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Zhao L, Guzman HP, Xagoraraki I. Comparative analyses of SARS-CoV-2 RNA concentrations in Detroit wastewater quantified with CDC N1, N2, and SC2 assays reveal optimal target for predicting COVID-19 cases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174140. [PMID: 38906283 DOI: 10.1016/j.scitotenv.2024.174140] [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: 03/17/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
To monitor COVID-19 through wastewater surveillance, global researchers dedicated significant endeavors and resources to develop and implement diverse RT-qPCR or RT-ddPCR assays targeting different genes of SARS-CoV-2. Effective wastewater surveillance hinges on the appropriate selection of the most suitable assay, especially for resource-constrained regions where scant technical and socioeconomic resources restrict the options for testing with multiple assays. Further research is imperative to evaluate the existing assays through comprehensive comparative analyses. Such analyses are crucial for health agencies and wastewater surveillance practitioners in the selection of appropriate methods for monitoring COVID-19. In this study, untreated wastewater samples were collected weekly from the Detroit wastewater treatment plant, Michigan, USA, between January and December 2023. Polyethylene glycol precipitation (PEG) was applied to concentrate the samples followed by RNA extraction and RT-ddPCR. Three assays including N1, N2 (US CDC Real-Time Reverse Transcription PCR Panel for Detection of SARS-CoV-2), and SC2 assay (US CDC Influenza SARS-CoV-2 Multiplex Assay) were implemented to detect SARS-CoV-2 in wastewater. The limit of blank and limit of detection for the three assays were experimentally determined. SARS-CoV-2 RNA concentrations were evaluated and compared through three statistical approaches, including Pearson and Spearman's rank correlations, Dynamic Time Warping, and vector autoregressive models. N1 and N2 demonstrated the highest correlation and most similar time series patterns. Conversely, N2 and SC2 assay demonstrated the lowest correlation and least similar time series patterns. N2 was identified as the optimal target to predict COVID-19 cases. This study presents a rigorous effort in evaluating and comparing SARS-CoV-2 RNA concentrations quantified with N1, N2, and SC2 assays and their interrelations and correlations with clinical cases. This study provides valuable insights into identifying the optimal target for monitoring COVID-19 through wastewater surveillance.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA
| | - Heidy Peidro Guzman
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA.
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2
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Tang L, Guo Z, Lu X, Zhao J, Li Y, Yang K. Wastewater multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages during the outbreak of infection in Chinese Mainland. Heliyon 2024; 10:e35332. [PMID: 39166043 PMCID: PMC11334792 DOI: 10.1016/j.heliyon.2024.e35332] [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: 09/15/2023] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
During the COVID-19, wastewater-based epidemiology (WBE) has become a powerful epidemic surveillance tool widely used worldwide. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we for the first time monitored the community circulation of SARS-CoV-2 lineages using WBE methods in Chinese Mainland. During the peak period of infection outbreak at the end of 2022, six precious sewage samples were collected from the manhole in the student dormitory area on Wangjiang Campus of Sichuan University. RT-qPCR revealed that the six sewage samples were all positive for SARS-CoV-2 RNA. Multiplex PCR amplicon sequencing of the sewage samples reflected the local transmission of SARS-CoV-2 variants. The results of two deconvolution methods indicate that the main virus lineages have clear evolutionary genetic correlations. Furthermore, the sampling time is consistent with the timeline of concern for these virus lineages, as well as the timeline of uploading the nucleic acid sequences from the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sewage sequencing results. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative detection of virus lineages transmission and evolution at the community level.
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Affiliation(s)
| | | | - Xiaoyi Lu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Junqiao Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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3
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Li S, Zhang Y, Tong P, Yang W. Diagnosis with Metagenomic Next-Generation Sequencing (mNGS) technology and real-time PCR for SARS-CoV-2 Omicron detection using various nasopharyngeal swabs in SARS-CoV-2 Omicron. PLoS One 2024; 19:e0305289. [PMID: 39106263 DOI: 10.1371/journal.pone.0305289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/27/2024] [Indexed: 08/09/2024] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant, with the main subtypes BA.5.2 and BF.7 in China, led to off-target effects on the S and N genes from December 1, 2022, to January 31, 2023. The kits used for studying and developing these agents were not adequately and independently evaluated. It is important to verify the performance of commercial Real-Time quantitative PCR (RT-qPCR) tests. OBJECTIVE We conducted a clinical evaluation of two Real Time SARS-CoV-2 Omicron assays to verify their performance using various detection reagents and clinical specimens. METHODS We performed clinical evaluations of two existing Chinese SARS-CoV-2 Omicron RT-qPCR kits 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, National instrument registration 20203400299, Shanghai, China) and COVID-19 nucleic acid detection kits (eDiagnosis Biomedicine, National instrument registration 20203400212, Wuhan, China) and using BSD (Bondson) (Guangzhou Bondson Biotechnology Co. Ltd, batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens. RESULTS The concordance rates for the Fosun and eDiagnosis kits were 95% and 100%, respectively. The detection limit for the Fosun and eDiagnosis kits was verified to be 300 copies/mL and 500 copies/mL. The Fosun assay exhibited the largest coefficient of variation (CV) for ORF1ab and N gene at the detection limit concentration (4.80%, 3.49%), whereas eDiagnosis showed a smaller CV (0.93%, 1.10%). In the reference product from the Hangzhou Clinical Laboratory Center test, it was found that Fosun had the lowest sensitivity of 93.47% and a specificity of 100%, while eDiagnosis exhibited 100% for both sensitivity and specificity. The lowest single target gene detection rate of Fosun reagents was 68.7% for the ORF1ab gene and 87.5% for the N gene, while eDiagnosis detection rate was 100%. Among the clinical group S specimens, the missed detection rate of the Fosun reagent was 10.9%, which was higher than the 3.9% of eDiagnosis. However, there was no significant difference in the clinical diagnostic efficiency of the two reagents. CONCLUSIONS The ORF1ab and N assays of SARS-CoV-2 Omicron on the eDiagnosis platform yielded higher values compared to those on the Fosun platform. Consequently, the eDiagnosis kit has also been used as standard detection reagents. Considering that the Fosun reagent has a relatively low detection limit and targets three single genes, it is more advantageous as a confirmatory reagent for the new museum.
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Affiliation(s)
- Sujuan Li
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yuanhang Zhang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Pengcheng Tong
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wei Yang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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St-Onge G, Davis JT, Hébert-Dufresne L, Allard A, Urbinati A, Scarpino SV, Chinazzi M, Vespignani A. Optimization and performance analytics of global aircraft-based wastewater surveillance networks. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.02.24311418. [PMID: 39132478 PMCID: PMC11312644 DOI: 10.1101/2024.08.02.24311418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Aircraft wastewater surveillance has been proposed as a novel approach to monitor the global spread of pathogens. Here we develop a computational framework to provide actionable information for designing and estimating the effectiveness of global aircraft-based wastewater surveillance networks (WWSNs). We study respiratory diseases of varying transmission potentials and find that networks of 10 to 20 strategically placed wastewater sentinel sites can provide timely situational awareness and function effectively as an early warning system. The model identifies potential blind spots and suggests optimization strategies to increase WWSNs effectiveness while minimizing resource use. Our findings highlight that increasing the number of sentinel sites beyond a critical threshold does not proportionately improve WWSNs capabilities, stressing the importance of resource optimization. We show through retrospective analyses that WWSNs can significantly shorten the detection time for emerging pathogens. The presented approach offers a realistic analytic framework for the analysis of WWSNs at airports.
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Affiliation(s)
- Guillaume St-Onge
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115, USA
- The Roux Institute, Northeastern University, Portland, ME 04101, USA
| | - Jessica T Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115, USA
| | - Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Département de physique, de génie physique et d'optique, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Antoine Allard
- Vermont Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Département de physique, de génie physique et d'optique, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Alessandra Urbinati
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115, USA
| | - Samuel V Scarpino
- Institute for Experiential AI, Northeastern University, Boston, MA 02115, USA
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115, USA
- The Roux Institute, Northeastern University, Portland, ME 04101, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA 02115, USA
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Alwahaibi N, Al Maskari M, Al-Jaaidi S, Al Dhahli B, Al Issaei H, Al Bahlani S. COVID-19 in the Arab countries: Three-year study. F1000Res 2024; 12:1448. [PMID: 38854702 PMCID: PMC11157493 DOI: 10.12688/f1000research.142541.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 06/11/2024] Open
Abstract
Background Twenty-two Arab countries share a common language, history, and culture. Nevertheless, governmental policies, healthcare systems, and resources differ from one Arab country to another. We have been following Coronavirus (COVID-19) from the beginning in each Arab country. In the present study, we aimed to assess the prevalence of COVID-19 in the Arab world and to compare these findings with other significantly affected countries. Methods Websites of the World Health Organization, World COVID-vaccinations tracker, Worldometer, and Ministries of Health were used to extract COVID-19 data in all Arab countries between the period January 2020 to December 2022. Results All Arab countries had 14,218,042 total confirmed COVID-19 cases, 13,384,924 total recovered cases and 173,544 total related deaths. The trend demonstrated that the third quarter of 2021 recorded the highest death toll and the first quarter of 2022 recorded the highest number of confirmed and recovered cases. Compared to the top 15 affected countries, the Arab world ranked last as it had the lowest overall incidence per million population (PMP) of 31,609. The data on total deaths PMP showed that India had the lowest number of deaths with only 377 cases followed by the Arab world with 386 cases. Conclusions Although the number of confirmed, death, and recovered cases of COVID-19 have greatly reduced in the last quarter of 2022 in most Arab countries, many Arab countries still need to re-campaign about COVID-19 vaccines and raise awareness programs about boosters. COVID-19 has had a relatively smaller impact on Arab countries than on other countries that have been significantly affected.
