1
|
Chai X, Liu S, Liu C, Bai J, Meng J, Tian H, Han X, Han G, Xu X, Li Q. Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China. Emerg Microbes Infect 2024; 13:2324502. [PMID: 38465692 DOI: 10.1080/22221751.2024.2324502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19 outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.
Collapse
Affiliation(s)
- Xiaoru Chai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Shiyou Liu
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Chao Liu
- Shijiazhuang Qiaodong Sewage Treatment Plant, Shijiazhuang, People's Republic of China
| | - Jiaxuan Bai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Juntao Meng
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xu Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Guangyue Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xiangdong Xu
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, People's Republic of China
| | - Qi Li
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| |
Collapse
|
2
|
Aravind Kumar N, Aradhana S, Harleen, Vishnuraj MR. SARS-CoV-2 in digital era: Diagnostic techniques and importance of nucleic acid quantification with digital PCRs. Rev Med Virol 2023; 33:e2471. [PMID: 37529971 DOI: 10.1002/rmv.2471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Studies related to clinical diagnosis and research of SARS-CoV-2 are important in the current pandemic era. Although molecular biology has emphasised the importance of qualitative analysis, quantitative analysis with nucleic acids in relation to SARS-CoV-2 needs to be clearly emphasised, which can provide perspective for viral dynamic studies of SARS-CoV-2. In this regard, the requirement and utilization of digital PCR in COVID-19 research has substantially increased during the pandemic, necessitating the aggregation of its cardinal applications and future scopes. Hence, this meta-review comprehensively addresses and emphasises the importance of nucleic acid quantification of SARS-CoV-2 RNA with digital PCR (dPCR). Various quantitative techniques of clinical significance like immunological, proteomic and nucleic acid-based diagnosis and quantification, have been comparatively discussed. Furthermore, the core part of the article focusses on the working principle and advantages of digital PCR, along with its applications in COVID-19 research. Several important applications like viral load quantitation, environmental surveillance and assay validation have been extensively investigated and discussed. Certain key future scopes of clinical importance, like mortality prediction, viral/variant-symbiosis, and antiviral studies were also identified, suggesting several possible digital PCR applications in COVID-19 research.
Collapse
Affiliation(s)
- N Aravind Kumar
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| | - S Aradhana
- Department of Biotechnology, School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Harleen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - M R Vishnuraj
- Meat Species Identification Laboratory, ICAR - National Meat Research Institute, Hyderabad, Telangana, India
| |
Collapse
|
3
|
Guterres A. Viral load: We need a new look at an old problem? J Med Virol 2023; 95:e29061. [PMID: 37638475 DOI: 10.1002/jmv.29061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The concept of viral load was introduced in the 1980s to measure the amount of viral genetic material in a person's blood, primarily for human immunodeficiency virus (HIV). It has since become crucial for monitoring HIV infection progression and assessing the efficacy of antiretroviral therapy. However, during the coronavirus disease 2019 pandemic, the term "viral load" became widely popularized, not only for the scientific community but for the general population. Viral load plays a critical role in both clinical patient management and research, providing valuable insights for antiviral treatment strategies, vaccination efforts, and epidemiological control measures. As measuring viral load is so important, why don't researchers discuss the best way to do it? Is it simply acceptable to use raw Ct values? Relying solely on Ct values for viral load estimation can be problematic due to several reasons. First, Ct values can vary between different quantitative polymerase chain reaction assays, platforms, and laboratories, making it difficult to compare data across studies. Second, Ct values do not directly measure the quantity of viral particles in a sample and they can be influenced by various factors such as initial viral load, sample quality, and assay sensitivity. Moreover, variations in viral RNA extraction and reverse-transcription steps can further impact the accuracy of viral load estimation, emphasizing the need for careful interpretation of Ct values in viral load assessment. Interestingly, we did not observe scientific articles addressing different strategies to quantify viral load. The absence of standardized and validated methods impedes the implementation of viral load monitoring in clinical management. The variability in cell quantities within samples and the variation in viral particle numbers within infected cells further challenge accurate viral load measurement and interpretation. To advance the field and improve patient outcomes, there is an urgent need for the development and validation of tailored, standardized methods for precise viral load quantification.
