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Panova N, Allan NP, Rubas NC, Lee RH, Kunihiro BP, Umeda L, Peres R, Juarez R, Maunakea AK. Sequencing the SARS-CoV-2 Genome from Stool Samples of Post-acute Cases Implicates a Novel Mutation Associated with Reduced Antibody Neutralization. EUROPEAN JOURNAL OF BIOMEDICAL RESEARCH 2023; 2:17-23. [PMID: 37525697 PMCID: PMC10389300 DOI: 10.24018/ejbiomed.2023.2.3.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Whole-genome SARS-CoV-2 sequencing tools are crucial for tracking the COVID-19 pandemic. However, current techniques require sampling of actively infectious patients following COVID-19 testing to recover enough SARS-CoV-2 RNA from the nasopharyngeal passage, which rapidly clears during the first few weeks of infection. A prospective assessment of the viral genome sourced from recovered non-infectious patients would greatly facilitate epidemiological tracking. Thus, we developed a protocol to isolate and sequence the genome of SARS-CoV-2 from stool samples of post-acute SARS-CoV-2 patients, at timepoints ranging from 10-120 days after onset of symptoms. Stool samples were collected from patients at varying timepoints post-convalescence, and viral DNA was isolated and sequenced using the QIAamp Viral RNA Mini Kit (Qiagen Inc.) and Ion Ampliseq™ Library Kit Plus (Life Technologies Corporation). Capacity of neutralizing antibodies in patient plasma was tested using a Luminex panel (Coronavirus Ig Total Human 11-Plex ProcartaPlex™ Panel, ThermoFisher). Of 64 samples obtained from post-acute patients, 21 (32.8%) yielded sufficient material for whole-genome sequencing. This allowed us to identify widely divergent phylogenetic relativity of the SARS-CoV-2 genome from post-acute patients living in the same households and infected around the same time. Additionally, we observed that individuals who recovered from infection expressed varying degrees of antibodies against SARS-CoV-2 structural proteins that corresponded to distinct variants. Interestingly, we identified a novel point mutation in the viral genome where infected patients expressed antibodies with a significantly reduced capacity to neutralize the virus in vitro relative to that of those infected with the wild-type strain. Altogether, we demonstrate a protocol to successfully sequence the SARS-CoV-2 genome from stool samples from patients up to 4 months post-infection, which can be applied to studies that assess the relationship between variants and immune response post-hoc and safe monitoring of the SARS-CoV-2 genome during the pandemic.
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Amahmid O, El Guamri Y, Rakibi Y, Ouizat S, Yazidi M, Razoki B, Kaid Rassou K, Asmama S, Bouhoum K, Belghyti D. Occurrence of SARS-CoV-2 in excreta, sewage, and environment: epidemiological significance and potential risks. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1686-1706. [PMID: 33752527 DOI: 10.1080/09603123.2021.1901865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 05/23/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients' excreta raises the issue of its occurrence and fate in sewage. This review has focused on the presence of the SARS-CoV-2 in human excreta, wastewater, sewage sludge, and river waters. It explored the potential use of the wastewater-based epidemiology approach to report on the situation of current and eventual future SARS-CoV-2 outbreaks. The main concern of the occurrence of SARS-CoV-2 in the environment is the public health risks at sites of sewage products disposal and reuse, especially in low-income countries with inadequate sanitation, where direct discharge and reuse of raw sewage are common practices. The review also addressed the role sewage-irrigated agriculture can have in SARS-CoV-2 spread in the environmental compartments reached through sewage products application. An overview was made on the interest of sewage management, water safety, and hygienic practices for controlling the environmental dissemination of SARS-CoV-2.
