRT-PCR assays, such as pan-poliovirus (PanPV), poliovirus serotype 2 (PV2), and wild poliovirus serotype 1 (WPV1). These important assays allow the identification and differentiation of PV genotypes and serotypes and are fundamental to the GPLN program. Validation of two additional kits provides feasible alternatives to the current piloted method of NA extraction for poliovirus rRT-PCR assays.
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Affiliation(s)
- Stacey Jeffries Miles
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Chelsea Harrington
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Hong Sun
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ashley Deas
- Cherokee Nation Assurance, Contracting Agency to the Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - M Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - W Allan Nix
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Everardo Vega
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Nancy Gerloff
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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17
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Bandyopadhyay AS, Lopez Cavestany R, Blake IM, Macklin G, Cooper L, Grassly N, Nery ALMDS, Mach O. Use of inactivated poliovirus vaccine for poliovirus outbreak response. THE LANCET. INFECTIOUS DISEASES 2024; 24:e328-e342. [PMID: 38012892 DOI: 10.1016/s1473-3099(23)00505-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 11/29/2023]
Abstract
With continued wild poliovirus transmission in Afghanistan and Pakistan and circulating vaccine-derived poliovirus in certain countries, there exists an ongoing risk of importation of polioviruses into other countries, including those that have been polio-free for decades. Diversifying the poliovirus outbreak response toolkit is essential to account for different public health and epidemiological contexts. In this Personal View, we discuss data on intestinal and pharyngeal mucosal immunity induced by inactivated poliovirus vaccine (IPV), previous programmatic experience of poliovirus outbreak response with IPV, and outbreak response guidelines in countries that exclusively use IPV. With recent reports of poliovirus detection in polio-free countries such as the USA and the UK, it is important to assess the interplay of virus transmission dynamics, vaccine impact on preventing paralysis and virus spread, and regulatory complexities of using oral poliovirus vaccine (OPV) and IPV options for outbreak response. As the global eradication programme navigates through cessation of routine OPV use with replacement by IPV and stockpiling of novel OPVs, clarity on the impact of IPV use will be important for informed decision making by global, regional, and national policy makers.
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Affiliation(s)
| | | | - Isobel M Blake
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Grace Macklin
- Polio Eradication Department, World Health Organization, Geneva, Switzerland
| | - Laura Cooper
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Nicholas Grassly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | | | - Ondrej Mach
- Polio Eradication Department, World Health Organization, Geneva, Switzerland
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18
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Singh R, Ryu J, Park SS, Kim S, Kim K. Monitoring viruses and beta-lactam resistance genes through wastewater surveillance during a COVID-19 surge in Suwon, South Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171223. [PMID: 38417514 DOI: 10.1016/j.scitotenv.2024.171223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
The present study reports data on a long-term campaign for monitoring SARS-CoV-2, norovirus, hepatitis A virus, and beta-lactam resistance genes in wastewater samples from a wastewater treatment plant during COVID-19 surge in Suwon, South Korea. Real-time digital PCR (RT-dPCR) assays indicated 100 % occurrence of all but hepatitis A virus and blaNDM gene in influent wastewater samples. CDC-N1 assay detected SARS-CoV-2 in all influent samples with an average log-transformed concentration of 5.1 ± 0.39 and the highest level at 6.02 gene copies/L. All samples were also positive for norovirus throughout the study with a mean concentration 5.67 ± 0.65 log10 gene copies/L. On the contrary, all treated wastewater (effluent) tested negative for both viruses' genetic materials. Furthermore, plasmid-mediated AmpC β-lactamases (PABLs) genes blaDHA, blaACC, and blaFOX, extended-spectrum β-lactamases (ESBLs) genes blaTEM and blaCTX, and Klebsiella pneumoniae carbapenemase (blaKPC) gene were measured at average concentrations of 7.05 ± 0.26, 5.60 ± 0.35, 7.82 ± 0.43, 8.38 ± 0.20, 7.64 ± 0.29, and 7.62 ± 0.41 log10 gene copies/L wastewater, respectively. Beta-lactam resistance genes showed strong correlations (r), the highest being 0.86 for blaKPC - blaFOX, followed by 0.82 for blaTEM - blaCTX and 0.79 for blaTEM - blaDHA. SARS-CoV-2 RNA occurrence in the wastewater was strongly associated (r = 0.796) with COVID-19 cases in the catchment during the initial study period of six months. A positive association of the SARS-CoV-2 RNA with the prevalence of COVID-19 cases showed a promising role of community-scale monitoring of pathogens to provide considerable early signals of infection dynamics. High concentrations of beta-lactam resistance genes in wastewater indicated a high concern for one of the biggest global health threats in South Korea and the need to find control measures. Moreover, antibiotic-resistance genes in treated wastewater flowing through water bodies and agricultural environments indicate further dissemination of antibiotic resistance traits and increasing microbial antibiotic resistance.
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Affiliation(s)
- Rajendra Singh
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Jaewon Ryu
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Sung Soo Park
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea
| | - Sungpyo Kim
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong City 30019, Republic of Korea
| | - Keugtae Kim
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, South Korea.
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19
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Thompson KM, Kalkowska DA, Routh JA, Brenner IR, Rosenberg ES, Zucker JR, Langdon-Embry M, Sugerman DE, Burns CC, Badizadegan K. Modeling Poliovirus Transmission and Responses in New York State. J Infect Dis 2024; 229:1097-1106. [PMID: 37596838 PMCID: PMC11284859 DOI: 10.1093/infdis/jiad355] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND In July 2022, New York State (NYS) reported a case of paralytic polio in an unvaccinated young adult, and subsequent wastewater surveillance confirmed sustained local transmission of type 2 vaccine-derived poliovirus (VDPV2) in NYS with genetic linkage to the paralyzed patient. METHODS We adapted an established poliovirus transmission and oral poliovirus vaccine evolution model to characterize dynamics of poliovirus transmission in NYS, including consideration of the immunization activities performed as part of the declared state of emergency. RESULTS Despite sustained transmission of imported VDPV2 in NYS involving potentially thousands of individuals (depending on seasonality, population structure, and mixing assumptions) in 2022, the expected number of additional paralytic cases in years 2023 and beyond is small (less than 0.5). However, continued transmission and/or reintroduction of poliovirus into NYS and other populations remains a possible risk in communities that do not achieve and maintain high immunization coverage. CONCLUSIONS In countries such as the United States that use only inactivated poliovirus vaccine, even with high average immunization coverage, imported polioviruses may circulate and pose a small but nonzero risk of causing paralysis in nonimmune individuals.