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Affiliation(s)
- Nasar Alwahaibi
- Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
| | - Muna Al Maskari
- Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
| | - Samiya Al-Jaaidi
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
| | - Buthaina Al Dhahli
- Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
| | - Halima Al Issaei
- Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
| | - Shadia Al Bahlani
- Department of Biomedical Science, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Muscat Governorate, Oman
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van der Drift AMR, Haver A, Kloosterman A, van der Beek RFHJ, Nagelkerke E, Eggink D, Laros JFJ, Nrs C, van Dissel JT, de Roda Husman AM, Lodder WJ. Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: A valuable addition to COVID-19 surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173535. [PMID: 38802021 DOI: 10.1016/j.scitotenv.2024.173535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Wastewater-based epidemiological surveillance at municipal wastewater treatment plants has proven to play an important role in COVID-19 surveillance. Considering international passenger hubs contribute extensively to global transmission of viruses, wastewater surveillance at this type of location may be of added value as well. The aim of this study is to explore the potential of long-term wastewater surveillance at a large passenger hub as an additional tool for public health surveillance during different stages of a pandemic. Here, we present an analysis of SARS-CoV-2 viral loads in airport wastewater by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) from the beginning of the COVID-19 pandemic in Feb 2020, and an analysis of SARS-CoV-2 variants by whole-genome next-generation sequencing from Sep 2020, both until Sep 2022, in the Netherlands. Results are contextualized using (inter)national measures and data sources such as passenger numbers, clinical surveillance data and national wastewater surveillance data. Our findings show that wastewater surveillance was possible throughout the study period, irrespective of measures, as viral loads were detected and quantified in 98.6 % (273/277) of samples. Emergence of SARS-CoV-2 variants, identified in 91.0 % (161/177) of sequenced samples, coincided with increases in viral loads. Furthermore, trends in viral load and variant detection in airport wastewater closely followed, and in some cases preceded, trends in national daily average viral load in wastewater and variants detected in clinical surveillance. Wastewater-based epidemiology at a large international airport is a valuable addition to classical COVID-19 surveillance and the developed expertise can be applied in pandemic preparedness plans for other (emerging) pathogens in the future.
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Affiliation(s)
- Anne-Merel R van der Drift
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Science (IRAS), Utrecht University (UU), Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Auke Haver
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Astrid Kloosterman
- Centre for Environmental Safety and Security (M&V), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Rudolf F H J van der Beek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Erwin Nagelkerke
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Applied Evolutionary Biology, 1105 AZ Amsterdam, the Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC); Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Department of BioInformatics and computational services (BIR), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Consortium Nrs
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Jaap T van Dissel
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Department of Infectious Diseases, Leiden University Medical Center (LUMC); Albinusdreef 2, 2333, ZA, Leiden, the Netherlands
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Science (IRAS), Utrecht University (UU), Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
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Patiño LH, Ballesteros N, Muñoz M, Ramírez AL, Castañeda S, Galeano LA, Hidalgo A, Paniz-Mondolfi A, Ramírez JD. Global and genetic diversity of SARS-CoV-2 in wastewater. Heliyon 2024; 10:e27452. [PMID: 38463823 PMCID: PMC10923837 DOI: 10.1016/j.heliyon.2024.e27452] [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: 10/16/2023] [Revised: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
The analysis of SARS-CoV-2 in wastewater has enabled us to better understand the spread and evolution of the virus worldwide. To deepen our understanding of its epidemiological and genomic characteristics, we analyzed 10,147 SARS-CoV-2 sequences from 5 continents and 21 countries that were deposited in the GISAID database up until January 31, 2023. Our results revealed over 100 independent lineages of the virus circulating in water samples from March 2020 to January 2023, including variants of interest and concern. We observed four clearly defined periods of global distribution of these variants over time, with one variant being replaced by another. Interestingly, we found that SARS-CoV-2 water-borne sequences from different countries had a close phylogenetic relationship. Additionally, 40 SARS-CoV-2 water-borne sequences from Europe and the USA did not show any phylogenetic relationship with SARS-CoV-2 human sequences. We also identified a significant number of non-synonymous mutations, some of which were detected in previously reported cryptic lineages. Among the countries analyzed, France and the USA showed the highest degree of sequence diversity, while Austria reported the highest number of genomes (6,296). Our study provides valuable information about the epidemiological and genomic diversity of SARS-CoV-2 in wastewater, which can be employed to support public health initiatives and preparedness.
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Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Angie Lorena Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Luis Alejandro Galeano
- Grupo de Investigación en Materiales Funcionales y Catálisis (GIMFC), Departamento de Química, Universidad de Nariño, Pasto, 52002, Colombia
| | - Arsenio Hidalgo
- Grupo de Investigación en Salud Pública, Departamento de Matemáticas, Universidad de Nariño, Pasto, 50002, Colombia
| | - Alberto Paniz-Mondolfi
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111321, Colombia
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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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Zafeiriadou A, Kaltsis L, Kostakis M, Kapes V, Thomaidis NS, Markou A. Wastewater surveillance of the most common circulating respiratory viruses in Athens: The impact of COVID-19 on their seasonality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:166136. [PMID: 37567285 DOI: 10.1016/j.scitotenv.2023.166136] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Due to governments' actions to contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the activity of common circulating respiratory viruses was significantly disrupted after the COVID-19 pandemic and thorough surveillance of respiratory pathogens was considered essential worldwide. Wastewater-based epidemiology has proven to be a valuable tool, that provides complementary information on disease outbreaks and is increasingly used to study the infection dynamics of other viruses, apart from SARS-CoV-2. The aims of the present study were the detection of four commonly circulating respiratory viruses: SARS-CoV-2, influenza A, B and Human Respiratory Syncytial Virus (RSV), the evaluation of the COVID-19 pandemic impact on their seasonality and the determination of the possible common trends in the viral load of these viruses in the wastewater of the Attica region. A standardized and validated concentration and extraction protocol was used, generic for all four viruses, followed by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) assays. The study proved that there was a prolonged period when all four viruses circulated in the population and an early outbreak of seasonal influenza and RSV in 2022-2023, compared to data from the pre-COVID-19 period. SARS-CoV-2, influenza A and RSV concentrations showed peak levels during December, followed by a slight decline in influenza A concentrations, followed by steady increase of influenza B concentrations in January 2023. SARS-CoV-2 was the dominant virus throughout the whole study period. This is the first study in Greece that investigated the most common circulating viruses simultaneously and in one of the largest timelines, providing crucial information about their infection dynamics during a period when an outbreak of respiratory diseases was declared by the National Public Health Organization. Presented results highlight the establishment of environmental surveillance as a non-invasive and complementary virus outbreak monitoring tool and the importance of influenza A, B and RSV integration into a wastewater-based surveillance system to help in disease management.
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Affiliation(s)
- Anastasia Zafeiriadou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Lazaros Kaltsis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771, Athens, Greece.
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10
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Ahmed W, Smith WJM, Tiwari A, Bivins A, Simpson SL. Unveiling indicator, enteric, and respiratory viruses in aircraft lavatory wastewater using adsorption-extraction and Nanotrap® Microbiome A Particles workflows. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165007. [PMID: 37348715 DOI: 10.1016/j.scitotenv.2023.165007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/17/2023] [Accepted: 06/17/2023] [Indexed: 06/24/2023]
Abstract
The effective detection of viruses in aircraft wastewater is crucial to establish surveillance programs for monitoring virus spread via aircraft passengers. This study aimed to compare the performance of two virus concentration workflows, adsorption-extraction (AE) and Nanotrap® Microbiome A Particles (NMAP), in detecting the prevalence and concentrations of 15 endogenous viruses including ssDNA, dsDNA, ssRNA in 24 aircraft lavatory wastewater samples. The viruses tested included two indicator viruses, four enteric viruses, and nine respiratory viruses. The results showed that cross-assembly phage (crAssphage), human polyomavirus (HPyV), rhinovirus A (RhV A), and rhinovirus B (RhV B) were detected in all wastewater samples using both workflows. However, enterovirus (EV), human norovirus GII (HNoV GII), human adenovirus (HAdV), bocavirus (BoV), parechovirus (PeV), epstein-barr virus (EBV). Influenza A virus (IAV), and respiratory syncytial virus B (RsV B) were infrequently detected by both workflows, and hepatitis A virus (HAV), influenza B virus (IBV), and respiratory syncytial virus B (RsV A) were not detected in any samples. The NMAP workflow had greater detection rates of RNA viruses (EV, PeV, and RsV B) than the AE workflow, while the AE workflow had greater detection rates of DNA viruses (HAdV, BoV, and EBV) than the NMAP workflow. The concentration of each virus was also analyzed, and the results showed that crAssphage had the highest mean concentration (6.76 log10 GC/12.5 mL) followed by HPyV (5.46 log10 GC/12.5 mL using the AE workflow, while the mean concentrations of enteric and respiratory viruses ranged from 2.48 to 3.63 log10 GC/12.5 mL. Using the NMAP workflow, the mean concentration of crAssphage was 5.18 log10 GC/12.5 mL and the mean concentration of HPyV was 4.20 log10 GC/12.5 mL, while mean concentrations of enteric and respiratory viruses ranged from 2.55 to 3.74 log10 GC/12.5 mL. Significantly higher (p < 0.05) mean concentrations of crAssphage and HPyV were observed when employing the AE workflow in comparison to the NMAP workflow. Conversely, the NMAP workflow yielded significantly greater (p < 0.05) concentrations of RhV A, and RhV B compared to the AE workflow. The findings of this study can aid in the selection of an appropriate concentration workflow for virus surveillance studies and contribute to the development of efficient virus detection methods.
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Affiliation(s)
- Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ananda Tiwari
- Expert Microbiology Research Unit, Finnish Institute for Health and Welfare, Kuopio 70701, Finland
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
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11
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Werbajh S, Larocca L, Carrillo C, Stolowicz F, Ogas L, Pallotto S, Cassará S, Mammana L, Zapiola I, Bouzas MB, Vojnov AA. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023; 15:1910. [PMID: 37766315 PMCID: PMC10537693 DOI: 10.3390/v15091910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas.
