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Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. Mol Diagn Ther 2024; 28:513-523. [PMID: 38992308 DOI: 10.1007/s40291-024-00727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Central nervous system (CNS) infections carry a substantial burden of morbidity and mortality worldwide, and accurate and timely diagnosis is required to optimize management. Metagenomic next-generation sequencing (mNGS) has proven to be a valuable tool in detecting pathogens in patients with suspected CNS infection. By sequencing microbial nucleic acids present in a patient's cerebrospinal fluid, brain tissue, or samples collected outside of the CNS, such as plasma, mNGS can detect a wide range of pathogens, including rare, unexpected, and/or fastidious organisms. Furthermore, its target-agnostic approach allows for the identification of both known and novel pathogens. This is particularly useful in cases where conventional diagnostic methods fail to provide an answer. In addition, mNGS can detect multiple microorganisms simultaneously, which is crucial in cases of mixed infections without a clear predominant pathogen. Overall, clinical mNGS testing can help expedite the diagnostic process for CNS infections, guide appropriate management decisions, and ultimately improve clinical outcomes. However, there are key challenges surrounding its use that need to be considered to fully leverage its clinical impact. For example, only a few specialized laboratories offer clinical mNGS due to the complexity of both the laboratory methods and analysis pipelines. Clinicians interpreting mNGS results must be aware of both false negatives-as mNGS is a direct detection modality and requires a sufficient amount of microbial nucleic acid to be present in the sample tested-and false positives-as mNGS detects environmental microbes and their nucleic acids, despite best practices to minimize contamination. Additionally, current costs and turnaround times limit broader implementation of clinical mNGS. Finally, there is uncertainty regarding the best practices for clinical utilization of mNGS, and further work is needed to define the optimal patient population(s), syndrome(s), and time of testing to implement clinical mNGS.
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Affiliation(s)
- LingHui David Su
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
| | - Charles Y Chiu
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Laboratory Medicine and Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - David Gaston
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Delve Bio, Inc., San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Dennis W Simon
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pediatric Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran T Thakur
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Neurology, Columbia University Irving Medical Center-New York Presbyterian Hospital, New York, NY, USA
| | - Shangxin Yang
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anne Piantadosi
- The Consortium for Clinical Metagenomics in Infectious Diseases, Nashville, TN, USA.
- Department of Pathology and Laboratory Medicine, and Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 101 Woodruff Circle, Atlanta, GA, USA.
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Van Nguyen T, Kasantikul T, Piewbang C, Techangamsuwan S. Evolutionary dynamics of canine kobuvirus in Vietnam and Thailand reveal the evidence of viral ability to evade host immunity. Sci Rep 2024; 14:12037. [PMID: 38802579 PMCID: PMC11130191 DOI: 10.1038/s41598-024-62833-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Canine kobuvirus (CaKoV) is a pathogen associated with canine gastrointestinal disease (GID). This study examined 327 rectal swabs (RS), including 113 from Vietnam (46 healthy, 67 with GID) and 214 from Thailand (107 healthy and 107 with GID). CaKoV was detected in both countries, with prevalences of 28.3% (33/113) in Vietnam and 7.9% (17/214) in Thailand. Additionally, CaKoV was found in both dogs with diarrhea and healthy dogs. CaKoV was mainly found in puppies under six months of age (30.8%). Co-detection with other canine viruses were also observed. The complete coding sequence (CDS) of nine Vietnamese and four Thai CaKoV strains were characterized. Phylogenetic analysis revealed a close genetic relationship between Vietnamese and Thai CaKoV strains, which were related to the Chinese strains. CDS analysis indicated a distinct lineage for two Vietnamese CaKoV strains. Selective pressure analysis on the viral capsid (VP1) region showed negative selection, with potential positive selection sites on B-cell epitopes. This study, the first of its kind in Vietnam, provides insights into CaKoV prevalence in dogs of different ages and healthy statuses, updates CaKoV occurrence in Thailand, and sheds light on its molecular characteristics and immune evasion strategies.
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Affiliation(s)
- Tin Van Nguyen
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Chutchai Piewbang
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Somporn Techangamsuwan
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Kantor RS, Jiang M. Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8161-8168. [PMID: 38691513 PMCID: PMC11097388 DOI: 10.1021/acs.est.4c02638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.
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Affiliation(s)
- Rose S. Kantor
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Minxi Jiang
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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Fernandez-Cassi X, Kohn T. Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09594-3. [PMID: 38647859 DOI: 10.1007/s12560-024-09594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/25/2024]
Abstract
Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.
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Affiliation(s)
- Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland.
- Departament of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona, Catalunya, Spain.
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Vaud, Lausanne, Switzerland
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Ibrahim C, Hammami S, Khelifi N, Pothier P, Hassen A. Activated sludge and UV-C 254 for Sapovirus, Aichivirus, Astrovirus, and Adenovirus processing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:1995-2014. [PMID: 37086061 DOI: 10.1080/09603123.2023.2203906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
In this study, the detection rates of four enteric viruses, Human Astrovirus (HAstVs), Aichivirus (AiVs), Human Adenovirus (HAdVs), and Sapovirus (SaVs) are carried out to assess the virological quality of the treated wastewater. A total of 140 samples was collected from wastewater treatment plant WWTP of Tunis-City. Real-time RT-PCR and conventional RT-PCR results showed high frequencies of detection of the four enteric viruses investigated at the entry and exit of the biological activated sludge procedure and a significant reduction in viral titers after tertiary treatment with UV-C254 irradiation. These results revealed the ineffectiveness of the biological activated sludge treatment in removing viruses and the poor quality of the treated wastewater intended for recycling, agricultural reuse, and safe discharge into the natural environment. The UV-C254 irradiation, selected while considering the non-release of known disinfection by-products because of eventual reactions with the large organic and mineral load commonly present in the wastewater.
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Affiliation(s)
- Chourouk Ibrahim
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, the University of Tunis El Manar, Tunis, Tunisia
- Microbiology Laboratory, Beja University Hospital, Beja,Tunisia
| | - Salah Hammami
- National School of Veterinary Medicine at Sidi Thabet, University of Manouba, Tunis, Tunisia
| | - Nesserine Khelifi
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
| | - Pierre Pothier
- National Reference Center for Enteric Viruses, Laboratory of Virology, University Hospital of Dijon, Dijon, France
| | - Abdennaceur Hassen
- Center of Research and Water Technologies (CERTE), Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Tunisia
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Kuczera K, Orłowska A, Smreczak M, Frant M, Trębas P, Rola J. Prevalence of Astroviruses in Different Animal Species in Poland. Viruses 2024; 16:80. [PMID: 38257780 PMCID: PMC10819871 DOI: 10.3390/v16010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal-oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.
