1
|
Paradis S, Van Der Pol B, Kaatz NA, Davis TE, Ledeboer NA, Faron ML, Laviers W, Lockamy E, Yanson KA. Clinical Performance of the BD Respiratory Viral Panel for BD MAX™ System in Detecting SARS-CoV-2, Influenza A and B, and Respiratory Syncytial Virus. Diagn Microbiol Infect Dis 2024; 110:116482. [PMID: 39142094 DOI: 10.1016/j.diagmicrobio.2024.116482] [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: 05/23/2024] [Revised: 07/18/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
Using a nasopharyngeal (NP) or anterior nasal (NS) swab from prospectively collected or retrospective specimens, we assessed the clinical performance of the BD Respiratory Viral Panel (BD RVP) for BD MAX System against FDA-cleared or authorized comparators. Across prospective and retrospective specimens, positive percent agreement (PPA) was ≥ 98.4% for SARS-CoV-2, ≥ 96.7% for influenza (flu) A, ≥ 91.7% for respiratory syncytial virus (RSV), and 100% for flu B (retrospective only) while negative percent agreement (NPA) was ≥ 97.7% across all targets, leading to the assay FDA clearance. A head-to-head comparison of NS versus NP results with BD RVP was also performed; PPA was ≥ 90% and NPA ≥ 98.2% for SARS-CoV-2, flu A and RSV. These findings confirm that the BD MAX RVP assay performs well for detection and differentiation of the three viruses in NP and NS specimens, with strong interrater agreements for NS versus NP comparisons.
Collapse
Affiliation(s)
- Sonia Paradis
- Becton, Dickinson and Company, BD Life Sciences - Diagnostic Solutions, 2100 Derry Rd. West, #100, Mississauga, Ontario, Canada.
| | - Barbara Van Der Pol
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Thomas E Davis
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nathan A Ledeboer
- The Medical College of Wisconsin, Department of Pathology and Laboratory Medicine, Milwaukee, WI, USA
| | - Matthew L Faron
- The Medical College of Wisconsin, Department of Pathology and Laboratory Medicine, Milwaukee, WI, USA
| | - William Laviers
- Becton, Dickinson and Company, BD Life Sciences - Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA
| | - Elizabeth Lockamy
- Becton, Dickinson and Company, BD Life Sciences - Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA
| | - Karen A Yanson
- Becton, Dickinson and Company, BD Life Sciences - Diagnostic Solutions, 7 Loveton Circle, Sparks, MD, USA
| |
Collapse
|
2
|
Islam ANMS, Farhana N, Choudhury R, Jahan NA, Uddin MJ, Refat MNH, Nasreen F, Khanam F. Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study. Access Microbiol 2024; 6:000727.v3. [PMID: 39165251 PMCID: PMC11334578 DOI: 10.1099/acmi.0.000727.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 07/16/2024] [Indexed: 08/22/2024] Open
Abstract
Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh. Design.This was a cross-sectional study. Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021. Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex. Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable. Interventions. Not applicable. Results.Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive. Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.
Collapse
Affiliation(s)
- A. N. M. Shamsul Islam
- Department of Public Health and Hospital Administration, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Nasreen Farhana
- Department of Microbiology and Mycology, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Rafaat Choudhury
- Department of Microbiology and Mycology, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Naznin Akter Jahan
- Department of Nutrition and Biochemistry, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Mohammad Jamal Uddin
- Department of Parasitology, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Md. Nazmul Hassan Refat
- Department of Public Health and Hospital Administration, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Fatima Nasreen
- Department of Microbiology and Mycology, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| | - Fahmida Khanam
- Department of Microbiology and Mycology, National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh
| |
Collapse
|
3
|
Ma H, Wang H, Han X, Fei J. Efficacy of targeted next generation sequencing for pathogen detection in lower respiratory tract infections. Am J Transl Res 2024; 16:3637-3645. [PMID: 39262714 PMCID: PMC11384368 DOI: 10.62347/fkwf4589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/29/2024] [Indexed: 09/13/2024]
Abstract
OBJECTIVE To investigate the diagnostic utility of targeted next-generation sequencing (tNGS) in the diagnosis of lower respiratory tract infections. METHODS Patients with lower respiratory tract infection in East Area of Yantai Yantaishan Hospital from December 2021 to September 2023 were retrospectively analyzed. Sputum samples were tested using both tNGS technology and conventional microbiological examination. Data were collected on general clinical features and test outcomes. The study evaluated the efficacy of tNGS by comparing its positive detection rate against traditional methods and analyzing detection differences among patients with varying clinical characteristics. Receiver operating characteristic (ROC) analysis was used to determine the diagnostic accuracy of both testing methods. RESULTS A total of 281 patients were included, with corresponding sputum specimens. The tNGS method showed a higher positivity rate of 90.0%, significantly outperforming the conventional method's rate of 70.82% (P<0.05). Among 199 patients with concordant positive results, 38.22% fully agreed, while 53.40% completely disagreed between the two methods. Mycobacterium tuberculosis, Candida albicans, and Pseudomonas aeruginosa were the most frequently detected pathogens, respectively. tNGS significantly reduced the time required for pathogen detection (P<0.001) and identified a higher rate of mixed infections compared to conventional methods (49.11% vs 2.85%, P<0.001). Positive tNGS detection rates significantly differed between patients with abnormal vs normal C-reactive protein or procalcitonin levels. The AUC for tNGS was 0.867, indicating superior diagnostic accuracy over the conventional method (P<0.05). CONCLUSIONS tNGS technology demonstrates a high positivity rate and rapid pathogen detection in lower respiratory tract infections, with notable advantages in identifying mixed infections. This method shows potential for enhancing diagnostic accuracy and treatment decisions in clinical settings.
Collapse
Affiliation(s)
- Hongfu Ma
- Department of Pulmonary and Critial Care Medicine, East Area of Yantai Yantaishan Hospital Yantai, Shandong, China
| | - Haixia Wang
- Department of Pulmonary and Critial Care Medicine, East Area of Yantai Yantaishan Hospital Yantai, Shandong, China
| | - Xiao Han
- Department of Pulmonary and Critial Care Medicine, East Area of Yantai Yantaishan Hospital Yantai, Shandong, China
| | - Jianwen Fei
- Department of Pulmonary and Critial Care Medicine, East Area of Yantai Yantaishan Hospital Yantai, Shandong, China
| |
Collapse
|
4
|
Xu C, Wang Z, Yu B, Pan Z, Ni J, Feng Y, Huang S, Wu M, Zhou J, Fang L, Wu Z. Simultaneous and ultrafast detection of pan-SARS-coronaviruses and influenza A/B viruses by a novel multiplex real-time RT-PCR assay. Virus Res 2024; 346:199410. [PMID: 38815870 PMCID: PMC11177080 DOI: 10.1016/j.virusres.2024.199410] [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: 10/30/2023] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Here we report an ultrafast quadruplex RT-qPCR assay with robust diagnostic ability to detect and distinguish pan-SARS-CoVs and influenza A/B viruses within 35 min. This quadruplex RT-qPCR assay comprised of one novel RNA-based internal control targeting human β2-microglobulin (B2M) for process accuracy and three newly-designed primers-probe sets targeting the envelope protein (E) of pan-SARS-CoV, matrix protein (MP) of influenza A virus and non-structural (NS) region of influenza B virus. This quadruplex assay exhibited a sensitivity comparable to its singleplex counterparts and a slightly higher to that of the Centers for Disease Control and Prevention-recommended SARS-CoV-2 and influenza A/B assays. The novel assay showed no false-positive amplifications with other common respiratory viruses, and its 95 % limits of detection for pan-SARS-CoV and influenza A/B virus was 4.26-4.52 copies/reaction. Moreover, the assay was reproducible with less than 1 % coefficient of variation and adaptable testing different clinical and environmental samples. Our ultrafast quadruplex RT-qPCR assay can serve as an attractive tool for effective differentiation of influenza A/B virus and SARS-CoV-2, but more importantly prognose the reemergence/emergence of SARS and novel coronaviruses or influenza viruses from animal spillover.