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Affiliation(s)
- Santiago Werbajh
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Luciana Larocca
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Carolina Carrillo
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Fabiana Stolowicz
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Lorena Ogas
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Sergio Pallotto
- Laboratorio Pablo Cassará S.R.L. Saladillo 2452, Buenos Aires C1440FFX, Argentina
| | - Solange Cassará
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Liliana Mammana
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Inés Zapiola
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - María Belén Bouzas
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Adrian A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
- Facultad de Medicina-Universidad del Salvador, Av. Córdoba 1601, Buenos Aires C1055AAG, Argentina
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12
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Hui KPY, Chin AWH, Ehret J, Ng KC, Peiris M, Poon LLM, Wong KHM, Chan MCW, Hosegood I, Nicholls JM. Stability of SARS-CoV-2 on Commercial Aircraft Interior Surfaces with Implications for Effective Control Measures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6598. [PMID: 37623181 PMCID: PMC10454724 DOI: 10.3390/ijerph20166598] [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: 06/12/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND The COVID-19 pandemic from 2019 to 2022 devastated many aspects of life and the economy, with the commercial aviation industry being no exception. One of the major concerns during the pandemic was the degree to which the internal aircraft environment contributed to virus transmission between humans and, in particular, the stability of SARS-CoV-2 on contact surfaces in the aircraft cabin interior. METHOD In this study, the stability of various major strains of SARS-CoV-2 on interior aircraft surfaces was evaluated using the TCID50 assessment. RESULTS In contrast to terrestrial materials, SARS-CoV-2 was naturally less stable on common contact points in the aircraft interior, and, over a 4 h time period, there was a 90% reduction in culturable virus. Antiviral and surface coatings were extremely effective at mitigating the persistence of the virus on surfaces; however, their benefit was diminished by regular cleaning and were ineffective after 56 days of regular use and cleaning. Finally, successive strains of SARS-CoV-2 have not evolved to be more resilient to survival on aircraft surfaces. CONCLUSIONS We conclude that the mitigation strategies for SARS-CoV-2 on interior aircraft surfaces are more than sufficient, and epidemiological evidence over the past three years has not found that surface spread is a major route of transmission.
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Affiliation(s)
- Kenrie P. Y. Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Alex W. H. Chin
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - John Ehret
- Qantas Airways Ltd., Qantas 10 Bourke Rd Mascot, Sydney, NSW 2020, Australia
| | - Ka-Chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Karen H. M. Wong
- Electron Microscopy Unit, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China
| | - Michael C. W. Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam HKG, Hong Kong SAR, China; (K.P.Y.H.)
- Centre for Immunology & Infection, Hong Kong Science Park HKG, Hong Kong SAR, China
| | - Ian Hosegood
- Qantas Airways Ltd., Qantas 10 Bourke Rd Mascot, Sydney, NSW 2020, Australia
| | - John M. Nicholls
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam HKG, Hong Kong SAR, China
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13
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Mothershead JL, Dembek ZF, Hadeed SJ, Schwartz-Watjen KT, Broadway KM, Tigabu B, Woodards AJ, Owens AN, Chekol T, Wu A. A Universal Travel Risk Assessment Questionnaire: Travel Assessment During COVID-19 Pandemic and Endemicity. Mil Med 2023; 188:e2606-e2614. [PMID: 36065513 DOI: 10.1093/milmed/usac261] [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: 06/17/2022] [Revised: 07/26/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Throughout the Coronavirus Disease 2019 (COVID-19) pandemic, military commanders have been challenged with providing appropriate travel guidance for their military and civilian personnel and dependents. This guidance, where promulgated, lacks uniformity. Travel aids and computer applications similarly differ and are not updated as often as jurisdictional travel health guidance is changed. Given the ever-evolving Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants with differing degrees of infectivity, COVID-19 travel guidance will remain relevant for military travelers during the transition from pandemic to endemic phases and for the foreseeable future. MATERIALS AND METHODS We reviewed all germane travel guidance promulgated by the U.S, Department of Defense; the U.S. Centers for Disease Control and Prevention; and other federal, state, and international agencies. From these materials, we identified and delineated applicable universal components for COVID-19 travel risk and created a universal Travel Risk Assessment Questionnaire (TRAQ). RESULTS We present a universal TRAQ that identifies and allows for a graded most-appropriate response to known travel risk assessment factors including travel restrictions, travel mode, travel time, travel party size, trip duration, COVID-19 incidence rate at travel destination, lodging, planned activities, personal interaction level, vaccination coverage at destination, travel location, traveler's vaccination status, previous COVID-19 infection, mask wear compliance, mask type, and work environment, along with additional considerations and post-travel COVID-19 questions. We provide examples of the use of this questionnaire that describe low, medium, and high risk to the traveler for contracting COVID-19. CONCLUSION Our TRAQ provides an easy-to-use format that can enable military, business, or personal travelers to more completely assess their likelihood of COVID-19 exposure and help them to reduce their potential for contracting COVID-19 during travel and subsequently transmitting it to others upon return. It should help commanders and traveling personnel to better assess COVID-19 travel risks through application of known travel risk factors.
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Affiliation(s)
- Jerry L Mothershead
- Applied Research Associates (ARA), Support to DTRA Technical Reachback, Albuquerque, NM 87110, USA
| | - Zygmunt F Dembek
- Battelle Memorial Institute, Support to DTRA Technical Reachback, Columbus, OH 43201, USA
- Guarantor
| | - Steven J Hadeed
- Battelle Memorial Institute, Support to DTRA Technical Reachback, Columbus, OH 43201, USA
| | | | - Katherine M Broadway
- Defense Sciences, Inc. (DSI), Support to DTRA Technical Reachback, San Antonio, TX 78230, USA
| | - Bersabeh Tigabu
- Global Systems Engineering, Support to DTRA Technical Reachback, Alexandria, VA 22312, USA
| | - Ashley J Woodards
- Battelle Memorial Institute, Support to DTRA Technical Reachback, Columbus, OH 43201, USA
| | - Akeisha N Owens
- Defense Threat Reduction Agency (DTRA), Fort Belvoir, VA 22060, USA
| | - Tesema Chekol
- Battelle Memorial Institute, Support to DTRA Technical Reachback, Columbus, OH 43201, USA
| | - Aiguo Wu
- Defense Threat Reduction Agency (DTRA), Fort Belvoir, VA 22060, USA
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14
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Wang J, Zhang Y, Dong S, Zha W, Liu C, Wang Y, Jiang Y, Xing H, Li X. Bivalent mRNA vaccines against three SARS-CoV-2 variants mediated by new ionizable lipid nanoparticles. Int J Pharm 2023:123155. [PMID: 37402442 DOI: 10.1016/j.ijpharm.2023.123155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/04/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023]
Abstract
Lipid nanoparticles (LNPs)-based mRNA vaccines have shown great potential in the fight against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. However, it remains still a challenge to improve the delivery efficiency of LNPs and the long-term stability of their mediated mRNA vaccines. Herein, a novel ionizable lipid 2-hexyldecyl 6-(ethyl(3-((2-hexyldecyl)oxy)-2-hydroxypropyl)amino)hexanoate (HEAH) derived LNPs were developed for delivering the receptor binding domain (RBD) mRNAs. In vitro cell assays confirmed that the ionizable lipid HEAH with one ether bond and one ester bond derived LNPs possessed higher mRNA delivery efficiency compared with the approved ALC-0315 with two ester bonds used in the BNT162b2 vaccine. Notably, the HEAH-derived LNPs powder lyophilized did not significantly change for 30 days after storage at 37 °C indicating good thermostability. After two RBD mRNAs of Delta and Omicron variants were encapsulated into the HEAH-derived LNPs, a bivalent mRNA vaccine was obtained as a nanoparticle formulation. Importantly, the bivalent mRNA vaccine not only resisted Delta and Omicron and also generated protective antibodies against ancestral SARS-CoV-2. The HEAH-mediated bivalent vaccine induced stronger humoral and cellular immunity than those of the ALC-0315 group. Taken together, the ionizable lipid HEAH-derived LNPs show outstanding potential in improving the delivery efficiency of mRNA and the stability of mRNA vaccine.
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Affiliation(s)
- Ji Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Yanhao Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Shuo Dong
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Wenhui Zha
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Chao Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Yang Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Yuhao Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Hanlei Xing
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China
| | - Xinsong Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 214122, PR China.
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15
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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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16
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Lyu H, Zhong X, Huang Q, Zheng L, Chen H, Cai S. High-rise buildings: A risk factor in the COVID-19 Omicron epidemic period. PUBLIC HEALTH IN PRACTICE 2023; 5:100389. [PMID: 37234095 PMCID: PMC10199749 DOI: 10.1016/j.puhip.2023.100389] [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: 03/16/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Objectives This study aimed to investigate possible viral transmission scenarios inside a high-rise building during the Omicron phase of the COVID-19 pandemic. Study design Cross-sectional study design. Methods In order to determine the pathogenicity of the Omicron variant of SARS-CoV-2, demographic, vaccination and clinical data were collected from COVID-19 positive cases during an outbreak in a high-rise residential building in Shenzhen, China, in early 2022. The pattern of viral transmission inside the building was determined through field investigation and engineering analysis. The results highlight the risk of Omicron infection in high-rise residential buildings. Results Symptoms of infection with the Omicron variant are predominantly mild. Younger age has a greater impact on the severity of disease than vaccination status. Each floor of the high-rise building investigated contained 7 apartments, numbered 01 to 07, positioned in the same layout on each floor. The drainage system included vertical pipes from the ground to the roof of the building. There were statistically significant differences in infection rates at different time points and incidence ratios between apartment numbers ending in 07 (type 07) and other apartments (P < 0.001). Households with early disease onset were concentrated in apartment type 07 and the severity of their disease was more severe. The incubation period of the outbreak was 5.21-5.31 days and the time-dependent reproduction number (Rt) was 12.08 (95% confidence interval [CI] 7.66, 18.29). Results suggest both non-contact and contact viral transmission may have contributed to the outbreak. The drainage system in the building allows aerosol regurgitation, thus indicating that the structure of the building may have led to spread of the virus from the sewage pipes. Infections in other apartments may have been as result of viral transmission in the elevators and intimate family contact. Conclusions Results from this study suggest that Omicron transmission was likely to be via the sewage system, supplemented by contact transmission in the stairs and elevators. The environmental spread of Omicron needs to be highlighted and prevented.