Collapse
Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| |
Collapse
|
4
|
Shinde M, Lavania M, Rawal J, Chavan N, Shinde P. Evaluation of droplet digital qRT-PCR (dd qRT-PCR) for quantification of SARS CoV-2 RNA in stool and urine specimens of COVID-19 patients. Front Med (Lausanne) 2023; 10:1148688. [PMID: 37469662 PMCID: PMC10352106 DOI: 10.3389/fmed.2023.1148688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction There have been a few reports of viral load detection in stool and urine samples of patients with coronavirus disease 2019 (COVID-19), and the transmission of the virus through faecal oral route. For clinical diagnosis and treatment, the widely used reverse transcription-polymerase chain reaction (qRT-PCR) method has some limitations. Methods The aim of our study to assess the presence and concentration of SARS CoV-2 RNA in stool and urine samples from COVID-19 patients with mild, moderate, and severe disease, we compared a traditional qRT-PCR approach with a ddPCR. ddPCR and qRT-PCR-based target gene analysis were performed on 107 COVID-19-confirmed patients paired samples (N1 and N2). The MagMax magnetic beads base method was used to isolate RNA. Real-time qRT-PCR and dd PCR were performed on all patients. Results and Discussion The average cycle threshold (Ct) of qRT-PCR was highly correlated with the average copy number of 327.10 copies/l analyzed in ddPCR. In ddPCR, urine samples showed 27.1% positivity while for stool it was 100%. Conclusion This study's findings not only show that SARS CoV-2 is present in urine and faeces, but also suggest that low concentrations of the viral target ddPCR make it easier to identify positive samples and help resolve for cases of inconclusive diagnosis.
Collapse
|
5
|
Comparison of RT-qPCR and RT-ddPCR with Rift valley fever virus (RVFV) RNA. Sci Rep 2023; 13:3085. [PMID: 36813787 PMCID: PMC9944419 DOI: 10.1038/s41598-023-29023-y] [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: 10/17/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Rift valley fever (RVF) is an important zoonotic disease caused by the Rift valley fever virus (RVFV) which can affect ruminants and humans. In this study, a comparison was done of the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription-droplet digital PCR (RT-ddPCR) assays with synthesized RVFV RNA, cultured viral RNA, and mock clinical RVFV RNA samples. The genomic segments (L, M, and S) of three RVFV strains (BIME01, Kenya56, and ZH548) were synthesized and used as templates for in vitro transcription (IVT). Both the RT-qPCR and RT-ddPCR assays for RVFV did not react with any of the negative reference viral genomes. Thus, both the RT-qPCR and RT-ddPCR assays are specific to RVFV. The comparison of both the RT-qPCR and RT-ddPCR assays with serially diluted templates showed that the LoD of both assays are similar, and a concordant of the results was observed. The LoD of both assays reached the practical measurable minimum concentration. Taken altogether, the sensitivity of the RT-qPCR and RT-ddPCR assays is similar, and the material measured by RT-ddPCR can be used as a reference material for RT-qPCR.
Collapse
|
6
|
Pandey SK, Mohanta GC, Kumar V, Gupta K. Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection. Vaccines (Basel) 2022; 10:1200. [PMID: 36016088 PMCID: PMC9414050 DOI: 10.3390/vaccines10081200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.
