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Bislava SB, Daja A, Oderinde BS, Uzairu SM. Prevalence of vaccine-derived poliovirus in sewage waters in Maiduguri, Borno State, Nigeria. LE INFEZIONI IN MEDICINA 2024; 32:90-98. [PMID: 38456020 PMCID: PMC10917565 DOI: 10.53854/liim-3201-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
After a long global battle with wild poliovirus, the virus has been defeated through researches and vaccination using the oral polio vaccine and inactivated polio vaccine as well as sensitization. The issue that is now of global concern is that of vaccine-derived poliovirus which emerged from the unstable oral polio vaccine. Ninety sewage water samples were collected from slums in Maiduguri using grab method, concentrated using two phase separation method and subjected to intratypic differentiation and vaccine-derived poliovirus screening. The result revealed the presence of Sabin 1in 17 samples (61.0%) and Sabin 3 in 22 samples (79.0%), all of which were positive after vaccine-derived poliovirus screening. The presence of strains of Sabin 1 and Sabin 3 in the sewage water samples collected is an indication of virus shedding in individuals which could be as a result of vaccination or contact with the faeces infected or vaccinated individuals.
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Affiliation(s)
| | - Aliyu Daja
- Department of Biochemistry, University of Maiduguri, Borno State, Nigeria
| | - Bamidele Soji Oderinde
- Department of Medical Laboratory Sciences, University of Maiduguri, Borno State, Nigeria
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2
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Bohrerova Z, Brinkman NE, Chakravarti R, Chattopadhyay S, Faith SA, Garland J, Herrin J, Hull N, Jahne M, Kang DW, Keely SP, Lee J, Lemeshow S, Lenhart J, Lytmer E, Malgave D, Miao L, Minard-Smith A, Mou X, Nagarkar M, Quintero A, Savona FDR, Senko J, Slonczewski JL, Spurbeck RR, Sovic MG, Taylor RT, Weavers LK, Weir M. Ohio Coronavirus Wastewater Monitoring Network: Implementation of Statewide Monitoring for Protecting Public Health. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2023; 29:845-853. [PMID: 37738597 PMCID: PMC10539008 DOI: 10.1097/phh.0000000000001783] [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] [Indexed: 09/24/2023]
Abstract
CONTEXT Prior to the COVID-19 pandemic, wastewater influent monitoring for tracking disease burden in sewered communities was not performed in Ohio, and this field was only on the periphery of the state academic research community. PROGRAM Because of the urgency of the pandemic and extensive state-level support for this new technology to detect levels of community infection to aid in public health response, the Ohio Water Resources Center established relationships and support of various stakeholders. This enabled Ohio to develop a statewide wastewater SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) monitoring network in 2 months starting in July 2020. IMPLEMENTATION The current Ohio Coronavirus Wastewater Monitoring Network (OCWMN) monitors more than 70 unique locations twice per week, and publicly available data are updated weekly on the public dashboard. EVALUATION This article describes the process and decisions that were made during network initiation, the network progression, and data applications, which can inform ongoing and future pandemic response and wastewater monitoring. DISCUSSION Overall, the OCWMN established wastewater monitoring infrastructure and provided a useful tool for public health professionals responding to the pandemic.
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Affiliation(s)
- Zuzana Bohrerova
- Ohio Water Resources Center (Drs Bohrerova, Lenhart, and Weavers), Civil, Environmental and Geodetic Engineering (Drs Bohrerova, Hull, Lenhart, and Weavers), Infectious Diseases Institute (Drs Faith and Lee and Ms Savona), Sustainability Institute (Dr Hull), Department of Food Science & Technology (Dr Lee), and Center for Applied Plant Sciences (Dr Sovic), The Ohio State University, Columbus, Ohio; Office of Research and Development, US Environmental Protection Agency, Washington, District of Columbia (Drs Brinkman, Garland, Jahne, Keely, and Nagarkar); Departments of Physiology and Pharmacology (Dr Chakravarti) and Medical Microbiology and Immunology (Drs Chattopadhyay and Taylor), University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; LuminUltra Technologies Inc, Hialeah, Florida (Mr Herrin and Dr Quintero); Department of Civil and Environmental Engineering, University of Toledo, Toledo, Ohio (Dr Kang); Divisions of Environmental Health Sciences (Drs Lee and Weir) and Biostatistics (Drs Lemeshow and Malgave and Ms Miao), The Ohio State University College of Public Health, Columbus, Ohio; Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio (Ms Lytmer); Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, Columbus, Ohio (Ms Minard-Smith and Dr Spurbeck); Department of Biological Sciences, Kent State University, Kent, Ohio (Dr Mou); Department of Geosciences and Department of Biology, The University of Akron, Akron, Ohio (Dr Senko); and Department of Biology, Kenyon College, Gambier, Ohio (Dr Slonczewski)
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3
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Bowes D, Darling A, Driver EM, Kaya D, Maal-Bared R, Lee LM, Goodman K, Adhikari S, Aggarwal S, Bivins A, Bohrerova Z, Cohen A, Duvallet C, Elnimeiry RA, Hutchison JM, Kapoor V, Keenum I, Ling F, Sills D, Tiwari A, Vikesland P, Ziels R, Mansfeldt C. Structured Ethical Review for Wastewater-Based Testing in Support of Public Health. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12969-12980. [PMID: 37611169 PMCID: PMC10484207 DOI: 10.1021/acs.est.3c04529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of WBT measured biomarkers for research activities and for the pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process, introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary workshop developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11 questions derived from primarily public health guidance. This study retrospectively applied these questions to SARS-CoV-2 monitoring programs covering the emergent phase of the pandemic (3/2020-2/2022 (n = 53)). Of note, 43% of answers highlight a lack of reported information to assess. Therefore, a systematic framework would at a minimum structure the communication of ethical considerations for applications of WBT. Consistent application of an ethical review will also assist in developing a practice of updating approaches and techniques to reflect the concerns held by both those practicing and those being monitored by WBT supported programs.
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Affiliation(s)
- Devin
A. Bowes
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
- Center on
Forced Displacement, Boston University, 111 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Amanda Darling
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Erin M. Driver
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Devrim Kaya
- School of
Chemical, Biological, and Environmental Engineering, Oregon State University, 105 26th St, Corvallis, Oregon 97331, United States
- School of
Public Health, San Diego State University, San Diego and Imperial Valley, California 92182, United States
| | - Rasha Maal-Bared
- Quality
Assurance and Environment, EPCOR Water Services Inc., EPCOR Tower, 2000−10423 101
Street NW, Edmonton, Alberta T5H 0E7, Canada
| | - Lisa M. Lee
- Department
of Population Health Sciences and Division of Scholarly Integrity
and Research Compliance, Virginia Tech, 300 Turner St. NW, Suite 4120 (0497), Blacksburg, Virginia 24061, United States
| | - Kenneth Goodman
- Institute
for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida 33101, United States
| | - Sangeet Adhikari
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Srijan Aggarwal
- Department
of Civil, Geological, and Environmental Engineering, University of Alaska Fairbanks, 1764 Tanana Loop, Fairbanks, Alaska 99775, United States
| | - Aaron Bivins
- Department
of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Zuzana Bohrerova
- The Ohio
State University, Department of Civil, Environmental
and Geodetic Engineering, 2070 Neil Avenue, 470 Hitchcock Hall, Columbus, Ohio 43210, United States
| | - Alasdair Cohen
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
- Department
of Population Health Sciences, Virginia
Tech, 205 Duck Pond Drive, Blacksburg, Virginia 24061, United States
| | - Claire Duvallet
- Biobot
Analytics, Inc., 501
Massachusetts Avenue; Cambridge, Massachusetts 02139, United States
| | - Rasha A. Elnimeiry
- Public
Health Outbreak Coordination, Informatics, Surveillance (PHOCIS) Office—Surveillance
Section, Division of Disease Control and Health Statistics, Washington State Department of Health, 111 Israel Rd SE, Tumwater, Washington 98501, United States
| | - Justin M. Hutchison
- Department
of Civil, Environmental, and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, Kansas 66045, United States
| | - Vikram Kapoor
- School
of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, Texas 78249, United States
| | - Ishi Keenum
- Complex
Microbial Systems Group, National Institute
of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Deborah Sills
- Department
of Civil and Environmental Engineering, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Ananda Tiwari
- Department
of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöberginkatu 2,
P.O. Box 66, FI 00014 Helsinki, Finland
- Expert
Microbiology Unit, Finnish Institute for
Health and Welfare, FI 70600 Kuopio, Finland
| | - Peter Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Ryan Ziels
- Department
of Civil Engineering, The University of
British Columbia, 6250
Applied Science Ln #2002, Vancouver, BC V6T 1Z4, Canada
| | - Cresten Mansfeldt
- Department
of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, UCB 428, Boulder, Colorado 80309, United States
- Environmental
Engineering Program, University of Colorado
Boulder, UCB 607, Boulder, Colorado 80309, United States
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4
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Liang Y, Chen J, Wang C, Yu B, Zhang Y, Liu Z. Investigating the mechanism of Echovirus 30 cell invasion. Front Microbiol 2023; 14:1174410. [PMID: 37485505 PMCID: PMC10359910 DOI: 10.3389/fmicb.2023.1174410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Viruses invade susceptible cells through a complex mechanism before injecting their genetic material into them. This causes direct damage to the host cell, as well as resulting in disease in the corresponding system. Echovirus type 30 (E30) is a member of the Enterovirus B group and has recently been reported to cause central nervous system (CNS) disorders, leading to viral encephalitis and viral meningitis in children. In this review, we aim to help in improving the understanding of the mechanisms of CNS diseases caused by E30 for the subsequent development of relevant drugs and vaccines.
