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Zheng X, Wang M, Deng Y, Xu X, Lin D, Zhang Y, Li S, Ding J, Shi X, Yau CI, Poon LLM, Zhang T. A rapid, high-throughput, and sensitive PEG-precipitation method for SARS-CoV-2 wastewater surveillance. Water Res 2023; 230:119560. [PMID: 36623382 PMCID: PMC9803703 DOI: 10.1016/j.watres.2022.119560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The effective application of wastewater surveillance is dependent on testing capacity and sensitivity to obtain high spatial resolution testing results for a timely targeted public health response. To achieve this purpose, the development of rapid, high-throughput, and sensitive virus concentration methods is urgently needed. Various protocols have been developed and implemented in wastewater surveillance networks so far, however, most of them lack the ability to scale up testing capacity or cannot achieve sufficient sensitivity for detecting SARS-CoV-2 RNA at low prevalence. In the present study, using positive raw wastewater in Hong Kong, a PEG precipitation-based three-step centrifugation method was developed, including low-speed centrifugation for large particles removal and the recovery of viral nucleic acid, and medium-speed centrifugation for the concentration of viral nucleic acid. This method could process over 100 samples by two persons per day to reach the process limit of detection (PLoD) of 3286 copies/L wastewater. Additionally, it was found that the testing capacity could be further increased by decreasing incubation and centrifugation time without significantly influencing the method sensitivity. The entire procedure uses ubiquitous reagents and instruments found in most laboratories to obtain robust testing results. This high-throughput, cost-effective, and sensitive tool will promote the establishment of nearly real-time wastewater surveillance networks for valuable public health information.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Mengying Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Danxi Lin
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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2
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Zheng X, Li S, Deng Y, Xu X, Ding J, Lau FTK, In Yau C, Poon LLM, Tun HM, Zhang T. Quantification of SARS-CoV-2 RNA in wastewater treatment plants mirrors the pandemic trend in Hong Kong. Sci Total Environ 2022; 844:157121. [PMID: 35787900 PMCID: PMC9249664 DOI: 10.1016/j.scitotenv.2022.157121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/12/2022] [Accepted: 06/28/2022] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) for the SARS-CoV-2 virus in wastewater treatment plants (WWTPs) has emerged as a cost-effective and unbiased tool for population-level testing in the community. In the present study, we conducted a 6-month wastewater monitoring campaign from three WWTPs of different flow rates and catchment area characteristics, which serve 28 % (2.1 million people) of Hong Kong residents in total. Wastewater samples collected daily or every other day were concentrated using ultracentrifugation and the SARS-CoV-2 virus RNA in the supernatant was detected using the N1 and E primer sets. The results showed significant correlations between the virus concentration and the number of daily new cases in corresponding catchment areas of the three WWTPs when using 7-day moving average values (Kendall's tau-b value: 0.227-0.608, p < 0.001). SARS-CoV-2 virus concentration was normalized to a fecal indicator using PMMoV concentration and daily flow rates, but the normalization did not enhance the correlation. The key factors contributing to the correlation were also evaluated, including the sampling frequency, testing methods, and smoothing days. This study demonstrates the applicability of wastewater surveillance to monitor overall SARS-CoV-2 pandemic dynamics in a densely populated city like Hong Kong, and provides a large-scale longitudinal reference for the establishment of the long-term sentinel surveillance in WWTPs for WBE of pathogens which could be combined into a city-wide public health observatory.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Frankie T K Lau
- Drainage Services Department, The Government of the Hong Kong Special Administrative Region of the People's Republic of China, Wanchai, Hong Kong, China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Hein M Tun
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Xu X, Deng Y, Zheng X, Li S, Ding J, Yang Y, On HY, Yang R, Chui HK, Yau CI, Tun HM, Chin AWH, Poon LLM, Peiris M, Leung GM, Zhang T. Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests. Environ Sci Technol 2022; 56:8875-8884. [PMID: 35584232 PMCID: PMC9128008 DOI: 10.1021/acs.est.2c00974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per μL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Hei Yin On
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Rong Yang
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Ho-Kwong Chui
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Hein Min Tun
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Alex W. H. Chin
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Gabriel M. Leung
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
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4
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Zheng X, Deng Y, Xu X, Li S, Zhang Y, Ding J, On HY, Lai JCC, In Yau C, Chin AWH, Poon LLM, Tun HM, Zhang T. Comparison of virus concentration methods and RNA extraction methods for SARS-CoV-2 wastewater surveillance. Sci Total Environ 2022; 824:153687. [PMID: 35134418 PMCID: PMC8816846 DOI: 10.1016/j.scitotenv.2022.153687] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/16/2022] [Accepted: 02/01/2022] [Indexed: 05/02/2023]
