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Smith AM, Ramudzulu M, Munk P, Avot BJP, Esterhuyse KCM, van Blerk N, Kwenda S, Sekwadi P. Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa. PLoS One 2024; 19:e0309409. [PMID: 39186711 PMCID: PMC11346938 DOI: 10.1371/journal.pone.0309409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.
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Affiliation(s)
- Anthony M. Smith
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Centre for Enteric Diseases, Johannesburg, South Africa
- Faculty of Health Sciences, Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Masindi Ramudzulu
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Centre for Enteric Diseases, Johannesburg, South Africa
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Baptiste J. P. Avot
- National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | | | - Nico van Blerk
- Ekurhuleni Water Care Company, Kempton Park, South Africa
| | - Stanford Kwenda
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Centre for Enteric Diseases, Johannesburg, South Africa
| | - Phuti Sekwadi
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Centre for Enteric Diseases, Johannesburg, South Africa
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2
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Kang S, Choi P, Maile-Moskowitz A, Brown CL, Gonzalez RA, Pruden A, Vikesland PJ. Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance. ACS ES&T WATER 2024; 4:1629-1636. [PMID: 38633369 PMCID: PMC11019537 DOI: 10.1021/acsestwater.3c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.
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Affiliation(s)
- Seju Kang
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Petra Choi
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Connor L. Brown
- Department
of Genetics, Bioinformatics, and Computational Biology, Blacksburg, Virginia 24061, United States
| | - Raul A. Gonzalez
- Hampton
Roads Sanitation District, Virginia Beach ,Virginia23455, United States
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Institute of Critical Technology and Applied Science (ICTAS),
Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
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3
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Rajput V, Pramanik R, Malik V, Yadav R, Samson R, Kadam P, Bhalerao U, Tupekar M, Deshpande D, Shah P, Shashidhara LS, Boargaonkar R, Patil D, Kale S, Bhalerao A, Jain N, Kamble S, Dastager S, Karmodiya K, Dharne M. Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118976-118988. [PMID: 37922087 DOI: 10.1007/s11356-023-30709-z] [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: 06/27/2023] [Accepted: 10/23/2023] [Indexed: 11/05/2023]
Abstract
The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (~28%), BA.1.X (1.0-72%), BA.2 (1.0-18%), BA.2.X (1.0-97.4%) BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-21.83%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.
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Affiliation(s)
- Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rinka Pramanik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinita Malik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Dipti Deshpande
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Priyanki Shah
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - L S Shashidhara
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | | | - Dhawal Patil
- Ecosan Services Foundation (ESF), Pune, Maharashtra, 411030, India
| | - Saurabh Kale
- Ecosan Services Foundation (ESF), Pune, Maharashtra, 411030, India
| | - Asim Bhalerao
- Fluid Robotics Private Limited (FRPL), Pune, Maharashtra, 411052, India
| | - Nidhi Jain
- Fluid Robotics Private Limited (FRPL), Pune, Maharashtra, 411052, India
| | - Sanjay Kamble
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Syed Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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4
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Wang X, Dong J, Lu Y. Circular mRNA: A novel therapeutic agent. BIOTECHNOLOGY NOTES (AMSTERDAM, NETHERLANDS) 2023; 4:58-63. [PMID: 39416918 PMCID: PMC11446363 DOI: 10.1016/j.biotno.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2024]
Abstract
Circular mRNA (circmRNA) is a covalent closed loop formed by reverse splicing of the 3' end to the 5' end of mRNA. Compared to traditional linear mRNAs, circmRNAs can mediate efficient, stable, and durable protein expression and are considered an alternative to linear mRNAs in terms of therapeutic reagents. With the continuous development of circmRNA research, circmRNA has also made significant progress in vaccines and cellular therapies. In this review, we present research advances in the in vitro synthesis of circmRNAs, focusing on the biological ligation methods of circmRNAs and current applications, with a summary of challenges regarding circmRNA design, synthesis, and applications. Based on the enhanced stability of circmRNAs, further research on circmRNAs could help expand their applications in biotherapeutics and strengthen their role in basic medical applications.
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Affiliation(s)
- Xiaoxue Wang
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jian Dong
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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5
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Asadi M, Oloye FF, Xie Y, Cantin J, Challis JK, McPhedran KN, Yusuf W, Champredon D, Xia P, De Lange C, El-Baroudy S, Servos MR, Jones PD, Giesy JP, Brinkmann M. A wastewater-based risk index for SARS-CoV-2 infections among three cities on the Canadian Prairie. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162800. [PMID: 36914129 PMCID: PMC10008033 DOI: 10.1016/j.scitotenv.2023.162800] [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: 09/19/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
Wastewater surveillance (WWS) is useful to better understand the spreading of coronavirus disease 2019 (COVID-19) in communities, which can help design and implement suitable mitigation measures. The main objective of this study was to develop the Wastewater Viral Load Risk Index (WWVLRI) for three Saskatchewan cities to offer a simple metric to interpret WWS. The index was developed by considering relationships between reproduction number, clinical data, daily per capita concentrations of virus particles in wastewater, and weekly viral load change rate. Trends of daily per capita concentrations of SARS-CoV-2 in wastewater for Saskatoon, Prince Albert, and North Battleford were similar during the pandemic, suggesting that per capita viral load can be useful to quantitatively compare wastewater signals among cities and develop an effective and comprehensible WWVLRI. The effective reproduction number (Rt) and the daily per capita efficiency adjusted viral load thresholds of 85 × 106 and 200 × 106 N2 gene counts (gc)/population day (pd) were determined. These values with rates of change were used to categorize the potential for COVID-19 outbreaks and subsequent declines. The weekly average was considered 'low risk' when the per capita viral load was 85 × 106 N2 gc/pd. A 'medium risk' occurs when the per capita copies were between 85 × 106 and 200 × 106 N2 gc/pd. with a rate of change <100 %. The start of an outbreak is indicated by a 'medium-high' risk classification when the week-over-week rate of change was >100 %, and the absolute magnitude of concentrations of viral particles was >85 × 106 N2 gc/pd. Lastly, a 'high risk' occurs when the viral load exceeds 200 × 106 N2 gc/pd. This methodology provides a valuable resource for decision-makers and health authorities, specifically given the limitation of COVID-19 surveillance based on clinical data.
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Affiliation(s)
- Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Warsame Yusuf
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - David Champredon
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Pu Xia
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chantel De Lange
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Seba El-Baroudy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada.
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6
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Lanzarini NM, Mannarino CF, Ribeiro AVC, Prado T, Vahia LS, Siqueira MM, Resende PC, Quintaes BR, Miagostovich MP. SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67368-67377. [PMID: 37101215 PMCID: PMC10132925 DOI: 10.1007/s11356-023-27019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.