Collapse
Affiliation(s)
- Changping Xu
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China; Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhengyang Wang
- Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Beibei Yu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Zhenhuang Pan
- Yiwu Center for Disease Control and Prevention, Yiwu, China
| | - Jun Ni
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Yan Feng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Shiwang Huang
- Shangcheng District Center for Disease Control and Prevention, Hangzhou, China
| | - Maomao Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Lei Fang
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China.
| | - Zhiwei Wu
- Center for Public Health Research, Medical School of Nanjing University, Nanjing, China.
| |
Collapse
|
5
|
Miguel F, Baleizão AR, Gomes AG, Caria H, Serralha FN, Justino MC. Strategies for Increasing the Throughput of Genetic Screening: Lessons Learned from the COVID-19 Pandemic within a University Community. BIOTECH 2024; 13:26. [PMID: 39051341 PMCID: PMC11270334 DOI: 10.3390/biotech13030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/29/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered in February 2021. With the emergence of new SARS-CoV-2 variants and safety concerns for students and staff, the lab was further challenged to develop rapid and sensitive diagnostic technologies. Methodologies such as sample-pooling extraction and multiplex protocols were developed to enhance testing efficiency without compromising accuracy. Through Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) analysis, the effectiveness of sample pooling was validated, proving to be a clear success in COVID-19 screening. Regarding multiplex analysis, the IPS COVID Lab developed an in-house protocol, achieving a sensitivity comparable to that of standard methods while reducing operational time and reagent consumption. This approach, requiring only two wells of a PCR plate (instead of three for samples), presents a more efficient alternative for future testing scenarios, increasing its throughput and testing capacity while upholding accuracy standards. The lessons learned during the SARS-CoV-2 pandemic provide added value for future pandemic situations.
Collapse
Affiliation(s)
- Fernanda Miguel
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
| | - A. Raquel Baleizão
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
| | - A. Gabriela Gomes
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
| | - Helena Caria
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Departamento de Ciências Biomédicas, Escola Superior de Saúde, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2914-503 Setúbal, Portugal
| | - Fátima N. Serralha
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
| | - Marta C. Justino
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
| |
Collapse
|
6
|
Middleton C, Larremore DB. Modeling the transmission mitigation impact of testing for infectious diseases. SCIENCE ADVANCES 2024; 10:eadk5108. [PMID: 38875334 PMCID: PMC11177932 DOI: 10.1126/sciadv.adk5108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/10/2024] [Indexed: 06/16/2024]
Abstract
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus but delayed by up to two days to control omicron-era severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, while rapid tests are superior to reverse transcription quantitative polymerase chain reaction (RT-qPCR) to control founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Last, we illustrate the model's flexibility by quantifying trade-offs in the use of post-diagnosis testing to shorten isolation times.
Collapse
Affiliation(s)
- Casey Middleton
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Daniel B. Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Santa Fe Institute, Santa Fe, NM, USA
| |
Collapse
|
7
|
Mosadegh M, Jalili S, Pourmand MR, Erfani Y, Panji M. Evaluating the efficiency of ELISA, monoplex and multiplex probe-based real-time reverse-transcription PCR assays in the detection of SARS-CoV-2 (COVID-19) and influenza A and B viruses: A cross-sectional study. Health Sci Rep 2024; 7:e2140. [PMID: 38915351 PMCID: PMC11194474 DOI: 10.1002/hsr2.2140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/26/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024] Open
Abstract
Background and Aims The current study aimed to evaluate the efficiency of Enzyme-linked immunosorbent assay (ELISA) assay and monoplex and multiplex real-time reverse-transcription PCR (rRT-PCR) in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A and B viruses (Flu A and Flu B). Methods The SARS-CoV-2 -specific IgG and IgM antibodies, as well as, Flu A (H1N1 and H3N2 serotypes) and Flu B virus antibodies were determined by ELISA assay. The one-step qRT-PCR method was used to detect the SARS-CoV-2 in nasopharyngeal swab samples. Furthermore, the presence of Flu A and B viruses was evaluated using probe-based RT-PCR. Simultaneous detection of SARS-CoV-2, Flu A and B viruses was performed by multiplex rRT-PCR assay. Results SARS CoV-2 IgM and IgG antibodies were detected in 33.3% and 58.3% of patients, respectively. In contrast, the SARS CoV-2 genome was detected in 50% of patients using the one-step monoplex RT-PCR assay. Flu A serotypes H1N1 and H3N2 were found in 16.7% and 8.3% of patients. Probe-based RT-PCR revealed that 39.3% of patients were positive for the Flu A virus. Multiplex rRT-PCR detect the SARS-CoV-2, Flu A, and Flu B in 50%, 39.3%, and 19% of samples, respectively. The sensitivity and specificity of multiplex rRT-PCR assay in comparison to monoplex RT-PCR were 100% and 55%, respectively. Coinfection with SARS-CoV-2, Flu A, and Flu B viruses was found in 9.5% of patients. Conclusion Multiplex rRT-PCR can be used as a repaid, cost-effective and suitable tool for molecular surveillance of SARS-CoV-2 and Flu A/B viruses.