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Affiliation(s)
- Hongxin Lyu
- Shenzhen Longhua Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Xianwu Zhong
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China
| | | | | | - Hongbiao Chen
- Shenzhen Longhua Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Song Cai
- Shenzhen University, Shenzhen, Guangdong, China
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17
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Li J, Hosegood I, Powell D, Tscharke B, Lawler J, Thomas KV, Mueller JF. A global aircraft-based wastewater genomic surveillance network for early warning of future pandemics. Lancet Glob Health 2023; 11:e791-e795. [PMID: 37061316 PMCID: PMC10101754 DOI: 10.1016/s2214-109x(23)00129-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 04/17/2023]
Abstract
International airports can have a key role in screening, detecting, and mitigating cross-border transmission of SARS-CoV-2 and potentially other infectious diseases. With aircraft passengers representing a subpopulation of a country or region, aircraft-based wastewater surveillance can be a promising approach to effectively identifying emerging viruses, tracing their evolution, and mapping global spread with international flights. Therefore, we propose the development of a global aircraft-based wastewater genomic surveillance network, with the busiest international airports as central nodes and continuing air travel journeys as vectors. This surveillance programme requires routinely collecting aircraft wastewater samples for microbiological analysis and sequencing and linking the resulting data with associated international air traffic information. With the creation of a strong international alliance between the airline industry and health authorities, this surveillance network will potentially complement public health systems with a true early warning ability to inform decision making for new variants and future global health risks.
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Affiliation(s)
- Jiaying Li
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia.
| | | | - David Powell
- International Air Transport Association, Geneva, Switzerland
| | - Ben Tscharke
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jenny Lawler
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Kevin V Thomas
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jochen F Mueller
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, QLD, Australia
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18
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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19
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Rasheed MK, Awrahman HA, Amin Al‐Jaf SM, Niranji SS. Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq. Immun Inflamm Dis 2023; 11:e801. [PMID: 36988244 PMCID: PMC10022420 DOI: 10.1002/iid3.801] [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: 10/07/2022] [Revised: 12/22/2022] [Accepted: 02/09/2023] [Indexed: 03/19/2023] Open
Abstract
Background Five variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS CoV‐2) have been globally recorded including Alpha, Beta, Gamma, Delta, and Omicron. The Omicron variant has outcompeted the other variants including the Delta variant. Molecular screenings of VOCs are important for surveillance, treatment, and vaccination programs. This study aimed to identify VOCs by using rapid inexpensive methods and partial sequencing of the virus's spike gene. Methods Mutation‐specific rRT PCR probes were used for both D614G and K417N mutations to potentially discriminate between Delta and Omicron variants. These were followed by sequencing of a fragment of spike gene (748 nucleotides), which covers the most notable VOC mutations in the receptor binding domain of SARS CoV‐2. Results Rapid methods showed that out of 24 SARS CoV‐2 positive samples, 19 carried the N417 mutation, which is present in the Omicron variant. Furthermore, 3 samples carried K417 wildtype, which is present in the Delta variant. Additionally, 2 samples containing both K417 and N417 suggested mixed infections between the two variants. The D614G mutation was present in all samples. Among the 4 samples sequenced, 3 samples carried 13 mutations, which are present in Omicron BA.1. The fourth sample contained the two common mutations (T478K and L452R) present in Delta, in addition to two more rare mutations (F456L and F490S), which are not commonly seen in Delta. Our data suggested that both Omicron variant BA.1 and a novel Delta variant might have circulated in this region that needs further investigations.
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Affiliation(s)
- Mariwan Kadir Rasheed
- College of Health ScienceUniversity of Human DevelopmentSulaymaniyahIraq,Sulaimani Veterinary DirectorateSulaimaniIraq
| | - Harem Abdalla Awrahman
- Hiwa Hospital, Sulaymaniyah General Directory of HealthMinistry of HealthSulaymaniyahIraq
| | - Sirwan M. Amin Al‐Jaf
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
| | - Sherko S. Niranji
- College of MedicineUniversity of GarmianKalarIraq,Coronavirus Research and Identification LabUniversity of GarmianKalarIraq
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20
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Agrawal S, Orschler L, Zachmann K, Lackner S. Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron. FEMS MICROBES 2023; 4:xtad006. [PMID: 37333432 PMCID: PMC10117852 DOI: 10.1093/femsmc/xtad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 02/11/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2024] Open
Abstract
Tracking SARS-CoV-2 variants in wastewater is primarily performed by detecting characteristic mutations of the variants. Unlike the Delta variant, the emergence of the Omicron variant and its sublineages as variants of concern has posed a challenge in using characteristic mutations for wastewater surveillance. In this study, we monitored the temporal and spatial variation of SARS-CoV-2 variants by including all the detected mutations and compared whether limiting the analyses to characteristic mutations for variants like Omicron impact the outcomes. We collected 24-hour composite samples from 15 wastewater treatment plants (WWTP) in Hesse and sequenced 164 wastewater samples with a targeted sequencing approach from September 2021 to March 2022. Our results show that comparing the number of all the mutations against the number of the characteristic mutations reveals a different outcome. A different temporal variation was observed for the ORF1a and S gene. As Omicron became dominant, we observed an increase in the overall number of mutations. Based on the characteristic mutations of the SARS-CoV-2 variants, a decreasing trend for the number of ORF1a and S gene mutations was noticed, though the number of known characteristic mutations in both genes is higher in Omicron than Delta.
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Affiliation(s)
- Shelesh Agrawal
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Laura Orschler
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Kira Zachmann
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Susanne Lackner
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
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21
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Girón-Guzmán I, Díaz-Reolid A, Cuevas-Ferrando E, Falcó I, Cano-Jiménez P, Comas I, Pérez-Cataluña A, Sánchez G. Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160914. [PMID: 36526211 PMCID: PMC9744676 DOI: 10.1016/j.scitotenv.2022.160914] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 05/05/2023]
Abstract
During the current COVID-19 pandemic, wastewater-based epidemiology (WBE) emerged as a reliable strategy both as a surveillance method and a way to provide an overview of the SARS-CoV-2 variants circulating among the population. Our objective was to compare two different concentration methods, a well-established aluminum-based procedure (AP) and the commercially available Maxwell® RSC Enviro Wastewater TNA Kit (TNA) for human enteric virus, viral indicators and SARS-CoV-2 surveillance. Additionally, both concentration methods were analyzed for their impact on viral infectivity, and nucleic acids obtained from each method were also evaluated by massive sequencing for SARS-CoV-2. The percentage of SARS-CoV-2 positive samples using the AP method accounted to 100 %, 83.3 %, and 33.3 % depending on the target region while 100 % positivity for these same three target regions was reported using the TNA procedure. The concentrations of norovirus GI, norovirus GII and HEV using the TNA method were significantly greater than for the AP method while no differences were reported for rotavirus, astrovirus, crAssphage and PMMoV. Furthermore, TNA kit in combination with the Artic v4 primer scheme yields the best SARS-CoV-2 sequencing results. Regarding impact on infectivity, the concentration method used by the TNA kit showed near-complete lysis of viruses. Our results suggest that although the performance of the TNA kit was higher than that of the aluminum procedure, both methods are suitable for the analysis of enveloped and non-enveloped viruses in wastewater by molecular methods.
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Affiliation(s)
- Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Pablo Cano-Jiménez
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain.
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
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22
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Sangsanont J, Rattanakul S, Makkaew P, Precha N, Rukthanapitak P, Sresung M, Siri Y, Kitajima M, Takeda T, Haramoto E, Puenpa J, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160317. [PMID: 36436629 PMCID: PMC9691270 DOI: 10.1016/j.scitotenv.2022.160317] [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: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Pratchaya Rukthanapitak
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 113-0033, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand.
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23
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Ahmed W, Bivins A, Korajkic A, Metcalfe S, Smith WJM, Simpson SL. Comparative analysis of Adsorption-Extraction (AE) and Nanotrap® Magnetic Virus Particles (NMVP) workflows for the recovery of endogenous enveloped and non-enveloped viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160072. [PMID: 36356768 PMCID: PMC10823496 DOI: 10.1016/j.scitotenv.2022.160072] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
In this study, two virus concentration methods, namely Adsorption-Extraction (AE) and Nanotrap® Magnetic Virus Particles (NMVP) along with commercially available extraction kits were used to quantify endogenous pepper mild mottle virus (PMMoV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in nucleic acid extracted from 48 wastewater samples collected over six events from eight wastewater treatment plants (WWTPs). The main aim was to determine which workflow (i.e., concentration and extraction methods) produces greater concentrations of endogenous PMMoV and SARS-CoV-2 gene copies (GC) in comparison with each other. Turbidity and total suspended solids (TSS) of wastewater samples within and among the eight WWTPs were highly variable (41-385 NTU and 77-668 mg/L TSS). In 58 % of individual wastewater samples, the log10 GC concentrations of PMMoV were greater by NMVP workflow compared to AE workflow. Paired measurements of PMMoV GC/10 mL from AE and NMVP across all 48 wastewater samples were weakly correlated (r = 0.455, p = 0.001) and demonstrated a poor linear relationship (r2 = 0.207). The log10 GC concentrations of SARS-CoV-2 in 69 % of individual samples were greater by AE workflow compared to NMVP workflow. In contrast to PMMoV, the AE and NMVP derived SARS-CoV-2 GC counts were strongly correlated (r = 0.859, p < 0.001) and demonstrated a strong linear relationship (r2 = 0.738). In general, the PMMoV GC achieved by the NMVP workflow decreased with increasing turbidity, but the PMMoV GC by the AE workflow did not appear to be as sensitive to either turbidity or TSS levels. These findings suggest that wastewater sample turbidity or suspended solids concentration, and the intended target for analysis should be considered when validating an optimal workflow for wastewater surveillance of viruses.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA
| | - Asja Korajkic
- United States Environmental Protection Agency, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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24
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Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Beaudet AB, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce C, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert‐May E, Kim J, Hrudey SE, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol 2023; 95:e28442. [PMID: 36579780 PMCID: PMC9880705 DOI: 10.1002/jmv.28442] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Barbara J. Waddell
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Jianwei Chen
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Kevin Xiang
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Leslie Chan
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Laura Vivas
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Kashtin Low
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Xuewen Lu
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Thierry Chekouo
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada,Division of Biostatistics, School of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Xiaotian Dai
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jason Cabaj
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Provincial Population & Public HealthAlberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
| | - Srijak Bhatnagar
- Faculty of Science and TechnologyAthabasca UniversityAthabascaAlbertaCanada
| | | | - Gopal Achari
- Department of Civil EngineeringUniversity of CalgaryCalgaryCanada
| | - Rhonda G. Clark
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Craig Pearce
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Joe J. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jon Meddings
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jenine Leal
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jennifer Ellison
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Bayan Missaghi
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jamil N. Kanji
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Oscar Larios
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
| | - Elissa Rennert‐May
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Joseph Kim
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Department of Analytical and Environmental ToxicologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Bonita E. Lee
- Department of PediatricsUniversity of AlbertaEdmontonAlbertaCanada,Women & Children's Health Research InstituteEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Xiaoli Pang
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin Frankowski
- Advancing Canadian Water AssetsUniversity of CalgaryCalgaryCanada
| | - John Conly
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
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25
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Jones DL, Rhymes JM, Wade MJ, Kevill JL, Malham SK, Grimsley JMS, Rimmer C, Weightman AJ, Farkas K. Suitability of aircraft wastewater for pathogen detection and public health surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159162. [PMID: 36202356 PMCID: PMC9528016 DOI: 10.1016/j.scitotenv.2022.159162] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
International air travel is now widely recognised as one of the primary mechanisms responsible for the transnational movement and global spread of SARS-CoV-2. Monitoring the viral load and novel lineages within human-derived wastewater collected from aircraft and at air transport hubs has been proposed as an effective way to monitor the importation frequency of viral pathogens. The success of this approach, however, is highly dependent on the bathroom and defecation habits of air passengers during their journey. In this study of UK adults (n = 2103), we quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights. The results were then used to assess the likelihood of capturing the signal from infected individuals at UK travel hubs. To obtain a representative cross-section of the population, the survey was stratified by geographical region, gender, age, parenting status, and social class. We found that an individual's likelihood to defecate on short-haul flights (< 6 h in duration) was low (< 13 % of the total), but was higher on long-haul flights (< 36 %; > 6 h in duration). This behaviour pattern was higher among males and younger age groups. The maximum likelihood of defecation was prior to departure (< 39 %). Based on known SARS-CoV-2 faecal shedding rates (30-60 %) and an equal probability of infected individuals being on short- (71 % of inbound flights) and long-haul flights (29 %), we estimate that aircraft wastewater is likely to capture ca. 8-14 % of SARS-CoV-2 cases entering the UK. Monte Carlo simulations predicted that SARS-CoV-2 would be present in wastewater on 14 % of short-haul flights and 62 % of long-haul flights under current pandemic conditions. We conclude that aircraft wastewater alone is insufficient to effectively monitor all the transboundary entries of faecal-borne pathogens but can form part of a wider strategy for public heath surveillance at national borders.