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Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Camille Ferreira Mannarino
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Leonardo Saboia Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
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7
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Yuan M, Zhu Y, Liu G, Wang Y, Wang G, Zhang G, Ye L, Qian Z, Liu P. An RBD bispecific antibody effectively neutralizes a SARS-CoV-2 Omicron variant. ONE HEALTH ADVANCES 2023; 1:12. [PMID: 37521533 PMCID: PMC10173222 DOI: 10.1186/s44280-023-00012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 08/01/2023]
Abstract
Potent neutralizing antibodies (nAbs) against SARS-CoV-2 are a promising therapeutic against the ongoing COVID-19 pandemic. However, the continuous emergence of neutralizing antibody escape variants makes it challenging for antibody therapeutics based on monospecific nAbs. Here, we generated an IgG-like bispecific antibody (bsAb), Bi-Nab, based on a pair of human neutralizing antibodies targeting multiple and invariant sites of the spike receptor binding domain (RBD): 35B5 and 32C7. We demonstrated that Bi-Nab exhibited higher binding affinity to the Delta spike protein than its parental antibodies and presented an extended inhibition breadth of preventing RBD binding to angiotensin-converting enzyme 2 (ACE2), the cellular receptor of SARS-CoV-2. In addition, pseudovirus neutralization results showed that Bi-Nab improved the neutralization potency and breadth with a lower half maximum inhibitory concentration (IC50) against wild-type SARS-CoV-2, variants being monitored (VBMs) and variants of concern (VOCs). Notably, the IgG-like Bi-Nab enhanced the neutralizing activity against Omicron variants with potent capabilities for transmission and immune evasion in comparison with its parental monoclonal antibody (mAb) 32C7 and a cocktail (with the lowest IC50 values of 31.6 ng/mL against the Omicron BA.1 and 399.2 ng/mL against the Omicron BA.2), showing evidence of synergistic neutralization potency of Bi-Nab against the Omicron variants. Thus, Bi-Nab represents a feasible and effective strategy against SARS-CoV-2 variants of concern.
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Affiliation(s)
- Mengqi Yuan
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Yanzhi Zhu
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Guanlan Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Yujie Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Guanxi Wang
- College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Lilin Ye
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038 China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176 China
| | - Pinghuang Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
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8
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Iwamoto R, Yamaguchi K, Katayama K, Ando H, Setsukinai KI, Kobayashi H, Okabe S, Imoto S, Kitajima M. Identification of SARS-CoV-2 variants in wastewater using targeted amplicon sequencing during a low COVID-19 prevalence period in Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 887:163706. [PMID: 37105480 PMCID: PMC10129341 DOI: 10.1016/j.scitotenv.2023.163706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Wastewater-based epidemiology is expected to be able to identify SARS-CoV-2 variants at an early stage via next-generation sequencing. In the present study, we developed a highly sensitive amplicon sequencing method targeting the spike gene of SARS-CoV-2, which allows for sequencing viral genomes from wastewater containing a low amount of virus. Primers were designed to amplify a relatively long region (599 bp) around the receptor-binding domain in the SARS-CoV-2 spike gene, which could distinguish initial major variants of concern. To validate the methodology, we retrospectively analyzed wastewater samples collected from a septic tank installed in a COVID-19 quarantine facility between October and December 2020. The relative abundance of D614G mutant in SARS-CoV-2 genomes in the facility wastewater increased from 47.5 % to 83.1 % during the study period. The N501Y mutant, which is the characteristic mutation of the Alpha-like strain, was detected from wastewater collected on December 24, 2020, which agreed with the fact that a patient infected with the Alpha-like strain was quarantined in the facility on this date. We then analyzed archived municipal wastewater samples collected between November 2020 and January 2021 that contained low SARS-CoV-2 concentrations ranging from 0.23 to 0.43 copies/qPCR reaction (corresponding to 3.30 to 4.15 log10 copies/L). The targeted amplicon sequencing revealed that the Alpha-like variant with D614G and N501Y mutations was present in municipal wastewater collected on December 4, 2020 and later, suggesting that the variant had already spread in the community before its first clinical confirmation in Japan on December 25, 2020. These results demonstrate that targeted amplicon sequencing of wastewater samples is a powerful surveillance tool applicable to low COVID-19 prevalence periods and may contribute to the early detection of emerging variants.
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Affiliation(s)
- Ryo Iwamoto
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kotoe Katayama
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroki Ando
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Ken-Ichi Setsukinai
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Hiroyuki Kobayashi
- Shionogi & Co., Ltd., 1-8, Doshomachi 3-Chome, Chuo-ku, Osaka 541-0045, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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9
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Child HT, O’Neill PA, Moore K, Rowe W, Denise H, Bass D, Wade MJ, Loose M, Paterson S, van Aerle R, Jeffries AR. Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLoS One 2023; 18:e0284211. [PMID: 37058515 PMCID: PMC10104291 DOI: 10.1371/journal.pone.0284211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Paul A. O’Neill
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - William Rowe
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Hubert Denise
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Weymouth, United Kingdom
| | - Matthew J. Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, Queen’s Medical Centre, The University of Nottingham, Nottingham, 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, Weymouth, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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10
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Yalamarty SSK, Filipczak N, Khan MM, Torchilin VP. Role of circular RNA and its delivery strategies to cancer - An overview. J Control Release 2023; 356:306-315. [PMID: 36878321 DOI: 10.1016/j.jconrel.2023.02.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
With the passage of years and the progress of research on ribonucleic acids, the range of forms in which these molecules have been observed grows. One of them, discovered relatively recently, is circular RNA - covalently closed circles (circRNA). In recent years, there has been a huge increase in the interest of researchers in this group of molecules. It entailed a significant increase in the state of knowledge about them, which in turn caused a dramatic change in their perception. Rather than seeing circular RNAs as curiosities that represent a minor information noise in a cell or a result of RNA misprocessing, they came to be regarded as a common, essential, and potentially extremely useful group of molecules. Nevertheless, the current state of the art of circRNA is full of white cards. A lot of valuable information has been obtained from high-throughput methods to study whole transcriptomes, but many issues related to circular RNAs still need to be clarified. Presumably, each answer obtained will raise several new questions. However, circRNAs have a wealth of potential applications, including therapeutic applications.
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Affiliation(s)
| | - Nina Filipczak
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA
| | | | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA; Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.
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11
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Gao X, Xia Y, Liu X, Xu Y, Lu P, dong Z, Liu J, Liang G. A perspective on SARS-CoV-2 virus-like particles vaccines. Int Immunopharmacol 2023; 115:109650. [PMID: 36649673 PMCID: PMC9832101 DOI: 10.1016/j.intimp.2022.109650] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/18/2022] [Accepted: 12/25/2022] [Indexed: 01/13/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) first appeared in Wuhan, China, in December 2019. The 2019 coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2, has spread to almost all corners of the world at an alarming rate. Vaccination is important for the prevention and control of the COVID-19 pandemic. Efforts are underway worldwide to develop an effective vaccine against COVID-19 using both traditional and innovative vaccine strategies. Compared to other vaccine platforms, SARS-CoV-2 virus-like particles (VLPs )vaccines, as a new vaccine platform, have unique advantages: they have artificial nanostructures similar to natural SARS-CoV-2, which can stimulate good cellular and humoral immune responses in the organism; they have no viral nucleic acids, have good safety and thermal stability, and can be mass-produced and stored; their surfaces can be processed and modified, such as the adjuvant addition, etc.; they can be considered as an ideal platform for COVID-19 vaccine development. This review aims to shed light on the current knowledge and progress of VLPs vaccines against COVID-19, especially those undergoing clinical trials.