Collapse
Affiliation(s)
- Satish Kumar Pandey
- Department of Biotechnology, School of Life Sciences, Mizoram University (Central University), Aizawl 796004, India
| | - Girish C. Mohanta
- Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh 160030, India;
| | - Vinod Kumar
- Department of Dermatology, Venerology and Leprology, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Kuldeep Gupta
- Russel H. Morgan, Department of Radiology and Radiological Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| |
Collapse
|
7
|
Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
Collapse
Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
| |
Collapse
|
8
|
Torres A, Motos A, Ceccato A, Bermejo-Martin J, de Gonzalo-Calvo D, Pérez R, Barroso M, Pascual IZ, Gonzalez J, Fernández-Barat L, Ferrer R, Riera J, García-Gasulla D, Peñuelas O, Lorente JÁ, Almansa R, Menéndez R, Kiarostami K, Canseco J, Villar RA, Añón JM, Mariño AB, Barberà C, Barberán J, Ortiz AB, Boado MV, Bustamante-Munguira E, Caballero J, Cantón-Bulnes ML, Pérez CC, Carbonell N, Catalán-González M, de Frutos R, Franco N, Galbán C, Gumucio-Sanguino VD, Torre MDCDL, Díaz E, Estella Á, Gallego E, Garmendia JLG, Gómez JM, Huerta A, García RNJ, Loza-Vázquez A, Marin-Corral J, Delgado MCM, Gándara AMDL, Varela IM, Messa JL, Albaiceta GM, Nieto M, Novo MA, Peñasco Y, Pérez-García F, Pozo-Laderas JC, Ricart P, Sagredo V, Sánchez-Miralles Á, Chinesta SS, Serra-Fortuny M, Socias L, Solé-Violan J, Suárez-Sipmann F, Lomas LT, Trenado J, Úbeda A, Valdivia LJ, Vidal P, Barbé F. Methodology of a Large Multicenter Observational Study of Patients with COVID-19 in Spanish Intensive Care Units. Arch Bronconeumol 2022; 58 Suppl 1:22-31. [PMID: 35491287 PMCID: PMC9012512 DOI: 10.1016/j.arbres.2022.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/17/2023]
Abstract
INTRODUCTION The COVID-19 pandemic created tremendous challenges for health-care systems. Intensive care units (ICU) were hit with a large volume of patients requiring ICU admission, mechanical ventilation, and other organ support with very high mortality. The Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES), a network of Spanish researchers to investigate in respiratory disease, commissioned the current proposal in response to the Instituto de Salud Carlos III (ISCIII) call. METHODS CIBERESUCICOVID is a multicenter, observational, prospective/retrospective cohort study of patients with COVID-19 admitted to Spanish ICUs. Several work packages were created, including study population and ICU data collection, follow-up, biomarkers and miRNAs, data management and quality. RESULTS This study included 6102 consecutive patients admitted to 55 ICUs homogeneously distributed throughout Spain and the collection of blood samples from more than 1000 patients. We enrolled a large population of COVID-19 ICU-admitted patients including baseline characteristics, ICU and MV data, treatments complications, and outcomes. The in-hospital mortality was 31%, and 76% of patients required invasive mechanical ventilation. A 3-6 month and 1 year follow-up was performed. Few deaths after 1 year discharge were registered. Low anti-SARS-CoV-2 S antibody levels predict mortality in critical COVID-19. These antibodies contribute to prevent systemic dissemination of SARS-CoV-2. The severity of COVID-19 impacts the circulating miRNA profile. Plasma miRNA profiling emerges as a useful tool for risk-based patient stratification in critically ill COVID-19 patients. CONCLUSIONS We present the methodology used in a large multicenter study sponsored by ISCIII to determine the short- and long-term outcomes in patients with COVID-19 admitted to more than 50 Spanish ICUs.