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Affiliation(s)
| | | | - Janell A Routh
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - I Ravi Brenner
- Office of Public Health, New York State Department of Health, Albany, New York, USA
| | - Eli S Rosenberg
- Office of Public Health, New York State Department of Health, Albany, New York, USA
- Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, New York, USA
| | - Jane R Zucker
- New York City Department of Health and Mental Hygiene, New York, New York, USA
- Immunization Services Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - David E Sugerman
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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20
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Verani M, Pagani A, Federigi I, Lauretani G, Atomsa NT, Rossi V, Viviani L, Carducci A. Wastewater-Based Epidemiology for Viral Surveillance from an Endemic Perspective: Evidence and Challenges. Viruses 2024; 16:482. [PMID: 38543847 PMCID: PMC10975420 DOI: 10.3390/v16030482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 05/23/2024] Open
Abstract
Wastewater-based epidemiology (WBE) is currently used to monitor not only the spread of the viral SARS-CoV-2 pandemic but also that of other viruses in endemic conditions, particularly in the absence of syndromic surveillance. The continuous monitoring of sewage requires high expenditure and significant time investments, highlighting the need for standardized methods and structured monitoring strategies. In this context, we conducted weekly wastewater monitoring in northwestern Tuscany (Italy) and targeted human adenovirus (HAdV), norovirus genogroup II (NoVggII), enterovirus (EV), and SARS-CoV-2. Samples were collected at the entrances of treatment plants and concentrated using PEG/NaCl precipitation, and viral nucleic acids were extracted and detected through real-time reverse transcription qPCR. NoVggII was the most identified target (84.4%), followed by HAdV, SARS-CoV-2, and EV. Only HAdV and EV exhibited seasonal peaks in spring and summer. Compared with data that were previously collected in the same study area (from February 2021 to September 2021), the results for SARS-CoV-2 revealed a shift from an epidemic to an endemic pattern, at least in the region under investigation, which was likely due to viral mutations that led to the spreading of new variants with increased resistance to summer environmental conditions. In conclusion, using standardized methods and an efficient monitoring strategy, WBE proves valuable for viral surveillance in pandemic and epidemic scenarios, enabling the identification of temporal-local distribution patterns that are useful for making informed public health decisions.
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Affiliation(s)
| | | | - Ileana Federigi
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56123 Pisa, Italy; (M.V.); (A.P.); (G.L.); (N.T.A.); (V.R.); (L.V.); (A.C.)
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21
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Leisman KP, Owen C, Warns MM, Tiwari A, Bian GZ, Owens SM, Catlett C, Shrestha A, Poretsky R, Packman AI, Mangan NM. A modeling pipeline to relate municipal wastewater surveillance and regional public health data. WATER RESEARCH 2024; 252:121178. [PMID: 38309063 DOI: 10.1016/j.watres.2024.121178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
As COVID-19 becomes endemic, public health departments benefit from improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging due to the high noise typical of environmental samples. We have developed a generalized pipeline using in- and out-of-sample model selection to test the ability of different correction models to reduce the variance in wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but the pipeline should be used to reevaluate any new data set as the sources of variance may change across locations, lab methods, and disease states. Using our best-fit model, we investigated the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We did this in a rolling manner for corrected wastewater data and for other prevalence indicators and statistically compared the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We found that wastewater trends often lead other COVID-19 indicators in predicting new surges.
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Affiliation(s)
- Katelyn Plaisier Leisman
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Christopher Owen
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Maria M Warns
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Anuj Tiwari
- Discovery Partners Institute, University of Illinois Chicago, Chicago, IL, USA
| | - George Zhixin Bian
- Department of Computer Science, Northwestern University, Evanston, IL, USA
| | - Sarah M Owens
- Biosciences, Argonne National Laboratory, Lemont, IL, USA
| | - Charlie Catlett
- Discovery Partners Institute, University of Illinois Chicago, Chicago, IL, USA; Computing, Environment, and Life Sciences, Argonne National Laboratory, Lemont, IL, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois Chicago, Chicago, IL, USA
| | - Rachel Poretsky
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Aaron I Packman
- Center for Water Research, Northwestern University, Evanston, IL, USA; Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA; Center for Water Research, Northwestern University, Evanston, IL, USA.
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22
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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23
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Tang J, Zhang X, Zhang J, Zhao Z, Ding Z. Environmental surveillance reveals co-circulation of distinctive lineages of enteroviruses in southwest China's border cities, 2020-2022. J Appl Microbiol 2024; 135:lxae060. [PMID: 38471668 DOI: 10.1093/jambio/lxae060] [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: 09/28/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
AIMS Enteroviruses are significant human pathogens associated with a range of mild to severe diseases. This study aims to understand the diversity and genetic characterization of enteroviruses circulated in southwest China's border cities by using environmental surveillance. METHODS AND RESULTS A total of 96 sewage samples were collected in three border cities and a port located in Yunnan Province, China from July 2020 to June 2022. After cell culture and VP1 sequencing, a total of 590 enterovirus isolates were identified, belonging to 21 types. All PV strains were Sabin-like with ≤6 nucleotide mutations in the VP1 coding region. Echovirus 6, echovirus 21 (a rare serotype in previous studies), and coxsackievirus B5 were the predominant serotypes, which accounted for 21.19%, 18.31%, and 13.39% of the total isolates, respectively. The prevalence of the common serotypes varied across different border cities and periods. Phylogenetic analysis revealed the presence of multiple evolutionary lineages for E21, E6, and E30, some of which formed distinct branches. CONCLUSIONS High diversity of enteroviruses and distinct lineages of predominant serotypes circulated in southwest China's border cities.
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Affiliation(s)
- Jingjing Tang
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Xiaodie Zhang
- Kunming Center for Disease Control and Prevention, No. 4 Ziyun Road, Kunming 650228, People's Republic of China
| | - Jie Zhang
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Zhixian Zhao
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
| | - Zhengrong Ding
- Yunnan Center for Disease Control and Prevention, No. 158 Dongsi Road, Kunming 650022, People's Republic of China
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24
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Zhao T, Li J, Huang T, Ying ZF, Che YC, Zhao ZM, Fu YT, Tao JH, Yang QH, Wei DK, Li GL, Yi L, Zhao YP, Chen HB, Wang JF, Jiang RJ, Yu L, Cai W, Yang W, Xie MX, Yin QZ, Pu J, Shi L, Hong C, Deng Y, Cai LK, Zhou J, Wen Y, Li HS, Huang W, Mo ZJ, Li CG, Li QH, Yang JS. Immune persistence after different polio sequential immunization schedules in Chinese infants. NPJ Vaccines 2024; 9:50. [PMID: 38424078 PMCID: PMC10904800 DOI: 10.1038/s41541-024-00831-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Trivalent oral poliovirus vaccine (tOPV) has been withdrawn and instead an inactivated poliovirus vaccine (IPV) and bivalent type 1 and type 3 OPV (bOPV) sequential immunization schedule has been implemented since 2016, but no immune persistence data are available for this polio vaccination strategy. This study aimed to assess immune persistence following different polio sequential immunization schedules. Venous blood was collected at 24, 36, and 48 months of age from participants who had completed sequential schedules of combined IPV and OPV in phase III clinical trials. The serum neutralizing antibody titers against poliovirus were determined, and the poliovirus-specific antibody-positive rates were evaluated. A total of 1104 participants were enrolled in this study. The positive rates of poliovirus type 1- and type 3-specific antibodies among the sequential immunization groups showed no significant difference at 24, 36, or 48 months of age. The positive rates of poliovirus type 2-specific antibody in the IPV-IPV-tOPV group at all time points were nearly 100%, which was significantly higher than the corresponding rates in other immunization groups (IPV-bOPV-bOPV and IPV-IPV-bOPV). Immunization schedules involving one or two doses of IPV followed by bOPV failed to maintain a high positive rate for poliovirus type 2-specific antibody.
