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Veneri C, Brandtner D, Mancini P, Bonanno Ferraro G, Iaconelli M, Suffredini E, Petrillo M, Leoni G, Paracchini V, Gawlik BM, Marchini A, La Rosa G. Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09607-1. [PMID: 38918335 DOI: 10.1007/s12560-024-09607-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.
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Affiliation(s)
- C Veneri
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - D Brandtner
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Petrillo
- Seidor Italy S.r.l., 20129, Milan, Italy
| | - G Leoni
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - V Paracchini
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - B M Gawlik
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - A Marchini
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - G La Rosa
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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2
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Li L, Haak L, Carine M, Pagilla KR. Temporal assessment of SARS-CoV-2 detection in wastewater and its epidemiological implications in COVID-19 case dynamics. Heliyon 2024; 10:e29462. [PMID: 38638959 PMCID: PMC11024598 DOI: 10.1016/j.heliyon.2024.e29462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
This research evaluated the relationship between daily new Coronavirus Disease 2019 (COVID-19) cases and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) concentrations in wastewater, followed by effects of differential SARS-CoV-2 shedding loads across various COVID-19 outbreaks. Linear regression analyses were utilized to examine the lead time of the SARS-CoV-2 signal in wastewater relative to new COVID-19 clinical cases. During the Delta wave, no lead time was evident, highlighting limited predictive capability of wastewater monitoring during this phase. However, significant lead times were observed during the Omicron wave, potentially attributed to testing capacity overload and subsequent case reporting delays or changes in shedding patterns. During the Post-Omicron wave (Febuary 23 to May 19, 2022), no lead time was discernible, whereas following the lifting of the COVID-19 state of emergency (May 30, 2022 to May 30, 2023), the correlation coefficient increased and demonstrated the potential of wastewater surveillance as an early warning system. Subsequently, we explored the virus shedding in wastewater through feces, operationalized as the ratio of SARS-CoV-2 concentrations to daily new COVID-19 cases. This ratio varied significantly across the Delta, Omicron, other variants and post-state-emergency phases, with the Kruskal-Wallis H test confirming a significant difference in medians across these stages (P < 0.0001). Despite its promise, wastewater surveillance of COVID-19 disease prevalence presents several challenges, including virus shedding variability, data interpretation complexity, the impact of environmental factors on viral degradation, and the lack of standardized testing procedures. Overall, our findings offer insights into the correlation between COVID-19 cases and wastewater viral concentrations, potential variation in SARS-CoV-2 shedding in wastewater across different pandemic phases, and underscore the promise and limitations of wastewater surveillance as an early warning system for disease prevalence trends.
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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Krishna R. Pagilla
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
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3
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Bolt K, Gil-González D, Oliver N. Unconventional data, unprecedented insights: leveraging non-traditional data during a pandemic. Front Public Health 2024; 12:1350743. [PMID: 38566798 PMCID: PMC10986850 DOI: 10.3389/fpubh.2024.1350743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction The COVID-19 pandemic prompted new interest in non-traditional data sources to inform response efforts and mitigate knowledge gaps. While non-traditional data offers some advantages over traditional data, it also raises concerns related to biases, representativity, informed consent and security vulnerabilities. This study focuses on three specific types of non-traditional data: mobility, social media, and participatory surveillance platform data. Qualitative results are presented on the successes, challenges, and recommendations of key informants who used these non-traditional data sources during the COVID-19 pandemic in Spain and Italy. Methods A qualitative semi-structured methodology was conducted through interviews with experts in artificial intelligence, data science, epidemiology, and/or policy making who utilized non-traditional data in Spain or Italy during the pandemic. Questions focused on barriers and facilitators to data use, as well as opportunities for improving utility and uptake within public health. Interviews were transcribed, coded, and analyzed using the framework analysis method. Results Non-traditional data proved valuable in providing rapid results and filling data gaps, especially when traditional data faced delays. Increased data access and innovative collaborative efforts across sectors facilitated its use. Challenges included unreliable access and data quality concerns, particularly the lack of comprehensive demographic and geographic information. To further leverage non-traditional data, participants recommended prioritizing data governance, establishing data brokers, and sustaining multi-institutional collaborations. The value of non-traditional data was perceived as underutilized in public health surveillance, program evaluation and policymaking. Participants saw opportunities to integrate them into public health systems with the necessary investments in data pipelines, infrastructure, and technical capacity. Discussion While the utility of non-traditional data was demonstrated during the pandemic, opportunities exist to enhance its impact. Challenges reveal a need for data governance frameworks to guide practices and policies of use. Despite the perceived benefit of collaborations and improved data infrastructure, efforts are needed to strengthen and sustain them beyond the pandemic. Lessons from these findings can guide research institutions, multilateral organizations, governments, and public health authorities in optimizing the use of non-traditional data.