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Affiliation(s)
- Konrad Kuczera
- Voivodship Veterinary Inspectorate Katowice, ul. Brynowska 25a, 40-585 Katowice, Poland;
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Maciej Frant
- Department of Swine Diseases, National Veterinary Research Institute, 24-100 Puławy, Poland;
| | - Paweł Trębas
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
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Torres-Franco AF, Leroy-Freitas D, Martinez-Fraile C, Rodríguez E, García-Encina PA, Muñoz R. Partitioning and inactivation of enveloped and nonenveloped viruses in activated sludge, anaerobic and microalgae-based wastewater treatment systems. WATER RESEARCH 2024; 248:120834. [PMID: 37984037 DOI: 10.1016/j.watres.2023.120834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
Anaerobic and microalgae-based technologies for municipal wastewater treatment have emerged as sustainable alternatives to activated sludge systems. However, viruses are a major sanitary concern for reuse applications of liquid and solid byproducts from these technologies. To assess their capacity to reduce viruses during secondary wastewater treatment, enveloped Phi6 and nonenveloped MS2 bacteriophages, typically used as surrogates of several types of wastewater viruses, were spiked into batch bioreactors treating synthetic municipal wastewater (SMWW). The decay of Phi6 and MS2 in anaerobic and microalgae-based reactors was compared with the decay in activated sludge batch reactors for 96 h (Phi6) and 144 h (MS2). In each reactor, bacteriophages in the soluble and solids fractions were titered, allowing the assessment of virus partitioning to biomass over time. Moreover, the influence of abiotic conditions such as agitation, oxygen absence and light excess in activated sludge, anaerobic and microalgae reactors, respectively, was assessed using dedicated SMWW control reactors. All technologies showed Phi6 and MS2 reductions. Phi6 was reduced in at least 4.7 to 6.5 log10 units, with 0 h concentrations ranging from 5.0 to 6.5 log10 PFU mL-1. Similarly, reductions achieved for MS2 were of at least 3.9 to 7.2 log10 units, from starting concentrations of 8.0 to 8.6 log10 PFU mL-1. Log-logistic models adjusted to bacteriophages' decay indicated T90 values in activated sludge and microalgae reactors of 2.2 and 7.9 h for Phi6 and of 1.0 and 11.5 h for MS2, respectively, all within typical hydraulic retention times (HRT) of full-scale operation. In the case of the microalgae technology, T99 values for Phi6 and MS2 of 12.7 h and 13.6 h were also lower than typical operating HRTs (2-10 d), while activated sludge and anaerobic treatment achieved less than 99 % of Phi6 and 50 % of MS2 inactivation within 12 h of typical HRT, respectively. Thus, the microalgae-based treatment exhibited a higher potential to reduce the disinfection requirements of treated wastewater.
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Affiliation(s)
- Andrés F Torres-Franco
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain.
| | - Deborah Leroy-Freitas
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Cristina Martinez-Fraile
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Elisa Rodríguez
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Pedro A García-Encina
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina. s/n, 47011 Valladolid, Spain.
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Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio 2023; 14:e0146823. [PMID: 37877702 PMCID: PMC10746264 DOI: 10.1128/mbio.01468-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel M. Maloney
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Kate Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Weymouth, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Matthew J. Wade
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
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Idrees S, Paudel KR, Sadaf T, Hansbro PM. How different viruses perturb host cellular machinery via short linear motifs. EXCLI JOURNAL 2023; 22:1113-1128. [PMID: 38054205 PMCID: PMC10694346 DOI: 10.17179/excli2023-6328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
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Potapov S, Gorshkova A, Krasnopeev A, Podlesnaya G, Tikhonova I, Suslova M, Kwon D, Patrushev M, Drucker V, Belykh O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. Int J Mol Sci 2023; 24:12049. [PMID: 37569424 PMCID: PMC10418309 DOI: 10.3390/ijms241512049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Andrey Krasnopeev
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Galina Podlesnaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Irina Tikhonova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Maria Suslova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Dmitry Kwon
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Maxim Patrushev
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Olga Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
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11
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Miścicka A, Lu K, Abaeva IS, Pestova TV, Hellen CUT. Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1051-1068. [PMID: 37041031 PMCID: PMC10275262 DOI: 10.1261/rna.079599.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
Initiation of translation on many viral mRNAs occurs by noncanonical mechanisms that involve 5' end-independent binding of ribosomes to an internal ribosome entry site (IRES). The ∼190-nt-long intergenic region (IGR) IRES of dicistroviruses such as cricket paralysis virus (CrPV) initiates translation without Met-tRNAi Met or initiation factors. Advances in metagenomics have revealed numerous dicistrovirus-like genomes with shorter, structurally distinct IGRs, such as nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1). Like canonical IGR IRESs, the ∼165-nt-long NediV-like IGRs comprise three domains, but they lack key canonical motifs, including L1.1a/L1.1b loops (which bind to the L1 stalk of the ribosomal 60S subunit) and the apex of stem-loop V (SLV) (which binds to the head of the 40S subunit). Domain 2 consists of a compact, highly conserved pseudoknot (PKIII) that contains a UACUA loop motif and a protruding CrPV-like stem--loop SLIV. In vitro reconstitution experiments showed that NediV-like IRESs initiate translation from a non-AUG codon and form elongation-competent 80S ribosomal complexes in the absence of initiation factors and Met-tRNAi Met Unlike canonical IGR IRESs, NediV-like IRESs bind directly to the peptidyl (P) site of ribosomes leaving the aminoacyl (A) site accessible for decoding. The related structures of NediV-like IRESs and their common mechanism of action indicate that they exemplify a distinct class of IGR IRES.
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Affiliation(s)
- Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Kristen Lu
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York 11203, USA
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12
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Pérez-Cataluña A, Randazzo W, Martínez-Blanch JF, Codoñer FM, Sánchez G. Sample and library preparation approaches for the analysis of the virome of irrigation water. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4450-4457. [PMID: 36823282 DOI: 10.1002/jsfa.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters. RESULTS Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families. CONCLUSION Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | | | - Francisco M Codoñer
- ADM-Lifesequencing - Health and Wellness - Adm Nutrition, Valencia, Spain
- Danone Nutricia Research, Singapore, Singapore
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
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13
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Coutinho CRM, Cardoso JF, Siqueira JAM, Machado RS, Chagas Júnior WDD, Tavares FN, Gabbay YB. Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019). J Med Virol 2023; 95:e28873. [PMID: 37349989 DOI: 10.1002/jmv.28873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.
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Affiliation(s)
| | - Jedson Ferreira Cardoso
- Laboratório de Bioinformática-BIOINFO, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Jones Anderson Monteiro Siqueira
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Raiana Scerni Machado
- Programa de Pós-graduação em Medicina Tropical, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Wanderley Dias das Chagas Júnior
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
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14
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Gh Jeelani P, Muzammil Munawar S, Khaleel Basha S, Krishna P G, Joshua Sinclair B, Dharshini Jenifer A, Ojha N, Mossa AT, Chidambaram R. Exploring possible strategies for treating SARS-CoV-2 in sewage wastewater: A review of current research and future directions. HYGIENE AND ENVIRONMENTAL HEALTH ADVANCES 2023; 6:100056. [PMID: 37131485 PMCID: PMC10088352 DOI: 10.1016/j.heha.2023.100056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/04/2023]
Abstract
The advent of acute respiratory coronavirus disease (COVID-19) is convoyed by the shedding of the virus in stool. Although inhalation from person-to-person and aerosol/droplet transmission are the main modes of SARS-Coronavirus-2 (SARS-CoV-2) transmission, currently available evidence indicates the presence of viral RNA in the sewerage wastewater, which highlights the need for more effective corona virus treatment options. In the existing COVID-19 pandemic, a substantial percentage of cases shed SARS-CoV-2 viral RNA in their faeces. Hence the treating this sewerage wastewater with proper surveillance is essential to contain this deadly pathogen from further transmission. Since, the viral disinfectants will not be very effective on sewerage waste as organic matter, and suspended solids in water can protect viruses that adsorb to these particles. More effective methods and measures are needed to prevent this virus from spreading. This review will explore some potential methods to treat the SARS-CoV-2 infected sewerage wastewater, current research and future directions.