Collapse
Affiliation(s)
- Antoni Torres
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Anna Motos
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Adrián Ceccato
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Jesús Bermejo-Martin
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
| | - David de Gonzalo-Calvo
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Translational Research in Respiratory Medicine, Respiratory Department, Hospital Universitari Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Raquel Pérez
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | - Marta Barroso
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
| | | | - Jessica Gonzalez
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain; Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain; Intensive Care Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain; Barcelona Supercomputing Centre (BSC), Barcelona, Spain; Hospital Universitario de Getafe, Universidad Europea, Madrid, Spain; Translational Research in Respiratory Medicine, Respiratory Department, Hospital Universitari Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Laia Fernández-Barat
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ricard Ferrer
- Intensive Care Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Jordi Riera
- Intensive Care Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | | | - Oscar Peñuelas
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Hospital Universitario de Getafe, Universidad Europea, Madrid, Spain
| | - José Ángel Lorente
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Hospital Universitario de Getafe, Universidad Europea, Madrid, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Rosario Menéndez
- Pulmonary Department, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Kasra Kiarostami
- Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Joan Canseco
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Department of Pneumology, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Research Institute-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Rosario Amaya Villar
- Intensive Care Clinical Unit, Hospital Universitario Virgen de Rocío, Sevilla, Spain
| | - José M Añón
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Servicio de Medicina Intensiva, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | | | | | - José Barberán
- Hospital Universitario HM Montepríncipe, Universidad San Pablo-CEU, Madrid, Spain
| | - Aaron Blandino Ortiz
- Servicio de Medicina Intensiva, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Elena Bustamante-Munguira
- Department of Intensive Care Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Jesús Caballero
- Critical Care Department, Hospital Universitari Arnau de Vilanova, IRBLleida, Lleida, Spain
| | | | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | | | - Raúl de Frutos
- Servicio de Anestesiología y Reanimación, Hospital Universitario de Basurto, Bilbao, Vizcaya, Spain
| | | | - Cristóbal Galbán
- Department of Medicine, CHUS, Complejo Hospitalario Universitario de Santiago, Santiago de Compostela, A Coruña, Spain
| | - Víctor D Gumucio-Sanguino
- Department of Intensive Care, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | - Emili Díaz
- Critical Care Department, Corporació Sanitària Parc Taulí, Department of Medicine, Universitat Autònoma de Barcelona (UAB), Sabadell, Barcelona, Spain
| | - Ángel Estella
- Departamento de Medicina, Facultad de Medicina, Universidad de Cádiz, Hospital Universitario de Jerez, Jerez de la Frontera, Cádiz, Spain
| | - Elena Gallego
- Unidad de Cuidados Intensivos, Hospital Universitario San Pedro de Alcántara, Cáceres, Spain
| | | | - José M Gómez
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Arturo Huerta
- Pulmonary and Critical Care Division, Emergency Department, Clínica Sagrada Família, Barcelona, Spain
| | | | - Ana Loza-Vázquez
- Unidad de Medicina Intensiva, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | | | | | | | | | | | - Guillermo M Albaiceta
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias, Hospital Central de Asturias, Oviedo, Asturias, Spain
| | - Maite Nieto
- Hospital Universitario de Segovia, Segovia, Spain
| | - Mariana Andrea Novo
- Servei de Medicina Intensiva, Hospital Universitari Son Espases, Palma de Mallorca, Illes Balears, Spain
| | - Yhivian Peñasco
- Servicio de Medicina Intensiva, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, Spain
| | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Departamento de Biomedicina y Biotecnología, Universidad de Alcalá de Henares, Madrid, Spain
| | - Juan Carlos Pozo-Laderas
- UGC-Medicina Intensiva, Hospital Universitario Reina Sofía, Instituto Maimónides IMIBIC, Córdoba, Spain
| | - Pilar Ricart
- Servei de Medicina Intensiva, Hospital Universitari Germans Trias, Badalona, Barcelona, Spain
| | | | | | - Susana Sancho Chinesta
- Servicio de Medicina Intensiva, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Lorenzo Socias
- Intensive Care Unit, Hospital Son Llàtzer, Palma de Mallorca, Illes Balears, Spain
| | - Jordi Solé-Violan
- Critical Care Department, Hospital de Gran Canaria Dr. Negrín, Las Palmas, Spain
| | | | - Luis Tamayo Lomas
- Critical Care Department, Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain
| | - José Trenado
- Servicio de Medicina Intensiva, Hospital Universitario Mútua de Terrassa, Terrassa, Barcelona, Spain
| | - Alejandro Úbeda
- Servicio de Medicina Intensiva, Hospital Punta de Europa, Algeciras, Cádiz, Spain
| | | | - Pablo Vidal
- Complexo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Ferran Barbé
- CIBER de Enfermedades Respiratorias (CIBERES), Spain; Translational Research in Respiratory Medicine, Respiratory Department, Hospital Universitari Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | | |
Collapse
|
9
|
Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [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: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
Collapse
Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| |
Collapse
|
10
|
Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
Collapse
Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| |
Collapse
|
11
|
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
Collapse
|
12
|
Luo X, Xue Y, Ju E, Tao Y, Li M, Zhou L, Yang C, Zhou J, Wang J. Digital CRISPR/Cas12b-based platform enabled absolute quantification of viral RNA. Anal Chim Acta 2022; 1192:339336. [PMID: 35057952 DOI: 10.1016/j.aca.2021.339336] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/07/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022]
Abstract
Early and accurate diagnosis of viruses is critical for control of the pandemic. CRISPR/Cas-based detection of nucleic acid is an emerging technology for molecular diagnostics, and has been applied for virus detection. Though these methods have excellent sensitivity and specificity, most of them were not able to measure the quantity of virus. We here developed a droplet digital reverse transcription loop-mediated isothermal amplification (RT-LAMP) enhanced Cas12b-based RNA detection platform (RECD), for quantitative detection of viral RNA. CRISPR/Cas12b, which is more thermally stable than other family members in CRISPR systems, is combined with digital RT-LAMP. Due to the innate characteristic of digital format detection and CRISPR/Cas system, droplet digital RECD (ddRECD) assay enables absolute quantification of viral RNA, with single-molecule sensitivity. We expect the ddRECD assay will be a powerful tool for molecular diagnostics.