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Affiliation(s)
- Kaylin Bolt
- Health Sciences Division (Assessment, Policy Development, and Evaluation Unit), Public Health - Seattle & King County, Seattle, WA, United States
| | - Diana Gil-González
- Department of Community Nursing, Preventive Medicine and Public Health and History of Science, University of Alicante, Alicante, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Nuria Oliver
- European Laboratory for Learning and Intelligent Systems (ELLIS) Alicante, Alicante, Spain
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4
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Tran DPH, You BC, Liu CW, Chen YN, Wang YF, Chung SN, Lee JJ, You SJ. Identifying spatiotemporal trends of SARS-CoV-2 RNA in wastewater: from the perspective of upstream and downstream wastewater-based epidemiology (WBE). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11576-11590. [PMID: 38221556 DOI: 10.1007/s11356-023-31769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
Recently, many efforts have been made to address the rapid spread of newly identified COVID-19 virus variants. Wastewater-based epidemiology (WBE) is considered a potential early warning tool for identifying the rapid spread of this virus. This study investigated the occurrence of SARS-CoV-2 in eight wastewater treatment plants (WWTPs) and their sewerage systems which serve most of the population in Taoyuan City, Taiwan. Across the entire study period, the wastewater viral concentrations were correlated with the number of COVID-19 cases in each WWTP (Spearman's r = 0.23-0.76). In addition, it is confirmed that several treatment technologies could effectively eliminate the virus RNA from WWTP influent (> 90%). On the other hand, further results revealed that an inverse distance weighted (IDW) interpolation and hotspot model combined with the geographic information system (GIS) method could be applied to analyze the spatiotemporal variations of SARS-CoV-2 in wastewater from the sewer system. In addition, socio-economic factors, namely, population density, land use, and income tax were successfully identified as the potential drivers which substantially affected the onset of the COVID-19 outbreak in Taiwan. Finally, the data obtained from this study can provide a powerful tool in public health decision-making not only in response to the current epidemic situation but also to other epidemic issues in the future.
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Affiliation(s)
- Duyen Phuc-Hanh Tran
- Department of Civil Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Bo-Cheng You
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Chen-Wuing Liu
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Yi-Ning Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Ya-Fen Wang
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Shu-Nu Chung
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Jin-Jing Lee
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Sheng-Jie You
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China.
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China.
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5
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Cutrupi F, Cadonna M, Postinghel M, Foladori P. SARS-CoV-2 removal in municipal wastewater treatment plants: Focus on conventional activated sludge, membrane bioreactor and anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167434. [PMID: 37774861 DOI: 10.1016/j.scitotenv.2023.167434] [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: 06/23/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
This work focuses on the removal of SARS-CoV-2 RNA in the various stages of a full-scale municipal WWTP characterised by two biological processes in parallel: (i) conventional activated sludge (CAS) and (ii) membrane bioreactor (MBR). The monitoring was carried out during the Omicron wave in 2022, a period characterised by a high concentration of SARS-CoV-2 in influent wastewater. The average concentration of SARS-CoV-2 in influent wastewater was 3.7 × 104 GU/L. In the primary sedimentation, the removal of SARS-CoV-2 was not appreciable. The largest log removal value of SARs-CoV-2 occurred in the biological stages, with 1.8 ± 0.9 and 2.2 ± 0.7 logs in CAS and MBR systems. The mean concentrations of SARS-CoV-2 in the CAS and MBR effluents were 6.8 × 102 GU/L and 6.4 × 102 GU/L, respectively. The MBR effluent showed more negative samples, because small particles are retained by membrane and cake layer. The analysis of the different types of sludge confirmed the accumulation of SARS-CoV-2 in primary (5.2 × 104 GU/L) and secondary sludge (3.5 × 104 GU/L), due to the affinity of enveloped viruses towards biosolids. A SARS-CoV-2 concentration in the digested sludge equal to 4.8 × 104 GU/L denotes a negligible reduction in the mesophilic anaerobic digester at temperature of 31-33 °C.