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Affiliation(s)
- Peerzada Gh Jeelani
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Syed Muzammil Munawar
- C. Abdul Hakeem College, (Automous) Melvisharam - 632 509, Ranipet District, Tamilnadu, India
| | - S Khaleel Basha
- C. Abdul Hakeem College, (Automous) Melvisharam - 632 509, Ranipet District, Tamilnadu, India
| | - Gopi Krishna P
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Bruce Joshua Sinclair
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - A Dharshini Jenifer
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu, India
| | - Nupur Ojha
- Department of Biotechnology, Indian Institute of Technology, Madras, Chennai 600036 Tamil Nadu, India
| | - Abdel-Tawab Mossa
- National Research Centre, Egypt | Cairo, Egypt | NRC 33 El Buhouth St 'Ad Doqi, Dokki, Cairo Governorate 12622, Egypt
| | - Ramalingam Chidambaram
- Nano-Food Research Group, Instrumental and Food Analysis Laboratory, Division of Industrial Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu, India
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15
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Li J, Hosegood I, Powell D, Tscharke B, Lawler J, Thomas KV, Mueller JF. A global aircraft-based wastewater genomic surveillance network for early warning of future pandemics. Lancet Glob Health 2023; 11:e791-e795. [PMID: 37061316 PMCID: PMC10101754 DOI: 10.1016/s2214-109x(23)00129-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 04/17/2023]
Abstract
International airports can have a key role in screening, detecting, and mitigating cross-border transmission of SARS-CoV-2 and potentially other infectious diseases. With aircraft passengers representing a subpopulation of a country or region, aircraft-based wastewater surveillance can be a promising approach to effectively identifying emerging viruses, tracing their evolution, and mapping global spread with international flights. Therefore, we propose the development of a global aircraft-based wastewater genomic surveillance network, with the busiest international airports as central nodes and continuing air travel journeys as vectors. This surveillance programme requires routinely collecting aircraft wastewater samples for microbiological analysis and sequencing and linking the resulting data with associated international air traffic information. With the creation of a strong international alliance between the airline industry and health authorities, this surveillance network will potentially complement public health systems with a true early warning ability to inform decision making for new variants and future global health risks.
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Affiliation(s)
- Jiaying Li
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia.
| | | | - David Powell
- International Air Transport Association, Geneva, Switzerland
| | - Ben Tscharke
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jenny Lawler
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Kevin V Thomas
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jochen F Mueller
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
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16
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Duarte MF, de Andrade IA, Silva JMF, de Melo FL, Machado AM, Inoue-Nagata AK, Nagata T. Metagenomic analyses of plant virus sequences in sewage water for plant viruses monitoring. TROPICAL PLANT PATHOLOGY 2023; 48:1-9. [PMID: 37362078 PMCID: PMC10147536 DOI: 10.1007/s40858-023-00575-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/25/2023] [Indexed: 06/28/2023]
Abstract
Frequent monitoring of emerging viruses of agricultural crops is one of the most important missions for plant virologists. A fast and precise identification of potential harmful viruses may prevent the occurrence of serious epidemics. Nowadays, high-throughput sequencing (HTS) technologies became an accessible and powerful tool for this purpose. The major discussion of this strategy resides in the process of sample collection, which is usually laborious, costly and nonrepresentative. In this study, we assessed the use of sewage water samples for monitoring the widespread, numerous, and stable plant viruses using HTS analysis and RT-qPCR. Plant viruses belonged to 12 virus families were found, from which Virgaviridae, Solemoviridae, Tymoviridae, Alphaflexiviridae, Betaflexiviridae, Closteroviridae and Secoviridae were the most abundant ones with more than 20 species. Additionally, we detected one quarantine virus in Brazil and a new tobamovirus species. To assess the importance of the processed foods as virus release origins to sewage, we selected two viruses, the tobamovirus pepper mild mottle virus (PMMoV) and the carlavirus garlic common latent virus (GarCLV), to detect in processed food materials by RT-qPCR. PMMoV was detected in large amount in pepper-based processed foods and in sewage samples, while GarCLV was less frequent in dried and fresh garlic samples, and in the sewage samples. This suggested a high correlation of virus abundance in sewage and processed food sources. The potential use of sewage for a virus survey is discussed in this study. Supplementary Information The online version contains supplementary material available at 10.1007/s40858-023-00575-8.
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Affiliation(s)
| | | | | | | | - Ana Maria Machado
- Companhia de Saneamento Ambiental Do DF, ETE-Norte, Brasília, DF 70800-130 Brazil
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17
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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18
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Genetic Diversity and Characterization of Circular Replication (Rep)-Encoding Single-Stranded (CRESS) DNA Viruses. Microbiol Spectr 2022; 10:e0105722. [PMID: 36346238 PMCID: PMC9769708 DOI: 10.1128/spectrum.01057-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The CRESS-DNA viruses are the ubiquitous virus detected in almost all eukaryotic life trees and play an essential role in the maintaining ecosystem of the globe. Still, their genetic diversity is not fully understood. Here, we bring to light the genetic diversity of replication (Rep) and capsid (Cap) proteins of CRESS-DNA viruses. We divided the Rep protein of the CRESS-DNA virus into 10 clusters using CLANS and phylogenetic analyses. Also, most of the Rep protein in Rep cluster 1 (R1) and R2 (Circoviridae, Smacoviridae, Nanoviridae, and CRESSV1-5) contain the Viral_Rep superfamily and P-loop_NTPase superfamily domains, while the Rep protein of viruses in other clusters has no such characterized functional domain. The Circoviridae, Nanoviridae, and CRESSV1-3 viruses contain two domains, such as Viral_Rep and P-loop_NTPase; the CRESSV4 and CRESSV5 viruses have only the Viral_Rep domain; most of the sequences in the pCRESS-related group have only P-loop_NTPase; and Smacoviridae do not have these two domains. Further, we divided the Cap protein of the CRESS-DNA virus into 20 clusters using CLANS and phylogenetic analyses. The Rep and Cap proteins of Circoviridae and Smacoviridae are grouped into a specific cluster. Cap protein of CRESS-DNA viruses grouped with one cluster and Rep protein with another cluster. Further, our study reveals that selection pressure plays a significant role in the evolution of CRESS-DNA viruses' Rep and Cap genes rather than mutational pressure. We hope this study will help determine the genetic diversity of CRESS-DNA viruses as more sequences are discovered in the future. IMPORTANCE The genetic diversity of CRESS-DNA viruses is not fully understood. CRESS-DNA viruses are classified as CRESSV1 to CRESSV6 using only Rep protein. This study revealed that the Rep protein of the CRESS-DNA viruses is classified as CRESSV1 to CRESSV6 groups and the new Smacoviridae-related, CRESSV2-related, pCRESS-related, Circoviridae-related, and 1 to 4 outgroups, according to the Viral_Rep and P-loop_NTPase domain organization, CLANS, and phylogenetic analysis. Furthermore, for the first time in this study, the Cap protein of CRESS-DNA viruses was classified into 20 distinct clusters by CLANS and phylogenetic analysis. Through this classification, the genetic diversity of CRESS-DNA viruses clarifies the possibility of recombinations in Cap and Rep proteins. Finally, it has been shown that selection pressure plays a significant role in the evolution and genetic diversity of Cap and Rep proteins. This study explains the genetic diversity of CRESS-DNA viruses and hopes that it will help classify future detected viruses.