Collapse
Affiliation(s)
- Mehrdad Mosadegh
- Department of Pathobiology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Shirin Jalili
- Institute of Police Equipment and TechnologiesPolicing Sciences and Social Studies Research InstituteTehranIran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical SciencesTehran University of Medical SciencesTehranIran
| | - Mohammad Panji
- Research Center for Life and Health Sciences and Biotechnology for the Police, Directorate of Health, Rescue and TreatmentPolice HeadquarterTehranIran
| |
Collapse
|
8
|
Wu F, Cai D, Shi X, Li P, Ma L. Multiplexed detection of eight respiratory viruses based on nanozyme colorimetric microfluidic immunoassay. Front Bioeng Biotechnol 2024; 12:1402831. [PMID: 38817925 PMCID: PMC11137192 DOI: 10.3389/fbioe.2024.1402831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024] Open
Abstract
Pandemics caused by respiratory viruses, such as the SARS-CoV-1/2, influenza virus, and respiratory syncytial virus, have resulted in serious consequences to humans and a large number of deaths. The detection of such respiratory viruses in the early stages of infection can help control diseases by preventing the spread of viruses. However, the diversity of respiratory virus species and subtypes, their rapid antigenic mutations, and the limited viral release during the early stages of infection pose challenges to their detection. This work reports a multiplexed microfluidic immunoassay chip for simultaneous detection of eight respiratory viruses with noticeable infection population, namely, influenza A virus, influenza B virus, respiratory syncytial virus, SARS-CoV-2, human bocavirus, human metapneumovirus, adenovirus, and human parainfluenza viruses. The nanomaterial of the nanozyme (Au@Pt nanoparticles) was optimized to improve labeling efficiency and enhance the detection sensitivity significantly. Nanozyme-binding antibodies were used to detect viral proteins with a limit of detection of 0.1 pg/mL with the naked eye and a microplate reader within 40 min. Furthermore, specific antibodies were screened against the conserved proteins of each virus in the immunoassay, and the clinical sample detection showed high specificity without cross reactivity among the eight pathogens. In addition, the microfluidic chip immunoassay showed high accuracy, as compared with the RT-PCR assay for clinical sample detection, with 97.2%/94.3% positive/negative coincidence rates. This proposed approach thus provides a convenient, rapid, and sensitive method for simultaneous detection of eight respiratory viruses, which is meaningful for the early diagnosis of viral infections. Significantly, it can be widely used to detect pathogens and biomarkers by replacing only the antigen-specific antibodies.
Collapse
Affiliation(s)
- Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Shenzhen Institute for Drug Control, Shenzhen, China
| | - Defeng Cai
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Department of Clinical Laboratory (Pathology) Centre, South China Hospital of Shenzhen University, Shenzhen, China
| | - Xueying Shi
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Ping Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China
| |
Collapse
|
9
|
Middleton C, Larremore DB. Modeling the Transmission Mitigation Impact of Testing for Infectious Diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.22.23295983. [PMID: 37808825 PMCID: PMC10557819 DOI: 10.1101/2023.09.22.23295983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus (RSV), but delayed by up to 2d to control omicron-era SARS-CoV-2. Furthermore, while rapid tests are superior to RT-qPCR for control of founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Finally, we illustrate the model's flexibility by quantifying tradeoffs in the use of post-diagnosis testing to shorten isolation times.
Collapse
Affiliation(s)
- Casey Middleton
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Daniel B Larremore
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Santa Fe Institute, Santa Fe, NM, USA
| |
Collapse
|
10
|
Lu X, Ding K, Fang Z, Liu Y, Ji T, Sun J, Zeng Z, He L. Lateral Flow Biosensor for On-Site Multiplex Detection of Viruses Based on One-Step Reverse Transcription and Strand Displacement Amplification. BIOSENSORS 2024; 14:103. [PMID: 38392022 PMCID: PMC10886883 DOI: 10.3390/bios14020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Respiratory pathogens pose a huge threat to public health, especially the highly mutant RNA viruses. Therefore, reliable, on-site, rapid diagnosis of such pathogens is an urgent need. Traditional assays such as nucleic acid amplification tests (NAATs) have good sensitivity and specificity, but these assays require complex sample pre-treatment and a long test time. Herein, we present an on-site biosensor for rapid and multiplex detection of RNA pathogens. Samples with viruses are first lysed in a lysis buffer containing carrier RNA to release the target RNAs. Then, the lysate is used for amplification by one-step reverse transcription and single-direction isothermal strand displacement amplification (SDA). The yield single-strand DNAs (ssDNAs) are visually detected by a lateral flow biosensor. With a secondary signal amplification system, as low as 20 copies/μL of virus can be detected in this study. This assay avoids the process of nucleic acid purification, making it equipment-independent and easier to operate, so it is more suitable for on-site molecular diagnostic applications.
Collapse
Affiliation(s)
- Xuewen Lu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; (X.L.); (K.D.); (Z.Z.)
| | - Kangning Ding
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; (X.L.); (K.D.); (Z.Z.)
| | - Zhiyuan Fang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China;
| | - Yilei Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
| | - Tianxing Ji
- Clinical Laboratory Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China;
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; (X.L.); (K.D.); (Z.Z.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- National Reference Laboratory of Veterinary Drug Residues (SCAU), College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; (X.L.); (K.D.); (Z.Z.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- National Reference Laboratory of Veterinary Drug Residues (SCAU), College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Limin He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; (X.L.); (K.D.); (Z.Z.)
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- National Reference Laboratory of Veterinary Drug Residues (SCAU), College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
11
|
Chung PYJ, Dhillon SK, Simoens C, Cuypers L, Laenen L, Bonde J, Corbisier P, Buttinger G, Cocuzza CE, Van Gucht S, Van Ranst M, Arbyn M. Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework. Microbiol Spectr 2024; 12:e0239723. [PMID: 38189291 PMCID: PMC10846132 DOI: 10.1128/spectrum.02397-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.
Collapse
Affiliation(s)
- Pui Yan Jenny Chung
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Sharonjit K. Dhillon
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Cindy Simoens
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, AHH-Hvidovre Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Clementina E. Cocuzza
- Laboratory of Clinical Microbiology and Virology, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
| |
Collapse
|
12
|
Kim J, Baek S, Nam J, Park J, Kim K, Kang J, Yeom G. Simultaneous Detection of Infectious Diseases Using Aptamer-Conjugated Gold Nanoparticles in the Lateral Flow Immunoassay-Based Signal Amplification Platform. Anal Chem 2024; 96:1725-1732. [PMID: 38240676 DOI: 10.1021/acs.analchem.3c04870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Various platforms for the accurate diagnosis of infectious diseases have been studied because of the emergence of coronavirus disease (COVID-19) in 2019. Recently, it has become difficult to distinguish viruses with similar symptoms due to the continuous mutation of viruses, and there is an increasing need for a diagnostic method to detect them simultaneously. Therefore, we developed a paper-based rapid antigen diagnostic test using DNA aptamers for the simultaneous detection of influenza A, influenza B, and COVID-19. Aptamers specific for each target viral antigen were selected and attached to AuNPs for application in a rapid antigen diagnosis kit using our company's heterogeneous sandwich-type aptamer screening method (H-SELEX). We confirmed that the three viruses could be detected on the same membrane without cross-reactivity based on the high stability, specificity, and binding affinity of the selected aptamers. Further, the limit of detection was 2.89 pg·mL-1 when applied to develop signal amplification technology; each virus antigen was detected successfully in diluted nasopharyngeal samples. We believe that the developed simultaneous diagnostic kit, based on such high accuracy, can distinguish various infectious diseases, thereby increasing the therapeutic effect and contributing to the clinical field.