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Affiliation(s)
- Yucai Liang
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Junbing Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing, China
| | - Congcong Wang
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Bowen Yu
- Department of Immunology, Weifang Medical University, Weifang, China
| | - Yong Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhijun Liu
- Department of Microbiology, Weifang Medical University, Weifang, China
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5
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Bowes DA, Darling A, Driver EM, Kaya D, Maal-Bared R, Lee LM, Goodman K, Adhikari S, Aggarwal S, Bivins A, Bohrerova Z, Cohen A, Duvallet C, Elnimeiry RA, Hutchison JM, Kapoor V, Keenum I, Ling F, Sills D, Tiwari A, Vikesland P, Ziels R, Mansfeldt C. Structured Ethical Review for Wastewater-Based Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.12.23291231. [PMID: 37398480 PMCID: PMC10312843 DOI: 10.1101/2023.06.12.23291231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of the field blurred the boundary between measuring biomarkers for research activities and for pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process (or associated data management safeguards), introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary group developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11-questions derived from primarily public health guidance because of the common exemption of wastewater samples to human subject research considerations. This study retrospectively applied the set of questions to peer- reviewed published reports on SARS-CoV-2 monitoring campaigns covering the emergent phase of the pandemic from March 2020 to February 2022 (n=53). Overall, 43% of the responses to the questions were unable to be assessed because of lack of reported information. It is therefore hypothesized that a systematic framework would at a minimum improve the communication of key ethical considerations for the application of WBT. Consistent application of a standardized ethical review will also assist in developing an engaged practice of critically applying and updating approaches and techniques to reflect the concerns held by both those practicing and being monitored by WBT supported campaigns. Abstract Figure Synopsis Development of a structured ethical review facilitates retrospective analysis of published studies and drafted scenarios in the context of wastewater-based testing.
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Affiliation(s)
- Devin A. Bowes
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
- Center on Forced Displacement, Boston University, 111 Cummington Mall, Boston, MA, 02215
| | - Amanda Darling
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 105 26th St, Corvallis, Oregon 97331
- School of Public Health, San Diego State University, San Diego and Imperial Valley, CA
| | - Rasha Maal-Bared
- Quality Assurance and Environment, EPCOR Water Services Inc., EPCOR Tower, 2000–10423 101 Street NW, Edmonton, Alberta, CA
| | - Lisa M. Lee
- Department of Population Health Sciences and Division of Scholarly Integrity and Research Compliance, Virginia Tech, 300 Turner St. NW, Suite 4120 (0497), Blacksburg, VA 24061
| | - Kenneth Goodman
- Institute for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
| | - Srijan Aggarwal
- Department of Civil, Geological, and Environmental Engineering, University of Alaska Fairbanks, 1764 Tanana Loop, Fairbanks, AK 99775
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803
| | - Zuzana Bohrerova
- The Ohio State University, Department of Civil, Environmental and Geodetic Engineering, 2070 Neil Avenue, 470 Hitchcock Hall, Columbus, OH 43210
| | - Alasdair Cohen
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
- Department of Population Health Sciences, Virginia Tech, 205 Duck Pond Drive, Blacksburg, VA 24061
| | - Claire Duvallet
- Biobot Analytics, Inc., 501 Massachusetts Avenue; Cambridge, MA; 02139
| | - Rasha A. Elnimeiry
- Public Health Outbreak Coordination, Informatics, Surveillance (PHOCIS) Office – Surveillance Section, Division of Disease Control and Health Statistics, Washington State Department of Health, 111 Israel Rd SE, Tumwater, WA 98501
| | - Justin M. Hutchison
- Department of Civil, Environmental, and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, KS 66045
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249
| | - Ishi Keenum
- Complex Microbial Systems Group, National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD 20899
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130
| | - Deborah Sills
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, 17837
| | - Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöberginkatu 2 P.O. Box 66 FI 00014 Helsinki, Finland
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Peter Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
| | - Ryan Ziels
- Department of Civil Engineering, the University of British Columbia, 6250 Applied Science Ln #2002, Vancouver, BC V6T 1Z4
| | - Cresten Mansfeldt
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, UCB 428, Boulder, CO 80309
- Environmental Engineering Program, University of Colorado Boulder, UCB 607, Boulder, CO 80309
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6
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Kisand V, Laas P, Palmik-Das K, Panksep K, Tammert H, Albreht L, Allemann H, Liepkalns L, Vooro K, Ritz C, Hauryliuk V, Tenson T. Prediction of COVID-19 positive cases, a nation-wide SARS-CoV-2 wastewater-based epidemiology study. WATER RESEARCH 2023; 231:119617. [PMID: 36682239 PMCID: PMC9845016 DOI: 10.1016/j.watres.2023.119617] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Taking advantage of Estonia's small size and population, we have employed wastewater-based epidemiology approach to monitor the spread of SARS-CoV-2, releasing weekly nation-wide updates. In this study we report results obtained between August 2020 and December 2021. Weekly 24 h composite samples were collected from wastewater treatment plants of larger towns already covered 65% of the total population that was complemented up to 40 additional grab samples from smaller towns/villages and the specific sites of concern. The N3 gene abundance was quantified by RT-qPCR. The N3 gene copy number (concentration) in wastewater fluctuated in accordance with the SARS-CoV-2 spread within the total population, with N3 abundance starting to increase 1.25 weeks (9 days) (95% CI: [1.10, 1.41]) before a rise in COVID-19 positive cases. Statistical model between the load of virus in wastewater and number of infected people validated with the Alpha variant wave (B.1.1.17) could be used to predict the order of magnitude in incidence numbers in Delta wave (B.1.617.2) in fall 2021. Targeted testing of student dormitories, retirement and nursing homes and prisons resulted in successful early discovery of outbreaks. We put forward a SARS-CoV-2 Wastewater Index (SARS2-WI) indicator of normalized virus load as COVID-19 infection metric to complement the other metrics currently used in disease control and prevention: dynamics of effective reproduction number (Re), 7-day mean of new cases, and a sum of new cases within last 14 days. In conclusion, an efficient surveillance system that combines analysis of composite and grab samples was established in Estonia. There is considerable discussion how the viral load in wastewater correlates with the number of infected people. Here we show that this correlation can be found. Moreover, we confirm that an increased signal in wastewater is observed before the increase in the number of infections. The surveillance system helped to inform public health policy and place direct interventions during the COVID-19 pandemic in Estonia via early warning of epidemic spread in various regions of the country.
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Affiliation(s)
- Veljo Kisand
- Institute of Technology, University of Tartu, Estonia.
| | - Peeter Laas
- Institute of Technology, University of Tartu, Estonia
| | | | | | - Helen Tammert
- Institute of Technology, University of Tartu, Estonia
| | | | - Hille Allemann
- Estonian Environmental Research Centre, Tallinn, Estonia
| | | | - Katri Vooro
- Estonian Environmental Research Centre, Tallinn, Estonia
| | - Christian Ritz
- Department of Population Health and Morbidity, National Institute of Public Health, University of Southern Denmark, Denmark
| | - Vasili Hauryliuk
- Institute of Technology, University of Tartu, Estonia; Department of Experimental Medical Science, Lund University, Sweden
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Estonia.