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Fomsgaard AS, Rasmussen M, Spiess K, Fomsgaard A, Belsham GJ, Fonager J. Improvements in metagenomic virus detection by simple pretreatment methods. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100120. [PMID: 36945677 PMCID: PMC10024160 DOI: 10.1016/j.jcvp.2022.100120] [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: 03/20/2022] [Revised: 09/26/2022] [Accepted: 10/24/2022] [Indexed: 11/21/2022] Open
Abstract
Early detection of pathogens at the point of care helps reduce the threats to human and animal health from emerging pathogens. Initially, the disease-causing agent will be unknown and needs to be identified; this often requires specific laboratory facilities. Here we describe the development of an unbiased detection assay for RNA and DNA viruses using metagenomic Nanopore sequencing and simple methods that can be transferred into a field setting. Human clinical samples containing the RNA virus SARS-CoV-2 or the DNA viruses human papillomavirus (HPV) and molluscum contagiosum virus (MCV) were used as a test of concept. Firstly, the virus detection potential was optimized by investigating different pretreatments for reducing non-viral nucleic acid components. DNase I pretreatment followed by filtration increased the proportion of SARS-CoV-2 sequenced reads > 500-fold compared with no pretreatments. This was sufficient to achieve virus detection with high confidence and allowed variant identification. Next, we tested individual SARS-CoV-2 samples with various viral loads (measured as CT-values determined by RT-qPCR). Lastly, we tested the assay on clinical samples containing the DNA virus HPV and co-infection with MCV to show the assay's detection potential for DNA viruses. This protocol is fast (same day results). We hope to apply this method in other settings for point of care detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.
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Affiliation(s)
- Anna S. Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
- Corresponding author.
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
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Genome Sequences of 16 Enterovirus Isolates from Environmental Sewage in Guatemala, 2019 to 2021. Microbiol Resour Announc 2022; 11:e0056222. [PMID: 35950869 PMCID: PMC9476903 DOI: 10.1128/mra.00562-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Enteroviruses can cause human infectious disease. We report 16 near-complete genome sequences of enteroviruses that were isolated through environmental surveillance of wastewater in Guatemala.
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Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM, Ng C, Chen H, Chandra F, Gin KY. A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant. IMETA 2022; 1:e39. [PMID: 38868719 PMCID: PMC10989988 DOI: 10.1002/imt2.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/30/2022] [Accepted: 06/19/2022] [Indexed: 06/14/2024]
Abstract
Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method. We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment. In all, bulk and FACS-coupled metagenomics are complementary approaches that enable a more thorough understanding of the community structure of DNA and RNA viruses in complex environmental samples, of which the latter is critical for increasing the sensitivity of detection of viral signatures that would otherwise be lost through bulk viral metagenomics.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Yi Yang
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
| | - Feijian Mao
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Fang You
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - David M. Needham
- Monterey Bay Aquarium Research InstituteMoss LandingCaliforniaUSA
- GEOMAR Helmholtz Centre for Ocean ResearchOcean EcoSystems Biology UnitKielGermany
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Charmaine Ng
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Hongjie Chen
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Franciscus Chandra
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Karina Yew‐Hoong Gin
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
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22
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Rosario K, Van Bogaert N, López-Figueroa NB, Paliogiannis H, Kerr M, Breitbart M. Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae. PeerJ 2022; 10:e13875. [PMID: 35990902 PMCID: PMC9390326 DOI: 10.7717/peerj.13875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Noémi Van Bogaert
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: FVPHouse, Berlare, Belgium
| | | | - Haris Paliogiannis
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: MIO-ECSDE, Athens, Greece
| | - Mason Kerr
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
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23
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Matsvay A, Dyachkova M, Sai A, Burskaia V, Artyushin I, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family. Microorganisms 2022; 10:1540. [PMID: 36013958 PMCID: PMC9416405 DOI: 10.3390/microorganisms10081540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Marina Dyachkova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Anna Sai
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia;
| | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
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24
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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: 5] [Impact Index Per Article: 2.5] [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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25
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Liu G, Qu J, Rose J, Medema G. Roadmap for Managing SARS-CoV-2 and Other Viruses in the Water Environment for Public Health. ENGINEERING (BEIJING, CHINA) 2022; 12:139-144. [PMID: 33654547 PMCID: PMC7909608 DOI: 10.1016/j.eng.2020.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/15/2020] [Accepted: 09/24/2020] [Indexed: 05/25/2023]
Abstract
The water sector needs to address viral-related public health issues, because water is a virus carrier, which not only spreads viruses (e.g., via drinking water), but also provides information about the circulation of viruses in the community (e.g., via sewage). It has been widely reported that waterborne viral pathogens are abundant, diverse, complex, and threatening the public health in both developed and developing countries. Meanwhile, there is great potential for viral monitoring that can indicate biosafety, treatment performance and community health. New developments in technology have been rising to meet the emerging challenges over the past decades. Under the current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the world's attention is directed to the urgent need to tackle the most challenging public health issues related to waterborne viruses. Based on critical analysis of the water viral knowledge progresses and gaps, this article offers a roadmap for managing COVID-19 and other viruses in the water environments for ensuring public health.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Joan Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
| | - Gertjan Medema
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA
- KWR Water Research Institute, Nieuwegein 3433 PE, Netherlands
- Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft 2628 CN, Netherlands
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26
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Gao Y, He W, Fu J, Li Y, He H, Chen Q. Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus. Front Public Health 2022; 10:865605. [PMID: 35517645 PMCID: PMC9062591 DOI: 10.3389/fpubh.2022.865605] [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: 02/02/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMurine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents.ResultsA total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%.ConclusionThe results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.
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27
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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28
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Jiang SC, Bischel HN, Goel R, Rosso D, Sherchan S, Whiteson KL, Yan T, Solo-Gabriele HM. Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse. WATER 2022; 14:1187. [PMID: 37622131 PMCID: PMC10448804 DOI: 10.3390/w14081187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.