Abstract
Wastewater surveillance is a promising tool for population-level monitoring of the spread of infectious diseases, such as the coronavirus disease 2019 (COVID-19). Different from clinical specimens, viruses in community-scale wastewater samples need to be concentrated before detection because viral RNA is highly diluted. The present study evaluated eleven different virus concentration methods for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. First, eight concentration methods of different principles were compared using spiked wastewater at a starting volume of 30 mL. Ultracentrifugation was the most effective method with a viral recovery efficiency of 25 ± 6%. The second-best option, AlCl3 precipitation method, yielded a lower recovery efficiency, only approximately half that of the ultracentrifugation method. Second, the potential of increasing method sensitivity was explored using three concentration methods starting with a larger volume of 1000 mL. Although ultracentrifugation using a large volume outperformed the other two large-volume methods, it only yielded a comparable method sensitivity as the ultracentrifugation using a small volume (30 mL). Thus, ultracentrifugation using less volume of wastewater is more preferable considering the sample processing throughput. Third, a comparison of two viral RNA extraction methods showed that the lysis-buffer-based extraction method resulted in higher viral recovery efficiencies, with cycle threshold (Ct) values 0.9-4.2 lower than those obtained for the acid-guanidinium-phenol-based method using spiked samples. These results were further confirmed by using positive wastewater samples concentrated by ultracentrifugation and extracted separately by the two viral RNA extraction methods. In summary, concentration using ultracentrifugation followed by the lysis buffer-based extraction method enables sensitive and robust detection of SARS-CoV-2 for wastewater surveillance.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hei Yin On
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Jimmy C C Lai
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Chung In Yau
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Hein M Tun
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong, China; HKU-Pasteur Research Pole, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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5
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Tam JCW, Chan YM, Tsang SY, Yau CI, Yeung SY, Au KK, Chow CK. Cover Image. Prenat Diagn 2020. [DOI: 10.1002/pd.5681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Yee Man Chan
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
| | - Shui Ying Tsang
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
| | - Chung In Yau
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
| | - Shuk Ying Yeung
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
| | - Ka Ki Au
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
| | - Chun Kin Chow
- Department of R&D, Medtimes Medical Group Limited Kwai Chung Hong Kong
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Tam JCW, Chan YM, Tsang SY, Yau CI, Yeung SY, Au KK, Chow CK. Noninvasive prenatal paternity testing by means of SNP-based targeted sequencing. Prenat Diagn 2020; 40:497-506. [PMID: 31674029 PMCID: PMC7154534 DOI: 10.1002/pd.5595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
Objective To develop a method for noninvasive prenatal paternity testing based on targeted sequencing of single nucleotide polymorphisms (SNPs). Method SNPs were selected based on population genetics data. Target‐SNPs in cell‐free DNA extracted from maternal blood (maternal cfDNA) were analyzed by targeted sequencing wherein target enrichment was based on multiplex amplification using QIAseq Targeted DNA Panels with Unique Molecular Identifiers. Fetal SNP genotypes were called using a novel bioinformatics algorithm, and the combined paternity indices (CPIs) and resultant paternity probabilities were calculated. Results Fetal SNP genotypes obtained from targeted sequencing of maternal cfDNA were 100% concordant with those from amniotic fluid‐derived fetal genomic DNA. From an initial panel of 356 target‐SNPs, an average of 148 were included in paternity calculations in 15 family trio cases, generating paternity probabilities of greater than 99.9999%. All paternity results were confirmed by short‐tandem‐repeat analysis. The high specificity of the methodology was validated by successful paternity discrimination between biological fathers and their siblings and by large separations between the CPIs calculated for the biological fathers and those for 60 unrelated men. Conclusion The novel method is highly effective, with substantial improvements over similar approaches in terms of reduced number of target‐SNPs, increased accuracy, and reduced costs.
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Affiliation(s)
| | - Yee Man Chan
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shui Ying Tsang
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chung In Yau
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shuk Ying Yeung
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Ka Ki Au
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chun Kin Chow
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
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