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Affiliation(s)
- Omar Amahmid
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Department of Biology, Laboratory of Water, Biodiversity and Climatic Change, Faculty of Sciences Semlalia, Cadi Ayyad Univesity, Marrakesh, Morocco
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
| | - Youssef El Guamri
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
| | - Youness Rakibi
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
- Engineering Laboratory of Organometallic, Molecular Materials and Environment (LIMOME), Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Saadia Ouizat
- Chemistry and Didactics Unit, Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Mohamed Yazidi
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Bouchra Razoki
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Khadija Kaid Rassou
- Department of Life and Earth Sciences, (Biology/geology Research Units), Regional Centre for Careers of Education and Training CRMEF Marrakech-Safi, Marrakesh, Morocco
| | - Souad Asmama
- Laboratory of Biomedical Analysis, University Hospital Centre Mohammad VI, Marrakech, Morocco
| | - Khadija Bouhoum
- Department of Biology, Laboratory of Water, Biodiversity and Climatic Change, Faculty of Sciences Semlalia, Cadi Ayyad Univesity, Marrakesh, Morocco
| | - Driss Belghyti
- Department of Biology, Laboratory of Natural Resources and Sustainable Development, University Ibn Tofail, Kenitra, Morocco
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Schang C, Crosbie ND, Nolan M, Poon R, Wang M, Jex A, John N, Baker L, Scales P, Schmidt J, Thorley BR, Hill K, Zamyadi A, Tseng CW, Henry R, Kolotelo P, Langeveld J, Schilperoort R, Shi B, Einsiedel S, Thomas M, Black J, Wilson S, McCarthy DT. Passive Sampling of SARS-CoV-2 for Wastewater Surveillance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10432-10441. [PMID: 34264643 PMCID: PMC8291133 DOI: 10.1021/acs.est.1c01530] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 05/17/2023]
Abstract
The shedding of pathogens by infected humans enables the use of sewage monitoring to conduct wastewater-based epidemiology (WBE). Although most WBE studies use data from large sewage treatment plants, timely data from smaller catchments are needed for targeted public health action. Traditional sampling methods, like autosamplers or grab sampling, are not conducive to quick ad hoc deployments and high-resolution monitoring at these smaller scales. This study develops and validates a cheap and easily deployable passive sampler unit, made from readily available consumables, with relevance to the COVID-19 pandemic but with broader use for WBE. We provide the first evidence that passive samplers can be used to detect SARS-CoV-2 in wastewater from populations with low prevalence of active COVID-19 infections (0.034 to 0.34 per 10,000), demonstrating their ability for early detection of infections at three different scales (lot, suburb, and city). A side by side evaluation of passive samplers (n = 245) and traditionally collected wastewater samples (n = 183) verified that the passive samplers were sensitive at detecting SARS-CoV-2 in wastewater. On all 33 days where we directly compared traditional and passive sampling techniques, at least one passive sampler was positive when the average SARS-CoV-2 concentration in the wastewater equaled or exceeded the quantification limit of 1.8 gene copies per mL (n = 7). Moreover, on 13 occasions where wastewater SARS-CoV-2 concentrations were less than 1.8 gene copies per mL, one or more passive samplers were positive. Finally, there was a statistically significant (p < 0.001) positive relationship between the concentrations of SARS-CoV-2 in wastewater and the levels found on the passive samplers, indicating that with further evaluation, these devices could yield semi-quantitative results in the future. Passive samplers have the potential for wide use in WBE with attractive feasibility attributes of cost, ease of deployment at small-scale locations, and continuous sampling of the wastewater. Further research will focus on the optimization of laboratory methods including elution and extraction and continued parallel deployment and evaluations in a variety of settings to inform optimal use in wastewater surveillance.