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Affiliation(s)
- Xiaoyang Gao
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China,School of Basic Medical Sciences, Henan University of Science & Technology, Luoyang 471023, China
| | - Yeting Xia
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xiaofang Liu
- The First People's Hospital of Nanyang Affiliated to Henan University, Nanyang 473000, China
| | - Yinlan Xu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province 453003, China
| | - Pengyang Lu
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Zhipeng dong
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Jing Liu
- Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.
| | - Gaofeng Liang
- School of Basic Medical Sciences, Henan University of Science & Technology, Luoyang 471023, China.
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12
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Castro GB, Bernegossi AC, Sousa BJDO, De Lima E Silva MR, Silva FRD, Freitas BLS, Ogura AP, Corbi JJ. Global occurrence of SARS-CoV-2 in environmental aquatic matrices and its implications for sanitation and vulnerabilities in Brazil and developing countries. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:2160-2199. [PMID: 34310248 DOI: 10.1080/09603123.2021.1949437] [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: 10/27/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
This paper includes a systematic review of the SARS-CoV-2 occurrence in environmental aquatic matrices and a critical sanitation analysis. We discussed the interconnection of sanitation services (wastewater, water supply, solid waste, and stormwater drainage) functioning as an important network for controlling the spread of SARS-CoV-2 in waters. We collected 98 studies containing data of the SARS-CoV-2 occurrence in aquatic matrices around the world, of which 40% were from developing countries. Alongside a significant number of people infected by the virus, developing countries face socioeconomic deficiencies and insufficient public investment in infrastructure. Therefore, our study focused on highlighting solutions to provide sanitation in developing countries, considering the virus control in waters by disinfection techniques and sanitary measures, including alternatives for the vulnerable communities. The need for multilateral efforts to improve the universal coverage of sanitation services demands urgent attention in a pandemic scenario.
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Affiliation(s)
- Gleyson B Castro
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
| | - Aline C Bernegossi
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
| | - Bruno José de O Sousa
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
| | | | - Fernando R Da Silva
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bárbara Luíza S Freitas
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
| | - Allan P Ogura
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
- PPG-SEA and CRHEA/SHS, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
| | - Juliano J Corbi
- Department of Hydraulic and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, Brazil
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13
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Joshi M, Kumar M, Srivastava V, Kumar D, Rathore DS, Pandit R, Graham DW, Joshi CG. Genetic sequencing detected the SARS-CoV-2 delta variant in wastewater a month prior to the first COVID-19 case in Ahmedabad (India). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119757. [PMID: 35853573 PMCID: PMC9287018 DOI: 10.1016/j.envpol.2022.119757] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 05/23/2023]
Abstract
Wastewater-based genomic surveillance can identify a huge majority of variants shed by the infected individuals within a population, which goes beyond genomic surveillance based on clinical samples (i.e., symptomatic patients only). We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis identified a total of 34 mutations in the spike protein across samples categorized into 23 types. The spike protein mutations were linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not seen in the samples from Sep/Nov 2020 but did appear before the massive second wave of COVID-19 cases, which in India started in early April 2021. In fact, genetic traces of the Delta variant were found in samples of early Feb 2021, more than a month before the first clinically confirmed case of this in March 2021 in Ahmedabad, Gujarat. The present work describes the circulating of SARS-CoV-2 variants in Ahmedabad and confirms the consequential value of wastewater surveillance for the early detection of variants of concerns (VOCs). Such monitoring must be included as a major component of future health protection systems.
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Affiliation(s)
- Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat, 382 355, India; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India.
| | - Vaibhav Srivastava
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Sector- 11, Gandhinagar, Gujarat, 382 011, India.
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14
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SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19. Vaccines (Basel) 2022; 10:vaccines10091538. [PMID: 36146616 PMCID: PMC9504858 DOI: 10.3390/vaccines10091538] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Over the past two years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections, resulting in an unprecedented pandemic of coronavirus disease 2019 (COVID-19). As the virus spreads through the population, ongoing mutations and adaptations are being discovered. There is now substantial clinical evidence that demonstrates the SARS-CoV-2 variants have stronger transmissibility and higher virulence compared to the wild-type strain of SARS-CoV-2. Hence, development of vaccines against SARS-CoV-2 variants to boost individual immunity has become essential. However, current treatment options are limited for COVID-19 caused by the SARS-CoV-2 variants. In this review, we describe current distribution, variation, biology, and clinical features of COVID-19 caused by SARS-CoV-2 variants (including Alpha (B.1.1.7 Lineage) variant, Beta (B.1.351 Lineage) variant, Gamma (P.1 Lineage) variant, Delta (B.1.617.2 Lineage) variant, and Omicron (B.1.1.529 Lineage) variant and others. In addition, we review currently employed vaccines in clinical or preclinical phases as well as potential targeted therapies in an attempt to provide better preventive and treatment strategies for COVID-19 caused by different SARS-CoV-2 variants.
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15
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Kumar A, O Pai M, Badoni G, Singh A, Agrawal A, Ji Omar B. Perspective Chapter: Tracking Trails of SARS CoV-2 - Variants to Therapy. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.106472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
A virus when replicates itself from one generation to another, tends to change a little bit of its structure. These variations are called mutations. History says that SARS CoV-2 originated from the virus reservoirs of animals, specifically non-human mammals like bats and minks. Since then, there are evolutionary changes in its genome due to recombination in divergent strains of different species. Thus, making the virus more robust and smarter to sustain and evade immune responses in humans. Probably, this has led to the 2019 SARS CoV-2 pandemic. This chapter tracks the evolutionary trails of the virus origin, its pathogenesis in humans, and varying variants with the coming times. Eventually, the chapter overviews the available vaccines and therapies to be followed for SARS CoV-2.
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16
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Lou EG, Sapoval N, McCall C, Bauhs L, Carlson-Stadler R, Kalvapalle P, Lai Y, Palmer K, Penn R, Rich W, Wolken M, Brown P, Ensor KB, Hopkins L, Treangen TJ, Stadler LB. Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35395314 DOI: 10.2139/ssrn.4022373] [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] [Indexed: 05/09/2023]
Abstract
Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3; hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Lauren Bauhs
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Russell Carlson-Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Yanlai Lai
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Kyle Palmer
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Ryker Penn
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Whitney Rich
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Pamela Brown
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Katherine B Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America; Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America.
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17
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Lou EG, Sapoval N, McCall C, Bauhs L, Carlson-Stadler R, Kalvapalle P, Lai Y, Palmer K, Penn R, Rich W, Wolken M, Brown P, Ensor KB, Hopkins L, Treangen TJ, Stadler LB. Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155059. [PMID: 35395314 PMCID: PMC8983075 DOI: 10.1016/j.scitotenv.2022.155059] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3; hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Lauren Bauhs
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Russell Carlson-Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Yanlai Lai
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Kyle Palmer
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Ryker Penn
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Whitney Rich
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Pamela Brown
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Katherine B Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America; Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America.