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Affiliation(s)
- Francesca Cutrupi
- Center Agriculture Food Environment (C3A) - University of Trento, via Edmund Mach 1, 38098 San Michele all' Adige, TN, Italy
| | - Maria Cadonna
- ADEP - Agenzia per la Depurazione, Autonomous Province of Trento, via Gilli, n. 3, 38121 Trento, Italy
| | - Mattia Postinghel
- ADEP - Agenzia per la Depurazione, Autonomous Province of Trento, via Gilli, n. 3, 38121 Trento, Italy
| | - Paola Foladori
- Department of Civil, Environmental and Mechanical Engineering (DICAM) - University of Trento, via Mesiano, n. 77, 38123 Trento, Italy.
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6
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La Rosa G, Mancini P, Iaconelli M, Veneri C, Bonanno Ferraro G, Del Giudice C, Suffredini E, Muratore A, Ferrara F, Lucentini L, Martuzzi M, Piccioli A. Tracing the footprints of SARS-CoV-2 in oceanic waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167343. [PMID: 37751837 DOI: 10.1016/j.scitotenv.2023.167343] [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: 07/15/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
The detection of SARS-CoV-2 in water environments has predominantly focused on wastewater, neglecting its presence in oceanic waters. This study aimed to fill this knowledge gap by investigating the occurrence of SARS-CoV-2 in remote sea and oceanic waters, at large distances from the coastline. Forty-three 500-liter samples were collected between May 2022 and January 2023 from the Atlantic Ocean, the Mediterranean Sea, the Arctic region, the Persian Gulf and the Red Sea. Using molecular detection methods including real-time RT-qPCR and nested PCR followed by sequencing, we successfully detected SARS-CoV-2 RNA in 7 of the 43 marine water samples (16.3 %), and specifically in samples taken from the Atlantic Ocean and the Mediterranean Sea. The estimated concentrations of SARS-CoV-2 genome copies in the positive samples ranged from 6 to 470 per 100 l. The presence of mutations characteristic of the Omicron variant was identified in these samples by amplicon sequencing. These findings provide evidence of the unforeseen presence of SARS-CoV-2 in marine waters even at distances of miles from the coastline and in open ocean waters. It is important to consider that these findings only display the occurrence of SARS-CoV-2 RNA, and further investigations are required to assess if infectious virus can be present in the marine environment.
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Affiliation(s)
- Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy.
| | - P Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Muratore
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - F Ferrara
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Martuzzi
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Piccioli
- Office of the Director General, Istituto Superiore di Sanità, Rome, Italy
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7
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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8
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Triggiano F, De Giglio O, Apollonio F, Brigida S, Fasano F, Mancini P, Bonanno Ferraro G, Veneri C, La Rosa G, Suffredini E, Lucentini L, Ungaro N, Di Vittorio G, Mongelli O, Albano N, Montagna MT. Wastewater-based Epidemiology and SARS-CoV-2: Variant Trends in the Apulia Region (Southern Italy) and Effect of Some Environmental Parameters. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:331-341. [PMID: 37735299 PMCID: PMC10654208 DOI: 10.1007/s12560-023-09565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
During the COVID-19 pandemic, wastewater monitoring has been used to monitor the levels of SARS-CoV-2 RNA entering the sewerage system. In Italy, the Istituto Superiore di Sanità coordinated the SARI project (Sorveglianza Ambientale Reflue in Italia) to detect SARS-CoV-2 and its variants. In this study, the concentration of SARS-CoV-2 and its variants in raw wastewater against COVID-19 cases was evaluated together with the effect of temperature and precipitation on virus spread. We validated a predictive model, proposed by De Giglio et al., 2021, to establish the number of COVID-19 cases/100,000 inhabitants. A receiver operating characteristic curve model was applied to predict the number of COVID-19 cases and Poisson regression was applied to study the effect of temperature and rainfall on viral load. In Apulia, from October 2021 to December 2022, we analyzed 1041 samples, of which 985 (94.6%) tested positive for SARS-CoV-2. Median atmospheric temperature was inversely proportional to viral load in wastewater; no correlation was found with precipitation. The predictive model confirmed that at least 11 cases/100,000 inhabitants would occur in the 15 days following the detection of the virus in wastewater. Environmental surveillance of SARS-CoV-2 can be used to map the virus and its variants.