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Affiliation(s)
- Ting Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jing Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Teng Huang
- Guangxi Province Center for Disease Control and Prevention, Nanning, China
| | - Zhi-Fang Ying
- National Institutes for Food and Drug Control, Beijing, China
| | - Yan-Chun Che
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Zhi-Mei Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yu-Ting Fu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jun-Hui Tao
- Liujiang District Center for Disease Prevention and Control, Liuzhou, China
| | - Qing-Hai Yang
- Liucheng County Center for Disease Prevention and Control, Liuzhou, China
| | - Ding-Kai Wei
- Rongan County Center for Disease Prevention and Control, Liuzhou, China
| | - Guo-Liang Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Li Yi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yu-Ping Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Hong-Bo Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jian-Feng Wang
- National Institutes for Food and Drug Control, Beijing, China
| | - Rui-Ju Jiang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Lei Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Wei Cai
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Wei Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Ming-Xue Xie
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Qiong-Zhou Yin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jing Pu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Chao Hong
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yan Deng
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Lu-Kui Cai
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jian Zhou
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yu Wen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Hong-Sen Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Wei Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Zhao-Jun Mo
- Guangxi Province Center for Disease Control and Prevention, Nanning, China.
| | - Chang-Gui Li
- National Institutes for Food and Drug Control, Beijing, China.
| | - Qi-Han Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China.
| | - Jing-Si Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China.
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25
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Thompson KM, Kalkowska DA, Kidd SE, Burns CC, Badizadegan K. Trade-offs of different poliovirus vaccine options for outbreak response in the United States and other countries that only use inactivated poliovirus vaccine (IPV) in routine immunization. Vaccine 2024; 42:819-827. [PMID: 38218668 PMCID: PMC10947589 DOI: 10.1016/j.vaccine.2023.12.081] [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: 10/11/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
Delays in achieving polio eradication have led to ongoing risks of poliovirus importations that may cause outbreaks in polio-free countries. Because of the low, but non-zero risk of paralysis with oral poliovirus vaccines (OPVs), countries that achieve and maintain high national routine immunization coverage have increasingly shifted to exclusive use of inactivated poliovirus vaccine (IPV) for all preventive immunizations. However, immunization coverage within countries varies, with under-vaccinated subpopulations potentially able to sustain transmission of imported polioviruses and experience local outbreaks. Due to its cost, ease-of-use, and ability to induce mucosal immunity, using OPV as an outbreak control measure offers a more cost-effective option in countries in which OPV remains in use. However, recent polio outbreaks in IPV-only countries raise questions about whether and when IPV use for outbreak response may fail to stop poliovirus transmission and what consequences may follow from using OPV for outbreak response in these countries. We systematically reviewed the literature to identify modeling studies that explored the use of IPV for outbreak response in IPV-only countries. In addition, applying a model of the 2022 type 2 poliovirus outbreak in New York, we characterized the implications of using different OPV formulations for outbreak response instead of IPV. We also explored the hypothetical scenario of the same outbreak except for type 1 poliovirus instead of type 2. We find that using IPV for outbreak response will likely only stop outbreaks for polioviruses of relatively low transmission potential in countries with very high overall immunization coverage, seasonal transmission dynamics, and only if IPV immunization interventions reach some unvaccinated individuals. Using OPV for outbreak response in IPV-only countries poses substantial risks and challenges that require careful consideration, but may represent an option to consider for some outbreaks in some populations depending on the properties of the available vaccines and coverage attainable.
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Affiliation(s)
| | | | - Sarah E Kidd
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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26
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Devaux CA, Pontarotti P, Levasseur A, Colson P, Raoult D. Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis? Front Public Health 2024; 11:1284337. [PMID: 38259741 PMCID: PMC10801389 DOI: 10.3389/fpubh.2023.1284337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
The polioviruses (PVs) are mainly transmitted by direct contact with an infected person through the fecal-oral route and respiratory secretions (or more rarely via contaminated water or food) and have a primary tropism for the gut. After their replication in the gut, in rare cases (far less than 1% of the infected individuals), PVs can spread to the central nervous system leading to flaccid paralysis, which can result in respiratory paralysis and death. By the middle of the 20th century, every year the wild polioviruses (WPVs) are supposed to have killed or paralyzed over half a million people. The introduction of the oral poliovirus vaccines (OPVs) through mass vaccination campaigns (combined with better application of hygiene measures), was a success story which enabled the World Health Organization (WHO) to set the global eradication of poliomyelitis as an objective. However this strategy of viral eradication has its limits as the majority of poliomyelitis cases today arise in individuals infected with circulating vaccine-derived polioviruses (cVDPVs) which regain pathogenicity following reversion or recombination. In recent years (between January 2018 and May 2023), the WHO recorded 8.8 times more cases of polio which were linked to the attenuated OPV vaccines (3,442 polio cases after reversion or recombination events) than cases linked to a WPV (390 cases). Recent knowledge of the evolution of RNA viruses and the exchange of genetic material among biological entities of the intestinal microbiota, call for a reassessment of the polio eradication vaccine strategies.
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Affiliation(s)
- Christian Albert Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Pierre Pontarotti
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Anthony Levasseur
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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27
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Jobling K, Quintela-Baluja M, Hassard F, Adamou P, Blackburn A, Research Team T, McIntyre-Nolan S, O'Mara O, Romalde JL, Di Cesare M, Graham DW. Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons. JOURNAL OF WATER AND HEALTH 2024; 22:64-76. [PMID: 38295073 PMCID: wh_2023_093 DOI: 10.2166/wh.2023.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p < 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.