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7
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Grube AM, Coleman CK, LaMontagne CD, Miller ME, Kothegal NP, Holcomb DA, Blackwood AD, Clerkin TJ, Serre ML, Engel LS, Guidry VT, Noble RT, Stewart JR. Detection of SARS-CoV-2 RNA in wastewater and comparison to COVID-19 cases in two sewersheds, North Carolina, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159996. [PMID: 36356771 PMCID: PMC9639408 DOI: 10.1016/j.scitotenv.2022.159996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be useful for monitoring population-wide coronavirus disease 2019 (COVID-19) infections, especially given asymptomatic infections and limitations in diagnostic testing. We aimed to detect SARS-CoV-2 RNA in wastewater and compare viral concentrations to COVID-19 case numbers in the respective counties and sewersheds. Influent 24-hour composite wastewater samples were collected from July to December 2020 from two municipal wastewater treatment plants serving different population sizes in Orange and Chatham Counties in North Carolina. After a concentration step via HA filtration, SARS-CoV-2 RNA was detected and quantified by reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) and quantitative PCR (RT-qPCR), targeting the N1 and N2 nucleocapsid genes. SARS-CoV-2 RNA was detected by RT-ddPCR in 100 % (24/24) and 79 % (19/24) of influent wastewater samples from the larger and smaller plants, respectively. In comparison, viral RNA was detected by RT-qPCR in 41.7 % (10/24) and 8.3 % (2/24) of samples from the larger and smaller plants, respectively. Positivity rates and method agreement further increased for the RT-qPCR assay when samples with positive signals below the limit of detection were counted as positive. The wastewater data from the larger plant generally correlated (⍴ ~0.5, p < 0.05) with, and even anticipated, the trends in reported COVID-19 cases, with a notable spike in measured viral RNA preceding a spike in cases when students returned to a college campus in the Orange County sewershed. Correlations were generally higher when using estimates of sewershed-level case data rather than county-level data. This work supports use of wastewater surveillance for tracking COVID-19 disease trends, especially in identifying spikes in cases. Wastewater-based epidemiology can be a valuable resource for tracking disease trends, allocating resources, and evaluating policy in the fight against current and future pandemics.
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Affiliation(s)
- Alyssa M Grube
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Collin K Coleman
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Connor D LaMontagne
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Megan E Miller
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Nikhil P Kothegal
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - David A Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - A Denene Blackwood
- Institute of Marine Sciences, Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, United States
| | - Thomas J Clerkin
- Institute of Marine Sciences, Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, United States
| | - Marc L Serre
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Lawrence S Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States
| | - Virginia T Guidry
- Occupational and Environmental Epidemiology Branch, NC Department of Health and Human Services, 5505 Six Forks Road, Raleigh, NC 27609, United States
| | - Rachel T Noble
- Institute of Marine Sciences, Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, NC 27599, United States.
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8
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Gao Z, Li P, Lin H, Lin W, Ren Y. Biomarker selection strategies based on compound stability in wastewater-based epidemiology. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:5516-5529. [PMID: 36418835 PMCID: PMC9684832 DOI: 10.1007/s11356-022-24268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The specific compositions of human excreta in sewage can be used as biomarkers to indicate the disease prevalence, health status, and lifestyle of the population living in the investigated catchment. It is important for guiding and evaluating public health policies as well as promoting human health development. Among several parameters of wastewater-based epidemiology (WBE), the decay of biomarkers during transportation in sewer and storage plays a crucial role in the back-calculation of population consumption. In this paper, we summarized the stability data of common biomarkers in storage at different temperatures and in-sewer transportation. Among them, cardiovascular drugs and antidiabetic drugs are very stable which can be used as biomarkers; most of the illicit drugs are stable except for cocaine, heroin, and tetrahydrocannabinol which could be substituted by their metabolites as biomarkers. There are some losses for part of antibiotics and antidepressants even in frozen storage. Rapid detection of contagious viruses is a new challenge for infectious disease control. With the deeper and broader study of biomarkers, it is expected that the reliable application of the WBE will be a useful addition to epidemiological studies.
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Affiliation(s)
- Zhihan Gao
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Ping Li
- Datansha Branch of Guangzhou Sewage Treatment Co., Ltd, Guangzhou, 510163, China
| | - Han Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Wenting Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China.
- The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institution, Guangzhou, 510006, China.
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Standards to support an enduring capability in wastewater surveillance for public health: Where are we? CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100247. [PMID: 37520917 PMCID: PMC9376981 DOI: 10.1016/j.cscee.2022.100247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/02/2023]
Abstract
The COVID-19 pandemic highlighted a wide range of public health system challenges for infectious disease surveillance. The discovery that the SARS-CoV-2 virus was shed in feces and can be characterized using PCR-based testing of sewage samples offers new possibilities and challenges for wastewater surveillance (WWS). However, WWS standardization of practices is needed to provide actionable data for a public health response. A workshop was convened consisting of academic, federal government, and industry stakeholders. The objective was to review WWS sampling protocols, testing methods, analyses, and data interpretation approaches for WWS employed nationally and identify opportunities for standardizing practices, including the development of documentary standards or reference materials in the case of SARS-CoV-2 surveillance. Other WWS potential future threats to public health were also discussed. Several aspects of WWS were considered and each offers the opportunity for standards development. These areas included sampling strategies, analytical methods, and data reporting practices. Each of these areas converged on a common theme, the challenge of results comparability across facilities and jurisdictions. For sampling, the consensus solution was the development of documentary standards to guide appropriate sampling practices. In contrast, the predominant opportunity for analytical methods was reference material development, such as PCR-based standards and surrogate recovery controls. For data reporting practices, the need for establishing the minimal required metadata, a metadata vocabulary, and standardizing data units of measure including measurement threshold definitions was discussed. Beyond SARS-CoV-2 testing, there was general agreement that the WWS platform will continue to be a valuable tool for a wide range of public health threats and that future cross-sector engagements are needed to guide an enduring WWS capability.
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Vaccine-associated paralytic poliomyelitis in a child: fast transformation from Sabin-like virus to vaccine-derived poliovirus triggered an epidemiological response in two countries of the European region. Int J Infect Dis 2022; 125:35-41. [PMID: 36180034 DOI: 10.1016/j.ijid.2022.09.034] [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: 06/01/2022] [Revised: 08/16/2022] [Accepted: 09/23/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The detection of a vaccine-derived poliovirus (VDPV) requires an epidemiological assessment and response. Using repeated stool sampling from a child who is immunocompetent and was vaccinated against poliomyelitis with acute flaccid paralysis, a case of an extremely rapid evolution of Sabin-like poliovirus (PV) type 3 was traced in the child's body. METHODS The case was independently identified in two countries-Tajikistan and Russia. Stool samples for the study were also independently collected in two countries on different days from the onset of paralysis. Virological, serological, and molecular methods; full genome Sanger; and high-throughput sequencing were performed to characterize isolates. RESULTS PV isolates from samples collected on days 2, 3, and 14 contained eight, seven, and seven mutations in the VP1-coding region, respectively, and were classified as Sabin-like PV type 3. The isolates from samples collected on days 15 and 18 had 11 mutations and were classified as vaccine-derived PVs, which required an epidemiological response in the two countries. CONCLUSION The results indicate the need to continue acute flaccid paralysis surveillance, maintain high vaccination coverage, and develop and introduce new effective, genetically stable PV vaccines.
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11
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Kilaru P, Hill D, Anderson K, Collins MB, Green H, Kmush BL, Larsen DA. Wastewater Surveillance for Infectious Disease: A Systematic Review. Am J Epidemiol 2022; 192:305-322. [PMID: 36227259 PMCID: PMC9620728 DOI: 10.1093/aje/kwac175] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 02/07/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to be a valuable source of information regarding SARS-CoV-2 transmission and coronavirus disease 2019 (COVID-19) cases. Although the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens that have been surveilled through wastewater. Herein we identify the infectious diseases that have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as were themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and nonpolio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did, the value reported varied by study. Wastewater surveillance should be considered as a potential public health tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.