Collapse
Affiliation(s)
- Jinwoo Kim
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sowon Baek
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jungmin Nam
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jeongeun Park
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kihyeun Kim
- Advanced Photonics Research Institute (APRI), Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Juyoung Kang
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Gyuho Yeom
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
13
|
Gao P, Fan Y, Kong X, Zhang R, Chen L, Jiang Y, Liu Y, Zhao M, Deng G, Cao Y, Ma L. A novel assay based on DNA melting temperature for multiplexed identification of SARS-CoV-2 and influenza A/B viruses. Front Microbiol 2023; 14:1249085. [PMID: 38173675 PMCID: PMC10762780 DOI: 10.3389/fmicb.2023.1249085] [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: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses can cause respiratory illnesses with similar clinical symptoms, making their differential diagnoses challenging. Additionally, in critically ill SARS-CoV-2-infected patients, co-infections with other respiratory pathogens can lead to severe cytokine storm and serious complications. Therefore, a method for simultaneous detection of SARS-CoV-2 and influenza A and B viruses will be clinically beneficial. Methods We designed an assay to detect five gene targets simultaneously via asymmetric PCR-mediated melting curve analysis in a single tube. We used specific probes that hybridize to corresponding single-stranded amplicons at low temperature and dissociate at high temperature, creating different detection peaks representing the targets. The entire reaction was conducted in a closed tube, which minimizes the risk of contamination. The limit of detection, specificity, precision, and accuracy were determined. Results The assay exhibited a limit of detection of <20 copies/μL for SARS-CoV-2 and influenza A and <30 copies/μL for influenza B, with high reliability as demonstrated by a coefficient of variation for melting temperature of <1.16% across three virus concentrations. The performance of our developed assay and the pre-determined assay showed excellent agreement for clinical samples, with kappa coefficients ranging from 0.98 (for influenza A) to 1.00 (for SARS-CoV-2 and influenza B). No false-positive, and no cross-reactivity was observed with six common non-influenza respiratory viruses. Conclusion The newly developed assay offers a straightforward, cost-effective and nucleic acid contamination-free approach for simultaneous detection of the SARS-CoV-2, influenza A, and influenza B viruses. The method offers high analytical sensitivity, reliability, specificity, and accuracy. Its use will streamline testing for co-infections, increase testing throughput, and improve laboratory efficacy.
Collapse
Affiliation(s)
- Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lida Chen
- Department of Blood Transfusion, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| |
Collapse
|
14
|
Ding J, Xu X, Deng Y, Zheng X, Zhang T. Circulation of SARS-CoV-2 Omicron sub-lineages revealed by multiplex genotyping RT-qPCR assays for sewage surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166300. [PMID: 37591390 DOI: 10.1016/j.scitotenv.2023.166300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Sewage surveillance has proven to be an essential complementary tool to clinical diagnosis in combating the COVID-19 pandemic by tracking the spread of the SARS-CoV-2 virus and evaluating infection levels in populations. With the striking spreading and continuous evolution of SARS-CoV-2 Omicron VOC that characterized with higher transmissibility and potential immune evasion, there is an urgent need for the rapid surveillance of this prevalent strain and its sub-lineages in sewage. In this study, based on three multiplex allele-specific (AS) RT-qPCR assays, we established a rapid and high-throughput detection workflow for the simultaneous discrimination of Omicron sub-lineages BA.2.2, BA.2.12.1, BA.4 and BA.5 (hereafter referred to as BA.4/BA.5) to track their community circulation in Hong Kong. All primer-probe sets in the multiplex assays could correctly discriminate and quantitate their target genotypes with high sensitivity and specificity, even when multiple variants co-existed in the sewage samples. Using the established multiplex assays, the trends of SARS-CoV-2 total viral load and variant dynamics in influent samples collected from 11 wastewater treatment plants (WWTPs) during June 2022 and September 2022, aligned with the clinical data, successfully unveiling the swift emergence and predominance of Omicron BA.4/BA.5 in Hong Kong. The study highlights the feasibility and applicability of multiplex RT-qPCR assays for monitoring epidemic trends and tracking variant displacement dynamics in sewage samples, providing a more rapid, high-throughput and cost-effective alternative to enhance the current sewage surveillance system.
Collapse
Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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.
| |
Collapse
|
15
|
Abbasi H, Nikoo HR, Fotouhi F, Khosravi A. Development of a robust TaqMan probe-based one-step multiplex RT-qPCR for simultaneous detection of SARS-CoV-2 and Influenza A/B viruses. BMC Microbiol 2023; 23:335. [PMID: 37951883 PMCID: PMC10640757 DOI: 10.1186/s12866-023-03048-9] [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: 11/23/2022] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND During the coronavirus disease 2019 (COVID-19) pandemic, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Influenza A, and Influenza B viruses is essential for rapid differential diagnosis in patients with similar symptoms, especially during "flu season" in the post-pandemic era. So far, several multiplex methods have been approved for the simultaneous detection of SARS-CoV-2, Influenza A, and Influenza B. However, due to the rapid mutation rate of the SARS-CoV-2 genome and the emergence of new variants, existing methods must be improved and updated. METHODS To identify a highly conserved region in the SARS-CoV-2 N-gene, a genomic survey was performed to increase the sensitivity and specificity of primer and probe sets targeting the SARS-CoV-2 genome. The 95% LLOD (95% lower limits of detection) were calculated by probit analysis. A total of 70 predetermined clinical samples using singleplex RT-qPCR assays, were included. The clinical performance of the multiplex RT-qPCR assay was determined and compared with a commercial multiplex kit. The Cohen's kappa coefficient, P-value (McNemar's test), Passing-Bablok regression, and Bland Altman agreement analysis were determined to monitor the agreement of the assays. RESULTS The novel SARS-CoV-2 primer and probe set designed in this assay was able to detect all variants of concern (VOCs) and variants of interest (VOIs) with high analytical and clinical performance. The 95% LLOD for the multiplex RT-qPCR was 20 copies per reaction for the N gene of SARS-CoV-2, 2 copies per reaction for M1 gene of Influenza A and NS1 gene of Influenza B. The diagnostic sensitivity of the multiplex RT-qPCR was 94.4%, 93.7%, and 100% for the detection of SARS-CoV-2, Influenza A, and Influenza B genomes, respectively. Moreover, the specificity was identical (100%) in both assays. According to the agreement analysis results, there was no statistical difference between our multiplex assay and the commercial kit. CONCLUSIONS In this study, we developed a novel in-house made multiplex RT-qPCR assay, with high sensitivity, specificity, and reliability for the diagnosis of SARS-CoV-2 infection in clinical samples. This is valuable during Influenza seasons when influenza co-circulates with SARS-CoV-2, as it saves costs, time, and thus specific and timely treatment of patients.