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Affiliation(s)
- Kelly Jobling
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; The authors contributed equally to the manuscript. E-mail:
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; The authors contributed equally to the manuscript
| | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, Cranfield MK43 0AL, UK
| | - Panagiota Adamou
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | | | | | - Jesus L Romalde
- CRETUS, Departamento de Microbiología y Parasitología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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28
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Kalkowska DA, Badizadegan K, Routh JA, Burns CC, Rosenberg ES, Brenner IR, Zucker JR, Langdon-Embry M, Thompson KM. Modeling undetected poliovirus circulation following the 2022 outbreak in the United States. Expert Rev Vaccines 2024; 23:186-195. [PMID: 38164695 PMCID: PMC11284832 DOI: 10.1080/14760584.2023.2299401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND New York State (NYS) reported a polio case (June 2022) and outbreak of imported type 2 circulating vaccine-derived poliovirus (cVDPV2) (last positive wastewater detection in February 2023), for which uncertainty remains about potential ongoing undetected transmission. RESEARCH DESIGN AND METHODS Extending a prior deterministic model, we apply an established stochastic modeling approach to characterize the confidence about no circulation (CNC) of cVDPV2 as a function of time since the last detected signal of transmission (i.e. poliovirus positive acute flaccid myelitis case or wastewater sample). RESULTS With the surveillance coverage for the NYS population majority and its focus on outbreak counties, modeling suggests a high CNC (95%) within 3-10 months of the last positive surveillance signal, depending on surveillance sensitivity and population mixing patterns. Uncertainty about surveillance sensitivity implies longer durations required to achieve higher CNC. CONCLUSIONS In populations that maintain high overall immunization coverage with inactivated poliovirus vaccine (IPV), rare polio cases may occur in un(der)-vaccinated individuals. Modeling demonstrates the unlikeliness of type 2 outbreaks reestablishing endemic transmission or resulting in large absolute numbers of paralytic cases. Achieving and maintaining high immunization coverage with IPV remains the most effective measure to prevent outbreaks and shorten the duration of imported poliovirus transmission.
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Affiliation(s)
| | | | - Janell A. Routh
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C. Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eli S. Rosenberg
- Office of Public Health, New York State Department of Health, Albany, NY, USA
- Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, NY, USA
| | - I. Ravi Brenner
- Office of Public Health, New York State Department of Health, Albany, NY, USA
| | - Jane R. Zucker
- New York City Department of Health and Mental Hygiene, New York, NY, USA
- Immunization Services Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Kimberly M. Thompson
- Kid Risk, Inc, Orlando, FL, USA
- Department of Public Health, Syracuse University, Syracuse, NY, USA
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29
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Maal-Bared R, Brisolara K, Knight M, Mansfeldt C. To sample or not to sample: A governance-focused decision tree for wastewater service providers considering participation in wastewater-based epidemiology (WBE) in support of public health programs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167128. [PMID: 37722431 DOI: 10.1016/j.scitotenv.2023.167128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Wastewater-based epidemiology (WBE) provides value to public health monitoring and protection. Participation of public and private wastewater system operators in WBE efforts is critical to public health surveillance program success and sustainability. However, given the number of WBE solicitations wastewater service providers receive, the limitation of service provider resources, the concerns around privacy, ethics, and equity, and the fatigue associated with responding to COVID-19, operators are becoming more hesitant to participate in WBE efforts. While various ethical concerns and sustainability challenges associated with WBE have been documented, no efforts to date have investigated what factors should systematically influence the decision to provide samples to a WBE effort. Therefore, this study develops a decision-making tool for WBE teams to proactively monitor, manage, and avoid wastewater system operators' operational risks and potential liabilities. Ultimately, using this tool allows WBE program partners in academia, government, and industry to better understand wastewater system operators' needs and challenges surrounding data quality and use, public health ethics, and daily wastewater infrastructure operation.
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Affiliation(s)
| | - Kari Brisolara
- LSUHSC, School of Public Health, 2020 Gravier St, New Orleans, LA, USA.
| | - Mark Knight
- LuminUltra Technologies Ltd, 520 King St, Fredericton, NB E3B 6G3, Canada.
| | - Cresten Mansfeldt
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO, USA; Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO, USA.
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30
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Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio 2023; 14:e0146823. [PMID: 37877702 PMCID: PMC10746264 DOI: 10.1128/mbio.01468-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel M. Maloney
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Kate Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Weymouth, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Matthew J. Wade
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
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31
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Sokoloski KJ, Holm RH, Smith M, Ford EE, Rouchka EC, Smith T. What is the functional reach of wastewater surveillance for respiratory viruses, pathogenic viruses of concern, and bacterial antibiotic resistance genes of interest? Hum Genomics 2023; 17:114. [PMID: 38105239 PMCID: PMC10726489 DOI: 10.1186/s40246-023-00563-8] [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: 05/12/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Despite a clear appreciation of the impact of human pathogens on community health, efforts to understand pathogen dynamics within populations often follow a narrow-targeted approach and rely on the deployment of specific molecular probes for quantitative detection or rely on clinical detection and reporting. MAIN TEXT Genomic analysis of wastewater samples for the broad detection of viruses, bacteria, fungi, and antibiotic resistance genes of interest/concern is inherently difficult, and while deep sequencing of wastewater provides a wealth of information, a robust and cooperative foundation is needed to support healthier communities. In addition to furthering the capacity of high-throughput sequencing wastewater-based epidemiology to detect human pathogens in an unbiased and agnostic manner, it is critical that collaborative networks among public health agencies, researchers, and community stakeholders be fostered to prepare communities for future public health emergencies or for the next pandemic. A more inclusive public health infrastructure must be built for better data reporting where there is a global human health risk burden. CONCLUSIONS As wastewater platforms continue to be developed and refined, high-throughput sequencing of human pathogens in wastewater samples will emerge as a gold standard for understanding community health.
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Affiliation(s)
- Kevin J Sokoloski
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
- Center for Predictive Medicine for Biodefense and Emerging Infectious Disease, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY, 40202, USA.
| | - Melissa Smith
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, 580 S. Preston St., Louisville, KY, 40202, USA
| | - Easton E Ford
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, 580 S. Preston St., Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY, 40202, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY, 40202, USA
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Kasstan B, Mounier-Jack S, Zuriaga-Alvaro A, Weil LG, Chantler T. "We're potentially worsening health inequalities": Evaluating how delivery of the 2022 London polio booster campaign was tailored to Orthodox Jewish families to reduce transmission vulnerability. SSM. QUALITATIVE RESEARCH IN HEALTH 2023; 4:100365. [PMID: 38169919 PMCID: PMC10759644 DOI: 10.1016/j.ssmqr.2023.100365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 01/05/2024]
Abstract
A polio booster campaign targeting all children aged 1-9 was implemented across London between August-December 2022 as part of a national enhanced poliovirus incident response. Orthodox Jewish (OJ) children were particularly vulnerable to transmission due to disparities in childhood vaccination coverage and the transnational spread of poliovirus affecting linked populations in New York and Israel. This study aimed to evaluate how the polio booster campaign was tailored to increase uptake and enable access for OJ families in northeast and north central London boroughs, and the impact of the campaign on local-level vaccine inequities. Semi-structured in-depth interviews (n = 36) were conducted with participants involved in the implementation and delivery of the polio booster campaign, and OJ mothers. Site visits (n = 5) were conducted at vaccine clinics, and rapid interviews (n = 26) were held to explore parental perceptions of the poliovirus incident and childhood immunisations. Enablers to vaccination during the campaign included the production of targeted printed communications and offering flexible clinic times in primary care settings or complementary delivery pathways embedded in family-friendly spaces. Barriers included digital booking systems. Mothers reported being aware of the poliovirus incident, but the majority of those interviewed did not feel their children were at risk of contracting polio. Healthcare provider participants raised concerns that the vaccine response had limited impact on reducing disparities in vaccine uptake. While OJ families were recognised as a priority for public health engagement during the poliovirus incident response, this evaluation identified limitations in reducing transmission vulnerability during the booster campaign. Lessons for future campaign delivery include effectively conveying transmission risk and the urgency to vaccinate. Priorities for mitigating vaccine inequities include public engagement to develop messaging strategies and strengthening the capacity of primary care and complementary delivery pathways to serve families with higher-than-average numbers of children.