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Affiliation(s)
- Davey L Jones
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch, WA 6105, Australia.
| | - Jennifer M Rhymes
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UK Centre for Ecology and Hydrology, Bangor, Gwynedd LL57 2UW, UK
| | - Matthew J Wade
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, London SW1H 0TL, UK
| | - Jessica L Kevill
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, London SW1H 0TL, UK; The London Data Company, London EC2N 2AT, UK
| | - Charlotte Rimmer
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Andrew J Weightman
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd LL57 2UW, UK; The London Data Company, London EC2N 2AT, UK
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26
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Galani A, Markou A, Dimitrakopoulos L, Kontou A, Kostakis M, Kapes V, Diamantopoulos MA, Adamopoulos PG, Avgeris M, Lianidou E, Scorilas A, Paraskevis D, Tsiodras S, Dimopoulos MA, Thomaidis N. Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159062. [PMID: 36181801 PMCID: PMC9519360 DOI: 10.1016/j.scitotenv.2022.159062] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.
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Affiliation(s)
- Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Aikaterini Kontou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, "P. & A. Kyriakou" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sotirios Tsiodras
- Fourth Department of Internal Medicine, School of Medicine, University General Hospital Attikon, National and Kapodistrian University of Athens, Greece
| | | | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece.
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Khan A, Khan SH, Saif M, Batool A, Sohail A, Waleed Khan M. A Survey of Deep Learning Techniques for the Analysis of COVID-19 and their usability for Detecting Omicron. J EXP THEOR ARTIF IN 2023. [DOI: 10.1080/0952813x.2023.2165724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Asifullah Khan
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
- PIEAS Artificial Intelligence Center (PAIC), Pakistan Institute of Engineering & Applied Sciences, Islamabad, Pakistan
- Center for Mathematical Sciences, Pakistan Institute of Engineering & Applied Sciences, Islamabad, Pakistan
| | - Saddam Hussain Khan
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
- Department of Computer Systems Engineering, University of Engineering and Applied Sciences (UEAS), Swat, Pakistan
| | - Mahrukh Saif
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
| | - Asiya Batool
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
| | - Anabia Sohail
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
- Department of Computer Science, Faculty of Computing & Artificial Intelligence, Air University, Islamabad, Pakistan
| | - Muhammad Waleed Khan
- Pattern Recognition Lab, Department of Computer & Information Sciences, Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad, Pakistan
- Department of Mechanical and Aerospace Engineering, Columbus, OH, USA
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28
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Farkas K, Williams R, Alex-Sanders N, Grimsley JMS, Pântea I, Wade MJ, Woodhall N, Jones DL. Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001346. [PMID: 36963000 PMCID: PMC10021541 DOI: 10.1371/journal.pgph.0001346] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/24/2022] [Indexed: 01/20/2023]
Abstract
It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with travel restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying the virus. Due to the limitation of current clinical surveillance approaches, complementary methods need to be developed to allow estimation of the frequency of SARS-CoV-2 entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing the unbiased sampling of SARS-CoV-2 carriage by passenger cohorts entering via airports. In this study, we monitored sewage in samples from terminals (n = 150) and aircraft (n = 32) at three major international airports in the UK for 1-3 weeks in March 2022. As the raw samples were more turbid than typical municipal wastewater, we used beef extract treatment followed by polyethylene glycol (PEG) precipitation to concentrate viruses, followed by reverse transcription quantitative PCR (RT-qPCR) for the detection of SARS-CoV-2 and a faecal indicator virus, crAssphage. All samples taken from sewers at the arrival terminals of Heathrow and Bristol airports, and 85% of samples taken from sites at Edinburgh airport, were positive for SARS-CoV-2. This suggests a high COVID-19 prevalence among passengers and/or airport staff members. Samples derived from aircraft also showed 93% SARS-CoV-2 positivity. No difference in viral prevalence was found before and after COVID-19 travel restrictions were lifted. Our results suggest that WBE is a useful tool for monitoring the global transfer rate of human pathogens and other disease-causing agents across international borders and should form part of wider international efforts to monitor and contain the spread of future disease outbreaks.
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Affiliation(s)
- Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, United Kingdom
| | - Rachel Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Natasha Alex-Sanders
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Jasmine M S Grimsley
- Data, Analytics, and Surveillance Group, UK Health Security Agency, London, United Kingdom
- The London Data Company, London, United Kingdom
| | - Igor Pântea
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Matthew J Wade
- Data, Analytics, and Surveillance Group, UK Health Security Agency, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Nick Woodhall
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Davey L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- Food Futures Institute, Murdoch University, Murdoch, Australia
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29
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Li J, Liang T, Hei A, Wang X, Li H, Yu X, Zhao R, Gao P, Fang C, Zhou J, Li M, He E, Skog S. Novel neutralizing chicken IgY antibodies targeting 17 potent conserved peptides identified by SARS-CoV-2 proteome microarray, and future prospects. Front Immunol 2022; 13:1074077. [PMID: 36618358 PMCID: PMC9815496 DOI: 10.3389/fimmu.2022.1074077] [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: 10/19/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction An approach toward novel neutralizing IgY polyclonal antibodies (N-IgY-pAb) against SARS-CoV-2 S-ECD was developed. Material and methods The novel N-IgY-pAb and its intranasal spray response against the wild type ("'WH-Human 1") SARS-CoV-2 virus, variants of Delta or Omicron were up to 98%. Unique virus peptides binding to N-IgY-pAb were screened by a SARS-CoV-2 proteome microarray. Results Seventeen mutation-free peptides with a Z-score > 3.0 were identified as potent targets from a total of 966 peptides. The new findings show that one is in the RBM domain (461LKPFERDISTEIYQA475 ), two are in the NTD domain (21RTQLPPAYTNSFTRG35, 291CALDPLSETKCTLKS305) four are in the C1/2-terminal (561PFQQFGRDIADTTDA575,571DTTDAVRDPQTLEIL585,581TLEILDITPCSFGGV595, 661ECDIPIGAGICASYQ675 ), three are in the S1/S2 border (741YICGDSTECSNLLLQ755, 811KPSKRSFIEDLLFNK825, 821LLFNKVTLADAGFIK835) one target is in HR2 (1161SPDVDLGDISGINAS1175) and one is in HR2-TM (1201QELGKYEQYIKWPWY1215). Moreover, five potential peptides were in the NSP domain: nsp3-55 (1361SNEKQEILGTVSWNL1375), nsp14-50 (614HHANEYRLYLDAYNM642, ORF10-3 (21MNSRNYIAQVDVVNFNLT38, ORF7a-1(1MKIILFLALITLATC15) and ORF7a-12 (1116TLCFTLKRKTE121). Discussion and conclusion We concluded that the N-IgY-pAb could effectively neutralize the SARS-CoV-2. The new findings of seventeen potent conserved peptides are extremely important for developing new vaccines and "cocktails" of neutralizing Abs for efficient treatments for patients infected with SARS-CoV-2.
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Affiliation(s)
- Jin Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ailian Hei
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Xiangbin Wang
- SciProtech Co., Ltd, Beijing Changping Science Park, Beijing, China
| | - Huijun Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Centre, National Centre for Protein Sciences-Beijing (PHOENIX Centre), Beijing Institute of LifeOmics, Beijing, China
| | - Rui Zhao
- SciProtech Co., Ltd, Beijing Changping Science Park, Beijing, China
| | - Peng Gao
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Cong Fang
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Ji Zhou
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Maogang Li
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Ellen He
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China
| | - Sven Skog
- Department of Medicine, Shenzhen Ellen-Sven Precision Medicine Institute, Shenzhen, China,*Correspondence: Sven Skog,
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30
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Harrington A, Vo V, Papp K, Tillett RL, Chang CL, Baker H, Shen S, Amei A, Lockett C, Gerrity D, Oh EC. Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158577. [PMID: 36087661 PMCID: PMC9450474 DOI: 10.1016/j.scitotenv.2022.158577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 05/31/2023]
Abstract
During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018-2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018-2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.
