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Andrianjakarivony FH, Bettarel Y, Cecchi P, Bouchard S, Chase E, Desnues C. Decoding the DNA and RNA viromes of a tropical urban lagoon. Environ Microbiol 2023; 25:2368-2387. [PMID: 37431274 DOI: 10.1111/1462-2920.16463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/19/2023] [Indexed: 07/12/2023]
Abstract
Human and livestock sewage is one of the major causes of excess nutrients, leading to the eutrophication of aquatic ecosystems and potentially to the emergence or spread of pathogenic viruses. This study aimed to investigate the composition and diversity of aquatic viromes in a highly anthropized lagoon, to identify the presence of pathogenic taxa and to explore their use as possible viral indicators of faecal contamination. For this, water and sediment samples were collected in the Ebrié Lagoon (Ivory Coast) at seven stations with contrasting levels of eutrophication. The DNA viromes of the planktonic and the benthic compartments were highly divergent, but were not influenced by the level of eutrophication. Conversely, the RNA viromes in the water column were comparable to those found in sediment, but showed significant differences between the stations. We detected the presence of viral DNA and RNA sequences we had assigned as indicators of faecal contamination (smacovirus, pecovirus and pepper mild mottle virus) as well as human pathogens (human cyclovirus, coxsackie B virus and picobirnavirus), which were all enriched in the most eutrophicated sites. These findings suggest that the examination of viromes represents a promising tool for assessing the state of human-induced contamination of aquatic ecosystems.
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Affiliation(s)
- Felana Harilanto Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Yvan Bettarel
- Marine Biodiversity, Exploitation & Conservation (MARBEC), University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Philippe Cecchi
- Marine Biodiversity, Exploitation & Conservation (MARBEC), University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Sonia Bouchard
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Emily Chase
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
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Kline A, Dean K, Kossik AL, Harrison JC, Januch JD, Beck NK, Zhou NA, Shirai JH, Boyle DS, Mitchell J, Meschke JS. Persistence of poliovirus types 2 and 3 in waste-impacted water and sediment. PLoS One 2022; 17:e0262761. [PMID: 35081146 PMCID: PMC8791527 DOI: 10.1371/journal.pone.0262761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022] Open
Abstract
Eradication of poliovirus (PV) is a global public health priority, and as clinical cases decrease, the role of environmental surveillance becomes more important. Persistence of PV and the environmental factors that influence it (such as temperature and sample type) are an important part of understanding and interpreting positive environmental surveillance samples. The objective of this study was to evaluate the persistence of poliovirus type 2 (PV2) and type 3 (PV3) in wastewater and sediment. Microcosms containing either 1) influent wastewater or 2) influent wastewater with a sediment matrix were seeded with either PV2 or PV3, and stored for up to 126 days at three temperatures (4°C, room temperature [RT], and 30°C). Active PV in the liquid of (1), and the sediment and liquid portions of (2) were sampled and quantified at up to 10 time points via plaque assay and RT-qPCR. A suite of 17 models were tested for best fit to characterize decay of PV2 and PV3 over time and determine the time points at which >90% (T90) and >99% (T99) reduction was reached. Linear models assessed the influence of experimental factors (matrix, temperature, virus type and method of detection) on the predicted T90 and T99 values. Results showed that when T90 was the dependent variable, virus type, matrix, and temperature significantly affected decay, and there was a clear interaction between the sediment matrix and temperature. When T99 was the dependent variable, only temperature and matrix type significantly influenced the decay metric. This study characterizes the persistence of both active and molecular PV2 and PV3 in relevant environmental conditions, and demonstrates that temperature and sediment both play important roles in PV viability. As eradication nears and clinical cases decrease, environmental surveillance and knowledge of PV persistence will play a key role in understanding the silent circulation in endemic countries.
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Affiliation(s)
- Allison Kline
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Kara Dean
- Biosystems & Agricultural Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Alexandra L. Kossik
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Joanna Ciol Harrison
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - James D. Januch
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicola K. Beck
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Jeffry H. Shirai
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | | | - Jade Mitchell
- Biosystems & Agricultural Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
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Di Cristanziano V, Weimer K, Böttcher S, Sarfo FS, Dompreh A, Cesar LG, Knops E, Heger E, Wirtz M, Kaiser R, Norman B, Phillips RO, Feldt T, Eberhardt KA. Molecular Characterization and Clinical Description of Non-Polio Enteroviruses Detected in Stool Samples from HIV-Positive and HIV-Negative Adults in Ghana. Viruses 2020; 12:v12020221. [PMID: 32079128 PMCID: PMC7077198 DOI: 10.3390/v12020221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
In the post-polio eradication era, increasing attention is given to non-polio enteroviruses. Most of the data about enteroviruses in sub-Saharan Africa are related to acute flaccid paralysis surveillance and target the pediatric population. This study aimed to investigate the presence of enterovirus in PLHIV (people living with HIV) and HIV-negative individuals in Ghana. Stool samples from HIV-positive individuals (n = 250) and healthy blood donors (n = 102) attending the Komfo Anokye Teaching Hospital in Kumasi, Ghana, were screened by real-time PCR for enterovirus. Molecular typing of the VP1 region was performed. Enterovirus-positive samples were tested for norovirus, adenovirus, rotavirus, sapovirus, and cosaviruses. Twenty-six out of 250 HIV-positive subjects (10.4%) and 14 out of 102 HIV-negative individuals (13.7%) were detected enterovirus-positive, not showing a significant different infection rate between the two groups. HIV-negative individuals were infected with Enterovirus C strains only. HIV-positive participants were detected positive for species Enterovirus A, Enterovirus B, and Enterovirus C. Co-infections with other viral enteric pathogens were almost exclusively detected among HIV-positive participants. Overall, the present study provides the first data about enteroviruses within HIV-positive and HIV-negative adults living in Ghana.