Collapse
Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran.
| |
Collapse
|
16
|
Toribio-Avedillo D, Gómez-Gómez C, Sala-Comorera L, Rodríguez-Rubio L, Carcereny A, García-Pedemonte D, Pintó RM, Guix S, Galofré B, Bosch A, Merino S, Muniesa M. Monitoring influenza and respiratory syncytial virus in wastewater. Beyond COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 892:164495. [PMID: 37245831 PMCID: PMC10214770 DOI: 10.1016/j.scitotenv.2023.164495] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
Wastewater-based surveillance can be a valuable tool to monitor viral circulation and serve as an early warning system. For respiratory viruses that share similar clinical symptoms, namely SARS-CoV-2, influenza, and respiratory syncytial virus (RSV), identification in wastewater may allow differentiation between seasonal outbreaks and COVID-19 peaks. In this study, to monitor these viruses as well as standard indicators of fecal contamination, a weekly sampling campaign was carried out for 15 months (from September 2021 to November 2022) in two wastewater treatment plants that serve the entire population of Barcelona (Spain). Samples were concentrated by the aluminum hydroxide adsorption-precipitation method and then analyzed by RNA extraction and RT-qPCR. All samples were positive for SARS-CoV-2, while the positivity rates for influenza virus and RSV were significantly lower (10.65 % for influenza A (IAV), 0.82 % for influenza B (IBV), 37.70 % for RSV-A and 34.43 % for RSV-B). Gene copy concentrations of SARS-CoV-2 were often approximately 1 to 2 logarithmic units higher compared to the other respiratory viruses. Clear peaks of IAV H3:N2 in February and March 2022 and RSV in winter 2021 were observed, which matched the chronological incidence of infections recorded in the Catalan Government clinical database. In conclusion, the data obtained from wastewater surveillance provided new information on the abundance of respiratory viruses in the Barcelona area and correlated favorably with clinical data.
Collapse
Affiliation(s)
- Daniel Toribio-Avedillo
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain
| | - Clara Gómez-Gómez
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain
| | - Laura Sala-Comorera
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - David García-Pedemonte
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Rosa Maria Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Susana Merino
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain; Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Maite Muniesa
- MARS Group (Health Related Water Microbiology Group), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Diagonal 643, E-08028 Barcelona, Spain.
| |
Collapse
|
17
|
Shen XX, Li FY, Qin M, Zhang GH, Zhang MY, Liu H, Sun XL, Xin ZJ, Ma XJ. Multicenter evaluation of a simple and sensitive nucleic acid self-testing for SARS-CoV-2. Virol Sin 2023; 38:620-626. [PMID: 37406815 PMCID: PMC10436039 DOI: 10.1016/j.virs.2023.06.009] [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: 02/04/2023] [Accepted: 06/29/2023] [Indexed: 07/07/2023] Open
Abstract
A rapid and accurate COVID-19 diagnosis is a prerequisite for blocking the source of infection as soon as possible and taking the appropriate medical action. Herein, we developed GeneClick, a device for nucleic acid self-testing of SARS-CoV-2, consisting of three modules: a sampling kit, a microfluidic chip-based disposable cartridge, and an amplification reader. In addition, we evaluated the clinical performance of GeneClick using 2162 nasal swabs collected at three medical institutions, using three commercial RT-qPCR kits and an antigen self-test as references. Compared to RT-qPCR, the sensitivity and specificity of the GeneClick assay were 97.93% and 99.72%, respectively, with a kappa value of 0.979 (P < 0.01). Of the 2162 samples, 2076 were also tested for SARS-CoV-2 antigens. Among the 314 positive samples identified by GeneClick assay, 63 samples were undetected by antigen tests. Overall, the GeneClick nucleic acid self-test demonstrated higher accuracy than the antigen-based detection. Based on the additional features, including simple operation, affordable price, portable device, and reliability of smartphone APP-driven sampling and result reporting, GeneClick offers a powerful tool for field-based SARS-CoV-2 detection in primary healthcare institutions or at-home use.
Collapse
Affiliation(s)
- Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Feng-Yu Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Hebei Medical University, Shijiazhuang, 050031, China
| | - Meng Qin
- Fengtai District Center for Disease Control and Prevention of Beijing, Beijing, 100071, China
| | - Guo-Hao Zhang
- Beijing Baicare Biotechnology Co., Ltd., Beijing, 102206, China
| | - Meng-Yi Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hong Liu
- Shandong University of Technology, School of Life Sciences and Medicine, Zibo, 255000, China
| | - Xiu-Li Sun
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhen-Jiang Xin
- Fengtai District Center for Disease Control and Prevention of Beijing, Beijing, 100071, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| |
Collapse
|
18
|
Kukushkin V, Ambartsumyan O, Subekin A, Astrakhantseva A, Gushchin V, Nikonova A, Dorofeeva A, Zverev V, Keshek A, Meshcheryakova N, Zaborova O, Gambaryan A, Zavyalova E. Multiplex Lithographic SERS Aptasensor for Detection of Several Respiratory Viruses in One Pot. Int J Mol Sci 2023; 24:ijms24098081. [PMID: 37175786 PMCID: PMC10178974 DOI: 10.3390/ijms24098081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Rapid and reliable techniques for virus identification are required in light of recurring epidemics and pandemics throughout the world. Several techniques have been distributed for testing the flow of patients. Polymerase chain reaction with reverse transcription is a reliable and sensitive, though not rapid, tool. The antibody-based strip is a rapid, though not reliable, and sensitive tool. A set of alternative tools is being developed to meet all the needs of the customer. Surface-enhanced Raman spectroscopy (SERS) provides the possibility of single molecule detection taking several minutes. Here, a multiplex lithographic SERS aptasensor was developed aiming at the detection of several respiratory viruses in one pot within 17 min. The four labeled aptamers were anchored onto the metal surface of four SERS zones; the caught viruses affect the SERS signals of the labels, providing changes in the analytical signals. The sensor was able to decode mixes of SARS-CoV-2 (severe acute respiratory syndrome coronavirus two), influenza A virus, respiratory syncytial virus, and adenovirus within a single experiment through a one-stage recognition process.
Collapse
Affiliation(s)
- Vladimir Kukushkin
- Osipyan Institute of Solid State Physics, Russian Academy of Science, 142432 Chernogolovka, Russia
| | | | - Alexei Subekin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anna Astrakhantseva
- Osipyan Institute of Solid State Physics, Russian Academy of Science, 142432 Chernogolovka, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Vladimir Gushchin
- N. F. Gamaleya Federal Research Center for Epidemiology & Microbiology, 123098 Moscow, Russia
| | - Alexandra Nikonova
- Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
| | | | - Vitaly Zverev
- Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - Anna Keshek
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
| | | | - Olga Zaborova
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for Research, Development of Immune and Biological Products RAS, 108819 Moscow, Russia
| | - Elena Zavyalova
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
| |
Collapse
|
19
|
Yan S, Yang F, Yao H, Dong D, Wu D, Wu N, Ye C, Wu H. A multiplex real-time RT-PCR assay for the detection of H1, H2 and H3 subtype avian influenza viruses. Virus Genes 2023; 59:333-337. [PMID: 36515804 DOI: 10.1007/s11262-022-01963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Avian influenza viruses (AIVs) are influenza A viruses, of which subtypes H1, H2 and H3 are highly transmissible in poultry and have the risk of transmission to human as well. It is important to establish an accurate, sensitive and convenient means of virus detection. In this study, we developed a multiplex real-time RT-PCR assay based on conserved sequences of the virus hemagglutinin and matrix, and designed primers and probes for the simultaneous and rapid detection of AIV subtypes H1, H2 and H3. We used different subtypes of AIVs and other avian respiratory viruses for evaluation of the specificity of this method. The results showed good sensitivity, specificity and reproducibility. The detection limit was 10-100 copies per reaction. The method also achieved good concordance with the virus isolation method when compared to 81 poultry samples evaluated. It provides a new method for detecting mixed infections of AIVs.