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Affiliation(s)
- Ben Kasstan
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Sandra Mounier-Jack
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Ana Zuriaga-Alvaro
- NHS Legacy and Health Equity Partnership, Primary Care and Public Health Commissioning, National Health Service England, London Region, London, SE1 8UG, United Kingdom
| | - Leonora G. Weil
- NHS Legacy and Health Equity Partnership, Primary Care and Public Health Commissioning, National Health Service England, London Region, London, SE1 8UG, United Kingdom
- United Kingdom Health Security Agency, London Region, South Colonnade, Canary Wharf, London, E14 4PU, United Kingdom
| | - Tracey Chantler
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
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33
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Zhdanov DD, Ivin YY, Shishparenok AN, Kraevskiy SV, Kanashenko SL, Agafonova LE, Shumyantseva VV, Gnedenko OV, Pinyaeva AN, Kovpak AA, Ishmukhametov AA, Archakov AI. Perspectives for the creation of a new type of vaccine preparations based on pseudovirus particles using polio vaccine as an example. BIOMEDITSINSKAIA KHIMIIA 2023; 69:253-280. [PMID: 37937429 DOI: 10.18097/pbmc20236905253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Traditional antiviral vaccines are currently created by inactivating the virus chemically, most often using formaldehyde or β-propiolactone. These approaches are not optimal since they negatively affect the safety of the antigenic determinants of the inactivated particles and require additional purification stages. The most promising platforms for creating vaccines are based on pseudoviruses, i.e., viruses that have completely preserved the outer shell (capsid), while losing the ability to reproduce owing to the destruction of the genome. The irradiation of viruses with electron beam is the optimal way to create pseudoviral particles. In this review, with the example of the poliovirus, the main algorithms that can be applied to characterize pseudoviral particles functionally and structurally in the process of creating a vaccine preparation are presented. These algorithms are, namely, the analysis of the degree of genome destruction and coimmunogenicity. The structure of the poliovirus and methods of its inactivation are considered. Methods for assessing residual infectivity and immunogenicity are proposed for the functional characterization of pseudoviruses. Genome integrity analysis approaches, atomic force and electron microscopy, surface plasmon resonance, and bioelectrochemical methods are crucial to structural characterization of the pseudovirus particles.
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Affiliation(s)
- D D Zhdanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu Yu Ivin
- Institute of Biomedical Chemistry, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A N Pinyaeva
- Institute of Biomedical Chemistry, Moscow, Russia; Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - A A Kovpak
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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34
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Ueno MK, Kitamura K, Nishimura Y, Arita M. Evaluation of Direct Detection Protocols for Poliovirus from Stool Samples of Acute Flaccid Paralysis Patients. Viruses 2023; 15:2113. [PMID: 37896890 PMCID: PMC10612058 DOI: 10.3390/v15102113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Polio surveillance in the Global Polio Eradication Initiative has been conducted with virus isolation from stool samples of acute flaccid paralysis (AFP) cases. Under the current biorisk management/regulations, challenges arise in the timelines of the report, sensitivity of the test and containment of poliovirus (PV) isolates. In the present study, we evaluated protocols of previously reported direct detection (DD) methods targeting the VP1 or VP4-VP2 regions of the PV genome in terms of sensitivity and sequencability. An optimized protocol targeting the entire-capsid region for the VP1 sequencing showed a high sensitivity (limit of detection = 82 copies of PV genome) with a simpler and faster reaction than reported ones (i.e., with the addition of all the primers at the start of the reaction, the RT-PCR reaction finishes within 2.5 h). The DD methods targeting the VP1 region detected PV in 60 to 80% of PV-positive stool samples from AFP cases; however, minor populations of PV strains in the samples with virus mixtures were missed by the methods. Sequencability of the DD methods was primarily determined by the efficiency of the PCRs for both Sanger and nanopore sequencing. The DD method targeting the VP4-VP2 region showed higher sensitivity than that targeting the VP1 region (limit of detection = 25 copies of PV genome) and successfully detected PV from all the stool samples examined. These results suggest that DD methods are effective for the detection of PV and that further improvement of the sensitivity is essential to serve as an alternative to the current polio surveillance algorithm.
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Affiliation(s)
| | | | | | - Minetaro Arita
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan; (M.K.U.); (K.K.); (Y.N.)
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35
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Bubba L, Benschop KSM, Blomqvist S, Duizer E, Martin J, Shaw AG, Bailly JL, Rasmussen LD, Baicus A, Fischer TK, Harvala H. Wastewater Surveillance in Europe for Non-Polio Enteroviruses and Beyond. Microorganisms 2023; 11:2496. [PMID: 37894154 PMCID: PMC10608818 DOI: 10.3390/microorganisms11102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Wastewater surveillance (WWS) was developed in the early 1960s for the detection of poliovirus (PV) circulation in the population. It has been used to monitor several pathogens, including non-polio enteroviruses (NPEVs), which are increasingly recognised as causes of morbidity in children. However, when applying WWS to a new pathogen, it is important to consider the purpose of such a study as well as the suitability of the chosen methodology. With this purpose, the European Non-Polio Enterovirus Network (ENPEN) organised an expert webinar to discuss its history, methods, and applications; its evolution from a culture-based method to molecular detection; and future implementation of next generation sequencing (NGS). The first simulation experiments with PV calculated that a 400 mL sewage sample is sufficient for the detection of viral particles if 1:10,000 people excrete poliovirus in a population of 700,000 people. If the method is applied correctly, several NPEV types are detected. Despite culture-based methods remaining the gold standard for WWS, direct methods followed by molecular-based and sequence-based assays have been developed, not only for enterovirus but for several pathogens. Along with case-based sentinel and/or syndromic surveillance, WWS for NPEV and other pathogens represents an inexpensive, flexible, anonymised, reliable, population-based tool for monitoring outbreaks and the (re)emergence of these virus types/strains within the general population.