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Affiliation(s)
- Anthony Harrington
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Van Vo
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Amei Amei
- Department of Mathematical Sciences, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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31
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Sawadogo Y, Galal L, Belarbi E, Zongo A, Schubert G, Leendertz F, Kanteh A, Sesay AK, Erhart A, Bañuls AL, Tarnagda Z, Godreuil S, Tinto H, Ouedraogo AS. Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa. Viruses 2022; 14:v14122788. [PMID: 36560792 PMCID: PMC9782145 DOI: 10.3390/v14122788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. METHODS Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. RESULTS The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. CONCLUSIONS This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves.
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Affiliation(s)
- Yacouba Sawadogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
| | - Lokman Galal
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
| | | | - Arsène Zongo
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
| | | | | | - Abdoulie Kanteh
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Abdul Karim Sesay
- Genomics Core Facility, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Annette Erhart
- Disease Control and Elimination Theme, Medical Research Council Unit the Gambia (MRCG), London School of Hygiene and Tropical Medicine, Fajara P.O. Box 273, The Gambia
| | - Anne-Laure Bañuls
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Zékiba Tarnagda
- Laboratoire National de Référence-Grippe (LNR-G), Institut de Recherche en Sciences de la Santé, Ouagadougou 03 BP 7192, Burkina Faso
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université de Montpellier—Institut de Recherche pour le Développement (IRD)—Centre National de la Recherche Scientifique (CNRS), 34394 Montpellier, France
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
| | - Halidou Tinto
- Centre National de la Recherche Scientifique et Technologique/Institut de Recherche en Sciences de la Santé (CNRST/IRSS), Nanoro BP 18, Burkina Faso
| | - Abdoul-Salam Ouedraogo
- Departement of Bacteriology and Virology, Souro Sanou University Hospital, Bobo Dioulasso 01 BP 676, Burkina Faso
- Laboratory of Emerging and Re-emerging Pathogens, School of Health Sciences Nazi Boni University, Bobo Dioulasso 01 BP 1091, Burkina Faso
- Muraz Center, Bobo Dioulasso 01 BP 390, Burkina Faso
- Jeune Equipe Associée (JEAI), Institut de Recherche pour le Développement (IRD), Résistances Antimicrobiennes au Burkina Faso (FASORAM), 34394 Montpellier, France
- Correspondence: or
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Li Y, Miyani B, Zhao L, Spooner M, Gentry Z, Zou Y, Rhodes G, Li H, Kaye A, Norton J, Xagoraraki I. Surveillance of SARS-CoV-2 in nine neighborhood sewersheds in Detroit Tri-County area, United States: Assessing per capita SARS-CoV-2 estimations and COVID-19 incidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158350. [PMID: 36041621 PMCID: PMC9419442 DOI: 10.1016/j.scitotenv.2022.158350] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 05/14/2023]
Abstract
Wastewater-based epidemiology (WBE) has been suggested as a useful tool to predict the emergence and investigate the extent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we screened appropriate population biomarkers for wastewater SARS-CoV-2 normalization and compared the normalized SARS-CoV-2 values across locations with different demographic characteristics in southeastern Michigan. Wastewater samples were collected between December 2020 and October 2021 from nine neighborhood sewersheds in the Detroit Tri-County area. Using reverse transcriptase droplet digital polymerase chain reaction (RT-ddPCR), concentrations of N1 and N2 genes in the studied sites were quantified, with N1 values ranging from 1.92 × 102 genomic copies/L to 6.87 × 103 gc/L and N2 values ranging from 1.91 × 102 gc/L to 6.45 × 103 gc/L. The strongest correlations were observed with between cumulative COVID-19 cases per capita (referred as COVID-19 incidences thereafter), and SARS-CoV-2 concentrations normalized by total Kjeldahl nitrogen (TKN), creatinine, 5-hydroxyindoleacetic acid (5-HIAA) and xanthine when correlating the per capita SARS-CoV-2 and COVID-19 incidences. When SARS-CoV-2 concentrations in wastewater were normalized and compared with COVID-19 incidences, the differences between neighborhoods of varying demographics were reduced as compared to differences observed when comparing non-normalized SARS-CoV-2 with COVID-19 cases. This indicates when studying the disease burden in communities of different demographics, accurate per capita estimation is of great importance. The study suggests that monitoring selected water quality parameters or biomarkers, along with RNA concentrations in wastewater, will allow adequate data normalization for spatial comparisons, especially in areas where detailed sanitary sewage flows and contributing populations in the catchment areas are not available. This opens the possibility of using WBE to assess community infections in rural areas or the developing world where the contributing population of a sample could be unknown.
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Affiliation(s)
- Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America.
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
| | - Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
| | - Maddie Spooner
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
| | - Zach Gentry
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
| | - Yangyang Zou
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
| | - Geoff Rhodes
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, United States of America
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, United States of America
| | - Andrew Kaye
- CDM Smith, 535 Griswold St, Detroit, MI 48226, United States of America
| | - John Norton
- Great Lakes Water Authority, 735 Randolph, Detroit, MI 48226, United States of America
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI 48823, United States of America
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Zhang X, Zhang L, Wang Y, Zhang M, Zhou J, Liu X, Wang Y, Qu C, Han W, Hou M, Deng F, Luo Y, Mao Y, Gu W, Dong Z, Pan Y, Zhang D, Tang S, Zhang L. Detection of the SARS-CoV-2 Delta Variant in the Transboundary Rivers of Yunnan, China. ACS ES&T WATER 2022; 2:2367-2377. [PMID: 37552741 PMCID: PMC9631342 DOI: 10.1021/acsestwater.2c00224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 05/30/2023]
Abstract
Ruili and Longchuan, two border counties in southwestern China, are facing epidemic control challenges due to the high rate of COVID-19 infections originating from neighboring Myanmar. Here, we aimed to establish the applicability of wastewater and environmental water surveillance of SARS-CoV-2 and conduct whole-genome sequencing (WGS) to trace the possible infection origin. In August 2021, total 72 wastewater and river water samples were collected from 32 sampling sites. SARS-CoV-2 ORF1ab and N genes were measured by RT-qPCR. We found that 19 samples (26.39%) were positive, and the viral loads of ORF1ab and N genes were 6.62 × 102-2.55×105 and 1.86 × 103-2.32 × 105 copies/L, respectively. WGS further indicated the sequences in two transboundary river samples, and one hospital wastewater sample belonged to the delta variant, suggesting that the infection source might be areas with high COVID-19 delta variant incidence in Southeast Asia (e.g., Myanmar). We reported for the first time the detection and quantification of SARS-CoV-2 RNA in the transboundary rivers of Myanmar-China. Our findings demonstrate that wastewater and environmental water may provide independent and nonintrusive surveillance points to monitor the global spread of emerging COVID-19 variants of concern, particularly in high-risk regions or border areas with considerable epidemic challenges and poor wastewater treatment facilities.
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Affiliation(s)
- Xiao Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Liang Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yuanyuan Wang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Meiling Zhang
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Jienan Zhou
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Xin Liu
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Yan Wang
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Changsheng Qu
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Wenxiang Han
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Min Hou
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yueyun Luo
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yixin Mao
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Wen Gu
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Zhaomin Dong
- School of Space and Environment, Beihang
University, Beijing100191, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Lan Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
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34
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Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, Ali I, Al-Ahdal T, Abdelazeem B, Sah R, Rodriguez-Morales AJ. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. LE INFEZIONI IN MEDICINA 2022; 30:480-494. [PMID: 36482957 PMCID: PMC9714996 DOI: 10.53854/liim-3004-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) has been the most recent variant of concern (VOC) established by the World Health Organization (WHO). Because of its greater infectivity and immune evasion, this variant quickly became the dominant type of circulating SARS-CoV-2 worldwide. Our literature review thoroughly explains the current state of Omicron emergence, particularly by comparing different omicron subvariants, including BA.2, BA.1, and BA.3. Such elaboration would be based on structural variations, mutations, clinical manifestation, transmissibility, pathogenicity, and vaccination effectiveness. The most notable difference between the three subvariants is the insufficiency of deletion (Δ69-70) in the spike protein, which results in a lower detection rate of the spike (S) gene target known as (S) gene target failure (SGTF). Furthermore, BA.2 had a stronger affinity to the human Angiotensin-converting Enzyme (hACE2) receptor than other Omicron sub-lineages. Regarding the number of mutations, BA.1.1 has the most (40), followed by BA.1, BA.3, and BA.3 with 39, 34, and 31 mutations, respectively. In addition, BA.2 and BA.3 have greater transmissibility than other sub-lineages (BA.1 and BA.1.1). These characteristics are primarily responsible for Omicron's vast geographical spread and high contagiousness rates, particularly BA.2 sub-lineages.
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Affiliation(s)
| | - Abdelaziz Abdelaal
- Harvard Medical School, Boston, MA,
USA,Boston University, MA,
USA,General Practitioner, Tanta University Hospitals,
Egypt
| | | | | | | | - Khaled Albakri
- Faculty of Medicine, The Hashemite University, Zarqa,
Jordan
| | - Iftikhar Ali
- Department of Pharmacy, Paraplegic Center, Peshawar,
Pakistan
| | - Tareq Al-Ahdal
- Institute of Global Health (HIGH), Heidelberg University, Heidelberg,
Germany
| | - Basel Abdelazeem
- Department of Internal Medicine, McLaren Health Care, Flint, Michigan,
USA,Department of Internal Medicine, Michigan State University, East Lansing, Michigan,
USA
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu,
Nepal,Dr. D.Y Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra,
India
| | - Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas, Pereira, Risaralda,
Colombia,Faculty of Medicine, Institución Universitaria Vision de Las Americas, Pereira, Risaralda,
Colombia,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36,
Lebanon,Master of Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima,
Perú
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35
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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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36
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Xie Y, Challis JK, Oloye FF, Asadi M, Cantin J, Brinkmann M, McPhedran KN, Hogan N, Sadowski M, Jones PD, Landgraff C, Mangat C, Servos MR, Giesy JP. RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern. ACS ES&T WATER 2022; 2:1852-1862. [PMID: 37552734 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
There are no standardized protocols for quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater to date, especially for population normalization. Here, a pipeline was developed, applied, and assessed to quantify SARS-CoV-2 and key variants of concern (VOCs) RNA in wastewater at Saskatoon, Canada. Normalization approaches using recovery ratio and extraction efficiency, wastewater parameters, or population indicators were assessed by comparing to daily numbers of new cases. Viral load was positively correlated with daily new cases reported in the sewershed. Wastewater surveillance (WS) had a lead time of approximately 7 days, which indicated surges in the number of new cases. WS revealed the variant α and δ driving the third and fourth wave, respectively. The adjustment with the recovery ratio and extraction efficiency improved the correlation between viral load and daily new cases. Normalization of viral concentration to concentrations of the artificial sweetener acesulfame K improved the trend of viral load during the Christmas and New Year holidays when populations were dynamic and variable. Acesulfame K performed better than pepper mild mottle virus, creatinine, and ammonia for population normalization. Hence, quality controls to characterize recovery ratios and extraction efficiencies and population normalization with acesulfame are promising for precise WS programs supporting decision-making in public health.