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18
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Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
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Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
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19
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Hyllestad S, Myrmel M, Lomba JAB, Jordhøy F, Schipper SK, Amato E. Effectiveness of environmental surveillance of SARS-CoV-2 as an early warning system during the first year of the COVID-19 pandemic: a systematic review. JOURNAL OF WATER AND HEALTH 2022; 20:1223-1242. [PMID: 36044191 DOI: 10.2166/wh.2022.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since infected persons shed SARS-CoV-2 in faeces before symptoms appear, environmental surveillance (ES) may serve as an early warning system (EWS) for COVID-19 and new variants of concern. The ES of SARS-CoV-2 has been widely reviewed; however, its effectiveness as an EWS for SARS-CoV-2 in terms of timeliness, sensitivity and specificity has not been systematically assessed. We conducted a systematic review to identify and synthesise evidence on the ES of SARS-CoV-2 as an EWS to evaluate the added value for public health. Of 1,014 studies identified, we considered 29 for a qualitative synthesis of the timeliness of ES as an EWS for COVID-19, while six studies were assessed for the ability to detect new variants and two for both aims. The synthesis indicates ES may serve as an EWS of 1-2 weeks. ES could complement clinical surveillance for SARS-CoV-2; however, its cost-benefit value for public health decisions needs to be assessed based on the stage of the pandemic and resources available. Studies focusing methodological knowledge gaps as well as how to use and interpret ES signals for public health actions are needed, as is the sharing of knowledge within countries/areas with long experience of such surveillance.
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Affiliation(s)
- Susanne Hyllestad
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jose Antonio Baz Lomba
- Department of Environmental Chemistry and Technology, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Fredrik Jordhøy
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Svanhild Kjørsvik Schipper
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Ettore Amato
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
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20
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Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nat Microbiol 2022; 7:1151-1160. [PMID: 35851854 PMCID: PMC9352586 DOI: 10.1038/s41564-022-01185-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/23/2022] [Indexed: 01/12/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK.
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Affiliation(s)
- Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Carola Bänziger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexander J Devaux
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Federica Cariti
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alex Tuñas Corzón
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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21
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Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nat Microbiol 2022. [PMID: 35851854 DOI: 10.1101/2021.01.08.21249379] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK.
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Affiliation(s)
- Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Carola Bänziger
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Alexander J Devaux
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Federica Cariti
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alex Tuñas Corzón
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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22
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Masachessi G, Castro G, Cachi AM, Marinzalda MDLÁ, Liendo M, Pisano MB, Sicilia P, Ibarra G, Rojas RM, López L, Barbás G, Cardozo D, Ré VE, Nates SV. Wastewater based epidemiology as a silent sentinel of the trend of SARS-CoV-2 circulation in the community in central Argentina. WATER RESEARCH 2022; 219:118541. [PMID: 35584586 PMCID: PMC9066365 DOI: 10.1016/j.watres.2022.118541] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 05/08/2023]
Abstract
Monitoring wastewater for the traces of viruses allows effective surveillance of entire communities, including symptomatic and asymptomatic infected individuals, providing information on whether a specific pathogen is circulating in a population. In the context of the COVID-19 pandemic, 261 wastewater samples from six communities of the province of Córdoba, Argentina were analyzed. From mid-May 2020 to the end of August 2021, raw sewage samples were collected from the central network pipe that enters into the Wastewater Treatment Plants (WWTP) in Córdoba city and five communities in the Punilla Valley. SARS-CoV-2 was concentrated by using the polyethylene glycol-6000 precipitation method. Viral genomes were extracted from concentrated samples, and N- and E-SARS-CoV-2 genes were detected by using real time RT-PCR. Wastewater samples that resulted positive for SARS-CoV-2 genome detection were subjected to viral variants of concern (VOCs) identification by real time RT-PCR. Overall, just by using the identification of the N gene or E gene, the rates of viral genome detection were 43.4% (86/198) and 51.5% (102/198) respectively, and by using both methodologies (positivity criterion: detection of N and / or E gene), the detection rate was 71.2% (141/198). Thereby, the optimal strategy to study the SARS-CoV-2 genome in wastewater would be the use of the combined detection of both genes. Detection of SARS-CoV-2 variants in wastewater reflected their circulation in the community, showing no VOCs detection in the first COVID-19 wave and their co-circulation with Gamma, Alpha and Delta VOCs during 2021. Therefore, SARS-CoV-2 Wastewater Based Epidemiology (WBE) described the introduction, permanence and/or the co-circulation of viral variants in the community. In geographical areas with a stable population, SARS-CoV-2 WBE could be used as an early warning sign of new COVID-19 cases, whereas in localities with a low number of inhabitants and high tourist influx, WBE may only be useful to reflect the circulation of the virus in the community. Overall, the monitoring of SARS-CoV-2 in wastewater can become a silent sentinel of the trend of viral circulation in the community, providing supplementary information for clinical surveillance to support public health measures.
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Affiliation(s)
- Gisela Masachessi
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina.
| | - Gonzalo Castro
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, T. Cáceres de Allende 421, Córdoba X5000HVE, Argentina
| | - Ariana Mariela Cachi
- Instituto Nacional de Medicina Aeronáutica y Espacial, FAA, Av. Fuerza Aérea Argentina Km 6 1/2 S/N B.0 Civico, Córdoba X5010, Argentina; Facultad de la Fuerza Aérea, Universidad de la Defensa Nacional, Av. Fuerza Aerea Argentina 5011, Córdoba X5000, Argentina
| | - María de Los Ángeles Marinzalda
- Instituto Nacional de Medicina Aeronáutica y Espacial, FAA, Av. Fuerza Aérea Argentina Km 6 1/2 S/N B.0 Civico, Córdoba X5010, Argentina; Facultad de la Fuerza Aérea, Universidad de la Defensa Nacional, Av. Fuerza Aerea Argentina 5011, Córdoba X5000, Argentina
| | - Matías Liendo
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina
| | - María Belén Pisano
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Paola Sicilia
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, T. Cáceres de Allende 421, Córdoba X5000HVE, Argentina
| | - Gustavo Ibarra
- Planta Municipal de tratamiento de efluente cloacales Bajo Grande-Laboratorio de análisis fisicoquímicos, bacteriológicos EDAR Bajo Grande, Cam. Chacra de la Merced 901, Córdoba X5000, Argentina
| | - Ricardo Manuel Rojas
- Cooperativa Integral Regional de Provisión de Servicios Públicos, Vivienda y Consumo Limitada (COOPI), Moreno 78, Villa Carlos Paz, X5152 Córdoba, Argentina
| | - Laura López
- Área de Epidemiología, Ministerio de Salud de la Provincia de Córdoba, Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Gabriela Barbás
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Diego Cardozo
- Ministerio de Salud de la Provincia de Córdoba, Argentina Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Viviana Elisabeth Ré
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Silvia Viviana Nates
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina
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23
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Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105282. [PMID: 35427787 PMCID: PMC9005225 DOI: 10.1016/j.meegid.2022.105282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
Background The massive increase in COVID-19 infection had generated a second wave in India during May–June 2021 with a critical pandemic situation. The Delta variant (B.1.617.2) was a significant factor during the second wave. Conversely, the UK had passed through the crucial phase of the pandemic from November to December 2020 due to B.1.1.7. The study tried to comprehend the pandemic response in the UK and India to the spread of the B.1.1.7 (Alpha, UK) variant and B.1.617.2 (Delta, India) variant. Methods This study was performed in three directions to understand the pandemic response of the two emerging variants. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). Second, we performed evolutionary epidemiology using molecular phylogenetics, scatter plots of the cluster evaluation, country-wise transmission pattern, and frequency pattern. Third, the receptor binding pattern was analyzed using the Wuhan reference strain and the other two variants. Results The study analyzed the country-wise and region-wise genome sequences and their submission pattern, molecular phylogenetics, scatter plot of the cluster evaluation, country-wise geographical distribution and transmission pattern, frequency pattern, entropy diversity, and mutational landscape of the two variants. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. The study found increased molecular interactivity between hACE2-RBD binding of B.1.1.7 and B.1.617.2 compared to the Wuhan reference strain. Our receptor binding analysis showed a similar indication pattern for hACE2-RBD of these two variants. However, B.1.617.2 offers slightly better stability in the hACE2-RBD binding pattern through MD simulation than B.1.1.7. Conclusion The increased hACE2-RBD binding pattern of B.1.1.7 and B.1.617.2 might help to increase the infectivity compared to the Wuhan reference strain.