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Affiliation(s)
- Pruthvi Kilaru
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Des Moines University College of Osteopathic Medicine, Des Moines, Iowa, United States
| | - Dustin Hill
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States
| | - Kathryn Anderson
- Department of Medicine, State University of New York Upstate Medical University, Syracuse, New York, United States
| | - Mary B Collins
- Department of Environmental Studies, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Hyatt Green
- Department of Environmental Biology, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Brittany L Kmush
- Department of Public Health, Syracuse University, Syracuse, New York, United States
| | - David A Larsen
- Correspondence to Dr. Dave Larsen, Department of Public Health, Syracuse University, 430C White Hall, Syracuse, NY 13244 ()
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12
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Jiménez-Rodríguez MG, Silva-Lance F, Parra-Arroyo L, Medina-Salazar DA, Martínez-Ruiz M, Melchor-Martínez EM, Martínez-Prado MA, Iqbal HMN, Parra-Saldívar R, Barceló D, Sosa-Hernández JE. Biosensors for the detection of disease outbreaks through wastewater-based epidemiology. Trends Analyt Chem 2022; 155:116585. [PMID: 35281332 PMCID: PMC8898787 DOI: 10.1016/j.trac.2022.116585] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Wastewater-Based Epidemiology (WBE) is a novel community-wide monitoring tool that provides comprehensive real-time data of the public and environmental health status and can contribute to public health interventions, including those related to infectious disease outbreaks (e.g., the ongoing COVID-19 pandemic). Nonetheless, municipalities without centralized laboratories are likely still not able to process WBE samples. Biosensors are a potentially cost-effective solution to monitor the development of diseases through WBE to prevent local outbreaks. This review discusses the economic and technical feasibility of eighteen recently developed biosensors for the detection and monitoring of infectious disease agents in wastewater, prospecting the prevention of future pandemics.
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Affiliation(s)
| | - Fernando Silva-Lance
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | - Lizeth Parra-Arroyo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | - D Alejandra Medina-Salazar
- Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Department of Chemical and Biochemical Engineering, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, Durango, Dgo, 34080, Mexico
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | | | - María Adriana Martínez-Prado
- Tecnológico Nacional de México-Instituto Tecnológico de Durango (TecNM-ITD), Department of Chemical and Biochemical Engineering, Blvd. Felipe Pescador 1830 Ote. Col. Nueva Vizcaya, Durango, Dgo, 34080, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico
| | | | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18-26, 08034, Barcelona, Spain
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, C/Emili Grahit, 101, Edifici H2O, 17003, Girona, Spain
- College of Environmental and Resources Sciences, Zhejiang A&F University, Hangzhou, 311300, China
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13
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Long term detection and quantification of SARS-CoV-2 RNA in wastewater in Bahrain. JOURNAL OF HAZARDOUS MATERIALS ADVANCES 2022. [PMID: 37520797 PMCID: PMC9088096 DOI: 10.1016/j.hazadv.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Wastewater-based epidemiology is a corroborated environmental surveillance tool in the global fight against SARS-CoV-2. The analysis of wastewater for detection of SARS-CoV-2 RNA may assist policymakers to survey a specific infectious community. Herein, we report on a long-term quantification study in Bahrain to investigate the incidence of the SARS-CoV-2 RNA in wastewater during the COVID-19 pandemic. The ∼260,000 population of Muharraq Island in Bahrain is served by a discrete sewerage catchment, and all wastewater flows to a single large Sewage Treatment Plant (STP) with a capacity of 100,000 m3/day. The catchment is predominately domestic, but also serves several hospitals and Bahrain's international airport. Flow-weighted 24-h composite wastewater samples for the period February 2020 to October 2021 were analyzed for the presence of SARS-CoV-2 N1, N2 and E genes. A Spearman rank correlation demonstrated a moderate correlation between the concentration of SARS-CoV-2 N1, N2 and E genes in the wastewater samples and the number of COVID-19 cases reported on the same day of the sampling. SARS-CoV-2 viral genes were detected in wastewater samples shortly after the first cases of COVID-19 were reported by the health authorities in Bahrain by reverse transcription-polymerase chain reaction (RT-qPCR). The viral genes were detected in 55 of 65 samples (84.62%) during the whole study period and the concentration range was found to be between 0 and 11,508 RNA copies/mL across the viral genes tested (in average N1: 518.4, N2: 366.8 and E: 649.3 copies/mL). Furthermore, wastewater samples from two COVID-19-dedicated quarantine facilities were analysed and detected higher SARS-CoV-2 gene concentrations (range 27-19,105 copies/mL; in average N1: 5044, N2: 4833 and E: 8663 copies/mL). Our results highlight the potential use of RT-qPCR for SARS-CoV-2 detection and quantification in wastewater and present the moderate correlation between concentration of SARS-CoV-2 genes with reported COVID-19 cases for a specified population. Indeed, this study identifies this technique as a mechanism for long term monitoring of SARS-CoV-2 infection levels and hence provides public health and policymakers with a useful environmental surveillance tool during and after the current pandemic.
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14
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Kissova R, Pastuchova K, Lengyelova V, Svitok M, Mikas J, Klement C, Bopegamage S. History of the Wastewater Assessment of Polio and Non-Polio Enteroviruses in the Slovak Republic in 1963-2019. Viruses 2022; 14:1599. [PMID: 35893665 PMCID: PMC9331368 DOI: 10.3390/v14081599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022] Open
Abstract
We describe the genesis of poliovirus (PV) and non-polio enterovirus (NPEV) surveillance program of sewage wastewaters from its inception to the present in the Slovak Republic (SR). Sampling procedures and evolution of the methodology used in the SR for the detection of PVs and NPEVs are presented chronologically. For statistical data processing, we divided our dataset into two periods, the first period from 1963 to 1998 (35 years), and the second period from 1999 to 2019 (21 years). Generalized additive models were used to assess temporal trends in the probability of occurrence of major EV serotypes during both periods. Canonical correspondence analysis on relative abundance data was used to test temporal changes in the composition of virus assemblages over the second period. The probability of occurrence of major viruses PV, coxsackieviruses (CVA, CVB), and Echoviruses (E)) significantly changed over time. We found that 1015 isolated PVs were of vaccine origin, called "Sabin-like" (isolates PV1, PV2, PV3). The composition of EV assemblages changed significantly during the second period. We conclude that during the whole period, CVB5, CVB4, and E3 were prominent NPEVS in the SR.
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Affiliation(s)
- Renata Kissova
- Department of Medical Microbiology, Regional Public Health Authority Banska Bystrica, Cesta k Nemocnici 25, 97401 Banska Bystrica, Slovakia; (R.K.); (C.K.)
| | - Katarina Pastuchova
- National Reference Laboratory of Poliomyelitis Public Health Authority, Trnavska Cesta, 82102 Bratislava, Slovakia;
| | - Viera Lengyelova
- Department of Medical Microbiology, Regional Public Health Authority Senny Trh, 82009 Kosice, Slovakia;
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 96001 Zvolen, Slovakia;
| | - Jan Mikas
- Public Health Authority, Trnavska Cesta, 82102 Bratislava, Slovakia;
| | - Cyril Klement
- Department of Medical Microbiology, Regional Public Health Authority Banska Bystrica, Cesta k Nemocnici 25, 97401 Banska Bystrica, Slovakia; (R.K.); (C.K.)
- Faculty of Public Health, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovakia
| | - Shubhada Bopegamage
- Faculty of Medicine, Enterovirus Laboratory, Institute of Microbiology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovakia
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15
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Tao Z, Lin X, Liu Y, Ji F, Wang S, Xiong P, Zhang L, Xu Q, Xu A, Cui N. Detection of multiple human astroviruses in sewage by next generation sequencing. WATER RESEARCH 2022; 218:118523. [PMID: 35525029 DOI: 10.1016/j.watres.2022.118523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/09/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Human astrovirus (HAstV) composes of classic HAstV serotypes 1-8 and recently discovered novel HAstV-MLB and HAstV-VA strains. A number of studies have demonstrated that wastewater analysis is an effective approach to understand the prevalence and diversity of enteric viruses in local population. However, a comprehensive analysis of classic and novel HAstVs in sewage is still lacking. In this study, sewage samples were collected monthly from Jinan, China during 2018-2019. Quantification of HAstV genomes was performed by real-time quantitative PCR. Different from previous studies which focused on partial ORF1b or ORF2 gene, complete ORF2 region of HAstV was amplified from sewage concentrates, and amplicons were subjected to next generation sequencing (NGS) and genetic analysis. This methodology allowed detection of 18 astroviruses, of which 7 (HAstV-1, -2, -4, -5, VA1, VA2, and VA3) were detected in all sewage samples. A new strain VA6 mapped to the HMO clade was identified in 20.8% of samples, with 82.4%-83.3% nucleotide identities to the closest strain VA5. The viral load of classic, MLB and VA clades in sewage samples ranged from 3.7 × 104 to 4.6 × 107, 3.4 × 104 to 3.9 × 106, and 3.3 × 104 to 4.1 × 106 copies per liter, respectively. Phylogenetic analysis based on complete ORF2 region reflected local HAstVs within each genotype constituted multiple co-circulating lineages. Existence of several new lineages composed exclusively or predominantly of Chinese sequences was observed as well. These results demonstrate sewage contains astroviruses with considerable high diversities. NGS based environmental surveillance greatly improves the understanding of HAstV circulation and should be encouraged.