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Affiliation(s)
- Sunny C Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Heather N Bischel
- Department of Civil & Environmental Engineering, University of California, Davis CA 95616
| | - Ramesh Goel
- Department of Civil & Environmental Engineering, University of Utah, Salt Lake City, Utah 84112
| | - Diego Rosso
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Samendra Sherchan
- Department of Environmental Health sciences, Tulane university, New Orleans, LA 70112
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Tao Yan
- Department of Civil and Environmental Engineering, and Water Resources Research Center, University of Hawaii at Manoa, HI 96822, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, 33146, USA
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Solomon C, Hewson I. Putative Invertebrate, Plant, and Wastewater Derived ssRNA Viruses in Plankton of the Anthropogenically Impacted Anacostia River, District of Columbia, USA. Microbes Environ 2022; 37:ME21070. [PMID: 35264468 PMCID: PMC9763036 DOI: 10.1264/jsme2.me21070] [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] [Indexed: 01/05/2023] Open
Abstract
The Anacostia River is a highly impacted watershed in the Northeastern United States which experiences combined sewage outfall in downstream waters. We examined the composition of RNA viruses at three sites in the river using viral metagenomics. Viromes had well represented Picornaviruses, Tombusviruses, Wolframviruses, Nodaviruses, with fewer Tobamoviruses, Sobemoviruses, and Densoviruses (ssDNA). Phylogenetic ana-lyses of detected viruses provide evidence for putatively autochthonous and allochthonous invertebrate, plant, and vertebrate host origin. The number of viral genomes matching Ribovaria increased downstream, and assemblages were most disparate between distant sites, suggesting impacts of the combined sewage overflows at these sites. Additionally, we recovered a densovirus genome fragment which was highly similar to the Clinch ambidensovirus 1, which has been attributed to mass mortality of freshwater mussels in Northeastern America. Taken together, these data suggest that RNA viromes of the Anacostia River reflect autochthonous production of virus particles by benthic metazoan and plants, and inputs from terrestrial habitats including sewage.
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Affiliation(s)
- Caroline Solomon
- School of Science, Technology, Accessibility, Mathematics and Public Health, Gallaudet University, 800 Florida Ave NE, Washington, DC 20002 USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Wing Hall 403, Ithaca NY 14853 USA, Corresponding author. E-mail: ; Tel: +1–607–255–0151; Fax: +1–607–255–3904
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Martínez-Puchol S, Itarte M, Rusiñol M, Forés E, Mejías-Molina C, Andrés C, Antón A, Quer J, Abril JF, Girones R, Bofill-Mas S. Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don't miss the forest for the trees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149562. [PMID: 34391155 PMCID: PMC8349739 DOI: 10.1016/j.scitotenv.2021.149562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 05/07/2023]
Abstract
In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Josep F Abril
- Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona; Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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31
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Kaiser FK, van Dyck L, Jo WK, Schreiner T, Pfankuche VM, Wohlsein P, Baumann I, Peters M, Baumgärtner W, Osterhaus ADME, Ludlow M. Detection of Systemic Canine Kobuvirus Infection in Peripheral Tissues and the Central Nervous System of a Fox Infected with Canine Distemper Virus. Microorganisms 2021; 9:microorganisms9122521. [PMID: 34946122 PMCID: PMC8705045 DOI: 10.3390/microorganisms9122521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Canine kobuvirus (CaKV) is a globally distributed pathogen of dogs and is predominantly associated with infection of the gastrointestinal tract. However, an etiological link to enteric disease has not been established since CaKV has been identified in both asymptomatic dogs and animals with diarrheic symptoms. In this study, an extraintestinal CaKV infection was detected by next-generation sequencing in a fox (Vulpes vulpes) in Germany concomitant with a canine distemper virus (canine morbillivirus; CDV) co-infection. Phylogenetic analysis of the complete coding region sequence showed that this strain was most closely related to a CaKV strain detected in a dog in the United Kingdom in 2008. The tissue and cellular tropism of CaKV was characterized by the detection of viral antigens and RNA. CaKV RNA was detected by in situ hybridization in different tissues, including epithelial cells of the stomach and ependymal cells in the brain. The use of a new RT-qPCR assay for CaKV confirmed the systemic distribution of CaKV with viral RNA also detected in the lymph nodes, bladder, trachea, and brain. The detection of a CDV infection in this fox suggests that immunosuppression should be further investigated as a contributing factor to the enhanced extraintestinal spread of CaKV.
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Affiliation(s)
- Franziska K. Kaiser
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Lydia van Dyck
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Wendy K. Jo
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Tom Schreiner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Ilka Baumann
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Albert D. M. E. Osterhaus
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Ludlow
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
- Correspondence:
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32
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High Frequency of Salivirus in Pediatric Patients with Acute Gastroenteritis. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2021. [DOI: 10.52547/jommid.9.4.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Xiao T, Leng H, Zhang Q, Chen Q, Guo H, Qi Y. Isolation and characterization of a Sabin 3/Sabin 1 recombinant vaccine-derived poliovirus from a child with severe combined immunodeficiency. Virus Res 2021; 308:198633. [PMID: 34793871 DOI: 10.1016/j.virusres.2021.198633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
An 8-month-old child diagnosed with severe combined immunodeficiency (SCID) was found to be excreting vaccine-derived poliovirus (VDPVs). Five stool samples from the child and stool samples from 24 contacts were collected during the following 7 months. Complete genome sequence by next generation sequencing (NGS) identified 0.7 to 1.4% nucleotide substitutions in the capsid P1 region of the first and the last isolates compared with Sabin 3 strain. Simplot analysis revealed that all isolates were Sabin 3/Sabin 1 recombinants, sharing a single recombination breakpoint in the 2C region. Multiple nucleotide variants were identified in the 5'UTR (T472→C and G395→A); amino acid mutations were identified in residues at VP1-6 (Thr to Ile), VP1-105 (Met to Thr), VP1-286 (Arg to Lys), VP2-155 (Lys to Glu), VP3-59 (Ser to Asn) and VP3-91 (Phe to Ser). These variants were commonly observed in other PV strains, which may contribute to attenuation and temperature sensitivity. None of the 24 tested contacts of the patient and related transmits was found to be infected with poliovirus. Our study provides a rapid and reliable method for the characterization of VDPV research in Poliovirus infection. In post-OPV era, immunodeficient people with persistent and chronic infection remain a major challenge for polio eradication in China.
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Affiliation(s)
- Tianhe Xiao
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China; Department of Bioengineering, University of California, San Diego, CA 92093, USA
| | - Hongying Leng
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Qian Zhang
- College of pharmacy, Nankai University, Tianjin 300353, China
| | - Qiang Chen
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Hongxiong Guo
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Yuhua Qi
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China.