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Affiliation(s)
- Yuwei Xie
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Jonathan K. Challis
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Femi F. Oloye
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
| | - Jenna Cantin
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Markus Brinkmann
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Kerry N. McPhedran
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Natacha Hogan
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- College of Agriculture and Bioresources, Department of
Animal and Poultry Sciences, University of Saskatchewan,
Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department,
City of Saskatoon, Saskatoon, Saskatchewan S7M 1X5,
Canada
| | - Paul D. Jones
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology
Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
R3E 3R2, Canada
- Food Science Department, University of
Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chand Mangat
- Antimicrobial Resistance and Nosocomial Infections,
National Microbiology Laboratory, Public Health Agency of
Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark R. Servos
- Department of Biology, University of
Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John P. Giesy
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Department of Veterinary Biomedical Sciences,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4,
Canada
- Department of Environmental Sciences,
Baylor University, Waco, Texas 76706, United
States
- Department of Zoology and Center for Integrative
Toxicology, Michigan State University, East Lansing, Michigan
48824, United States
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37
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Langan LM, O’Brien M, Lovin LM, Scarlett KR, Davis H, Henke AN, Seidel SE, Archer N, Lawrence E, Norman RS, Bojes HK, Brooks BW. Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States. ACS ES&T WATER 2022; 2:2211-2224. [PMID: 37552718 PMCID: PMC9291321 DOI: 10.1021/acsestwater.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
After its emergence in late November/December 2019, the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) rapidly spread globally. Recognizing that this virus is shed in feces of individuals and that viral RNA is detectable in wastewater, testing for SARS-CoV-2 in sewage collections systems has allowed for the monitoring of a community's viral burden. Over a 9 month period, the influents of two regional wastewater treatment facilities were concurrently examined for wild-type SARS-CoV-2 along with variants B.1.1.7 and B.1.617.2 incorporated as they emerged. Epidemiological data including new confirmed COVID-19 cases and associated hospitalizations and fatalities were tabulated within each location. RNA from SARS-CoV-2 was detectable in 100% of the wastewater samples, while variant detection was more variable. Quantitative reverse transcription PCR (RT-qPCR) results align with clinical trends for COVID-19 cases, and increases in COVID-19 cases were positively related with increases in SARS-CoV-2 RNA load in wastewater, although the strength of this relationship was location specific. Our observations demonstrate that clinical and wastewater surveillance of SARS-CoV-2 wild type and constantly emerging variants of concern can be combined using RT-qPCR to characterize population infection dynamics. This may provide an early warning for at-risk communities and increases in COVID-19 related hospitalizations.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
| | - Lea M. Lovin
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Kendall R. Scarlett
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Haley Davis
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Abigail N. Henke
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Biology, Baylor
University, One Bear Place #97388, Waco, Texas 76798, United
States
| | - Sarah E. Seidel
- Center for Health
Statistics, Texas Department of State Health Services, Austin, Texas
78756, United States
| | - Natalie Archer
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Eric Lawrence
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - R. Sean Norman
- Department of Environmental Health Sciences, Arnold School of
Public Health, University of South Carolina, 921 Assembly
Street Columbia, South Carolina 29208, United States
| | - Heidi K. Bojes
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
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38
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Wilhelm A, Schoth J, Meinert-Berning C, Agrawal S, Bastian D, Orschler L, Ciesek S, Teichgräber B, Wintgens T, Lackner S, Weber FA, Widera M. Wastewater surveillance allows early detection of SARS-CoV-2 omicron in North Rhine-Westphalia, Germany. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157375. [PMID: 35850355 PMCID: PMC9287496 DOI: 10.1016/j.scitotenv.2022.157375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 05/25/2023]
Abstract
Wastewater-based epidemiology (WBE) has demonstrated its importance to support SARS-CoV-2 epidemiology complementing individual testing strategies. Due to their immune-evasive potential and the resulting significance for public health, close monitoring of SARS-CoV-2 variants of concern (VoC) is required to evaluate the regulation of early local countermeasures. In this study, we demonstrate a rapid workflow for wastewater-based early detection and monitoring of the newly emerging SARS-CoV-2 VoCs Omicron in the end of 2021 at the municipal wastewater treatment plant (WWTP) Emschermuendung (KLEM) in the Federal State of North-Rhine-Westphalia (NRW, Germany). Initially, available primers detecting Omicron-related mutations were rapidly validated in a central laboratory. Subsequently, RT-qPCR analysis of purified SARS-CoV-2 RNA was performed in a decentral PCR laboratory in close proximity to KLEM. This decentralized approach enabled the early detection of K417N present in Omicron in samples collected on 8th December 2021 and the detection of further mutations (N501Y, Δ69/70) in subsequent biweekly sampling campaigns. The presence of Omicron in wastewater was confirmed by next generation sequencing (NGS) in a central laboratory with samples obtained on 14th December 2021. Moreover, the relative increase of the mutant fraction of Omicron was quantitatively monitored over time by dPCR in a central PCR laboratory starting on 12th December 2021 confirming Omicron as the dominant variant by the end of 2021. In conclusions, WBE plays a crucial role in surveillance of SARS-CoV-2 variants and is suitable as an early warning system to identify variant emergence. In particular, the successive workflow using RT-qPCR, RT-dPCR and NGS demonstrates the strength of WBE as a versatile tool to monitor variant spreading.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany
| | - Laura Orschler
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, D-60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany; Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074, Aachen, Germany
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
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39
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35753493 DOI: 10.1101/2022.01.28.21268186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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40
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Chassalevris T, Chaintoutis SC, Koureas M, Petala M, Moutou E, Beta C, Kyritsi M, Hadjichristodoulou C, Kostoglou M, Karapantsios T, Papadopoulos A, Papaioannou N, Dovas CI. SARS-CoV-2 wastewater monitoring using a novel PCR-based method rapidly captured the Delta-to-Omicron ΒΑ.1 transition patterns in the absence of conventional surveillance evidence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156932. [PMID: 35753493 PMCID: PMC9225927 DOI: 10.1016/j.scitotenv.2022.156932] [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: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/21/2023]
Abstract
Conventional SARS-CoV-2 surveillance based on genotyping of clinical samples is characterized by challenges related to the available sequencing capacity, population sampling methodologies, and is time, labor, and resource-demanding. Wastewater-based variant surveillance constitutes a valuable supplementary practice, since it does not require extensive sampling, and provides information on virus prevalence in a timely and cost-effective manner. Consequently, we developed a sensitive real-time RT-PCR-based approach that exclusively amplifies and quantifies SARS-CoV-2 genomic regions carrying the S:Δ69/70 deletion, indicative of the Omicron BA.1 variant, in wastewater. The method was incorporated in the analysis of composite daily samples taken from the main Wastewater Treatment Plant of Thessaloniki, Greece, from 1 December 2021. The applicability of the methodology is dependent on the epidemiological situation. During Omicron BA.1 global emergence, Thessaloniki was experiencing a massive epidemic wave attributed solely to the Delta variant, according to genomic surveillance data. Since Delta does not possess the S:Δ69/70, the emergence of Omicron BA.1 could be monitored via the described methodology. Omicron BA.1 was detected in sewage samples on 19 December 2021 and a rapid increase of its viral load was observed in the following 10-day period, with an estimated early doubling time of 1.86 days. The proportion of the total SARS-CoV-2 load attributed to BA.1 reached 91.09 % on 7 January, revealing a fast Delta-to-Omicron transition pattern. The detection of Omicron BA.1 subclade in wastewater preceded the outburst of reported (presumable) Omicron cases in the city by approximately 7 days. The proposed wastewater surveillance approach based on selective PCR amplification of a genomic region carrying a deletion signature enabled rapid, real-time data acquisition on Omicron BA.1 prevalence and dynamics during the slow remission of the Delta wave. Timely provision of these results to State authorities readily influences the decision-making process for targeted public health interventions, including control measures, awareness, and preparedness.
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Affiliation(s)
- Taxiarchis Chassalevris
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Michalis Koureas
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Evangelia Moutou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece
| | - Christina Beta
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Kyritsi
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Christos Hadjichristodoulou
- Department of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi str., 41222 Larissa, Greece
| | - Margaritis Kostoglou
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Thodoris Karapantsios
- Laboratory of Chemical and Environmental Technology, School of Chemistry, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636 Thessaloniki, Greece
| | - Nikolaos Papaioannou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 11 Stavrou Voutyra str., 54627, Thessaloniki, Greece.