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Affiliation(s)
- Zexin Tao
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Xiaojuan Lin
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Yao Liu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Feng Ji
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Suting Wang
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Ping Xiong
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Li Zhang
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Qing Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China.
| | - Ning Cui
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Jinan 250355, China.
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Yanaç K, Adegoke A, Wang L, Uyaguari M, Yuan Q. Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153906. [PMID: 35218826 PMCID: PMC8864809 DOI: 10.1016/j.scitotenv.2022.153906] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
Although numerous studies have detected SARS-CoV-2 RNA in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 RNA and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 RNA in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 RNA in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 RNA concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in 15.27 ± 3.32% recovery of an internal positive control, Armored RNA, and a high positivity rate of SARS-CoV-2 RNA in stored wastewater samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids in fresh wastewater samples. Our results suggested that SARS-CoV-2 RNA may predominate in solids, and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 RNA was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 RNA was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 RNA concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 RNA loads in wastewater.
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Affiliation(s)
- Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada
| | - Adeola Adegoke
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Liqun Wang
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Miguel Uyaguari
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada.
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Krzysztoszek A, Gad B, Diedrich S, Böttcher S, Wieczorek M. Investigation of airport sewage to detect importation of poliovirus, Poland, 2017 to 2020. Euro Surveill 2022; 27:2100674. [PMID: 35713024 PMCID: PMC9205162 DOI: 10.2807/1560-7917.es.2022.27.24.2100674] [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: 04/09/2023] Open
Abstract
BackgroundPolioviruses are human pathogens which may easily be imported via travellers from endemic areas and countries where oral polio vaccine (OPV) is still routinely used to polio-free countries. Risk of reintroduction strictly depends on polio immunisation coverage. Sustaining a polio-free status requires strategies that allow rapid detection and control of potential poliovirus reintroductions.AimThe aim of this study was to apply environmental surveillance at an international airport in Poland to estimate the probability of poliovirus importation via air transport.MethodsBetween 2017 and 2020, we collected 142 sewage samples at Warsaw Airport. After sewage concentration, virus was isolated in susceptible cell cultures. Poliovirus isolates were characterised by intratypic differentiation and sequencing.ResultsSeven samples were positive for polioviruses. All isolates were characterised as Sabin-like polioviruses type 3 (SL-3). No wild or vaccine-derived polioviruses were found. The number of mutations accumulated in most isolates suggested a limited circulation in humans. Only one SL-3 isolate contained seven mutations, which is compatible with more than half a year of circulation.ConclusionSince OPV was withdrawn from the immunisation schedule in Poland in 2016, detection of SL-3 in airport sewage may indicate the events of importation from a region where OPV is still in use. Our study shows that environmental surveillance, including airport sewage investigation, has the capacity to detect emerging polioviruses and monitor potential exposure to poliovirus importation. Poliovirus detection in sewage samples indicates the need for sustaining a high level of polio immunisation coverage in the population.
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Affiliation(s)
- Arleta Krzysztoszek
- Department of Virology, National Institute of Public Health NIH - National Institute of Research, Warsaw, Poland
| | - Beata Gad
- Department of Virology, National Institute of Public Health NIH - National Institute of Research, Warsaw, Poland
| | - Sabine Diedrich
- Regional Reference Laboratory for Poliomyelitis, Robert Koch Institute, Berlin, Germany
| | - Sindy Böttcher
- Regional Reference Laboratory for Poliomyelitis, Robert Koch Institute, Berlin, Germany
| | - Magdalena Wieczorek
- Department of Virology, National Institute of Public Health NIH - National Institute of Research, Warsaw, Poland
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Dzinamarira T, Murewanhema G, Iradukunda PG, Madziva R, Herrera H, Cuadros DF, Tungwarara N, Chitungo I, Musuka G. Utilization of SARS-CoV-2 Wastewater Surveillance in Africa-A Rapid Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:969. [PMID: 35055789 PMCID: PMC8775514 DOI: 10.3390/ijerph19020969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 02/06/2023]
Abstract
Wastewater-based epidemiology for SARS-CoV-2 RNA detection in wastewater is desirable for understanding COVID-19 in settings where financial resources and diagnostic facilities for mass individual testing are severely limited. We conducted a rapid review to map research evidence on the utilization of SARS-CoV-2 wastewater surveillance in Africa. We searched PubMed, Google Scholar, and the World Health Organization library databases for relevant reports, reviews, and primary observational studies. Eight studies met the inclusion criteria. Narrative synthesis of the findings from included primary studies revealed the testing methodologies utilized and that detected amount of SARS-CoV-2 viral RNA correlated with the number of new cases in the studied areas. The included reviews revealed the epidemiological significance and environmental risks of SARS-CoV-2 wastewater. Wastewater surveillance data at the community level can be leveraged for the rapid assessment of emerging threats and aid pandemic preparedness. Our rapid review revealed a glaring gap in the primary literature on SARS-CoV-2 wastewater surveillance on the continent, and accelerated and adequate investment into research is urgently needed to address this gap.
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Affiliation(s)
- Tafadzwa Dzinamarira
- School of Health Systems & Public Health, University of Pretoria, Pretoria 0002, South Africa
- ICAP at Columbia University, Harare, Zimbabwe;
| | - Grant Murewanhema
- Unit of Obstetrics and Gynaecology, Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Patrick Gad Iradukunda
- London School of Hygiene and Tropical Medicine, University of London, London WC1E 7HU, UK;
| | - Roda Madziva
- School of Sociology and Social Policy, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Helena Herrera
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2UP, UK;
| | - Diego F. Cuadros
- Department of Geography and Geographic Information Science, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Nigel Tungwarara
- Department of Health Studies, University of South Africa, Pretoria 0002, South Africa;
| | - Itai Chitungo
- Chemical Pathology Unit, Department of Laboratory Diagnostic and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
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Ivanova OE, Shakaryan AK, Morozova NS, Vakulenko YA, Eremeeva TP, Kozlovskaya LI, Baykova OY, Shustova EY, Mikhailova YM, Romanenkova NI, Rozaeva NR, Dzhaparidze NI, Novikova NA, Zverev VV, Golitsyna LN, Lukashev AN. Cases of Acute Flaccid Paralysis Associated with Coxsackievirus A2: Findings of a 20-Year Surveillance in the Russian Federation. Microorganisms 2022; 10:microorganisms10010112. [PMID: 35056561 PMCID: PMC8780984 DOI: 10.3390/microorganisms10010112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Surveillance for acute flaccid paralysis syndrome (AFP) in children under 15 is the backbone of the Global Polio Eradication Initiative. Laboratory examination of stool samples from AFP cases allows the detection of, along with polioviruses, a variety of non-polio enteroviruses (NPEV). The etiological significance of these viruses in the occurrence of AFP cases has been definitively established only for enteroviruses A71 and D68. Enterovirus Coxsackie A2 (CVA2) is most often associated with vesicular pharyngitis and hand, foot and mouth disease. Among 7280 AFP cases registered in Russia over 20 years (2001–2020), CVA2 was isolated only from five cases. However, these included three children aged 3 to 4 years, without overt immune deficiency, immunized with 4–5 doses of poliovirus vaccine in accordance with the National Vaccination Schedule. The disease resulted in persistent residual paralysis. Clinical and laboratory data corresponded to poliomyelitis developing during poliovirus infection. These findings are compatible with CVA2 being the cause of AFP. Molecular analysis of CVA2 from these patients and a number of AFP cases in other countries did not reveal association with a specific phylogenetic group, suggesting that virus genetics is unlikely to explain the pathogenic profile. The overall results highlight the value of AFP surveillance not just for polio control but for studies of uncommon AFP agents.