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Liu S, Zhang SM, Buddenborg SK, Loker ES, Bonning BC. Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya. PeerJ 2021; 9:e12290. [PMID: 34820163 PMCID: PMC8601052 DOI: 10.7717/peerj.12290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, Iowa, United States
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Sarah K. Buddenborg
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Eric S. Loker
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Bryony C. Bonning
- Entomology & Nematology Department, University of Florida, Gainesville, Florida, United States
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Rothman JA, Loveless TB, Kapcia J, Adams ED, Steele JA, Zimmer-Faust AG, Langlois K, Wanless D, Griffith M, Mao L, Chokry J, Griffith JF, Whiteson KL. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants. Appl Environ Microbiol 2021; 87:e0144821. [PMID: 34550753 PMCID: PMC8579973 DOI: 10.1128/aem.01448-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Theresa B. Loveless
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Joseph Kapcia
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Eric D. Adams
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - David Wanless
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Lucy Mao
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jeffrey Chokry
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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36
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Zhang M, You F, Wu F, He H, Li Q, Chen Q. Epidemiology and genetic characteristics of murine kobuvirus from faecal samples of Rattus losea, Rattus tanezumi and Rattus norvegicus in southern China. J Gen Virol 2021; 102. [PMID: 34486970 PMCID: PMC8567428 DOI: 10.1099/jgv.0.001646] [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] [Indexed: 01/05/2023] Open
Abstract
Recently, murine kobuvirus (MuKV), a novel member of the family Picornaviridae, was identified in faecal samples of Rattus norvegicus in China. The limited information on the circulation of MuKV in other murine rodent species prompted us to investigate its prevalence and conduct a genetic characterization of MuKV in Rattus losea, Rattus tanezumi and Rattus norvegicus in China. Between 2015 and 2017, 243 faecal samples of these three murine rodent species from three regions in southern China were screened for the presence of MuKV. The overall prevalence was 23.0% (56/243). Three complete MuKV polyprotein sequences were acquired, and the genome organization was determined. Phylogenetic analyses suggested that our sequences were closely related to Chinese strains and belong to the species Aichivirus A in the genus Kobuvirus. Additional studies are required to understand the true prevalence of MuKV in murine rodent populations in China.
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Affiliation(s)
- Minyi Zhang
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Fangfei You
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Fei Wu
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Qiushuang Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, PR China
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021. [PMID: 34451505 DOI: 10.3390/pathogens10081042.pmid:34451505;pmcid:pmc8401729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | | | | | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
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38
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021; 10:1042. [PMID: 34451505 PMCID: PMC8401729 DOI: 10.3390/pathogens10081042] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Christophe Soumagnac
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Annessi
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Lacoste
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
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Roach M, Cantu A, Vieri MK, Cotten M, Kellam P, Phan M, van der Hoek L, Mandro M, Tepage F, Mambandu G, Musinya G, Laudisoit A, Colebunders R, Edwards R, Mokili JL. No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study. Pathogens 2021; 10:pathogens10070787. [PMID: 34206564 PMCID: PMC8308762 DOI: 10.3390/pathogens10070787] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the increasing epidemiological evidence that the Onchocerca volvulus parasite is strongly associated with epilepsy in children, hence the name onchocerciasis-associated epilepsy (OAE), the pathophysiological mechanism of OAE remains to be elucidated. In June 2014, children with unprovoked convulsive epilepsy and healthy controls were enrolled in a case control study in Titule, Bas-Uélé Province in the Democratic Republic of the Congo (DRC) to identify risk factors for epilepsy. Using a subset of samples collected from individuals enrolled in this study (16 persons with OAE and 9 controls) plasma, buffy coat, and cerebrospinal fluid (CSF) were subjected to random-primed next-generation sequencing. The resulting sequences were analyzed using sensitive computational methods to identify viral DNA and RNA sequences. Anneloviridae, Flaviviridae, Hepadnaviridae (Hepatitis B virus), Herpesviridae, Papillomaviridae, Polyomaviridae (Human polyomavirus), and Virgaviridae were identified in cases and in controls. Not unexpectedly, a variety of bacteriophages were also detected in all cases and controls. However, none of the identified viral sequences were found enriched in OAE cases, which was our criteria for agents that might play a role in the etiology or pathogenesis of OAE.
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Affiliation(s)
- Michael Roach
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia; (M.R.); (R.E.)
| | - Adrian Cantu
- Computational Sciences Research Center, Biology Department, San Diego State University, San Diego, CA 92182, USA;
| | - Melissa Krizia Vieri
- Global Health Institute, University of Antwerp, 2160 Antwerp, Belgium; (M.K.V.); (R.C.)
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton CB10 1RQ, UK;
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
| | - Paul Kellam
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
| | - My Phan
- MRC/UVRI and London School of Hygiene and Tropical Medicine, Entebbe, Uganda; (P.K.); (M.P.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands;
| | - Michel Mandro
- Provincial Health Division Ituri, Ministry of Health, Ituri, Congo;
| | - Floribert Tepage
- Provincial Health Division Bas Uélé, Ministry of Health, Bas Uélé, Congo;
| | - Germain Mambandu
- Provincial Health Division Tshopo, Ministry of Health, Tshopo, Congo;
| | | | | | - Robert Colebunders
- Global Health Institute, University of Antwerp, 2160 Antwerp, Belgium; (M.K.V.); (R.C.)
| | - Robert Edwards
- College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia; (M.R.); (R.E.)
- Computational Sciences Research Center, Biology Department, San Diego State University, San Diego, CA 92182, USA;
- Viral Information Institute, Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - John L. Mokili
- Viral Information Institute, Biology Department, San Diego State University, San Diego, CA 92182, USA
- Correspondence:
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing. Viruses 2021; 13:v13040641. [PMID: 33918088 PMCID: PMC8070635 DOI: 10.3390/v13040641] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation sequencing (NGS) analysis of amplicons covering the entire capsid coding region directly synthesized from clinical samples. One hundred and twelve clinical samples from England; previously shown to be positive for EVs, were analyzed. There was high concordance between the results obtained by the new NGS approach and those from the conventional Sanger method used originally with agreement in the serotypes identified in the 83 samples that were typed by both methods. The sensitivity and specificity of the NGS method compared to those of the conventional Sanger sequencing typing assay were 94.74% (95% confidence interval, 73.97% to 99.87%) and 97.85% (92.45% to 99.74%) for Enterovirus A, 93.75% (82.80% to 98.69%) and 89.06% (78.75% to 95.49%) for Enterovirus B, 100% (59.04% to 100%) and 98.10% (93.29% to 99.77%) for Enterovirus C, and 100% (75.29% to 100%) and 100% (96.34% to 100%) for Enterovirus D. The NGS method identified five EVs in previously untyped samples as well as additional viruses in some samples, indicating co-infection. This method can be easily expanded to generate whole-genome EV sequences as we show here for EV-D68. Information from capsid and whole-genome sequences is critical to help identifying the genetic basis for changes in viral properties and establishing accurate spatial-temporal associations between EV strains of public health relevance.