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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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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022; 44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant is spreading rapidly throughout several countries. Thus, we comprehensively analyzed Omicron's mutational landscape and compared mutations with VOC/VOI. We analyzed SNVs throughout the genome, and AA variants (NSP and SP) in VOC/VOI, including Omicron. We generated heat maps to illustrate the AA variants with high mutation prevalence (> 75% frequency) of Omicron, which demonstrated eight mutations with > 90% prevalence in ORF1a and 29 mutations with > 75% prevalence in S-glycoprotein. A scatter plot for Omicron and VOC/VOI's cluster evaluation was computed. We performed a risk analysis of the antibody-binding risk among four mutations (L452, F490, P681, D614) and observed three mutations (L452R, F490S, D614G) destabilized antibody interactions. Our comparative study evaluated the properties of 28 emerging mutations of the S-glycoprotein of Omicron, and the ΔΔG values. Our results showed K417N with minimum and Q954H with maximum ΔΔG value. Furthermore, six important RBD mutations (G339D, S371L, N440K, G446S, T478K, Q498R) were chosen for comprehensive analysis for stabilizing/destabilizing properties and molecular flexibility. The G339D, S371L, N440K, and T478K were noted as stable mutations with 0.019 kcal/mol, 0.127 kcal/mol, 0.064 kcal/mol, and 1.009 kcal/mol. While, G446S and Q498R mutations showed destabilizing results. Simultaneously, among six RBD mutations, G339D, G446S, and Q498R mutations increased the molecular flexibility of S-glycoprotein. This study depicts the comparative mutational pattern of Omicron and other VOC/VOI, which will help researchers to design and deploy novel vaccines and therapeutic antibodies to fight against VOC/VOI, including Omicron.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Rd, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020, Odisha, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156741. [PMID: 35716745 PMCID: PMC9212401 DOI: 10.1016/j.scitotenv.2022.156741] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 05/21/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, 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
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, 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 Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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44
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022:acsestwater.1c00349. [PMID: 35716745 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349&ref=pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, 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
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, 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 Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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45
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Rana R, Kant R, Huirem RS, Bohra D, Ganguly NK. Omicron variant: Current insights and future directions. Microbiol Res 2022; 265:127204. [PMID: 36152612 PMCID: PMC9482093 DOI: 10.1016/j.micres.2022.127204] [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: 07/05/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.
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Affiliation(s)
- Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, Delhi, India.
| | - Ravi Kant
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
| | | | - Deepika Bohra
- Department of Research, Sir Ganga Ram Hospital, Delhi, India
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46
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La Rosa G, Iaconelli M, Veneri C, Mancini P, Bonanno Ferraro G, Brandtner D, Lucentini L, Bonadonna L, Rossi M, Grigioni M, Suffredini E. The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155767. [PMID: 35533857 DOI: 10.5281/zenodo.5985319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 05/25/2023]
Abstract
The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool.
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Affiliation(s)
- G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
| | - M Iaconelli
- 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
| | - G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Rossi
- Independent Researcher, Rome, Italy
| | - M Grigioni
- National Center for Innovative Technologies in 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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47
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La Rosa G, Iaconelli M, Veneri C, Mancini P, Bonanno Ferraro G, Brandtner D, Lucentini L, Bonadonna L, Rossi M, Grigioni M, Suffredini E. The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155767. [PMID: 35533857 PMCID: PMC9074219 DOI: 10.1016/j.scitotenv.2022.155767] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 05/21/2023]
Abstract
The SARS-CoV-2 Omicron variant emerged in South Africa in November 2021, and has later been identified worldwide, raising serious concerns. A real-time RT-PCR assay was designed for the rapid screening of the Omicron variant, targeting characteristic mutations of the spike gene. The assay was used to test 737 sewage samples collected throughout Italy (19/21 Regions) between 11 November and 25 December 2021, with the aim of assessing the spread of the Omicron variant in the country. Positive samples were also tested with a real-time RT-PCR developed by the European Commission, Joint Research Centre (JRC), and through nested RT-PCR followed by Sanger sequencing. Overall, 115 samples tested positive for Omicron SARS-CoV-2 variant. The first occurrence was detected on 7 December, in Veneto, North Italy. Later on, the variant spread extremely fast in three weeks, with prevalence of positive wastewater samples rising from 1.0% (1/104 samples) in the week 5-11 December, to 17.5% (25/143 samples) in the week 12-18, to 65.9% (89/135 samples) in the week 19-25, in line with the increase in cases of infection with the Omicron variant observed during December in Italy. Similarly, the number of Regions/Autonomous Provinces in which the variant was detected increased from one in the first week, to 11 in the second, and to 17 in the last one. The presence of the Omicron variant was confirmed by the JRC real-time RT-PCR in 79.1% (91/115) of the positive samples, and by Sanger sequencing in 66% (64/97) of PCR amplicons. In conclusion, we designed an RT-qPCR assay capable to detect the Omicron variant, which can be successfully used for the purpose of wastewater-based epidemiology. We also described the history of the introduction and diffusion of the Omicron variant in the Italian population and territory, confirming the effectiveness of sewage monitoring as a powerful surveillance tool.
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Affiliation(s)
- G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
| | - M Iaconelli
- 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
| | - G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Rossi
- Independent Researcher, Rome, Italy
| | - M Grigioni
- National Center for Innovative Technologies in 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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48
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Xu A, Hong B, Lou F, Wang S, Li W, Shafqat A, An X, Zhao Y, Song L, Tong Y, Fan H. Sub-lineages of the SARS-CoV-2 Omicron variants: Characteristics and prevention. MedComm (Beijing) 2022; 3:e172. [PMID: 35992968 PMCID: PMC9380698 DOI: 10.1002/mco2.172] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, new variants of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have emerged, accelerating the spread of the virus. Omicron was defined by the World Health Organization in November 2021 as the fifth "variant of concern" after Alpha, Beta, Gamma, and Delta. In recent months, Omicron has become the main epidemic strain. Studies have shown that Omicron carries more mutations than Alpha, Beta, Gamma, Delta, and wild-type, facilitating immune escape and accelerating its transmission. This review focuses on the Omicron variant's origin, transmission, main biological features, subvariants, mutations, immune escape, vaccination, and detection methods. We also discuss the appropriate preventive and therapeutic measures that should be taken to address the new challenges posed by the Omicron variant. This review is valuable to guide the surveillance, prevention, and development of vaccines and other therapies for Omicron variants. It is desirable to develop a more efficient vaccine against the Omicron variant and take more effective measures to constrain the spread of the epidemic and promote public health.
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Affiliation(s)
- Ailan Xu
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Bixia Hong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Fuxing Lou
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Shuqi Wang
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Wenye Li
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Amna Shafqat
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Xiaoping An
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yunwei Zhao
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Lihua Song
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yigang Tong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Huahao Fan
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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49
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Blumenfeld NR, Bolene MAE, Jaspan M, Ayers AG, Zarrandikoetxea S, Freudman J, Shah N, Tolwani AM, Hu Y, Chern TL, Rogot J, Behnam V, Sekhar A, Liu X, Onalir B, Kasumi R, Sanogo A, Human K, Murakami K, Totapally GS, Fasciano M, Sia SK. Multiplexed reverse-transcriptase quantitative polymerase chain reaction using plasmonic nanoparticles for point-of-care COVID-19 diagnosis. NATURE NANOTECHNOLOGY 2022; 17:984-992. [PMID: 35879456 DOI: 10.1038/s41565-022-01175-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) offers the capabilities of real-time monitoring of amplified products, fast detection, and quantitation of infectious units, but poses technical hurdles for point-of-care miniaturization compared with end-point polymerase chain reaction. Here we demonstrate plasmonic thermocycling, in which rapid heating of the solution is achieved via infrared excitation of nanoparticles, successfully performing reverse-transcriptase qPCR (RT-qPCR) in a reaction vessel containing polymerase chain reaction chemistry, fluorescent probes and plasmonic nanoparticles. The method could rapidly detect SARS-CoV-2 RNA from human saliva and nasal specimens with 100% sensitivity and 100% specificity, as well as two distinct SARS-CoV-2 variants. The use of small optical components for both thermocycling and multiplexed fluorescence monitoring renders the instrument amenable to point-of-care use. Overall, this study demonstrates that plasmonic nanoparticles with compact optics can be used to achieve real-time and multiplexed RT-qPCR on clinical specimens, towards the goal of rapid and accurate molecular clinical diagnostics in decentralized settings.
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Affiliation(s)
- Nicole R Blumenfeld
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | - Michael Anne E Bolene
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | | | - Abigail G Ayers
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Sabin Zarrandikoetxea
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | | | - Nikhil Shah
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | - Angela M Tolwani
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | - Yuhang Hu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | - Terry L Chern
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Vira Behnam
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Aditya Sekhar
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Xinyi Liu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Rover Diagnostics, New York, NY, USA
| | | | - Robert Kasumi
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Abdoulaye Sanogo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kelia Human
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kasey Murakami
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Goutham S Totapally
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Samuel K Sia
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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50
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Le Targa L, Wurtz N, Lacoste A, Penant G, Jardot P, Annessi A, Colson P, La Scola B, Aherfi S. SARS-CoV-2 Testing of Aircraft Wastewater Shows That Mandatory Tests and Vaccination Pass before Boarding Did Not Prevent Massive Importation of Omicron Variant into Europe. Viruses 2022; 14:1511. [PMID: 35891491 PMCID: PMC9319773 DOI: 10.3390/v14071511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Most new SARS-CoV-2 epidemics in France occurred following the importation from abroad of emerging viral variants. Currently, the risk of new variants being imported is controlled based on a negative screening test (PCR or antigenic) and proof of up-to-date vaccine status, such as the International Air Transport Association travel pass. METHODS The wastewater from two planes arriving in Marseille (France) from Addis Ababa (Ethiopia) in December 2021 was tested by RT-PCR to detect SARS-CoV2 and screen for variants. These tests were carried out between landing and customs clearance and were then sequenced by MiSeq Illumina. Antigenic tests and sequencing by NovaSeq were carried out on respiratory samples collected from the 56 passengers on the second flight. RESULTS SARS-CoV-2 RNA suspected of being from the Omicron BA.1 variant was detected in the aircraft's wastewater. SARS-CoV2 RNA was detected in 11 [20%) passengers and the Omicron BA.1 variant was identified. CONCLUSION Our work shows the efficiency of aircraft wastewater testing to detect SARS-CoV-2 cases among travellers and to identify the viral genotype. It also highlights the low efficacy of the current control strategy for flights entering France from outside Europe, which combines a requirement to produce a vaccine pass and proof of a negative test before boarding.
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Affiliation(s)
- Lorlane Le Targa
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Biosellal, 27 Chemin des Peupliers, 69570 Lyon, France
| | - Nathalie Wurtz
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Gwilherm Penant
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Priscilla Jardot
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Annessi
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Philippe Colson
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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