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Affiliation(s)
- Francesco Triggiano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Osvalda De Giglio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy.
| | - Francesca Apollonio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Silvia Brigida
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Campus Ecotekne, Monteroni di Lecce, Lecce, 73047, Italy
| | - Fabrizio Fasano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Luca Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Nicola Ungaro
- Agency for the Environmental Prevention and Protection (ARPA Puglia), Corso Trieste 27, Bari, 70126, Italy
| | | | - Onofrio Mongelli
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Nelhudoff Albano
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Maria Teresa Montagna
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
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9
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Cutrupi F, Rossi M, Cadonna M, Poznanski E, Manara S, Postinghel M, Palumbi G, Bellisomi M, Nicosia E, Allaria G, Dondero L, Veneri C, Mancini P, Ferraro GB, Rosa G, Suffredini E, Foladori P, Grasselli E. Evaluation of concentration procedures, sample pre-treatment, and storage condition for the detection of SARS-CoV-2 in wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106660-106670. [PMID: 37733200 PMCID: PMC10579110 DOI: 10.1007/s11356-023-29696-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Crucial information on the pandemic's spread has been gathered by monitoring the trend of SARS-CoV-2 in wastewater. This surveillance has highlighted that the initial concentration is a critical step of the analytical procedure due to the low viral titer that may be present in this matrix. This paper presents the results of the evaluation of two different wastewater concentration protocols to determine the most efficient and cost-effective. The two methods tested were the following: (a) a biphasic separation system with PEG-dextran and (b) a PEG/NaCl precipitation protocol. Other aspects of the detection method were also investigated including the influence of storage temperature on virus recovery and the heat treatment of pasteurization, which aims to make samples safer for operators and the environment. The PEG/NaCl precipitation method was found to perform better than the biphasic separation system, allowing for more sensitive identification of the presence of the virus and the detection of a higher viral titer than that identified with the biphasic separation in all results. Storage of the samples at 4.3±0.2°C for up to 3 weeks did not adversely affect the virus titer and the pasteurization pre-treatment increases operator safety and maintains the identification of the viral concentration.
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Affiliation(s)
- Francesca Cutrupi
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy.