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McCall C, Wu H, O'Brien E, Xagoraraki I. Assessment of enteric viruses during a hepatitis outbreak in Detroit MI using wastewater surveillance and metagenomic analysis. J Appl Microbiol 2021; 131:1539-1554. [PMID: 33550682 DOI: 10.1111/jam.15027] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022]
Abstract
AIMS This study investigates enteric viruses in wastewater during an outbreak of acute hepatitis caused by hepatitis A virus (HAV) in a large metropolitan area. Emphasis is given to caliciviruses and HAV. METHODS AND RESULTS Metagenomic analysis was performed to characterize enteric viruses excreted by the population of Detroit MI, during a hepatitis A outbreak that occurred in 2017 and 2018. Additionally, HAV, norovirus GII, and sapovirus were quantified, using qPCR, in 54 untreated wastewater samples collected over the course of 4 months. Correlation analysis was performed to identify associations between the number of disease cases and HAV concentrations in wastewater. HAV obtained the highest relative abundance among other enteric viruses detected in wastewater metagenomes. Metagenomic analysis also detected several other enteric viruses including astrovirus, enterovirus and hepatitis E virus. Average sapovirus concentrations of 1·36 × 106 gc l-1 were significantly greater than norovirus GII concentrations (2·94 × 104 gc l-1 ). Additionally, norovirus GI and GII along with sapovirus GI.1 were detected using metagenomics. HAV loads in wastewater were significantly correlated with the number of disease cases reported 1 week after wastewater sampling. CONCLUSIONS Surveying untreated wastewater is a promising method for detecting early signs of hepatitis A outbreaks and for routine environmental monitoring of enteric viruses circulating in the environment. SIGNIFICANCE AND IMPACT OF THE STUDY Authors demonstrate the usefulness of metagenomics for genogrouping and enteric viral surveillance.
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Affiliation(s)
- C McCall
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - H Wu
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - E O'Brien
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - I Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
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Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil. Arch Virol 2021; 166:905-913. [PMID: 33462673 DOI: 10.1007/s00705-020-04944-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/13/2020] [Indexed: 01/24/2023]
Abstract
From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.
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Majumdar M, Klapsa D, Wilton T, Bujaki E, Fernandez-Garcia MD, Faleye TOC, Oyero AO, Adewumi MO, Ndiaye K, Adeniji JA, Martin J. High Diversity of Human Non-Polio Enterovirus Serotypes Identified in Contaminated Water in Nigeria. Viruses 2021; 13:v13020249. [PMID: 33562806 PMCID: PMC7914538 DOI: 10.3390/v13020249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/06/2023] Open
Abstract
Human enteroviruses (EVs) are highly prevalent in sewage and have been associated with human diseases with complications leading to severe neurological syndromes. We have used a recently developed molecular method to investigate the presence of EVs in eight samples collected in 2017–2018 from water streams contaminated by drainage channels in three different locations in Nigeria. A total of 93 human EV strains belonging to 45 different serotypes were identified, far exceeding the number of strains and serotypes found in similar samples in previous studies. Next generation sequencing analysis retrieved whole-capsid genomic nucleotide sequences of EV strains belonging to all four A, B, C, and D species. Our results further demonstrate the value of environmental surveillance for the detection of EV transmission of both serotypes commonly associated with clinical syndromes, such as EV-A71, and those that appear to circulate silently but could eventually cause outbreaks and disease. Several uncommon serotypes, rarely reported elsewhere, were detected such as EV-A119, EV-B87, EV-C116, and EV-D111. Ten EV serotypes were detected in Nigeria for the first time and two of them, CV-A12 and EV-B86, firstly described in Africa. This method can be expanded to generate whole-genome EV sequences as we show here for one EV-D111 strain. Our data revealed phylogenetic relationships of Nigerian sewage strains with EV strains reported elsewhere, mostly from African origin, and provided new insights into the whole-genome structure of emerging serotype EV-D111 and recombination events among EV-D serotypes.
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Affiliation(s)
- Manasi Majumdar
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Dimitra Klapsa
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Thomas Wilton
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Erika Bujaki
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | | | - Temitope Oluwasegun Cephas Faleye
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
| | | | - Moses Olubusuyi Adewumi
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
| | - Kader Ndiaye
- Department of Virology, Institute Pasteur, Dakar, Senegal; (M.D.F.-G.); (K.N.)
| | - Johnson Adekunle Adeniji
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
- World Health Organization National Polio Laboratory, Ibadan, Oyo State, Nigeria;
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
- Correspondence:
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45
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Schneider J, Engler M, Hofmann J, Selinka HC, Jones TC, Drosten C, Diedrich S, Corman VM, Böttcher S. Molecular detection of cosaviruses in a patient with acute flaccid paralysis and in sewage samples in Germany. Virus Res 2021; 297:198285. [PMID: 33548413 DOI: 10.1016/j.virusres.2020.198285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/02/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
Cosaviruses (CoSV) were first identified in stool samples collected from non-polio acute flaccid paralysis (AFP) cases and their healthy contacts in Pakistan in 2003. The clinical importance of CoSV remains unclear as data on epidemiology are scarce and no routine diagnostic testing is done. In this study, we characterized human CoSV (HCoSV) in a child with non-polio AFP and in sewage samples collected in Berlin, Germany. Using unbiased high-throughput sequencing and specific PCR, we characterized a HCoSV-D in stool samples of a three-year-old child hospitalized in Germany with non-polio AFP and travel history to Pakistan. The shedding pattern and absence of other relevant pathogens suggests that HCoSV-D may have been involved in the genesis of AFP. The HCoSV-RNA concentration was high, with 2.57 × 106 copies per mL fecal/suspension, decreasing in follow-up samples. To investigate the possibility of local circulation of HCoSV, we screened Berlin sewage samples collected between 2013 and 2018. Molecular testing of sewage samples has shown the presence of CoSV in several parts of the world, but until now not in Germany. Of our sewage samples, 54.3 % were positive for CoSV, with up to three viral species identified in samples. Phylogenetically, the German sequences clustered intermixed with sequences obtained globally. Together, these findings emphasize the need for further clinical, epidemiological, environmental, pathogenicity and phylogenetic studies of HCoSV.
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Affiliation(s)
- J Schneider
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - M Engler
- Department of Paediatrics, Sana Klinikum Offenbach GmbH, Starkenburgring 66, 63069, Offenbach am Main, Germany
| | - J Hofmann
- Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - H C Selinka
- German Environment Agency, Microbiological Risks, Corrensplatz 1, 14195, Berlin, Germany
| | - T C Jones
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - C Drosten
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany
| | - S Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
| | - V M Corman
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany.
| | - S Böttcher
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany.
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Mohan SV, Hemalatha M, Kopperi H, Ranjith I, Kumar AK. SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 405:126893. [PMID: 32901196 PMCID: PMC7471803 DOI: 10.1016/j.cej.2020.126893] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/03/2023]
Abstract
The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (βCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.