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24
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Barbé L, Schaeffer J, Besnard A, Jousse S, Wurtzer S, Moulin L, Le Guyader FS, Desdouits M. SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters. Front Microbiol 2022; 13:889811. [PMID: 35756003 PMCID: PMC9218694 DOI: 10.3389/fmicb.2022.889811] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.
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Affiliation(s)
- Laure Barbé
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Sarah Jousse
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | | | - Laurent Moulin
- R&D Laboratory, DRDQE, Eau de Paris, Ivry-sur-Seine, France
| | | | - Marion Desdouits
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
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25
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Heger LA, Elsen N, Rieder M, Gauchel N, Sommerwerck U, Bode C, Duerschmied D, Oette M, Ahrens I. Clinical analysis on diagnostic accuracy of Bosch Vivalytic SARS-CoV-2 point-of-care test and evaluation of cycle threshold at admission for COVID-19 risk assessment. BMC Infect Dis 2022; 22:486. [PMID: 35606698 PMCID: PMC9125343 DOI: 10.1186/s12879-022-07447-7] [Citation(s) in RCA: 4] [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: 09/27/2021] [Accepted: 05/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce. OBJECTIVE To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients. METHODS Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients' nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed. RESULTS 120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS < 10 days (27.82 (± 4.648) vs. 36.2 (25.9-39.18); p = 0.0191). There was a negative correlation of CT at admission and LOS (r[44]s = - 0.31; p = 0.038) but only age was associated with the probability of an increased LOS in a multiple logistic regression analysis (OR 1.105 [95% CI, 1.03-1.19]; p = 0.006). CONCLUSION Our data indicate that POC testing with Bosch Vivalytic SARS-CoV-2 is a valid strategy to identify COVID-19 patients and decrease turnaround time to definite COVID-19 diagnosis. Also, our data suggest that age at admission possibly with CT value as a combined parameter could be a promising tool for risk assessment of increased length of hospital stay and severity of disease in COVID-19 patients.
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Affiliation(s)
- Lukas Andreas Heger
- Department of Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany.
| | - Nils Elsen
- Department of Cardiology and Medical Intensive Care, Augustinerinnen Hospital, Academic Teaching Hospital University of Cologne, Cologne, Germany
| | - Marina Rieder
- Department of Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Nadine Gauchel
- Department of Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Urte Sommerwerck
- Department of Pneumology, Augustinerinnen Hospital, Academic Teaching Hospital University of Cologne, Cologne, Germany
| | - Christoph Bode
- Department of Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Daniel Duerschmied
- Department of Cardiology and Angiology I, Heart Center Freiburg University, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Mark Oette
- Department of General Medicine, Gastroenterology and Infectious Diseases, Augustinerinnen Hospital, Academic Teaching Hospital University of Cologne, Cologne, Germany
| | - Ingo Ahrens
- Department of Cardiology and Medical Intensive Care, Augustinerinnen Hospital, Academic Teaching Hospital University of Cologne, Cologne, Germany
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Radu E, Masseron A, Amman F, Schedl A, Agerer B, Endler L, Penz T, Bock C, Bergthaler A, Vierheilig J, Hufnagl P, Korschineck I, Krampe J, Kreuzinger N. Emergence of SARS-CoV-2 Alpha lineage and its correlation with quantitative wastewater-based epidemiology data. WATER RESEARCH 2022; 215:118257. [PMID: 35303559 PMCID: PMC8898540 DOI: 10.1016/j.watres.2022.118257] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 02/22/2022] [Accepted: 03/05/2022] [Indexed: 05/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) gave rise to an international public health emergency in 3 months after its emergence in Wuhan, China. Typically for an RNA virus, random mutations occur constantly leading to new lineages, incidental with a higher transmissibility. The highly infective alpha lineage, firstly discovered in the UK, led to elevated mortality and morbidity rates as a consequence of Covid-19, worldwide. Wastewater surveillance proved to be a powerful tool for early detection and subsequent monitoring of the dynamics of SARS-CoV-2 and its variants in a defined catchment. Using a combination of sequencing and RT-qPCR approaches, we investigated the total SARS-CoV-2 concentration and the emergence of the alpha lineage in wastewater samples in Vienna, Austria linking it to clinical data. Based on a non-linear regression model and occurrence of signature mutations, we conclude that the alpha variant was present in Vienna sewage samples already in December 2020, even one month before the first clinical case was officially confirmed and reported by the health authorities. This provides evidence that a well-designed wastewater monitoring approach can provide a fast snapshot and may detect the circulating lineages in wastewater weeks before they are detectable in the clinical samples. Furthermore, declining 14 days prevalence data with simultaneously increasing SARS-CoV-2 total concentration in wastewater indicate a different shedding behavior for the alpha variant. Overall, our results support wastewater surveillance to be a suitable approach to spot early circulating SARS-CoV-2 lineages based on whole genome sequencing and signature mutations analysis.
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Affiliation(s)
- Elena Radu
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria; Institute of Virology Stefan S. Nicolau, Romanian Academy of Science, 285 Mihai Bravu Avenue, 030304, Bucharest, Romania
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Julia Vierheilig
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety AGES, Department for Medical Microbiology and Hygiene, Währingerstraße 25A, 1090, Vienna, Austria
| | - Irina Korschineck
- Ingenetix GmbH, Arsenalstraße 11/Hüttenbrennergasse 5, 1030, Vienna, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria.