| | - Michele Rossi
- Department of Biosciences, University of Milano, Via Celoria 26, 20134, Milano, Italy
| | - Maria Cadonna
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | | | - Serena Manara
- Department of Cellular Computational and Integrative Biology-CIBIO, Via Sommarive 9, 38123, Trento, Italy
| | - Mattia Postinghel
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | - Giulia Palumbi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Marta Bellisomi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Elena Nicosia
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
- Department of Health and Social Services, Liguria Region Administration, Piazza della Vittoria 119, 16121, Genova, Italy
| | - Giorgia Allaria
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Lorenzo Dondero
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Giuseppina Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Foladori
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy
| | - Elena Grasselli
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
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10
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Lombardi A, Voli A, Mancusi A, Girardi S, Proroga YTR, Pierri B, Olivares R, Cossentino L, Suffredini E, La Rosa G, Fusco G, Pizzolante A, Porta A, Campiglia P, Torre I, Pennino F, Tosco A. SARS-CoV-2 RNA in Wastewater and Bivalve Mollusk Samples of Campania, Southern Italy. Viruses 2023; 15:1777. [PMID: 37632119 PMCID: PMC10459311 DOI: 10.3390/v15081777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
SARS-CoV-2 can be detected in the feces of infected people, consequently in wastewater, and in bivalve mollusks, that are able to accumulate viruses due to their ability to filter large amounts of water. This study aimed to monitor SARS-CoV-2 RNA presence in 168 raw wastewater samples collected from six wastewater treatment plants (WWTPs) and 57 mollusk samples obtained from eight harvesting sites in Campania, Italy. The monitoring period spanned from October 2021 to April 2022, and the results were compared and correlated with the epidemiological situation. In sewage, the ORF1b region of SARS-CoV-2 was detected using RT-qPCR, while in mollusks, three targets-RdRp, ORF1b, and E-were identified via RT-dPCR. Results showed a 92.3% rate of positive wastewater samples with increased genomic copies (g.c.)/(day*inhabitant) in December-January and March-April 2022. In the entire observation period, 54.4% of mollusks tested positive for at least one SARS-CoV-2 target, and the rate of positive samples showed a trend similar to that of the wastewater samples. The lower SARS-CoV-2 positivity rate in bivalve mollusks compared to sewages is a direct consequence of the seawater dilution effect. Our data confirm that both sample types can be used as sentinels to detect SARS-CoV-2 in the environment and suggest their potential use in obtaining complementary information on SARS-CoV-2.
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Affiliation(s)
- Annalisa Lombardi
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Andrea Mancusi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Santa Girardi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Biancamaria Pierri
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Renato Olivares
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Luigi Cossentino
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giovanna Fusco
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Antonio Pizzolante
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Ida Torre
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Francesca Pennino
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
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11
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Kutteyil SS, Pattassery SA, Jayaswamy MM, Potdar V, Rajagopal PM, Munivenkatappa A. Trend of coronavirus disease 2019 pandemic in Bengaluru, Karnataka, India. Indian J Public Health 2023; 67:468-470. [PMID: 37929393 DOI: 10.4103/ijph.ijph_68_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
The study reports the trend of coronavirus disease 2019 (COVID-19) infection observed from 2020 to 2022 in the city of Bengaluru, Karnataka, India, across each week in relation to the corresponding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sewage positivity data and other non-COVID-19 respiratory viral infections such as influenza and respiratory syncytial virus (RSV). The data on COVID-19 cases were procured from public domains, whereas the molecular testing of sewage samples and clinical samples for influenza and RSV was performed at our unit. The pattern of sewage positivity matched the waves of COVID-19, and few sewage samples in 2021 and 2022 tested positive before the onset of clinical cases. Influenza and RSV cases were reported during the periods of low COVID-19 cases. Thus, sewage surveillance is effective in monitoring the circulating SARS-CoV-2 virus, while laboratory surveillance of SARS-CoV-2, influenza, and RSV cases is pertinent to identify the common viral etiology of respiratory infections in the community.