Collapse
Affiliation(s)
- Sijing Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Fan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China
| | - Dalu Dong
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China
| | - Danna Wu
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China
| | - Chunsheng Ye
- Hangzhou Biotest Biotech Co.,Ltd, 27 Tuyi Road, Cangqian Street, Yuhang District, Hangzhou, 311121, Zhejiang, China.
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
| |
Collapse
|
20
|
Maltezou HC, Papanikolopoulou A, Vassiliu S, Theodoridou K, Nikolopoulou G, Sipsas NV. COVID-19 and Respiratory Virus Co-Infections: A Systematic Review of the Literature. Viruses 2023; 15:865. [PMID: 37112844 PMCID: PMC10142898 DOI: 10.3390/v15040865] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Τhe COVID-19 pandemic highly impacted the circulation, seasonality, and morbidity burden of several respiratory viruses. We reviewed published cases of SARS-CoV-2 and respiratory virus co-infections as of 12 April 2022. SARS-CoV-2 and influenza co-infections were reported almost exclusively during the first pandemic wave. It is possible that the overall incidence of SARS-CoV-2 co-infections is higher because of the paucity of co-testing for respiratory viruses during the first pandemic waves when mild cases might have been missed. Animal models indicate severe lung pathology and high fatality; nevertheless, the available literature is largely inconclusive regarding the clinical course and prognosis of co-infected patients. Animal models also indicate the importance of considering the sequence timing of each respiratory virus infection; however, there is no such information in reported human cases. Given the differences between 2020 and 2023 in terms of epidemiology and availability of vaccines and specific treatment against COVID-19, it is rational not to extrapolate these early findings to present times. It is expected that the characteristics of SARS-CoV-2 and respiratory virus co-infections will evolve in the upcoming seasons. Multiplex real-time PCR-based assays have been developed in the past two years and should be used to increase diagnostic and infection control capacity, and also for surveillance purposes. Given that COVID-19 and influenza share the same high-risk groups, it is essential that the latter get vaccinated against both viruses. Further studies are needed to elucidate how SARS-CoV-2 and respiratory virus co-infections will be shaped in the upcoming years, in terms of impact and prognosis.
Collapse
Affiliation(s)
- Helena C. Maltezou
- Directorate of Research, Studies and Documentation, National Public Health Organization, 15123 Athens, Greece
| | - Amalia Papanikolopoulou
- Third Department of Internal Medicine, Sotiria General Hospital for Thoracic Diseases, National and Kapodistrian University of Athens, School of Medicine, Sotiria General Hospital, 11527 Athens, Greece
| | | | - Kalliopi Theodoridou
- Department of Microbiology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Georgia Nikolopoulou
- Department of Hepatitides, National Public Health Organization, 15123 Athens, Greece
| | - Nikolaos V. Sipsas
- Pathophysiology Department, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| |
Collapse
|
21
|
Yang HH, Huang IT, Wu RC, Chen LK. A highly efficient and accurate method of detecting and subtyping Influenza A pdm H1N1 and H3N2 viruses with newly emerging mutations in the matrix gene in Eastern Taiwan. PLoS One 2023; 18:e0283074. [PMID: 36952488 PMCID: PMC10035893 DOI: 10.1371/journal.pone.0283074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 03/01/2023] [Indexed: 03/25/2023] Open
Abstract
The rapid identification of Influenza A virus and its variants, which cause severe respiratory diseases, is imperative to providing timely treatment and improving patient outcomes. Conventionally, two separate assays (total test duration of up to 6 h) are required to initially differentiate Influenza A and B viruses and subsequently distinguish the pdm H1N1 and H3N2 serotypes of Influenza A virus. In this study, we developed a multiplex real-time RT-PCR method for simultaneously detecting Influenza A and B viruses and subtyping Influenza A virus, with a substantially reduced test duration. Clinical specimens from hospitalized patients and outpatients with influenza-like symptoms in Eastern Taiwan were collected between 2011 and 2015, transported to Hualien Tzu Chi Hospital, and analyzed. Conventional RT-PCR was used to subtype the isolated Influenza A viruses. Thereafter, for rapid identification, the multiplex real-time RT-PCR method was developed and applied to identify the conserved regions that aligned with the available primers and probes. Accordingly, a multiplex RT-PCR assay with three groups of primers and probes (MAF and MAR primers and MA probe; InfAF and InfAR primers and InfA probe; and MBF and MBR primers and MB probe) was established to distinguish these viruses in the same reaction. Thus, with this multiplex RT-PCR assay, Influenza B, Influenza A pdm H1N1, and Influenza A H3N2 viruses were accurately detected and differentiated within only 2.5 h. This multiplex RT-PCR assay showed similar analytical sensitivity to the conventional singleplex assay. Further, the phylogenetic analyses of our samples revealed that the characteristics of these viruses were different from those reported previously using samples collected during 2012–2013. In conclusion, we developed a multiplex real-time RT-PCR method for highly efficient and accurate detection and differentiation of Influenza A and B viruses and subtyping Influenza A virus with a substantially reduced test duration for diagnosis.
Collapse
Affiliation(s)
- Hui-Hua Yang
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Taiwan CDC Collaborating Laboratories of Virology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - I-Tsong Huang
- Taiwan CDC Collaborating Laboratories of Virology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Ren-Chieh Wu
- Branch of Clinical Pathology, Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Emergency Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- PhD Program in Pharmacology and Toxicology, Tzu Chi University, Hualien, Taiwan
| | - Li-Kuang Chen
- Taiwan CDC Collaborating Laboratories of Virology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Branch of Clinical Pathology, Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Emergency Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- PhD Program in Pharmacology and Toxicology, Tzu Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Department of Laboratory Diagnostic, College of Medicine, Tzu Chi University, Hualien, Taiwan
- * E-mail:
| |
Collapse
|
22
|
Karas BY, Sitnikova VE, Nosenko TN, Dedkov VG, Arsentieva NA, Gavrilenko NV, Moiseev IS, Totolian AA, Kajava AV, Uspenskaya MV. ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals. JOURNAL OF BIOPHOTONICS 2023:e202200166. [PMID: 36869427 DOI: 10.1002/jbio.202200166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/08/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detect seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built classification models based on PCA associated with LDA and ANN. Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA.