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Affiliation(s)
- Olga E. Ivanova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
| | - Armen K. Shakaryan
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Pirogov Russian National Research Medical University, 119121 Moscow, Russia
| | - Nadezhda S. Morozova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Tatyana P. Eremeeva
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Liubov I. Kozlovskaya
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Olga Y. Baykova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Elena Y. Shustova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Yulia M. Mikhailova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | | | - Nadezhda R. Rozaeva
- Saint-Petersburg Pasteur Institute, 197101 Saint-Petersburg, Russia; (N.I.R.); (N.R.R.)
| | - Natela I. Dzhaparidze
- Federal Budgetary Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in the Vladimir Region”, 600005 Vladimir, Russia;
| | - Nadezhda A. Novikova
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Vladimir V. Zverev
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Lyudmila N. Golitsyna
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
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20
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Keeren K, Böttcher S, Diedrich S. Enterovirus Surveillance (EVSurv) in Germany. Microorganisms 2021; 9:2005. [PMID: 34683328 PMCID: PMC8538599 DOI: 10.3390/microorganisms9102005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
The major aim of the enterovirus surveillance (EVSurv) in Germany is to prove the absence of poliovirus circulation in the framework of the Global Polio Eradication Program (GPEI). Therefore, a free-of-charge enterovirus diagnostic is offered to all hospitals for patients with symptoms compatible with a polio infection. Within the quality proven laboratory network for enterovirus diagnostic (LaNED), stool and cerebrospinal fluid (CSF) samples from patients with suspected aseptic meningitis/encephalitis or acute flaccid paralysis (AFP) are screened for enterovirus (EV), typing is performed in all EV positive sample to exclude poliovirus infections. Since 2006, ≈200 hospitals from all 16 German federal states have participated annually. On average, 2500 samples (70% stool, 28% CSF) were tested every year. Overall, the majority of the patients studied are children <15 years. During the 15-year period, 53 different EV serotypes were detected. While EV-A71 was most frequently detected in infants, E30 dominated in older children and adults. Polioviruses were not detected. The German enterovirus surveillance allows monitoring of the circulation of clinically relevant serotypes resulting in continuous data about non-polio enterovirus epidemiology.
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Affiliation(s)
- Kathrin Keeren
- Secretary of the National Commission for Polio Eradication in Germany, Robert Koch Institute, 13353 Berlin, Germany;
| | - Sindy Böttcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | | | - Sabine Diedrich
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
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21
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Tian X, Han Z, He Y, Sun Q, Wang W, Xu W, Li H, Zhang Y. Temporal phylogeny and molecular characterization of echovirus 30 associated with aseptic meningitis outbreaks in China. Virol J 2021; 18:118. [PMID: 34092258 PMCID: PMC8182919 DOI: 10.1186/s12985-021-01590-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An outbreak of aseptic meningitis occurred from June to August 2016, in Inner Mongolia Autonomous Region, China. METHODS To determine its epidemiological characteristics, etiologic agent, and possible origin, specimens were collected for virus isolation and identification, followed by molecular epidemiological analysis. RESULTS A total of 363 patients were clinically diagnosed from June 1st to August 31st 2016, and most cases (63.1%, n = 229) were identified between June 22nd and July 17th, with children aged 6 to 12 years constituting the highest percentage (68.9%, n = 250). All viral isolates from this study belonged to genotype C of echovirus 30 (E30), which dominated transmission in China. To date, two E30 transmission lineages have been identified in China, of which Lineage 2 was predominant. We observed fluctuant progress of E30 genetic diversity, with Lineage 2 contributing to increased genetic diversity after 2002, whereas Lineage 1 was significant for the genetic diversity of E30 before 2002. CONCLUSIONS We identified the epidemiological and etiological causes of an aseptic meningitis outbreak in Inner Mongolia in 2016, and found that Lineage 2 played an important role in recent outbreaks. Moreover, we found that Gansu province could play an important role in E30 spread and might be a possible origin site. Furthermore, Fujian, Shandong, Taiwan, and Zhejiang provinces also demonstrated significant involvement in E30 evolution and persistence over time in China.
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Affiliation(s)
- Xiaoling Tian
- Inner Mongolia Center for Disease Control and Prevention, Huhhot, 010031, People's Republic of China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yulong He
- Tongliao City Center for Disease Control and Prevention, Tongliao, 028000, People's Republic of China
| | - Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Wenrui Wang
- Inner Mongolia Center for Disease Control and Prevention, Huhhot, 010031, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Hongying Li
- Tongliao City Hospital, Tongliao, 028000, People's Republic of China.
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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22
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Anderson-Coughlin BL, Shearer AEH, Omar AN, Wommack KE, Kniel KE. Recovery of SARS-CoV-2 from Wastewater Using Centrifugal Ultrafiltration. Methods Protoc 2021; 4:mps4020032. [PMID: 34065842 PMCID: PMC8162551 DOI: 10.3390/mps4020032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 01/13/2023] Open
Abstract
The COVID-19 pandemic is a global crisis and continues to impact communities as the disease spreads. Clinical testing alone provides a snapshot of infected individuals but is costly and difficult to perform logistically across whole populations. The virus which causes COVID-19, SARS-CoV-2, is shed in human feces and urine and can be detected in human waste. SARS-CoV-2 can be shed in high concentrations (>107 genomic copies/mL) due to its ability to replicate in the gastrointestinal tract of humans through attachment to the angiotensin-converting enzyme 2 (ACE-2) receptors there. Monitoring wastewater for SARS-CoV-2, alongside clinical testing, can more accurately represent the spread of disease within a community. This protocol describes a reliable and efficacious method to recover SARS-CoV-2 in wastewater, quantify genomic RNA levels, and evaluate concentration fluctuations over time. Using this protocol, viral levels as low as 10 genomic copies/mL were successfully detected from 30 mL of wastewater in more than seven-hundred samples collected between August 2020 and March 2021. Through the adaptation of traditional enteric virus methods used in food safety research, targets have been reliably detected with no inhibition of detection (RT-qPCR) observed in any sample processed. This protocol is currently used for surveillance of wastewater systems across New Castle County, Delaware.
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Affiliation(s)
- Brienna L. Anderson-Coughlin
- Center for Environmental and Wastewater-Based Epidemiological Research, Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA; (B.L.A.-C.); (A.E.H.S.); (A.N.O.)
| | - Adrienne E. H. Shearer
- Center for Environmental and Wastewater-Based Epidemiological Research, Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA; (B.L.A.-C.); (A.E.H.S.); (A.N.O.)
| | - Alexis N. Omar
- Center for Environmental and Wastewater-Based Epidemiological Research, Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA; (B.L.A.-C.); (A.E.H.S.); (A.N.O.)
| | - K. Eric Wommack
- Center for Environmental and Wastewater-Based Epidemiological Research, Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Kalmia E. Kniel
- Center for Environmental and Wastewater-Based Epidemiological Research, Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA; (B.L.A.-C.); (A.E.H.S.); (A.N.O.)
- Correspondence:
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23
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Cheng W, Ji T, Zhou S, Shi Y, Jiang L, Zhang Y, Yan D, Yang Q, Song Y, Cai R, Xu W. Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018. Arch Virol 2021; 166:1305-1312. [PMID: 33638089 PMCID: PMC8036204 DOI: 10.1007/s00705-020-04934-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/04/2020] [Indexed: 11/26/2022]
Abstract
Echovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.
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Affiliation(s)
- Wenjun Cheng
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Tianjiao Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuaifeng Zhou
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Yong Shi
- Jiangxi Provincial Centers for Disease Control and Prevention, Nanchang, People's Republic of China
| | - Lili Jiang
- Yunnan Provincial Centers for Disease Control and Prevention, Kunming, People's Republic of China
| | - Yong Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongmei Yan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Qian Yang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yang Song
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Ru Cai
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
| | - Wenbo Xu
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
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24
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Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases. Viruses 2021; 13:v13010120. [PMID: 33477302 PMCID: PMC7829892 DOI: 10.3390/v13010120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011-2012, and then in 2017-2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017-2018. There was a predominance of types from EV-C in 2017-2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011-2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.
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Zhao C, Lin X, Ji F, Xiong P, Liu Y, Wang S, Chen P, Xu Q, Zhang L, Tao Z, Xu A. Prevalence and Bayesian Phylogenetics of Enteroviruses Derived From Environmental Surveillance Around Polio Vaccine Switch Period in Shandong Province, China. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:321-332. [PMID: 33108600 DOI: 10.1007/s12560-020-09449-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
We present the results of environmental surveillance for poliovirus (PV) and non-poliovirus (NPEV) around the switch from trivalent to bivalent oral polio-vaccine (OPV) which occurred in China in May 2016. Sewage samples were collected in Jinan and Linyi city from 2015 to 2017. Enterovirus (EV) isolation, VP1 amplification, Sanger sequencing, and phylogenetic analyses were performed. Among105 sewage samples (36 in Jinan and 69 in Linyi), 101 were positive for EV, with 74.3% (78/105) PV-positive samples and 90.5% (95/105) NPEV-positive samples. A total of 893 EV isolates were obtained, including 326 (36.5%) PVs and 567 (63.5%) NPEVs. Echovirus (E) -11 was the most common serotype out of 18 detected NPEV types (120/567), followed by E-3 (75/567) and E-6 (74/567). PV2 vanished and PV3 came to be the ascendant PV type in sewage after May 2016. Eight PV isolates were judged as pre-vaccine-derived poliovirus (pre-VDPV) and no VDPV or wild PV isolates were monitored. Bayesian phylogenetics demonstrated global E-11 originated in 1876 and evolved with the estimated rate of 4.63 × 10-3 nucleotide substitutions per site per year (s/s/y). Multiple circulating clusters that originated at different times were coexisting in Shandong province. The most recently common ancestor of global coxsackievirus B5 could date back to 1867, at the evolutionary rate of 3.95 × 10-3 s/s/y. In conclusion, our study described the changes of PVs and NPEVs around the polio vaccine switch period and provided meaningful global molecular epidemiological data for further studies of EV-related diseases among the population.