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Affiliation(s)
- Susha Subash Kutteyil
- Scientist "B", ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Sakib Akther Pattassery
- Scientist "B", ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | | | - Varsha Potdar
- Scientist "E", Group Leader, National Influenza Centre, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Padma Mudalappa Rajagopal
- Deputy Director, Department of Health and Family Welfare, State Surveillance Unit, Bengaluru, Karnataka, India
| | - Ashok Munivenkatappa
- Scientist "C", ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
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12
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La Rosa G, Brandtner D, Bonanno Ferraro G, Veneri C, Mancini P, Iaconelli M, Lucentini L, Del Giudice C, Orlandi L, Suffredini E. Wastewater surveillance of SARS-CoV-2 variants in October-November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162339. [PMID: 36813191 DOI: 10.1016/j.scitotenv.2023.162339] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
This study adds insight regarding the occurrence and spread of SARS-CoV-2 Variants of Concern (VOCs) and Variants of Interest (VOIs) in Italy in October and November 2022, by testing urban wastewater collected throughout the country. A total of 332 wastewater samples were collected from 20 Italian Regions/Autonomous Provinces (APs) within the framework of national SARS-CoV-2 environmental surveillance. Of these, 164 were collected in the first week of October and 168 in the first week of November. A ∼1600 bp fragment of the spike protein was sequenced by Sanger (for individual samples) and long-read nanopore sequencing (for pooled Region/AP samples). In October, mutations characteristic of Omicron BA.4/BA.5 were detected in the vast majority (91 %) of the samples amplified by Sanger sequencing. A fraction of these sequences (9 %) also displayed the R346T mutation. Despite the low prevalence documented in clinical cases at the time of sampling, amino acid substitutions characteristic of sublineages BQ.1 or BQ.1.1 were detected in 5 % of sequenced samples from four Regions/APs. A significantly higher variability of sequences and variants was documented in November 2022, when the rate of sequences harbouring mutations of lineages BQ.1 and BQ1.1 increased to 43 %, and the number of Regions/APs positive for the new Omicron subvariant more than tripled (n = 13) compared to October. Moreover, an increase in the number of sequences with the mutation package BA.4/BA.5 + R346T (18 %), as well as the detection of variants never observed before in wastewater in Italy, such as BA.2.75 and XBB.1 (the latter in a Region where no clinical cases associated with this variant had ever been documented) was recorded. The results suggest that, as predicted by the ECDC, BQ.1/BQ.1.1 is rapidly becoming dominant in late 2022. Environmental surveillance proves to be a powerful tool for tracking the spread of SARS-CoV-2 variants/subvariants in the population.
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Affiliation(s)
- G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
| | | | - G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Orlandi
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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13
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La Rosa G, Mancini P, Veneri C, Ferraro GB, Lucentini L, Iaconelli M, Suffredini E. Detection of Monkeypox Virus DNA in Airport Wastewater, Rome, Italy. Emerg Infect Dis 2023; 29:193-196. [PMID: 36476335 PMCID: PMC9796218 DOI: 10.3201/eid2901.221311] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Environmental surveillance can be a complementary tool for detecting pathogens circulating in communities. We detected monkeypox virus DNA in wastewater from Italy's largest airport by using real-time PCR assays targeting the G2R region and F3L and N3R genes and sequencing. Wastewater surveillance can be quickly adapted to investigate emerging threats.
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14
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Armas F, Chandra F, Lee WL, Gu X, Chen H, Xiao A, Leifels M, Wuertz S, Alm EJ, Thompson J. Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era. ENVIRONMENT INTERNATIONAL 2023; 171:107718. [PMID: 36584425 PMCID: PMC9783150 DOI: 10.1016/j.envint.2022.107718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of a population's infections. In the past two years, WBS has proven to be crucial for managing the pandemic across different geographical regions. However, the changing context of the pandemic due to high levels of COVID-19 vaccination warrants a closer examination of its implication towards SARS-CoV-2 WBS. Two main questions were raised: 1) Does vaccination cause shedding of viral signatures without infection? 2) Does vaccination affect the relationship between wastewater and clinical data? To answer, we review historical reports of shedding from viral vaccines in use prior to the COVID-19 pandemic including for polio, rotavirus, influenza and measles infection and provide a perspective on the implications of different COVID-19 vaccination strategies with regard to the potential shedding of viral signatures into the sewershed. Additionally, we reviewed studies that looked into the relationship between wastewater and clinical data and how vaccination campaigns could have affected the relationship. Finally, analyzing wastewater and clinical data from the Netherlands, we observed changes in the relationship concomitant with increasing vaccination coverage and switches in dominant variants of concern. First, that no vaccine-derived shedding is expected from the current commercial pipeline of COVID-19 vaccines that may confound interpretation of WBS data. Secondly, that breakthrough infections from vaccinated individuals contribute significantly to wastewater signals and must be interpreted in light of the changing dynamics of shedding from new variants of concern.