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27
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Yu M, Zhu Y, Li Y, Chen Z, Li Z, Wang J, Li Z, Zhang F, Ding J. Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches. Front Immunol 2022; 13:884433. [PMID: 35603198 PMCID: PMC9120605 DOI: 10.3389/fimmu.2022.884433] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023] Open
Abstract
The development of an effective multivalent vaccine against SARS-CoV-2 variants is an important means to improve the global public health situation caused by COVID-19. In this study, we identified the antigen epitopes of the main global epidemic SARS-CoV-2 and mutated virus strains using immunoinformatics approach, and screened out 8 cytotoxic T lymphocyte epitopes (CTLEs), 17 helper T lymphocyte epitopes (HTLEs), 9 linear B-cell epitopes (LBEs) and 4 conformational B-cell epitopes (CBEs). The global population coverage of CTLEs and HTLEs was 93.16% and 99.9% respectively. These epitopes were spliced together by corresponding linkers and recombined into multivalent vaccine. In silico tests, the vaccine protein was a non-allergen and the docking with TLR-3 molecule showed a strong interaction. The results of immune simulation showed that the vaccine may be helpful to initiate both cellular and humoral immunity against all VOC. The optimistic immunogenicity of the vaccine was confirmed in vivo and in vitro finally. Therefore, our vaccine may have potential protection against SARS-CoV-2 and its variants.
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jing Wang
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Zheng Li
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
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Zhang Y, Wang R, He C, Zhang YF, Luo Z, Luo J, Chen S, Jin Y, Xie B, Liu Y. Amantadine-assembled nanostimulator enhances dimeric RBD antigen-elicited cross-neutralization against SARS-CoV-2 strains. NANO TODAY 2022; 43:101393. [PMID: 35035515 PMCID: PMC8752318 DOI: 10.1016/j.nantod.2022.101393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
There is an urgent need to develop new vaccination strategies to elevate the cross-neutralization against different SARS-CoV-2 strains. In this study, we construct the spherical amantadine-assembled nanostimulator (AAS). Amantadine as immunostimulating molecules are displayed on the outermost layer of AAS. Molecular mechanism analysis reveals that AAS can activate RIG-I-like receptor (RLR) signaling pathway to increase the expression of type I interferons in vivo. AAS-mediated activation of RLR signaling pathway further promotes the maturation and proliferation of dendritic cells (DCs) and T helper cells (Ths), finally activating B cells to produce potent antibody responses. In performance evaluation experiments, the mixture of AAS and dimeric RBD significantly enhances RBD-specific humoral responses (4-fold IgG, 3.5-fold IgG2a, 3.3-fold IgG2b, 3.8-fold IgG3 and 1.3-fold IgM), in comparison to aluminum adjuvant-assistant dimeric RBD. Importantly, AAS dramatically elevates dimeric RBD-elicited cross-neutralization against different SARS-CoV-2 strains such as Wuhan-Hu-1 (9-fold), B.1.1.7 (UK variant, 15-fold), B.1.351 (South African variant, 4-fold) and B.1.617.2 (India variant, 7-fold). Our study verifies the mechanism of AAS in activating RLR signaling pathway in host immune system and highlights the power of AAS in improving antigen-elicited cross-neutralization against different SARS-CoV-2 strains.
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Affiliation(s)
- Ye Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Ruixin Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Chunyan He
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Yu-Fang Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Zhongrui Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Jia Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Sisi Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Yu Jin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Bowen Xie
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
| | - Ye Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650000, China
- National Medical Products Administration (NMPA) Key Laboratory for Quality Control and Evaluation of Vaccines and Biological Products, Kunming, Yunnan 650000, China
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Caduff L, Dreifuss D, Schindler T, Devaux AJ, Ganesanandamoorthy P, Kull A, Stachler E, Fernandez-Cassi X, Beerenwinkel N, Kohn T, Ort C, Julian TR. Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021. Euro Surveill 2022; 27:2100806. [PMID: 35272748 PMCID: PMC8915404 DOI: 10.2807/1560-7917.es.2022.27.10.2100806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/21/2022] [Indexed: 04/19/2023] Open
Abstract
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.AimHere, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.MethodsWe developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69-70 and ORF1a Δ3675-3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.ResultsBased on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69-70 was 0.34 (95% confidence interval (CI): 0.30-0.39) and based on ORF1a Δ3675-3677 was 0.53 (95% CI: 0.49-0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38-0.61).ConclusionDigital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
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Affiliation(s)
- Lea Caduff
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander J Devaux
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | - Anina Kull
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Elyse Stachler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Xavier Fernandez-Cassi
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph Ort
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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30
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Cai H, Hu J, Huang L, Gao C, Xu M, Gao Y, Sun T, Fang X. The Relationship Between Convergent IGH Signatures and Severity of COVID-19 Patients by Next-Generation Sequencing of B-Cell Repertoire. Front Microbiol 2022; 12:833054. [PMID: 35222317 PMCID: PMC8865457 DOI: 10.3389/fmicb.2021.833054] [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: 12/10/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
Object To reveal convergent IGH signatures and the association with severity of coronavirus disease 2019 (COVID-19) patients. Method A total of 25 COVID-19 inpatients were classified into three clinical conditions: mild, severe, and critical. We analyzed convergent IGH signatures by ImmuHub® B-cell receptor (BCR) profiling system. Results IGH singleton frequency in patients is significantly lower than that of healthy donors (HDs). The clonality index of IGH in patients is significantly higher than that in HDs. Nevertheless, no significant difference was observed among the three groups. The difference in IGH clonality (top five clones) between post- and pretreatment was significant in the improvement and deterioration groups. Three common public motifs were shared by all COVID-19 patients: ARDYGG, RWYFDY, and YYYYGMDV. Conclusion B cells could recognize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and produce clonal expansion. Patients who had better outcomes after treatment had higher IGH clonality. Three common public motifs—ARDYGG, RWYFDY, and YYYYGMDV—might be used for vaccine development (ChiCTR2000029626).
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Affiliation(s)
- Hongliu Cai
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Juan Hu
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingtong Huang
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunhua Gao
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mi Xu
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuzhi Gao
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Sun
- Zhejiang California International NanoSystems Institute, Zhejiang University, Hangzhou, China
| | - Xueling Fang
- Department of Critical Care Units, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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31
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Castiglioni S, Schiarea S, Pellegrinelli L, Primache V, Galli C, Bubba L, Mancinelli F, Marinelli M, Cereda D, Ammoni E, Pariani E, Zuccato E, Binda S. SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 pandemic in Lombardy, Italy (March-June 2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150816. [PMID: 34627901 PMCID: PMC8497959 DOI: 10.1016/j.scitotenv.2021.150816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 04/15/2023]
Abstract
Wastewater-based viral surveillance was proposed as a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, and apply it to follow the trends of epidemic in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe and was severely affected. Composite 24 h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the pandemic). The method developed and optimized, involved virus concentration using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E + 05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities corresponding to the very low number of cases recorded in the same period. Viral loads were calculated considering the wastewater daily flow rate and the population served by each wastewater treatment plant, and were used for inter- city comparison. The highest viral loads were found in Brembate, Ranica and Lodi corresponding to the hotspots of the first peak of pandemic. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. This study tested wastewater surveillance of SARS-CoV-2 to follow the pandemic trends in one of most affected areas worldwide, demonstrating that it can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.