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Affiliation(s)
- Chenxu Zhao
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Ping Xiong
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Yao Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Suting Wang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Peng Chen
- Hospital of Stomatology, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Cheeloo College of Medicine, Shandong University, 44-1 Wenhuaxi Road, Jinan, 250012, Shandong, China
| | - Qing Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Li Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China.
| | - Aiqiang Xu
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhuaxi Road, Jinan, 250012, Shandong, China.
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan, 250014, Shandong, China.
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26
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Venugopal A, Ganesan H, Sudalaimuthu Raja SS, Govindasamy V, Arunachalam M, Narayanasamy A, Sivaprakash P, Rahman PKSM, Gopalakrishnan AV, Siama Z, Vellingiri B. Novel wastewater surveillance strategy for early detection of coronavirus disease 2019 hotspots. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2020; 17:8-13. [PMID: 32501429 PMCID: PMC7245214 DOI: 10.1016/j.coesh.2020.05.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The novel coronavirus disease 2019, a pandemic of global concern, caused by the novel severe acute respiratory syndrome coronavirus 2 has severely revealed the need for public monitoring and efficient screening techniques. Despite the various advancements made in the medical and research field, containment of this virus has proven to be difficult on several levels. As such, it is a necessary requirement to identify possible hotspots in the early stages of any disease. Based on previous studies carried out on coronaviruses, there is a high likelihood that severe acute respiratory syndrome coronavirus 2 may also survive in wastewater. Hence, we propose the use of nanofiber filters as a wastewater pretreatment routine and upgradation of existing wastewater evaluation and treatment systems to serve as a beneficial surveillance tool.
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Affiliation(s)
- Anila Venugopal
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Harsha Ganesan
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Suresh Selvapuram Sudalaimuthu Raja
- Department of Microbiology, Government Arts and Science College (Affiliated to Bharathidasan University, Trichy), Perambalur 621107, Tamil Nadu, India
| | | | - Manimekalan Arunachalam
- Department of Environmental Sciences, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Arul Narayanasamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Palanisamy Sivaprakash
- Centre for Environmental Awareness, Department of Mechanical Engineering, Dr.N.G.P. Institute of Technology, Coimbatore 641048, Tamil Nadu, India
| | - Pattanathu K S M Rahman
- Deploy Lead - Centre for Enzyme Innovation, Office No: 6.06, King Henry Building, School of Biological Science, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, VIT, Vellore 632014, Tamil Nadu, India
| | - Zothan Siama
- Department of Zoology, School of Life-science, Mizoram University, Aizawl 796004, Mizoram, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
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Korotkova EA, Prostova MA, Gmyl AP, Kozlovskaya LI, Eremeeva TP, Baikova OY, Krasota AY, Morozova NS, Ivanova OE. Case of Poliomyelitis Caused by Significantly Diverged Derivative of the Poliovirus Type 3 Vaccine Sabin Strain Circulating in the Orphanage. Viruses 2020; 12:v12090970. [PMID: 32883046 PMCID: PMC7552002 DOI: 10.3390/v12090970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/26/2022] Open
Abstract
Significantly divergent polioviruses (VDPV) derived from the oral poliovirus vaccine (OPV) from Sabin strains, like wild polioviruses, are capable of prolonged transmission and neuropathology. This is mainly shown for VDPV type 2. Here we describe a molecular-epidemiological investigation of a case of VDPV type 3 circulation leading to paralytic poliomyelitis in a child in an orphanage, where OPV has not been used. Samples of feces and blood serum from the patient and 52 contacts from the same orphanage were collected twice and investigated. The complete genome sequencing was performed for five polioviruses isolated from the patient and three contact children. The level of divergence of the genomes of the isolates corresponded to approximately 9–10 months of evolution. The presence of 61 common substitutions in all isolates indicated a common intermediate progenitor. The possibility of VDPV3 transmission from the excretor to susceptible recipients (unvaccinated against polio or vaccinated with inactivated poliovirus vaccine, IPV) with subsequent circulation in a closed children’s group was demonstrated. The study of the blood sera of orphanage residents at least twice vaccinated with IPV revealed the absence of neutralizing antibodies against at least two poliovirus serotypes in almost 20% of children. Therefore, a complete rejection of OPV vaccination can lead to a critical decrease in collective immunity level. The development of new poliovirus vaccines that create mucosal immunity for the adequate replacement of OPV from Sabin strains is necessary.
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Affiliation(s)
- Ekaterina A. Korotkova
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia;
- Correspondence: (E.A.K.); (O.E.I.); Tel.: +7-916-169-86-12 (E.A.K.); +7-916-677-24-03 (O.E.I.)
| | - Maria A. Prostova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Anatoly P. Gmyl
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Liubov I. Kozlovskaya
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Tatiana P. Eremeeva
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Olga Y. Baikova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Alexandr Y. Krasota
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia;
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
| | - Nadezhda S. Morozova
- Federal Centre of Hygiene and Epidemiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 117105 Moscow, Russia;
| | - Olga E. Ivanova
- Federal State Budgetary Scientific Institution “Chumakov Federal Scientific Centre for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (FSBSI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (M.A.P.); (L.I.K.); (T.P.E.); (O.Y.B.)
- Institute for Bionic Technologies and Engineering, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (E.A.K.); (O.E.I.); Tel.: +7-916-169-86-12 (E.A.K.); +7-916-677-24-03 (O.E.I.)
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Baicus A, Joffret ML, Bessaud M, Delpeyroux F, Oprisan G. Reinforced poliovirus and enterovirus surveillance in Romania, 2015-2016. Arch Virol 2020; 165:2627-2632. [PMID: 32776175 DOI: 10.1007/s00705-020-04772-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Due to the risk of poliovirus importation from Ukraine in 2015, a combined surveillance program monitoring the circulation of enteroviruses (EVs) in healthy children from at-risk areas and in the environment was conducted in Romania. Virological testing of stool samples collected from 155 healthy children aged from two months to six years and of 186 sewage water samples collected from different areas was performed. A total of 58 (37.42%) stool samples and 50 (26.88%) sewage water samples were positive for non-polio EVs, but no poliovirus was detected. A high level of circulation of echovirus (E) types 6 and 7 and coxsackievirus (CV) type B5 was observed.
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Affiliation(s)
- Anda Baicus
- Cantacuzino Medico Military National Institute of Research and Development, Bucharest, Romania. .,Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
| | | | | | | | - Gabriela Oprisan
- Cantacuzino Medico Military National Institute of Research and Development, Bucharest, Romania.,Faculty of Pharmacy, Titu Maiorescu University, Bucharest, Romania
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Tao Z, Chen P, Cui N, Lin X, Ji F, Liu Y, Xiong P, Zhang L, Xu Q, Song Y, Xu A. Detection of enteroviruses in urban sewage by next generation sequencing and its application in environmental surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138818. [PMID: 32570328 DOI: 10.1016/j.scitotenv.2020.138818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/26/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Environmental surveillance has been used successfully in monitoring enterovirus (EV) circulation; however cell culture method may introduce a selective bias in those EV strains that are recovered from the environment. In this study, urban sewage samples were collected monthly in Jinan, China in 2018 and concentrated via membrane adsorption/elution method. A P1 seminested RT-PCR (RT-snPCR) and NGS method was developed, by which amplicons of 4000 nucleotide in length covering the entire P1 region of EVs were obtained from sewage concentrates and were further analyzed by next generation sequencing (NGS). In addition, for each sewage concentrate, two other assays - cell culture and NGS based partial VP1 amplicon sequencing - were conducted in parallel and compared. The results showed that the P1 RT-snPCR and NGS method generated the most data, with 32 serotypes identified belonging to species EV-A (n = 11), EV-B (n = 14), and EV-C (n = 7). These serotypes covered all those detected from the methods of cell culture (n = 10) and partial VP1 amplicon sequencing (n = 16). EV serotypes from acute flaccid paralysis surveillance correlated with those from sewage. Phylogenetic analysis on coxsackievirus B5, a common pathogen of meningitis, revealed close genetic relationship between environmental and clinical sequences. These results demonstrate sewage contains different EVs related to a variety of diseases. Traditional cell culture method underestimates the existence of some serotypes. NGS based environmental surveillance provides data which are consistent with those from clinical diseases, greatly improves our understanding on the actual circulation in the population, and should be encouraged for public health surveillance.