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Affiliation(s)
- Christelle Schang
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Nicolas D. Crosbie
- Melbourne Water Corp., 990
La Trobe St., Docklands, Victoria 3001, Australia
| | - Monica Nolan
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Rachael Poon
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Miao Wang
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Aaron Jex
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Nijoy John
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Louise Baker
- The Walter and Eliza Hall Institute of
Medical Research, Parkville, Victoria 3052,
Australia
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Scales
- The University of
Melbourne, Parkville, Victoria 3010, Australia
| | | | - Bruce R. Thorley
- Victorian Infectious Diseases Reference Laboratory,
Royal Melbourne Hospital at the Peter Doherty Institute for Infection and
Immunity, Melbourne, Victoria 3000, Australia
| | - Kelly Hill
- Water Research Australia,
Adelaide Office, Level 2, 250 Victoria Square, Adelaide 5000, South
Australia
| | - Arash Zamyadi
- Water Research Australia,
Melbourne Office, 990 La Trobe St., Docklands, Victoria 3001,
Australia
| | - Chi-Wen Tseng
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Rebekah Henry
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Peter Kolotelo
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Jeroen Langeveld
- Department of Water Management, TU
Delft, Delft, CN 2628, The Netherlands
- Partners4UrbanWater, Nijmegen
6532 ZV, The Netherlands
| | | | - Baiqian Shi
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
| | - Steve Einsiedel
- ALS Hydrographics, 22
Dalmore Drive, Scoresby, Victoria 3179, Australia
| | - Michael Thomas
- Barwon Water, 55-67 Ryrie
St., Geelong, Victoria 3220, Australia
| | - James Black
- Department of Health, Victoria Department
of Health and Human Services, 50 Lonsdale St., Melbourne, Victoria 3000,
Australia
| | - Simon Wilson
- Melbourne Water Corp., 990
La Trobe St., Docklands, Victoria 3001, Australia
| | - David T. McCarthy
- Environmental and Public Health Microbiology Lab (EPHM
Lab), Department of Civil Engineering, Monash University,
Clayton, Victoria 3800, Australia
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Rimoldi SG, Stefani F, Gigantiello A, Polesello S, Comandatore F, Mileto D, Maresca M, Longobardi C, Mancon A, Romeri F, Pagani C, Cappelli F, Roscioli C, Moja L, Gismondo MR, Salerno F. Presence and infectivity of SARS-CoV-2 virus in wastewaters and rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020. [PMID: 32693284 DOI: 10.1101/2020.05.01.20086009] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The presence of SARS-CoV-2 in raw wastewaters has been demonstrated in many countries affected by this pandemic. Nevertheless, virus presence and infectivity in treated wastewaters, but also in the receiving water bodies are still poorly investigated. In this study, raw and treated samples from three wastewater treatment plants, and three river samples within the Milano Metropolitan Area, Italy, were surveyed for SARS-CoV-2 RNA detection by means of real time RT-PCR and infectivity test on culture cells. SARS-CoV-2 RNA was detected in raw, but not in treated wastewaters (four and two samples, respectively, sampled in two dates). The isolated virus genome was sequenced, and belonged to the strain most spread in Europe and similar to another found in the same region. RNA presence in raw wastewater samples decreased after eight days, probably following the epidemiological trend estimated for the area. Virus infectivity was always null, indicating the natural decay of viral pathogenicity in time from emission. Samples from receiving rivers (three sites, sampled in the same dates as wastewaters) showed in some cases a positivity to real time RT-PCR, probably due to non-treated, or inefficiently treated discharges, or to the combined sewage overflows. Nevertheless, also for rivers infectivity was null. Risks for public health should be limited, although a precautionary approach to risk assessment is here advocated, giving the preliminary nature of the presented data.
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Affiliation(s)
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy.
| | - Anna Gigantiello
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Stefano Polesello
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
| | | | - Davide Mileto
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Mafalda Maresca
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Alessandro Mancon
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Francesca Romeri
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Cristina Pagani
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Francesca Cappelli
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy; Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Claudio Roscioli
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
| | - Lorenzo Moja
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | | | - Franco Salerno
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
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5
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Rimoldi SG, Stefani F, Gigantiello A, Polesello S, Comandatore F, Mileto D, Maresca M, Longobardi C, Mancon A, Romeri F, Pagani C, Cappelli F, Roscioli C, Moja L, Gismondo MR, Salerno F. Presence and infectivity of SARS-CoV-2 virus in wastewaters and rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140911. [PMID: 32693284 PMCID: PMC7358170 DOI: 10.1016/j.scitotenv.2020.140911] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/13/2023]
Abstract
The presence of SARS-CoV-2 in raw wastewaters has been demonstrated in many countries affected by this pandemic. Nevertheless, virus presence and infectivity in treated wastewaters, but also in the receiving water bodies are still poorly investigated. In this study, raw and treated samples from three wastewater treatment plants, and three river samples within the Milano Metropolitan Area, Italy, were surveyed for SARS-CoV-2 RNA detection by means of real time RT-PCR and infectivity test on culture cells. SARS-CoV-2 RNA was detected in raw, but not in treated wastewaters (four and two samples, respectively, sampled in two dates). The isolated virus genome was sequenced, and belonged to the strain most spread in Europe and similar to another found in the same region. RNA presence in raw wastewater samples decreased after eight days, probably following the epidemiological trend estimated for the area. Virus infectivity was always null, indicating the natural decay of viral pathogenicity in time from emission. Samples from receiving rivers (three sites, sampled in the same dates as wastewaters) showed in some cases a positivity to real time RT-PCR, probably due to non-treated, or inefficiently treated discharges, or to the combined sewage overflows. Nevertheless, also for rivers infectivity was null. Risks for public health should be limited, although a precautionary approach to risk assessment is here advocated, giving the preliminary nature of the presented data.