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Affiliation(s)
- Sara Castiglioni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy.
| | - Silvia Schiarea
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Federica Mancinelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | | | | | | | - Elena Pariani
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Ettore Zuccato
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
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Monitoring of SARS-CoV-2 Variants by Wastewater-Based Surveillance as a Sustainable and Pragmatic Approach—A Case Study of Jaipur (India). WATER 2022. [DOI: 10.3390/w14030297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wastewater-based surveillance has been emerging as an efficient and advantageous tool to predict COVID-19 prevalence in the population, much earlier (7–28 days) than reported clinical cases, thus providing sufficient time to organize resources and optimize their use in managing COVID-19. Since the commencement of the COVID-19 pandemic, SARS-CoV-2 genetic lineages have emerged and are circulating all over the world. The assessment of SARS-CoV-2 variants of concern (VOCs) in wastewater has recently been proven to be successful. The present research demonstrates a case study utilizing an established approach to perform monitoring of SARS-CoV-2 variants from 11 distinct wastewater treatment plants across Jaipur (India) during the second peak period of COVID-19 (from 19 February 2021 to 8 June 2021). The sequences obtained were analyzed to detect lineage using the Pangolin tool and SNPs using the mpileup utility of Samtools, which reported high genome coverage. The mutation analyses successfully identified the penetration of the B.1. in the first two weeks of sampling (19–26 February), followed by the B.1.617.2 variant into Jaipur in the first week of March 2021. B.1.617.2 was initially discovered in India in October 2020; however, it was not reported until early April 2021.The present study identified the presence of B.1.617.2 in early March, which correlates well with the clinical patient’s data (290 cases were reported much later by the government on 10 May 2021). The average total genome coverage of the samples is 94.39% when mapped onto the severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1; a complete genome (NC_045512.2) sequence and SNP analysis showed that 37–51 SNPs were identified in each sample. The current study demonstrates that sewage surveillance for variant characterization is a reliable and practical method for tracking the diversity of SARS-CoV-2 strains in the community that is considerably faster than clinical genomic surveillance. As a result, this method can predict the advent of epidemiologically or clinically important mutations/variants, which can help with public health decision making.
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33
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Jiang Y, Wu Q, Song P, You C. The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines. Front Med (Lausanne) 2022; 8:806641. [PMID: 35118097 PMCID: PMC8804231 DOI: 10.3389/fmed.2021.806641] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.
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Affiliation(s)
| | | | | | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
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34
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Shah S, Gwee SXW, Ng JQX, Lau N, Koh J, Pang J. Wastewater surveillance to infer COVID-19 transmission: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150060. [PMID: 34798721 PMCID: PMC8423771 DOI: 10.1016/j.scitotenv.2021.150060] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 05/18/2023]
Abstract
Successful detection of SARS-COV-2 in wastewater suggests the potential utility of wastewater-based epidemiology (WBE) for COVID-19 community surveillance. This systematic review aims to assess the performance of wastewater surveillance as early warning system of COVID-19 community transmission. A systematic search was conducted in PubMed, Medline, Embase and the WBE Consortium Registry according to PRISMA guidelines for relevant articles published until 31st July 2021. Relevant data were extracted and summarized. Quality of each paper was assessed using an assessment tool adapted from Bilotta et al.'s tool for environmental science. Of 763 studies identified, 92 studies distributed across 34 countries were shortlisted for qualitative synthesis. A total of 26,197 samples were collected between January 2020 and May 2021 from various locations serving population ranging from 321 to 11,400,000 inhabitants. Overall sample positivity was moderate at 29.2% in all examined settings with the spike (S) gene having maximum rate of positive detections and nucleocapsid (N) gene being the most targeted. Wastewater signals preceded confirmed cases by up to 63 days, with 13 studies reporting sample positivity before the first cases were detected in the community. At least 50 studies reported an association of viral load with community cases. While wastewater surveillance cannot replace large-scale diagnostic testing, it can complement clinical surveillance by providing early signs of potential transmission for more active public health responses. However, more studies using standardized and validated methods are required along with risk analysis and modelling to understand the dynamics of viral outbreaks.
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Affiliation(s)
- Shimoni Shah
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Sylvia Xiao Wei Gwee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Jamie Qiao Xin Ng
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Nicholas Lau
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Jiayun Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Junxiong Pang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
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Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021. Viruses 2022; 14:v14010143. [PMID: 35062346 PMCID: PMC8781944 DOI: 10.3390/v14010143] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
Infection with enterovirus D68 (EV-D68) has been linked with severe neurological disease such as acute flaccid myelitis (AFM) in recent years. However, active surveillance for EV-D68 is lacking, which makes full assessment of this association difficult. Although a high number of EV-D68 infections were expected in 2020 based on the EV-D68's known biannual circulation patterns, no apparent increase in EV-D68 detections or AFM cases was observed during 2020. We describe an upsurge of EV-D68 detections in wastewater samples from the United Kingdom between July and November 2021 mirroring the recently reported rise in EV-D68 detections in clinical samples from various European countries. We provide the first publicly available 2021 EV-D68 sequences showing co-circulation of EV-D68 strains from genetic clade D and sub-clade B3 as in previous years. Our results show the value of environmental surveillance (ES) for the early detection of circulating and clinically relevant human viruses. The use of a next-generation sequencing (NGS) approach helped us to estimate the prevalence of EV-D68 viruses among EV strains from other EV serotypes and to detect EV-D68 minor variants. The utility of ES at reducing gaps in virus surveillance for EV-D68 and the possible impact of nonpharmaceutical interventions introduced to control the COVID-19 pandemic on EV-D68 transmission dynamics are discussed.