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Affiliation(s)
- Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
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15
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Keck JW, Berry SM. Wastewater Surveillance-"Messy" Science With Public Health Potential. Am J Public Health 2023; 113:6-8. [PMID: 36356276 PMCID: PMC9755940 DOI: 10.2105/ajph.2022.307141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/12/2022]
Affiliation(s)
- James W Keck
- James W. Keck is with the Department of Family and Community Medicine, College of Medicine, University of Kentucky, Lexington. Scott M. Berry is with the Department of Mechanical Engineering, College of Engineering, University of Kentucky
| | - Scott M Berry
- James W. Keck is with the Department of Family and Community Medicine, College of Medicine, University of Kentucky, Lexington. Scott M. Berry is with the Department of Mechanical Engineering, College of Engineering, University of Kentucky
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16
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Zapata-Cardona MI, Flórez-Álvarez L, Lopera TJ, Chvatal-Medina M, Zapata-Builes W, Diaz FJ, Aguilar-Jimenez W, Taborda N, Hernandez JC, Rugeles MT. Neutralizing antibody titers to Omicron six months after vaccination with BNT162b2 in Colombia. Front Immunol 2022; 13:1102384. [PMID: 36618393 PMCID: PMC9811190 DOI: 10.3389/fimmu.2022.1102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence of the Omicron variant has generated concerns about the efficacy of COVID-19 vaccines. We evaluated the serum neutralizing activity of antibodies against the Omicron (lineage BA.1.1) by plaque reduction neutralizing test, as well as its correlation with age and gender, in a Colombian cohort six months after being vaccinated with BNT162b2 (Pfizer/BioNTech). Compared to all other variants analyzed, a significantly lower neutralizing activity (p<0.001) was observed against Omicron. Interestingly, older individuals exhibited lower titers against Omicron than those younger than 40. No statistical differences in neutralizing activity were observed according to gender. Our results showed that two doses of BNT162b2 might not provide robust protection against the Omicron variant over time. It is necessary to consider including changes in the composition of the vaccines to protect against new emerging variants of SARS-CoV-2 and campaigns to implement additional booster vaccinations.
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Affiliation(s)
- María I. Zapata-Cardona
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tulio J. Lopera
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Francisco J. Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Natalia Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - Juan C. Hernandez
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia., Medellín, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia,*Correspondence: Maria T. Rugeles,
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17
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Hegazy N, Cowan A, D'Aoust PM, Mercier É, Towhid ST, Jia JJ, Wan S, Zhang Z, Kabir MP, Fang W, Graber TE, MacKenzie AE, Guilherme S, Delatolla R. Understanding the dynamic relation between wastewater SARS-CoV-2 signal and clinical metrics throughout the pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158458. [PMID: 36075428 PMCID: PMC9444583 DOI: 10.1016/j.scitotenv.2022.158458] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 05/27/2023]
Abstract
Wastewater surveillance (WWS) of SARS-CoV-2 was proven to be a reliable and complementary tool for population-wide monitoring of COVID-19 disease incidence but was not as rigorously explored as an indicator for disease burden throughout the pandemic. Prior to global mass immunization campaigns and during the spread of the wildtype COVID-19 and the Alpha variant of concern (VOC), viral measurement of SARS-CoV-2 in wastewater was a leading indicator for both COVID-19 incidence and disease burden in communities. As the two-dose vaccination rates escalated during the spread of the Delta VOC in Jul. 2021 through Dec. 2021, relations weakened between wastewater signal and community COVID-19 disease incidence and maintained a strong relationship with clinical metrics indicative of disease burden (new hospital admissions, ICU admissions, and deaths). Further, with the onset of the vaccine-resistant Omicron BA.1 VOC in Dec. 2021 through Mar. 2022, wastewater again became a strong indicator of both disease incidence and burden during a period of limited natural immunization (no recent infection), vaccine escape, and waned vaccine effectiveness. Lastly, with the populations regaining enhanced natural and vaccination immunization shortly prior to the onset of the Omicron BA.2 VOC in mid-Mar 2022, wastewater is shown to be a strong indicator for both disease incidence and burden. Hospitalization-to-wastewater ratio is further shown to be a good indicator of VOC virulence when widespread clinical testing is limited. In the future, WWS is expected to show moderate indication of incidence and strong indication of disease burden in the community during future potential seasonal vaccination campaigns.