Collapse
Affiliation(s)
- Xinyi Luo
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yingying Xue
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Enguo Ju
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Chongguang Yang
- School of Public Health, Sun Yat-sen University (Shenzhen), Shenzhen, 518107, China
| | - Jianhua Zhou
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China; Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, China.
| | - Jiasi Wang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China; Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, China.
| |
Collapse
|
13
|
Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 34818780 DOI: 10.20944/preprints202104.0481.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
Collapse
Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| |
Collapse
|
14
|
Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
Collapse
Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| |
Collapse
|
15
|
Neagu M, Constantin C, Surcel M. Testing Antigens, Antibodies, and Immune Cells in COVID-19 as a Public Health Topic—Experience and Outlines. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182413173. [PMID: 34948782 PMCID: PMC8700871 DOI: 10.3390/ijerph182413173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022]
Abstract
The current COVID-19 pandemic has triggered an accelerated pace in all research domains, including reliable diagnostics methodology. Molecular diagnostics of the virus and its presence in biological samples relies on the RT-PCR method, the most used and validated worldwide. Nonconventional tests with improved parameters that are in the development stages will be presented, such as droplet digital PCR or CRISPR-based assays. These molecular tests were followed by rapid antigen testing along with the development of antibody tests, whether based on ELISA platform or on a chemiluminescent microparticle immunoassay. Less-conventional methods of testing antibodies (e.g., lateral flow immunoassay) are presented as well. Left somewhere in the backstage of COVID-19 research, immune cells and, furthermore, immune memory cells, are gaining the spotlight, more so in the vaccination context. Recently, methodologies using flow-cytometry evaluate circulating immune cells in infected/recovered patients. The appearance of new virus variants has triggered a surge for tests improvement. As the pandemic has entered an ongoing or postvaccination era, all methodologies that are used to monitor public health focus on diagnostic strategies and this review points out where gaps should be filled in both clinical and research settings.
Collapse
Affiliation(s)
- Monica Neagu
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
- Pathology Department, Colentina University Hospital, 19-21 Șoseaua Ștefan cel Mare, 020125 Bucharest, Romania
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, 91-93 Splaiul Independentei, 050095 Bucharest, Romania
| | - Carolina Constantin
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
- Pathology Department, Colentina University Hospital, 19-21 Șoseaua Ștefan cel Mare, 020125 Bucharest, Romania
- Correspondence:
| | - Mihaela Surcel
- Immunology Laboratory, Victor Babes National Institute of Pathology, 99-101 Splaiul Independentei, 050096 Bucharest, Romania; (M.N.); (M.S.)