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Affiliation(s)
- Zexin Tao
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Peng Chen
- School and Hospital of Stomatology, Shandong University, 44-1 Wenhuaxi Road, Jinan 250012, China
| | - Ning Cui
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Jinan 250355, China
| | - Xiaojuan Lin
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Feng Ji
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Yao Liu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Ping Xiong
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Li Zhang
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Qing Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Yanyan Song
- School of Public Health, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China.
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China; School of Public Health, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China.
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30
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Environmental Surveillance Complements Case-Based Surveillance of Acute Flaccid Paralysis in Polio Endgame Strategy 2019-2023. Appl Environ Microbiol 2020; 86:AEM.00702-20. [PMID: 32444474 DOI: 10.1128/aem.00702-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 11/20/2022] Open
Abstract
The Polio Endgame Strategy 2019-2023 has been developed. However, more effective and efficient surveillance activities should be conducted with the preparedness of emergence for vaccine-derived poliovirus (VDPV) or wild poliovirus (WPV). We reviewed the impact of the case-based acute flaccid paralysis (AFP) surveillance (1991 to 2018) and environmental surveillance (2011 to 2018) in polio eradication in Shandong province of China. Clinical characteristics of AFP cases and enterovirus (EV) investigation of research samples were assessed. During the period, 10,224 AFP cases were investigated, and 352 sewage samples were collected. The nonpolio AFP rate sustained at over 2.0/100,000 since 1997. Of 10,224 cases, males and young children experienced a higher risk of severe diseases, and 68.5% suffered lower limb paralysis. We collected 1,707 EVs from AFP cases, including 763 polioviruses and 944 nonpolio enteroviruses (NPEVs). No WPV was isolated since 1992. The AFP surveillance showed high sensitivity in detecting 143 vaccine-associated paralytic poliomyelitis (VAPP) cases and 6 VDPVs. For environmental surveillance, 217 (61.6%) samples were positive for poliovirus, and altogether, 838 polioviruses and 2,988 NPEVs were isolated. No WPV was isolated in environmental surveillance, although one VDPV2 was identified. Phylogenetic analysis revealed environmental surveillance had the capacity to detect a large scope of NPEVs. The case-based AFP surveillance will be indispensable for detecting VAPP cases and VDPV circulation in countries using oral polio vaccine. Environmental surveillance is advantageous in identifying EV circulation and responding to ongoing circulating VDPV outbreaks and should be expanded to complement the AFP surveillance.IMPORTANCE Interrupting wild poliovirus transmission and stopping circulating vaccine-derived poliovirus (cVDPV) outbreaks have been proposed as two global goals by the World Health Organization in the Global Polio Eradication Initiative (GPEI). This analysis, based on the 28-year acute flaccid paralysis (AFP) surveillance and 8-year environmental surveillance, provides continued high-quality surveillance performance in achieving the GPEI and detecting the circulation of enterovirus. Given the ongoing cVDPV outbreaks in the world, we present the surveillance capacity of environmental surveillance in capturing enterovirus circulation. The final poliovirus (especially VDPV) elimination has become increasingly complex, and the case-based AFP surveillance alone will lead to difficulties in early detecting dynamics of poliovirus transmission and monitoring the extent of environmental circulation. This study goes beyond previous work to provide a detailed comprehensive evaluation of the enterovirus surveillance and can be used to formulate a set of implementation plan and performance indicators for environmental surveillance.
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Beyer S, Szewzyk R, Gnirss R, Johne R, Selinka HC. Detection and Characterization of Hepatitis E Virus Genotype 3 in Wastewater and Urban Surface Waters in Germany. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:137-147. [PMID: 32172512 PMCID: PMC7225198 DOI: 10.1007/s12560-020-09424-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/04/2020] [Indexed: 05/18/2023]
Abstract
In highly populated areas, environmental surveillance of wastewater and surface waters is a key factor to control the circulation of viruses and risks for public health. Hepatitis E virus (HEV) genotype 3 is considered as an emerging pathogen in industrialized countries. Therefore, this study was carried out to determine the prevalence of HEV in environmental waters in urban and suburban regions in Germany. HEV was monitored in water samples using quantitative RT-PCR (RT-qPCR) and nested RT-PCR without or with virus concentration via polyethylene glycol precipitation or ultracentrifugation. By RT-qPCR, 84-100% of influent samples of wastewater treatment plants were positive for HEV RNA. Genotypes HEV-3c and 3f were identified in wastewater, with HEV-3c being the most prevalent genotype. These data correlate with subtypes identified earlier in patients from the same area. Comparison of wastewater influent and effluent samples revealed a reduction of HEV RNA of about 1 log10 during passage through wastewater treatment plants. In addition, combined sewer overflows (CSOs) after heavy rainfalls were shown to release HEV RNA into surface waters. About 75% of urban river samples taken during these CSO events were positive for HEV RNA by RT-qPCR. In contrast, under normal weather conditions, only around 30% of river samples and 15% of samples from a bathing water located at an urban river were positive for HEV. Median concentrations of HEV RNA of all tested samples at this bathing water were below the limit of detection.
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Affiliation(s)
- Sophia Beyer
- Section II 1.4 Microbiological Risks, German Environment Agency (UBA), Corrensplatz 1, 14195, Berlin, Germany
| | - Regine Szewzyk
- Section II 1.4 Microbiological Risks, German Environment Agency (UBA), Corrensplatz 1, 14195, Berlin, Germany
| | - Regina Gnirss
- Berliner Wasserbetriebe (BWB), Cicerostr. 24, 10709, Berlin, Germany
| | - Reimar Johne
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, German Environment Agency (UBA), Corrensplatz 1, 14195, Berlin, Germany.
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Popova AY, Ezhlova EB, Melnikova AA, Morozova NS, Mikhailova YM, Ivanova OE, Kozlovskaya LI, Eremeeva TP, Gmyl AP, Korotkova EA, Baykova OY, Krasota AY, Ivanenko АV, Yarmolskaya MS, Kovalchuk IV, Romanenko EN. Measures counteracting 2016 spread of vaccine-derived poliomyelitis virus type 2 in Russian Federation. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-mcs-1303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Since April 2016 after global cessation of using trivalent oral poliovirus vaccine (tOPV) and switch to bivalent OPV consisting of polioviruses types 1 and 3 (the “switch”), any isolation of type 2 poliovirus has been regarded as an event of extreme importance requiring investigation, risk assessment and decision making. In 2016, 2 cases of isolated vaccine-derived poliovirus type 2 from healthy children was registered in Russia. Our study was aimed at on the assessing a risk of further spread of vaccine-derived poliovirus type 2 and provide measures for preventing its further spread based on epidemiological investigation and genetic characteristics of the isolated viruses. The cases were revealed within the surveillance program for poliomyelitis and acute flaccid paralysis syndrome conducted in the Russian Federation. The laboratory investigation was carried out in accordance with the algorithm adopted in the Russian Federation and recommended by the WHO standards: virus isolation on RD, L20B and Hep2C cell cultures, identification in the neutralization reaction, intratyping differentiation by using RT-PCR in real-time mode, sequencing of the poliovirus genome fragments encoding the VP1 protein. A risk assessment for spread of vaccine-derived poliovirus type 2 was performed in accordance with the WHO recommendations. There was uncovered a genetic relationship between virus strains isolated in September and December from unvaccinated Moscow resident boy (1 year old) who arrived from the Chechen Republic and from unvaccinated girl resident of the Chechen Republic (1 year old) with impaired humoral and cellular immunity. The virus strains were found to bear 10 and 13 genomic nucleotide substitutions, respectively, at the site encoding the VP1 protein compared with the Sabin type 2 vaccine strain that allowed to classify them as vaccine-derived polioviruses. In particular, both virus strains were shown to originate from the type 2 strain presented in the tOPV used shortly before the “switch”. Epidemiological investigation revealed family ties and probable contact between both children in the same premises. A series of organizational and vaccination measures was undertaken, as well as polio surveillance was strengthened in the region. No new type 2 polioviruses of vaccine origin were detected in the territory of the Chechen Republic during 18-month monitoring follow-up. The risk assessment of spread for vaccine-derived poliovirus type 2 in a region, Russian Federation as well as cross-boundary spread identified it as “low,” requiring no use of type 2 monovalent OPV. Such experience for countermeasures may be taken into account to oppose the risks before and after the global certification for poliomyelitis eradication.
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