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Affiliation(s)
- Laura Bubba
- European Non-Polio Enterovirus Network (E.N.P.E.N.), 1207 Geneva, Switzerland
| | - Kimberley S. M. Benschop
- National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (K.S.M.B.); (E.D.)
| | - Soile Blomqvist
- Finnish Institute for Health and Welfare, P.O. Box 95, 70701 Kuopio, Finland;
| | - Erwin Duizer
- National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands; (K.S.M.B.); (E.D.)
| | - Javier Martin
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Potters Bar EN6 3QG, UK;
| | - Alexander G. Shaw
- MRC Centre for Global Infectious Disease Analysis, London SW7 2AZ, UK;
- Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London SW7 2BX, UK
| | - Jean-Luc Bailly
- Laboratoire Micro-Organismes Genome Environnement (LMGE), Université Clermont Auvergne CNRS, 63001 Clermont-Ferrand, France;
| | - Lasse D. Rasmussen
- Virus Surveillance and Research Section Department of Virus and Microbiological Special Diagnostics Statens Serum Institut, DK-2300 Copenhagen, Denmark;
| | - Anda Baicus
- Enteric Viral Infections Laboratory, Cantacuzino National Institute for Medical-Military Research and Development, 020123 Bucharest, Romania;
| | - Thea K. Fischer
- Department of Clinical Research, University Hospital of Nordsjaelland, 3400 Hilleroed, Denmark
- Department of Public Health, University of Copenhagen, 1172 Copenhagen, Denmark
| | - Heli Harvala
- Microbiology Services National Health Service (NHS) Blood and Transplant, London NW9 5BG, UK;
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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36
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Maréchal V, Maday Y, Wallet C, Cluzel N, Borde C. Wastewater-based epidemiology: Retrospective, current status, and future prospects. Anaesth Crit Care Pain Med 2023; 42:101251. [PMID: 37236316 DOI: 10.1016/j.accpm.2023.101251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Vincent Maréchal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012 Paris, France; Groupement d'Intérêt Scientifique OBEPINE.
| | - Yvon Maday
- Sorbonne Université, CNRS, Université de Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), F-75005 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Clémentine Wallet
- Université de Strasbourg, Unit 7292, DHPI, IUT Louis Pasteur, Schiltigheim, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Nicolas Cluzel
- Sorbonne Université, Maison des Modélisations Ingénieries et Technologies (SUMMIT), 75005 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
| | - Chloé Borde
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, F-75012 Paris, France; Groupement d'Intérêt Scientifique OBEPINE
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37
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Shaw AG, Mampuela TK, Lofiko EL, Pratt C, Troman C, Bujaki E, O'Toole Á, Akello JO, Aziza AA, Lusamaki EK, Makangara JC, Akonga M, Lay Y, Nsunda B, White B, Jorgensen D, Pukuta E, Riziki Y, Rankin KE, Rambaut A, Ahuka-Mundeke S, Muyembe JJ, Martin J, Grassly NC, Mbala-Kingebeni P. Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study. Nat Microbiol 2023; 8:1634-1640. [PMID: 37591995 PMCID: PMC10465353 DOI: 10.1038/s41564-023-01453-4] [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: 03/16/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
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Affiliation(s)
- Alexander G Shaw
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - Tresor Kabeya Mampuela
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Catherine Pratt
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Troman
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Erika Bujaki
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Joyce Odeke Akello
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Adrienne Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- TransVIHMI (Recherches Translationnelles sur le VIH et les Maladies Infectieuses endémiques et émergentes), University of Montpellier (UM), French National Research Institute for Sustainable Development (IRD), INSERM, Montpellier, France
| | - Jean Claude Makangara
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Marceline Akonga
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yvonne Lay
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bibiche Nsunda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Bailey White
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Elizabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Yogolelo Riziki
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Steve Ahuka-Mundeke
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Javier Martin
- Department of Vaccines, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare products Regulatory Agency, Potters Bar, UK
| | - Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Placide Mbala-Kingebeni
- Service de Microbiologie, Departement de Biologie Médicale, Cliniques Universitaires de Kinshasa (CUK), Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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Kasstan B, Mounier-Jack S, Chantler T, Masters N, Flores SA, Stokley S, Meek H, Easton D, De Luna-Evans T, Souto M, Punjabi C, Ruppert PS, Rosenberg E, Routh J. Poliovirus outbreak in New York State, August 2022: qualitative assessment of immediate public health responses and priorities for improving vaccine coverage. Epidemiol Infect 2023; 151:e120. [PMID: 37435800 PMCID: PMC10468811 DOI: 10.1017/s0950268823001127] [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: 04/21/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023] Open
Abstract
In 2022, a case of paralysis was reported in an unvaccinated adult in Rockland County (RC), New York. Genetically linked detections of vaccine-derived poliovirus type 2 (VDPV2) were reported in multiple New York counties, England, Israel, and Canada. The aims of this qualitative study were to: i) review immediate public health responses in New York to assess the challenges in addressing gaps in vaccination coverage; ii) inform a longer-term strategy to improving vaccination coverage in under-vaccinated communities, and iii) collect data to support comparative evaluations of transnational poliovirus outbreaks. Twenty-three semi-structured interviews were conducted with public health professionals, healthcare professionals, and community partners. Results indicate that i) addressing suboptimal vaccination coverage in RC remains a significant challenge after recent disease outbreaks; ii) the poliovirus outbreak was not unexpected and effort should be invested to engage mothers, the key decision-makers on childhood vaccination; iii) healthcare providers (especially paediatricians) received technical support during the outbreak, and may require resources and guidance to effectively contribute to longer-term vaccine engagement strategies; vi) data systems strengthening is required to help track under-vaccinated children. Public health departments should prioritize long-term investments in appropriate communication strategies, countering misinformation, and promoting the importance of the routine immunization schedule.
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Affiliation(s)
- Ben Kasstan
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - Sandra Mounier-Jack
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - Tracey Chantler
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
- The Vaccine Centre, Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | - Nina Masters
- Centers for Disease Control and Prevention, Epidemic Intelligence Service, Atlanta, GA, USA
| | - Stephen A Flores
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shannon Stokley
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Haillie Meek
- Centers for Disease Control and Prevention, Epidemic Intelligence Service, Atlanta, GA, USA
- New York State Department of Health, Albany, NY, USA
| | - Delia Easton
- New York State Department of Health, Albany, NY, USA
| | | | - Maria Souto
- Rockland County Department of Health, Pomona, NY, USA
| | | | | | - Eli Rosenberg
- New York State Department of Health, Albany, NY, USA
| | - Janell Routh
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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40
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Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Toward a global virus genomic surveillance network. Cell Host Microbe 2023; 31:861-873. [PMID: 36921604 PMCID: PMC9986120 DOI: 10.1016/j.chom.2023.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
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41
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Singanayagam A, Klapsa D, Burton-Fanning S, Hand J, Wilton T, Stephens L, Mate R, Shillitoe B, Celma C, Slatter M, Flood T, Gopal R, Martin J, Zambon M. Asymptomatic immunodeficiency-associated vaccine-derived poliovirus infections in two UK children. Nat Commun 2023; 14:3413. [PMID: 37296153 PMCID: PMC10251316 DOI: 10.1038/s41467-023-39094-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Increasing detections of vaccine-derived poliovirus (VDPV) globally, including in countries previously declared polio free, is a public health emergency of international concern. Individuals with primary immunodeficiency (PID) can excrete polioviruses for prolonged periods, which could act as a source of cryptic transmission of viruses with potential to cause neurological disease. Here, we report on the detection of immunodeficiency-associated VDPVs (iVDPV) from two asymptomatic male PID children in the UK in 2019. The first child cleared poliovirus with increased doses of intravenous immunoglobulin, the second child following haematopoetic stem cell transplantation. We perform genetic and phenotypic characterisation of the infecting strains, demonstrating intra-host evolution and a neurovirulent phenotype in transgenic mice. Our findings highlight a pressing need to strengthen polio surveillance. Systematic collection of stool from asymptomatic PID patients who are at high risk for poliovirus excretion could improve the ability to detect and contain iVDPVs.