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Affiliation(s)
- Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stéphanie Guilherme
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada.
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18
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Wurtzer S, Levert M, Dhenain E, Accrombessi H, Manco S, Fagour N, Goulet M, Boudaud N, Gaillard L, Bertrand I, Challant J, Masnada S, Azimi S, Gillon-Ritz M, Robin A, Mouchel JM, Sig O, Moulin L. From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157740. [PMID: 35917966 PMCID: PMC9338838 DOI: 10.1016/j.scitotenv.2022.157740] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 05/17/2023]
Abstract
Throughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the prevalent populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and the proportions of VOCs identified by sequencing of strains isolated from patient. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation within human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.
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Affiliation(s)
- Sebastien Wurtzer
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France.
| | - Morgane Levert
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Eloïse Dhenain
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Heberte Accrombessi
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Sandra Manco
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Nathalie Fagour
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Marion Goulet
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | | | - Lucie Gaillard
- ACTALIA, Food Safety Department, F-50000 Saint-Lô, France
| | | | - Julie Challant
- University of Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Sophie Masnada
- SIAM - STV, Avenue de la courtiere, FR-77400 Saint Thibault des vignes, France
| | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, FR-92700 Colombes, France
| | - Miguel Gillon-Ritz
- Direction de la Proprete et de l'Eau - Service Technique de l'Eau et de l'Assainissement, Rue du Commandeur, FR-75014 Paris, France
| | - Alban Robin
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
| | - Jean-Marie Mouchel
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Obepine Sig
- Sorbonne Universite, CNRS, EPHE, UMR 7619 Metis, e-LTER Zone Atelier Seine, F-75005 Paris, France
| | - Laurent Moulin
- Eau de Paris, Research & Development, 33 avenue Jean Jaures, FR-94200 Ivry sur Seine, France
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Soni V, Paital S, Raizada P, Ahamad T, Khan AAP, Thakur S, Singh P, Hussain CM, Sharma S, Nadda AK. Surveillance of omicron variants through wastewater epidemiology: Latest developments in environmental monitoring of pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156724. [PMID: 35716753 PMCID: PMC9197784 DOI: 10.1016/j.scitotenv.2022.156724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
WBE has been a monitoring system that can give purposeful and inclusive real-time assessments of civic society as well as environmental health. This concept review introduces WBE as a surveillance scheme and initial warning outbreaks of contagious diseases caused by harmful SARS-CoV-2 with pandemic potential. Examining biomarkers of contagious diseases as evidence in polluted water taken from wastewater treatment plants suggests that these systems can be examined to get epidemiological data for checking the transmission of infectious B.1.1.529 to different areas. Thereafter, various benefits of surveillance are provided to analyse health information and pinpoint different problems that may be occurring in the workstation. Surveillance is followed by intervention steps that improved the work environment and prevent further progression of the disease. This information will help to improve early detection strategies, designing a prevention strategy to reduce their spread, infection control and therapies, thus, strengthening our global preparedness to fight future epidemics. In the end, a comprehensive discussion on the remaining challenges and opportunities for epidemiology has been given for future research perspectives.
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Affiliation(s)
- Vatika Soni
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Shilpa Paital
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Tansir Ahamad
- Department of Chemistry, College of Science, King Saud University, Saudi Arabia.
| | - Aftab Aslam Parwaz Khan
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, P. O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India.
| | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
| | - Swati Sharma
- University Institute of Biotechnology, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
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Lee WL, Armas F, Guarneri F, Gu X, Formenti N, Wu F, Chandra F, Parisio G, Chen H, Xiao A, Romeo C, Scali F, Tonni M, Leifels M, Chua FJD, Kwok GW, Tay JY, Pasquali P, Thompson J, Alborali GL, Alm EJ. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. WATER RESEARCH 2022; 221:118809. [PMID: 35841797 PMCID: PMC9250349 DOI: 10.1016/j.watres.2022.118809] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/01/2022] [Indexed: 05/06/2023]
Abstract
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Matteo Tonni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Germaine Wc Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Joey Yr Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Paolo Pasquali
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Italy
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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