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Ahmed W, Bivins A, Simpson SL, Bertsch PM, Ehret J, Hosegood I, Metcalfe SS, Smith WJM, Thomas KV, Tynan J, Mueller JF. Wastewater surveillance demonstrates high predictive value for COVID-19 infection on board repatriation flights to Australia. ENVIRONMENT INTERNATIONAL 2022; 158:106938. [PMID: 34735954 PMCID: PMC8514683 DOI: 10.1016/j.envint.2021.106938] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 10/12/2021] [Indexed: 05/23/2023]
Abstract
Controlling importation and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from overseas travelers is essential for countries, such as Australia, New Zealand, and other island nations, that have adopted a suppression strategy to manage very low community transmission. Wastewater surveillance of SARS-CoV-2 RNA has emerged as a promising tool employed in public health response in many countries globally. This study aimed to establish whether the surveillance of aircraft wastewater can be used to provide an additional layer of information to augment individual clinical testing. Wastewater from 37 long-haul flights chartered to repatriate Australians was tested for the presence of SARS-CoV-2 RNA. Children 5 years or older on these flights tested negative for coronavirus disease 19 (COVID-19) (deep nasal and oropharyngeal reverse-transcription (RT)-PCR swab) 48 h before departure. All passengers underwent mandatory quarantine for 14-day post arrival in Howard Springs, NT, Australia. Wastewater from 24 (64.9 %) of the 37 flights tested positive for SARS-CoV-2 RNA. During the 14 day mandatory quarantine, clinical testing identified 112 cases of COVID-19. Surveillance for SARS-CoV-2 RNA in repatriation flight wastewater using pooled results from three RT-qPCR assays demonstrated a positive predictive value (PPV) of 87.5 %, a negative predictive value (NPV) of 76.9 % and 83.7% accuracy for COVID-19 cases during the post-arrival 14-day quarantine period. The study successfully demonstrates that the surveillance of wastewater from aircraft for SARS-CoV-2 can provide an additional and effective tool for informing the management of returning overseas travelers and for monitoring the importation of SARS CoV-2 and other clinically significant pathogens.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, QLD 4102, Australia
| | - John Ehret
- Qantas Airways Limited, 10 Bourke Rd Mascot, 2020, NSW, Australia
| | - Ian Hosegood
- Qantas Airways Limited, 10 Bourke Rd Mascot, 2020, NSW, Australia
| | - Suzanne S Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, QLD 4102, Australia
| | - Kevin V Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4103, Australia
| | - Josh Tynan
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4103, Australia
| | - Jochen F Mueller
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4103, Australia
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Kazybay B, Ahmad A, Mu C, Mengdesh D, Xie Y. Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Travel Med Infect Dis 2022; 45:102242. [PMID: 34929375 PMCID: PMC8677628 DOI: 10.1016/j.tmaid.2021.102242] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Variants of SARS-CoV-2 lineages including the most recently circulated Omicron, and previous pandemic B.1.351, B.1.1.7, which have been public concerns, contain a N501Y mutation located in the spike receptor binding domain. However, the potential interactions with host cells linking N501Y mutation to pathogenic relevance remain elusive. Recently, we and others report that kinases such as PI3K/AKT signaling are essential in SARS-CoV-2 entry. Here we analyzed the predicted potential kinases interacting with the mutation. Bioinformatics tools including structure-prediction based molecular docking analysis were applied. We found kinases such as EGFR might potentially act as new factors involving the N501Y mutation binding through possible phosphorylation at Y501 and enhanced affinity in certain variants. To our surprise, the Omicron receptor binding domain harboring N501Y mutation did not enhance binding to EGFR which might be due to the mutations of charged polar to uncharged polar side chains located on the interaction interfaces. Similarly, potent gains of phosphorylation in B.1.351 and B.1.1.7 by mutations were predicted and interaction networks were analyzed with enrichment of pathways. Given kinases might be elevated in cancer patients, the N501Y mutation containing lineages may be possibly much more infectious and additional care for cancer management might be taken into consideration by precision prevention, therapy or recovery.
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Affiliation(s)
- Bexultan Kazybay
- Biology Department, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, 21300, Pakistan
| | - Chenglin Mu
- Zhejiang University, Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Diana Mengdesh
- Biology Department, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Yingqiu Xie
- Biology Department, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan.
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Zhao X, Zhong Y, Wang X, Shen J, An W. Advances in Circular RNA and Its Applications. Int J Med Sci 2022; 19:975-985. [PMID: 35813288 PMCID: PMC9254372 DOI: 10.7150/ijms.71840] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022] Open
Abstract
Circular RNA (circRNA) is a novel endogenous non-coding RNA (ncRNA) that, like microRNA (miRNA), is a rapidly emerging RNA research topic. CircRNA, unlike traditional linear RNAs (which have 5' and 3' ends), has a closed-loop structure that is unaffected by RNA exonucleases. Thus, circRNA has sustained expression and is less sensitive to degradation. Since circRNAs have many miRNAs binding sites, eliminating their repressive effects on their target genes can strongly enhance their expression. CircRNAs serve an important regulatory role in disease onset and progression via specific circRNA-miRNA interactions. We summarized the current progress in elucidating mechanisms and biogenesis of circRNAs in this review. In particular, circRNAs can function mainly as miRNA sponges, regulating host gene expression and protein transportation. Finally, we discussed the application prospects and significant challenges for the development of circRNA-based therapeutics.
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Affiliation(s)
- Xian Zhao
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Youxiu Zhong
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Xudong Wang
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Jiuheng Shen
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Wenlin An
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
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Preparing for COVID-2x: Urban Planning Needs to Regard Urological Wastewater as an Invaluable Communal Public Health Asset and Not as a Burden. URBAN SCIENCE 2021. [DOI: 10.3390/urbansci5040075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prior to the COVID-19 pandemic, the analysis of urological wastewater had been a matter of academic curiosity and community-wide big-picture studies looking at drug use or the presence of select viruses such as Hepatitis. The COVID-19 pandemic saw systematic testing of urological wastewater emerge as a significant early detection tool for the presence of SARS-CoV-2 in a community. Even though the pandemic still rages in all continents, it is time to consider the post-pandemic world. This paper posits that urban planners should treat urological wastewater as a communal public health asset and that future sewer design should allow for stratified multi-order sampling.
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40
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Mishra S, Mindermann S, Sharma M, Whittaker C, Mellan TA, Wilton T, Klapsa D, Mate R, Fritzsche M, Zambon M, Ahuja J, Howes A, Miscouridou X, Nason GP, Ratmann O, Semenova E, Leech G, Sandkühler JF, Rogers-Smith C, Vollmer M, Unwin HJT, Gal Y, Chand M, Gandy A, Martin J, Volz E, Ferguson NM, Bhatt S, Brauner JM, Flaxman S. Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine 2021; 39:101064. [PMID: 34401689 PMCID: PMC8349999 DOI: 10.1016/j.eclinm.2021.101064] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. METHODS We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. FINDINGS Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. INTERPRETATION The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts. FUNDING National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.
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Affiliation(s)
- Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Sören Mindermann
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK
| | - Mrinank Sharma
- Department of Statistics, University of Oxford, UK
- Department of Engineering Science, University of Oxford, UK
- Future of Humanity Institute, University of Oxford, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Thomas Wilton
- National Institute for Biological Standards and Control (NIBSC), UK
| | - Dimitra Klapsa
- National Institute for Biological Standards and Control (NIBSC), UK
| | - Ryan Mate
- National Institute for Biological Standards and Control (NIBSC), UK
| | - Martin Fritzsche
- National Institute for Biological Standards and Control (NIBSC), UK
| | | | - Janvi Ahuja
- Future of Humanity Institute, University of Oxford, UK
- Medical Sciences Division, University of Oxford, UK
| | - Adam Howes
- Department of Mathematics, Imperial College London, UK
| | | | - Guy P Nason
- Department of Mathematics, Imperial College London, UK
| | | | | | - Gavin Leech
- Department of Computer Science, University of Bristol, UK
| | | | - Charlie Rogers-Smith
- OATML Group (work done while at OATML as an external collaborator), Department of Computer Science, University of Oxford, UK
| | - Michaela Vollmer
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
- Public Health England, London, UK
| | - H Juliette T Unwin
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Yarin Gal
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK
| | | | - Axel Gandy
- Department of Mathematics, Imperial College London, UK
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), UK
| | - Erik Volz
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Neil M Ferguson
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark
| | - Jan M Brauner
- Oxford Applied and Theoretical Machine Learning (OATML) Group, Department of Computer Science, University of Oxford, UK
- Future of Humanity Institute, University of Oxford, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, UK
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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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42
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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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