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Affiliation(s)
- Anika Singanayagam
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK.
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Shirelle Burton-Fanning
- Microbiology and Virology Services, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Julian Hand
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Laura Stephens
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Ryan Mate
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Benjamin Shillitoe
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
- Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Cristina Celma
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Mary Slatter
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Terry Flood
- Paediatric Stem Cell Transplant Unit, Great North Children's Hospital, Newcastle upon Tyne, UK
| | - Robin Gopal
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Potters Bar, London, UK
| | - Maria Zambon
- Polio Reference Service, UK Health Security Agency, Colindale, London, UK.
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42
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Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
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Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
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Weil M, Sofer D, Shulman LM, Weiss L, Levi N, Aguvaev I, Cohen Z, Kestin K, Vasserman R, Elul M, Fratty IS, Zuckerman NS, Erster O, Yishai R, Hecht L, Alroy-Preis S, Mendelson E, Bar-Or I. Environmental surveillance detected type 3 vaccine-derived polioviruses in increasing frequency at multiple sites prior to detection of a poliomyelitis case. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161985. [PMID: 36739034 DOI: 10.1016/j.scitotenv.2023.161985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Israel conducts routine environmental (15 sites) and acute flaccid paralysis (AFP) surveillance for poliovirus. During September 2021, increasing numbers of wastewater samples collected from more than one site in the Jerusalem region proved positive for ambiguous type 3 vaccine-derived poliovirus (aVDPV3), while environmental samples from remaining sampling sites were negative. In late February 2022, a VDPV3, genetically related to the Jerusalem environmental surveillance samples, was isolated from a stool sample collected from a non-immunodeficient, non-immunized child from Jerusalem who developed AFP, indicating that the aVDPV3s were circulating (cVDPV3s) rather than immunodeficiency-related VDPV3s (iVDPVs). In response to these isolations, the Israel Ministry of Health launched a catch-up immunization program.
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Affiliation(s)
- Merav Weil
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Lester M Shulman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Leah Weiss
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Nofar Levi
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Irina Aguvaev
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Zvi Cohen
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Klil Kestin
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Rinat Vasserman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Elul
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ilana S Fratty
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; The Israel Center for Disease Control, Israel Ministry of Health, Ramat-Gan, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ruth Yishai
- Department of Laboratories, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Lior Hecht
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Bar-Or
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.
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Arita M, Fuchino H. Characterization of Anti-Poliovirus Compounds Isolated from Edible Plants. Viruses 2023; 15:v15040903. [PMID: 37112883 PMCID: PMC10145814 DOI: 10.3390/v15040903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
Poliovirus (PV) is the causative agent of poliomyelitis and is a target of the global eradication programs of the World Health Organization (WHO). After eradication of type 2 and 3 wild-type PVs, vaccine-derived PV remains a substantial threat against the eradication as well as type 1 wild-type PV. Antivirals could serve as an effective means to suppress the outbreak; however, no anti-PV drugs have been approved at present. Here, we screened for effective anti-PV compounds in a library of edible plant extracts (a total of 6032 extracts). We found anti-PV activity in the extracts of seven different plant species. We isolated chrysophanol and vanicoside B (VCB) as the identities of the anti-PV activities of the extracts of Rheum rhaponticum and Fallopia sachalinensis, respectively. VCB targeted the host PI4KB/OSBP pathway for its anti-PV activity (EC50 = 9.2 μM) with an inhibitory effect on in vitro PI4KB activity (IC50 = 5.0 μM). This work offers new insights into the anti-PV activity in edible plants that may serve as potent antivirals for PV infection.
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Affiliation(s)
- Minetaro Arita
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi 208-0011, Tokyo, Japan
| | - Hiroyuki Fuchino
- Research Center for Medicinal Plant Resources, National Institutes of Biomedical Innovation, Health and Nutrition, 1-2 Hachimandai, Tsukuba 305-0843, Ibaraki, Japan
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45
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Yang H, Qi Q, Zhang Y, Wen N, Cao L, Liu Y, Fan C, Yan D, Zhu X, Hao L, Zhu S, Ma Q, Liu J, Ma C, Nan L, Chen Y, Ma X, Chen N, Deng K, Shao G, Ding X, An Z, Rodewald LE, Li X, Wang D, Zhu H, Wang H, Feng Z, Xu W, Zhou J, Yin Z. Analysis of a Sabin-Strain Inactivated Poliovirus Vaccine Response to a Circulating Type 2 Vaccine-Derived Poliovirus Event in Sichuan Province, China 2019-2021. JAMA Netw Open 2023; 6:e2249710. [PMID: 36602797 PMCID: PMC9856606 DOI: 10.1001/jamanetworkopen.2022.49710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
IMPORTANCE The Sabin-strain inactivated poliovirus vaccine (IPV) may be a tool for polio outbreak response in certain situations. OBJECTIVE To investigate the response to a type 2 vaccine-derived poliovirus (VDPV2) outbreak. DESIGN, SETTING, AND PARTICIPANTS This case series was conducted in China after a VDPV2 was detected in stool specimens from a child with acute flaccid paralysis (AFP) in Sichuan Province in 2019, 3 years after the global withdrawal of live, attenuated type 2 oral poliovirus vaccine (OPV). Investigation followed National Health Commission and World Health Organization guidance and included searching hospitals for unreported AFP cases; testing stool specimens from the child, his contacts, and local children; enhanced environmental surveillance for VDPV2s in wastewater; and measuring vaccination coverage. Sabin-strain IPV campaigns were conducted in a wide geographic area. MAIN OUTCOMES AND MEASURES Any VDPV2 detection after completion of the supplementary immunization activities. RESULTS A 28-nucleotide-change VDPV2 was isolated from a young boy. Three VDPV2s were detected in healthy children; 2 were contacts of the original child, and none had paralysis. A search of 31 million hospital records found 10 unreported AFP cases; none were polio. No type 2 polioviruses were found in wastewater. Prior to the event, polio vaccine coverage was 65% among children younger than 5 years. Sabin-strain IPV campaigns reached more than 97% of targeted children, administering 1.4 million doses. No transmission source was identified. More than 1 year of enhanced poliovirus environmental and AFP surveillance detected no additional VDPVs. CONCLUSIONS AND RELEVANCE These findings suggest that the circulating VPDV2 outbreak in 2019 was associated with low vaccine coverage. An investigation discovered 3 infected but otherwise healthy children and no evidence of the virus in wastewater. Following Sabin-strain IPV-only campaigns expanding from county to prefecture, the poliovirus was not detected, and the outbreak response was considered by an expert panel and the World Health Organization to have been successful. This success suggests that the Sabin-strain IPV may be a useful tool for responding to circulating VDPV2 outbreaks when high-quality supplementary immunization activities can be conducted and carefully monitored in settings with good sanitation.