Collapse
Affiliation(s)
- Boris Y Karas
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | - Vera E Sitnikova
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | | | - Vladimir G Dedkov
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia A Arsentieva
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Natalia V Gavrilenko
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Ivan S Moiseev
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Areg A Totolian
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, Université Montpellier, Montpellier, France
| | | |
Collapse
|
23
|
da Costa VG, Gomes AJC, Bittar C, Geraldini DB, Previdelli da Conceição PJ, Cabral ÁS, Carvalho T, Biselli JM, Provazzi PJS, Campos GRF, Sanches PRDS, Costa PI, Nogueira ML, Araujo JP, Spilki FR, Calmon MF, Rahal P. Burden of Influenza and Respiratory Syncytial Viruses in Suspected COVID-19 Patients: A Cross-Sectional and Meta-Analysis Study. Viruses 2023; 15:665. [PMID: 36992374 PMCID: PMC10055802 DOI: 10.3390/v15030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/11/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Non-SARS-CoV-2 respiratory viral infections, such as influenza virus (FluV) and human respiratory syncytial virus (RSV), have contributed considerably to the burden of infectious diseases in the non-COVID-19 era. While the rates of co-infection in SARS-CoV-2-positive group (SCPG) patients have been determined, the burden of other respiratory viruses in the SARS-CoV-2-negative group (SCNG) remains unclear. Here, we conducted a cross-sectional study (São José do Rio Preto county, Brazil), and we collected our data using a meta-analysis to evaluate the pooled prevalence of FluV and RSV among SCNG patients. Out of the 901 patients suspected of COVID-19, our molecular results showed positivity of FluV and RSV in the SCNG was 2% (15/733) and 0.27% (2/733), respectively. Co-infection with SARS-CoV-2 and FluV, or RSV, was identified in 1.7% of the patients (3/168). Following our meta-analysis, 28 studies were selected (n = 114,318 suspected COVID-19 patients), with a pooled prevalence of 4% (95% CI: 3-6) for FluV and 2% (95% CI: 1-3) for RSV among SCNG patients were observed. Interestingly, FluV positivity in the SCNG was four times higher (OR = 4, 95% CI: 3.6-5.4, p < 0.01) than in the SCPG. Similarly, RSV positivity was significantly associated with SCNG patients (OR = 2.9, 95% CI: 2-4, p < 0.01). For subgroup analysis, cold-like symptoms, including fever, cough, sore throat, headache, myalgia, diarrhea, and nausea/vomiting, were positively associated (p < 0.05) with the SCPG. In conclusion, these results show that the pooled prevalence of FluV and RSV were significantly higher in the SCNG than in the SCPG during the early phase of the COVID-19 pandemic.
Collapse
Affiliation(s)
- Vivaldo Gomes da Costa
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Ana Júlia Chaves Gomes
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Cíntia Bittar
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Dayla Bott Geraldini
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Pâmela Jóyce Previdelli da Conceição
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Ágata Silva Cabral
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Tamara Carvalho
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Joice Matos Biselli
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Paola Jocelan Scarin Provazzi
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Guilherme Rodrigues Fernandes Campos
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
| | - Paulo Ricardo da Silva Sanches
- Laboratório de Virologia Molecular, Departamento de Ciências Biológicas, Faculdade de Ciências Farmacêuticas (UNESP), Araraquara 14800-903, SP, Brazil
| | - Paulo Inácio Costa
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas (UNESP), Araraquara 14801-360, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
| | - João Pessoa Araujo
- Instituto de Biotecnologia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu 18607-440, SP, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo 93525-075, RS, Brazil
| | - Marília Freitas Calmon
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| |
Collapse
|
24
|
Krumbein H, Kümmel LS, Fragkou PC, Thölken C, Hünerbein BL, Reiter R, Papathanasiou KA, Renz H, Skevaki C. Respiratory viral co-infections in patients with COVID-19 and associated outcomes: A systematic review and meta-analysis. Rev Med Virol 2023; 33:e2365. [PMID: 35686619 PMCID: PMC9347814 DOI: 10.1002/rmv.2365] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
Abstract
The aim of this systematic review and meta-analysis was to critically assess the published literature related to community-acquired viral co-infections and COVID-19 and to evaluate the prevalence, most identified co-pathogens, and relevant risk factors. Furthermore, we aimed to examine the clinical features and outcomes of co-infected compared to mono-infected COVID-19 patients. We systematically searched PubMed, Web of Science, Embase, Scopus, and The Cochrane Library for studies published from 1 November 2019 to 13 August 2021. We included patients of all ages and any COVID-19 severity who were screened for respiratory viral co-infection within 48 h of COVID-19 diagnosis. The main outcome was the proportion of patients with a respiratory viral co-infection. The systematic review was registered to PROSPERO (CRD42021272235). Out of 6053 initially retrieved studies, 59 studies with a total of 16,643 SARS-CoV-2 positive patients were included. The global pooled prevalence was 5.01% (95% CI 3.34%-7.27%; I2 = 95%) based on a random-effects model, with Influenza Viruses (1.54%) and Enteroviruses (1.32%) being the most prevalent pathogens. Subgroup analyses showed that co-infection was significantly higher in paediatric (9.39%) than adult (3.51%) patients (p-value = 0.02). Furthermore, co-infected patients were more likely to be dyspnoeic and the odds of fatality (OR = 1.66) were increased. Although a relatively low proportion of COVID-19 patients have a respiratory viral co-infection, our findings show that multiplex viral panel testing may be advisable in patients with compatible symptoms. Indeed, respiratory virus co-infections may be associated with adverse clinical outcomes and therefore have therapeutic and prognostic implications.
Collapse
Affiliation(s)
- Hanna Krumbein
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Lara S. Kümmel
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Paraskevi C. Fragkou
- Fourth Department of Internal MedicineMedical School of AthensNational and Kapodistrian University of AthensAttikon University HospitalAthensGreece
| | - Clemens Thölken
- Institute of Medical Bioinformatics and BiostatisticsMedical FacultyPhilipps University of MarburgMarburgGermany
| | - Ben L. Hünerbein
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Rieke Reiter
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | | | - Harald Renz
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Chrysanthi Skevaki
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| |
Collapse
|
25
|
Li Y, Qiao J, Han X, Zhao Z, Kou J, Zhang W, Man S, Ma L. Needs, Challenges and Countermeasures of SARS-CoV-2 Surveillance in Cold-Chain Foods and Packaging to Prevent Possible COVID-19 Resurgence: A Perspective from Advanced Detections. Viruses 2022; 15:120. [PMID: 36680157 PMCID: PMC9864631 DOI: 10.3390/v15010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
The pandemic caused by SARS-CoV-2 has a huge impact on the global economy. SARS-CoV-2 could possibly and potentially be transmitted to humans through cold-chain foods and packaging (namely good-to-human), although it mainly depends on a human-to-human route. It is imperative to develop countermeasures to cope with the spread of viruses and fulfil effective surveillance of cold-chain foods and packaging. This review outlined SARS-CoV-2-related cold-chain food incidents and current methods for detecting SARS-CoV-2. Then the needs, challenges and practicable countermeasures for SARS-CoV-2 detection, specifically for cold-chain foods and packaging, were underlined. In fact, currently established detection methods for SARS-CoV-2 are mostly used for humans; thus, these may not be ideally applied to cold-chain foods directly. Therefore, it creates a need to develop novel methods and low-cost, automatic, mini-sized devices specifically for cold-chain foods and packaging. The review intended to draw people's attention to the possible spread of SARS-CoV-2 with cold-chain foods and proposed perspectives for futuristic cold-chain foods monitoring during the pandemic.