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Affiliation(s)
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy.
| | - Anna Gigantiello
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Stefano Polesello
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
| | | | - Davide Mileto
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Mafalda Maresca
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Alessandro Mancon
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Francesca Romeri
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Cristina Pagani
- University Hospital "L. Sacco", ASST Fatebenefratelli Sacco, Milan, Italy
| | - Francesca Cappelli
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy; Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Claudio Roscioli
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
| | - Lorenzo Moja
- Department of Biomedical Sciences for Health, University of Milan, Italy
| | | | - Franco Salerno
- Water Research Institute-National Research Council (IRSA-CNR), Brugherio, MB, Italy
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6
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Simmonds P. Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other Coronaviruses. mBio 2020; 11:e01661-20. [PMID: 33127861 PMCID: PMC7642675 DOI: 10.1128/mbio.01661-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
The ultimate outcome of the coronavirus disease 2019 (COVID-19) pandemic is unknown and is dependent on a complex interplay of its pathogenicity, transmissibility, and population immunity. In the current study, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated for the presence of large-scale internal RNA base pairing in its genome. This property, termed genome-scale ordered RNA structure (GORS) has been previously associated with host persistence in other positive-strand RNA viruses, potentially through its shielding effect on viral RNA recognition in the cell. Genomes of SARS-CoV-2 were remarkably structured, with minimum folding energy differences (MFEDs) of 15%, substantially greater than previously examined viruses such as hepatitis C virus (HCV) (MFED of 7 to 9%). High MFED values were shared with all coronavirus genomes analyzed and created by several hundred consecutive energetically favored stem-loops throughout the genome. In contrast to replication-associated RNA structure, GORS was poorly conserved in the positions and identities of base pairing with other sarbecoviruses-even similarly positioned stem-loops in SARS-CoV-2 and SARS-CoV rarely shared homologous pairings, indicative of more rapid evolutionary change in RNA structure than in the underlying coding sequences. Sites predicted to be base paired in SARS-CoV-2 showed less sequence diversity than unpaired sites, suggesting that disruption of RNA structure by mutation imposes a fitness cost on the virus that is potentially restrictive to its longer evolution. Although functionally uncharacterized, GORS in SARS-CoV-2 and other coronaviruses represents important elements in their cellular interactions that may contribute to their persistence and transmissibility.IMPORTANCE The detection and characterization of large-scale RNA secondary structure in the genome of SARS-CoV-2 indicate an extraordinary and unsuspected degree of genome structural organization; this could be effectively visualized through a newly developed contour plotting method that displays positions, structural features, and conservation of RNA secondary structure between related viruses. Such RNA structure imposes a substantial evolutionary cost; paired sites showed greater restriction in diversity and represent a substantial additional constraint in reconstructing its molecular epidemiology. Its biological relevance arises from previously documented associations between possession of structured genomes and persistence, as documented for HCV and several other RNA viruses infecting humans and mammals. Shared properties potentially conferred by large-scale structure in SARS-CoV-2 include increasing evidence for prolonged infections and induced immune dysfunction that prevents development of protective immunity. The findings provide an additional element to cellular interactions that potentially influences the natural history of SARS-CoV-2, its pathogenicity, and its transmission.
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Affiliation(s)
- P Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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