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Affiliation(s)
- Hong Yang
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qi Qi
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Yong Zhang
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ning Wen
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lei Cao
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Liu
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Chunxiang Fan
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoping Zhu
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Lixin Hao
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qianli Ma
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Jiajie Liu
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Chao Ma
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lei Nan
- Liangshan Prefectural Center for Disease Control and Prevention, Liangshan, China
| | - Yong Chen
- Leibo County Center for Disease Control and Prevention, Liangshan, China
| | - Xiaozhen Ma
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Na Chen
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Kun Deng
- Liangshan Prefectural Center for Disease Control and Prevention, Liangshan, China
| | - Ge Shao
- Chinese Field Epidemiology Training Program, Beijing, China
| | - Xianxiang Ding
- Chinese Field Epidemiology Training Program, Beijing, China
| | - Zhijie An
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lance E. Rodewald
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaolei Li
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongyan Wang
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Zhu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huaqing Wang
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zijian Feng
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiushun Zhou
- Sichuan Provincial Center for Disease Control and Prevention, Chengdu, China
| | - Zundong Yin
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing, China
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46
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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47
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Bermingham WH, Canning B, Wilton T, Kidd M, Klapsa D, Majumdar M, Sooriyakumar K, Martin J, Huissoon AP. Case report: Clearance of longstanding, immune-deficiency-associated, vaccine-derived polio virus infection following remdesivir therapy for chronic SARS-CoV-2 infection. Front Immunol 2023; 14:1135834. [PMID: 36936936 PMCID: PMC10022663 DOI: 10.3389/fimmu.2023.1135834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
The global polio eradication campaign has had remarkable success in reducing wild-type poliovirus infection, largely built upon the live attenuated Sabin oral poliovirus vaccine. Whilst rare, vaccine poliovirus strains may cause infection and subsequently revert to a neurovirulent type, termed vaccine-derived poliovirus (VDPV). Persistent, vaccine derived infection may occur in an immunocompromised host (iVDPV), where it is a recognised complication following receipt of the Sabin vaccine. This has significant implications for the global polio eradication campaign and there is currently no agreed global strategy to manage such patients.Here we describe a case of a 50-year-old man with common variable immune deficiency, persistently infected with a neurovirulent vaccine-derived type 2 poliovirus following vaccination in childhood. iVDPV infection had proven resistant to multiple prior attempts at treatment with human breast milk, ribavirin and oral administration of a normal human pooled immunoglobulin product. His iVDPV infection subsequently resolved after 12 days treatment with remdesivir, an adenosine analogue prodrug that is an inhibitor of viral RNA-dependent RNA polymerase, administered as treatment for a prolonged, moderate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. iVDPV from the patient, isolated prior to treatment, was subsequently demonstrated to be sensitive to remdesivir in vitro. Based on the observations made in this case, and the mechanistic rationale for use with iVDPV, there is strong justification for further clinical studies of remdesivir treatment as a potentially curative intervention in patients with iVDPV infection.
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Affiliation(s)
- William Hywel Bermingham
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
- *Correspondence: William Hywel Bermingham,
| | - Benjamin Canning
- Department of Virology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Thomas Wilton
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Michael Kidd
- Public Health Laboratory, UK Health Security Agency, Birmingham, United Kingdom
| | - Dimitra Klapsa
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Manasi Majumdar
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Kavitha Sooriyakumar
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Javier Martin
- Division of Vaccines, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, Potters Bar, United Kingdom
| | - Aarnoud P. Huissoon
- Department of Immunology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
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48
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John TJ, Dharmapalan D. Lessons from Vaccine-Related Poliovirus in Israel, UK and USA. Vaccines (Basel) 2022; 10:1969. [PMID: 36423064 PMCID: PMC9695509 DOI: 10.3390/vaccines10111969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2023] Open
Abstract
Genetic variants of vaccine poliovirus type 2, imported from an unknown source, were detected in waste waters in Jerusalem, London and New York in early 2022. Wild poliovirus type 2 was globally eradicated in 1999, but vaccine virus type 2 continued for 16 more years; routine use of the vaccine was discontinued in 2016 and reintroduced occasionally on purpose. As an unintended consequence, type 2 vaccine virus variants (circulating vaccine-derived polioviruses, cVDPVs) that mimic wild viruses' contagiousness and neurovirulence, have been emerging and spreading. To illustrate, in just the past four years (2018-2021), 2296 children developed cVDPV polio in 35 low-income countries. Many assume that virus transmission is via the faecal-oral route. Sustained virus transmission was documented in London and New York, in spite of high standards of sanitation and hygiene. Here, virus transmission cannot be attributed to faecal contamination of food or drinking water (for faecal-oral transmission). Hence, contagious transmission can only be explained by inhalation of droplets/aerosol containing virus shed in pharyngeal fluids (respiratory transmission), as was the classical teaching of polio epidemiology. If transmission efficiency of VDPV is via the respiratory route where hygiene is good, it stands to reason that it is the same case in countries with poor hygiene, since poor hygiene cannot be a barrier against respiratory transmission. By extrapolation, the extreme transmission efficiency of wild polioviruses must also have been due to their ability to exploit respiratory route transmission. These lessons have implications for global polio eradication. It was as a result of assuming faecal-oral transmission that eradication was attempted with live attenuated oral polio vaccine (OPV), ignoring its safety problems and very low efficacy in low-income countries. Inactivated poliovirus vaccine (IPV) is completely safe and highly efficacious in protecting children against polio, with just three routine doses. Protecting all children from polio must be the interim goal of eradication, until poliovirus circulation dies out under sustained immunisation pressure. OPV should be discontinued under cover of immunity induced by IPV to stop the emergence of new lineages of VDPVs, not only type 2, but also types 1 and 3, to expedite the completion of polio eradication.
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Affiliation(s)
- T. Jacob John
- Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Dhanya Dharmapalan
- Department of Pediatrics, Apollo Hospitals, CBD Belapur, Navi, Mumbai 400614, Maharashtra, India
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49
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Hill M, Pollard AJ. Detection of poliovirus in London highlights the value of sewage surveillance. Lancet 2022; 400:1491-1492. [PMID: 36243023 DOI: 10.1016/s0140-6736(22)01885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023]
Affiliation(s)
- Matilda Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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