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Affiliation(s)
- Veronica Di Cristanziano
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Kristina Weimer
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Sindy Böttcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | - Fred Stephen Sarfo
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
| | | | | | - Elena Knops
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Eva Heger
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Maike Wirtz
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Betty Norman
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
| | - Richard Odame Phillips
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
- Kumasi Center for Collaborative Research in Tropical Medicine, Kumasi 00233, Ghana
| | - Torsten Feldt
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, 40225 Düsseldorf, Germany;
| | - Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
- Correspondence: ; Tel.: +49-40-428-180
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Ndiaye AK, Diop PAM, Diop OM. Environmental surveillance of poliovirus and non-polio enterovirus in urban sewage in Dakar, Senegal (2007-2013). Pan Afr Med J 2014; 19:243. [PMID: 25848458 PMCID: PMC4377292 DOI: 10.11604/pamj.2014.19.243.3538] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 07/23/2014] [Indexed: 11/16/2022] Open
Abstract
Introduction Global poliomyelitis eradication initiative relies on (i) laboratory based surveillance of acute flaccid surveillance (AFP) to monitor the circulation of wild poliovirus in a population, and (ii) vaccination to prevent its diffusion. However, as poliovirus can survive in the environment namely in sewage, environmental surveillance (ES) is of growing importance as the eradication target is close. This study aimed to assess polioviruses and non polio enteroviruses circulation in sewage drains covering a significant population of Dakar. Methods From April 2007 to May 2013, 271 specimens of raw sewage were collected using the grab method in 6 neighborhoods of Dakar. Samples were processed to extract and concentrate viruses using polyethylene glycol and Dextran (two-phase separation method). Isolation of enteroviruses was attempted in RD, L20B and Hep2 cell lines. Polioviruses were identified by RT-PCR and Elisa. Non Polio Enteroviruses (NPEVs) were identified by RT-PCR and microneutralisation tests. Results Polioviruses and NPEVs were respectively detected in 34,3% and 42,8% sewage samples. No wild poliovirus neither circulating vaccine-derived Poliovirus (cVDPV) was detected. Neutralization assays have identified 49 non polio enteroviruses that were subsequently classified in 13 serotypes belonging to HEV-A (22, 4%), HEV-B (12, 24%), HEV-C (26, 53%) and HEV-D (6, 12%) species. Conclusion This study is the first documentation of enteroviruses environmental detection in Senegal. It shows the usefulness of environmental surveillance for indirect monitoring of the circulation and distribution of enteroviruses in the community.
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Affiliation(s)
- Abdou Kader Ndiaye
- National Reference Center for Enteric Viruses, Medical Virology Unit, Institut Pasteur de Dakar, Senegal
| | - Pape Amadou Mbathio Diop
- National Reference Center for Enteric Viruses, Medical Virology Unit, Institut Pasteur de Dakar, Senegal
| | - Ousmane Madiagne Diop
- National Reference Center for Enteric Viruses, Medical Virology Unit, Institut Pasteur de Dakar, Senegal
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Momou KJ, Akoua-Koffi C, Dosso M. Detection of Enteroviruses in Water Samples from Yopougon, Côte d'Ivoire by Cell Culture and Polymerase Chain Reaction. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:23-30. [PMID: 24185752 DOI: 10.1007/s12560-013-9130-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 10/23/2013] [Indexed: 06/02/2023]
Abstract
The objective of this study was to compare sensitivities of enterovirus isolation from wastewater in different cell lines as well as to compare the sensitivity and specificity of isolation in cell culture with direct detection by reverse transcription polymerase chain reaction (RT-PCR). Sixty-eight samples of wastewaters were collected between September 2008 and January 2009 in Yopougon, Abidjan. Enteroviruses were concentrated according to World Health Organization recommendations. Viruses were inoculated into various cell lines while direct RT-PCR was performed on water concentrates. The buffalo green monkey kidney cell line was the most sensitive with 58.8 % of viral isolation. This was followed by the rhabdomyosarcoma cell line with sensitivity of 51.6 %, with human epidermoid carcinoma cell line showing sensitivity of 50 % and fibroblastic cells derived from transgenic mice LTK-1 (L20B) cell showing 23.50 % sensitivity. However, a lower specificity of 2.9 % was observed with the L20B cell line. 44.1 % of the samples were positive by direct RT-PCR detection while 51.47 % samples were positive by using RT-PCR on infected cell cultures. No difference in percentage positivity was observed using RT-PCR on infected tissue culture isolates or using RT-PCR directly on wastewater samples.
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Affiliation(s)
- K J Momou
- Unité des virus du système nerveux, Département virus épidémique, Institut Pasteur de Cote d'Ivoire, BP 490, Abidjan 01, Ivory Coast.
- UFR sciences et gestion de l'environnement, Laboratoire des sciences de l'environnement université Nangui Abrogoua, BP 801, Abidjan 02, Ivory Coast.
| | - C Akoua-Koffi
- UFR des sciences médicales de Bouaké, Université de Bouaké, Abidjan, Ivory Coast
| | - M Dosso
- Département bactériologie virologie, Institut Pasteur de Cote d'Ivoire, BP V153, Abidjan 01, Ivory Coast
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