| |
Collapse
|
16
|
Ishak A, AlRawashdeh MM, Esagian SM, Nikas IP. Diagnostic, Prognostic, and Therapeutic Value of Droplet Digital PCR (ddPCR) in COVID-19 Patients: A Systematic Review. J Clin Med 2021; 10:5712. [PMID: 34884414 PMCID: PMC8658157 DOI: 10.3390/jcm10235712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Accurate detection of SARS-CoV-2, the pathogen causing the global pandemic of COVID-19, is essential for disease surveillance and control. Quantitative reverse transcription PCR (RT-qPCR) is considered the reference standard test for the diagnosis of SARS-CoV-2 by the World Health Organization and Centers for Disease Control and Prevention. However, its limitations are a prompt for a more accurate assay to detect SARS-CoV-2, quantify its levels, and assess the prognosis. This article aimed to systematically review the literature and assess the diagnostic performance of droplet digital PCR (ddPCR), also to evaluate its potential role in prognosis and management of COVID-19 patients. PubMed and Scopus databases were searched to identify relevant articles published until 13 July 2021. An additional PubMed search was performed on 21 October 2021. Data from the 39 eligible studies were extracted and an overall 3651 samples from 2825 patients and 145 controls were used for our qualitative analysis. Most studies reported ddPCR was more accurate than RT-qPCR in detecting and quantifying SARS-CoV-2 levels, especially in patients with low viral loads. ddPCR was also found highly effective in quantifying SARS-CoV-2 RNAemia levels in hospitalized patients, monitoring their disease course, and predicting their response to therapy. These findings suggest ddPCR could serve as a complement or alternative SARS-CoV-2 tool with emerging diagnostic, prognostic, and therapeutic value, especially in hospital settings. Additional research is still needed to standardize its laboratory protocols, also to accurately assess its role in monitoring COVID-19 therapy response and in identifying SARS-CoV-2 emerging variants.
Collapse
Affiliation(s)
- Angela Ishak
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Mousa M. AlRawashdeh
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Stepan M. Esagian
- Jacobi Medical Center, Department of Medicine, Albert Einstein College of Medicine, The Bronx, New York, NY 10461, USA;
| | - Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| |
Collapse
|
17
|
Niu C, Wang X, Zhang Y, Lu L, Wang D, Gao Y, Wang S, Luo J, Jiang Y, Wang N, Guo Y, Zhu L, Dong L. Interlaboratory assessment of quantification of SARS-CoV-2 RNA by reverse transcription digital PCR. Anal Bioanal Chem 2021; 413:7195-7204. [PMID: 34697653 PMCID: PMC8545465 DOI: 10.1007/s00216-021-03680-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/06/2021] [Accepted: 09/20/2021] [Indexed: 01/23/2023]
Abstract
The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused severe harm to the health of people all around the world. Molecular detection of the pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), played a crucial role in the control of the disease. Reverse transcription digital PCR (RT-dPCR) has been developed and used in the detection of SARS-CoV-2 RNA as an absolute quantification method. Here, an interlaboratory assessment of quantification of SARS-CoV-2 RNA was organized by the National Institute of Metrology, China (NIMC), using in vitro transcribed RNA samples, among ten laboratories on six different dPCR platforms. Copy number concentrations of three genes of SARS-CoV-2 were measured by all participants. Consistent results were obtained with dispersion within 2.2-fold and CV% below 23% among different dPCR platforms and laboratories, and Z′ scores of all the reported results being satisfactory. Possible reasons for the dispersion included PCR assays, partition volume, and reverse transcription conditions. This study demonstrated the comparability and applicability of RT-dPCR method for quantification of SARS-CoV-2 RNA and showed the capability of the participating laboratories at SARS-CoV-2 test by RT-dPCR platform.
Collapse
Affiliation(s)
- Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Lin Lu
- Center for Reference Materials Research and Management (Office of National Research Center for Certified Reference Materials), National Institute of Metrology, Beijing, China
| | - Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Shangjun Wang
- Biological Metrology Center, Nanjing Institute of Measurement and Testing Technology, Nanjing, China
| | - Jingyan Luo
- R & D Department, Guangdong Forevergen Medical Technology Co., Ltd, Foshan, China
| | - Ying Jiang
- R & D Department, Mission Medical Technologies (Ningbo) Co., Ltd, Ningbo, China
| | - Nuo Wang
- Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | | | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
| |
Collapse
|