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Key Words
- (h+), Photoholes
- +ssRNA, Positive Sense Single-Stranded RNA
- A-WWTS, Algal-WWTS
- ACE2, Angiotensin-converting enzyme 2
- AH, Absolute Humidity
- AOPs, Advanced Oxidation Processes
- ASP, Activate Sludge Process
- Aerosols
- BCoV, Bovine Enteric Coronavirus)
- BSL, Biosafety Level
- BVDV1, Bovine Viral Diarrhea Virus Type 1
- BVDV2, Bovine Viral Diarrhea Virus Type 2
- BoRv, Bovine Rotavirus Group A
- CCA, Carbon Covered Alumina
- CNT, Carbon Nanotubes
- COVID-19
- COVID-19, Coronavirus Disease 2019
- CRFK, Crandell Reese feline kidney cell line (CRFK)
- CVE, Coxsackievirus B5
- ClO2, Chlorine dioxide
- Cl−, Chlorine
- Cys, Cysteine
- DBP, Disinfection by-products
- DBT, L2 and Delayed Brain Tumor Cell Cultures
- DMEM, Dulbecco’s Modified Eagle Medium
- DNA, deoxyribose nucleic acid
- Disinfection
- E gene, Envelope protein gene
- EV, Echovirus 11
- Enteric virus
- Enveloped virus
- FC, Free Chlorine
- FFP3, Filtering Face Piece
- FIPV, Feline infectious peritonitis virus
- GI, Gastrointestinal tract
- H2O2, Hydrogen Peroxide
- H3N2, InfluenzaA
- H6N2, Avian influenza virus
- HAV, Hepatitis A virus (HAV)
- HAdV, Human Adenovirus
- HCoV, Human CoV
- HEV, Hepatitis E virus
- HKU1, Human CoV1
- ICC-PCR, Integrated Cell Culture with PCR
- JCV, JCV polyomavirus
- MALDI-TOF MS, Mass Spectrometry
- MBR, Membrane Bioreactor (MBR)
- MERS-CoV, Middle East Respiratory Syndrome Coronavirus
- MHV, Murine hepatitis virus
- MNV-1, Murine Norovirus
- MWCNTs, Multiwalled Carbon Nanotubes
- Met, Methionine
- N gene, Nucleocapsid protein gene
- NCoV, Novel coronavirus
- NGS, Next generation sequencing
- NTP, Non-Thermal Plasma
- O2, Singlet Oxygen
- O3, Ozone
- ORF, Open Reading Frame
- PAA, Para Acetic Acid
- PCR, Polymerase Chain Reaction
- PEC, Photoelectrocatalytical
- PEG, Polyethylene Glycol
- PFU, Plaque Forming Unit
- PMMoV, Pepper Mild Mottle Virus
- PMR, Photocatalytic Membrane Reactors
- PPE, Personal Protective Equipment
- PTAF, Photocatalytic Titanium Apatite Filter
- PV-1, Polivirus-1
- PV-3, Poliovirus 3
- PVDF, Polyvinylidene Fluoride
- Qβ, bacteriophages
- RH, Relative Humidity
- RNA, Ribose nucleic acid
- RONS, Reactive Oxygen and/or Nitrogen Species
- RT-PCR, Real Time Polymerase Chain Reaction
- RVA, Rotaviruses A
- SARS-CoV-1, Severe Acute Respiratory Syndrome Coronavirus 1
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- SBR, Sequential Batch Reactor
- SODIS, Solar water disinfection
- STP, Sewage Treatment Plant
- Sewage
- T90, First order reaction time required for completion of 90%
- T99.9, First order reaction time required for completion of 99.9%
- TGEV, Porcine Coronavirus Transmissible Gastroenteritis Virus
- TGEV, Transmissible Gastroenteritis
- Trp, Tryptophan
- Tyr, Tyrosine
- US-EPA, United States Environmental Protection Agency
- UV, Ultraviolet
- WBE, Wastewater-Based Epidemiology
- WWT, Wastewater Treatment
- WWTPs, Wastewater Treatment Plants
- dPCR, Digital PCR
- ds, Double Stranded
- dsDNA, Double Stranded DNA
- log10, logarithm with base 10
- qRT-PCR, quantitative RT-PCR
- ss, Single Stranded
- ssDNA, Single Stranded DNA
- ssRNA, Single Stranded RNA
- αCoV, Alphacoronavirus
- βCoV, Betacoronavirus
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Affiliation(s)
- S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Manupati Hemalatha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Harishankar Kopperi
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - I Ranjith
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - A Kiran Kumar
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Dispensary, Hyderabad 500007, India
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Yang Q, Rivailler P, Zhu S, Yan D, Xie N, Tang H, Zhang Y, Xu W. Detection of multiple viruses potentially infecting humans in sewage water from Xinjiang Uygur Autonomous Region, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142322. [PMID: 33254887 DOI: 10.1016/j.scitotenv.2020.142322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
The progress of sequencing technologies has facilitated metagenomics projects on environmental samples like sewage water. The present study concerned the analysis of sewage samples collected from 3 locations in Xinjiang Uygur Autonomous Region in China. The analysis focused on RNA viruses known to infect humans and identified viruses from 10 families. The proportion of human virus species in the sewage samples was relatively stable with an average of 17%. Thirty virus species known to infect humans were identified and they belonged to 6 families: Picornaviridae (12), Astroviridae (11), Reoviridae (3), Caliciviridae (2), Papillomaviridae (1) and Picobirnaviridae (1). A total of 16 full-length genomes were generated from Astroviridae, Picornaviridae (Salivirus and Kobuvirus) and Picobirnaviridae. Astroviruses appeared to be the most present viruses and were detected in all sewage samples. Analyzing the virome of sewage samples should help to monitor any potential risks to public health.
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Affiliation(s)
- Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Pierre Rivailler
- WHO WPRO Regional Reference Measles/Rubella Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China
| | - Na Xie
- Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Jianquanyi Road, Urumqi 830002, China
| | - Haishu Tang
- Xinjiang Uygur Autonomous Region Center for Disease Control and Prevention, Jianquanyi Road, Urumqi 830002, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; WHO WPRO Regional Reference Measles/Rubella Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, 155 Changbai Road, Beijing 102206, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
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Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, Flamholz A, Kennedy LC, Greenwald H, Hinkle A, Hetzel J, Spitzer S, Koble J, Tan A, Hyde F, Schroth G, Kuersten S, Banfield JF, Nelson KL. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio 2021; 12:e02703-20. [PMID: 33468686 PMCID: PMC7845645 DOI: 10.1128/mbio.02703-20] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
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Affiliation(s)
- Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Avi Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | | | | | | | - Asako Tan
- Illumina, San Diego, California, USA
| | | | | | | | - Jillian F Banfield
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Kara L Nelson
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
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49
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Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, Flamholz A, Kennedy LC, Greenwald H, Hinkle A, Hetzel J, Spitzer S, Koble J, Tan A, Hyde F, Schroth G, Kuersten S, Banfield JF, Nelson KL. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio 2021. [PMID: 33468686 DOI: 10.1101/2020.09.13.20193805] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
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Affiliation(s)
- Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Avi Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | | | | | | | - Asako Tan
- Illumina, San Diego, California, USA
| | | | | | | | - Jillian F Banfield
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Kara L Nelson
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
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50
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Crits-Christoph A, Kantor RS, Olm MR, Whitney ON, Al-Shayeb B, Lou YC, Flamholz A, Kennedy LC, Greenwald H, Hinkle A, Hetzel J, Spitzer S, Koble J, Tan A, Hyde F, Schroth G, Kuersten S, Banfield JF, Nelson KL. Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants. mBio 2021. [PMID: 33468686 DOI: 10.1128/mbio.02703-20%j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.
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Affiliation(s)
- Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
| | - Avi Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
| | | | | | | | - Asako Tan
- Illumina, San Diego, California, USA
| | | | | | | | - Jillian F Banfield
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Kara L Nelson
- Innovative Genomics Institute, Berkeley, California, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA
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