Collapse
Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenlu Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Tianjin 300457, China
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin 300457, China
- Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin 300457, China
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin 300457, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| |
Collapse
|
26
|
Kim TY, Bae GE, Kim JY, Kang M, Jang JH, Huh HJ, Chung DR, Lee NY. Evaluation of the Kaira COVID-19/Flu/RSV Detection Kit for detection of SARS-CoV-2, influenza A/B, and respiratory syncytial virus: A comparative study with the PowerChek SARS-CoV-2, influenza A&B, RSV Multiplex Real-time PCR Kit. PLoS One 2022; 17:e0278530. [PMID: 36516190 PMCID: PMC9750031 DOI: 10.1371/journal.pone.0278530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Co-circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses, such as influenza and respiratory syncytial virus (RSV), can be a severe threat to public health. The accurate detection and differentiation of these viruses are essential for clinical laboratories. Herein, we comparatively evaluated the performance of the Kaira COVID-19/Flu/RSV Detection Kit (Kaira; Optolane, Seongnam, Korea) for detection of SARS-CoV-2, influenza A and B, and RSV in nasopharyngeal swab (NPS) specimens with that of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea). METHODS A total of 250 archived NPS specimens collected for routine clinical testing were tested in parallel by the Kaira and PowerChek assays. RNA standards were serially diluted and tested by the Kaira assay to calculate the limit of detection (LOD). RESULTS The positive and negative percent agreements between the Kaira and PowerChek assays were as follows: 100% (49/49) and 100% (201/201) for SARS-CoV-2; 100% (50/50) and 99.0% (198/200) for influenza A; 100% (50/50) and 100% (200/200) for influenza B; and 100% (51/51) and 100% (199/199) for RSV, respectively. The LODs of the Kaira assay for SARS-CoV-2, influenza A and B, and RSV were 106.1, 717.1, 287.3, and 442.9 copies/mL, respectively. CONCLUSIONS The Kaira assay showed comparable performance to the PowerChek assay for detection of SARS-CoV-2, influenza A and B, and RSV in NPS specimens, indicating that the Kaira assay could be a useful diagnostic tool when these viruses are co-circulating.
Collapse
Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Go Eun Bae
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- * E-mail:
| | - Doo Ryeon Chung
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, Korea
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
27
|
Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Chen CW, Yang YS, Hsieh SS, Chen ES, Yang MH, Tang SH, Perng CL, Yang JR, Liu MT, Chang FY, Shang HS. Multicenter study evaluating novel multi-specimen pooling assay for the detection of SARS-CoV-2: High sensitivity and high throughput testing. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1069-1075. [PMID: 34538568 PMCID: PMC8411585 DOI: 10.1016/j.jmii.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND/PURPOSE Mass screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important to prevent the spread of coronavirus disease 2019 (COVID-19). Pooling samples can increase the number of tests processed. LabTurbo AIO 48 is an automated platform that allows ribonucleic acid extraction and sample analysis on the same instrument. We created a novel pooling assay on this platform for SARS-CoV-2 detection and demonstrated that the pooling strategy increases testing capacity without affecting accuracy and sensitivity. METHODS Comparative limit of detection (LoD) assessment was performed on the LabTurbo AIO 48 platform and the current standard detection system based on real-time reverse transcription polymerase chain reaction (rRT-PCR) using 55 clinically positive samples. An additional 330 primary clinical samples were assessed. RESULTS Six samples pooled into one reaction tube were detected in approximately 2.5 h using the World Health Organization rRT-PCR protocol. LabTurbo AIO 48 also demonstrated a higher throughput than our reference rRT-PCR assay, with an LoD of 1000 copies/mL. The overall percentage agreement between the methods for the 330 samples was 100%. CONCLUSION We created a novel multi-specimen pooling assay using LabTurbo AIO 48 for the robust detection of SARS-CoV-2, allowing high-throughput results; this assay will aid in better control and prevention of COVID-19. The diagnostic assay was cost-effective and time-efficient; thus, the pooling strategy is a practical and effective method for diagnosing large quantities of specimens without compromising precision.
Collapse
Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - En-Sung Chen
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Mei-Hsiu Yang
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | | | | | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC,Corresponding author. Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan, ROC. Fax: +886 2 87927226
| |
Collapse
|
28
|
Akarapipad P, Bertelson E, Pessell A, Wang TH, Hsieh K. Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19. BIOSENSORS 2022; 12:bios12110978. [PMID: 36354487 PMCID: PMC9688249 DOI: 10.3390/bios12110978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.
Collapse
Affiliation(s)
- Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Bertelson
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Pessell
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
29
|
Distribution of Viral Respiratory Infections during the COVID-19 Pandemic Using the FilmArray Respiratory Panel. Biomedicines 2022; 10:biomedicines10112734. [DOI: 10.3390/biomedicines10112734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
This study was conducted to evaluate the distribution of respiratory viral pathogens in the emergency department during the coronavirus disease 2019 (COVID-19) pandemic. Between May 2020 and September 2022, patients aged between 0.1 and 98 years arrived at the emergency department of Asia University Hospital, and samples from nasopharyngeal swabs were tested by the FilmArrayTM Respiratory Panel (RP). SARS-CoV-2 positivity was subsequently retested by the cobas Liat system. There were 804 patients for whom the FilmArrayTM RP was tested, and 225 (27.9%) of them had positive results for respiratory viruses. Rhinovirus/enterovirus was the most commonly detected pathogen, with 170 (61.8%) cases, followed by adenovirus with 38 (13.8%), SARS-CoV-2 with 16 (5.8%) cases, and coronavirus 229E, with 16 (5.8%) cases. SARS-CoV-2 PCR results were positive in 16 (5.8%) cases, and there were two coinfections of SARS-CoV-2 with adenovirus and rhinovirus/enterovirus. A total of 43 (5.3%) patients were coinfected; the most coinfection was adenovirus plus rhinovirus/enterovirus, which was detectable in 18 (41.9%) cases. No atypical pathogens were found in this study. Intriguingly, our results showed that there was prefect agreement between the detection of SARS-CoV-2 conducted with the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test and the FilmArrayTM RP. Therefore, the FilmArrayTM RP assay is a reliable and feasible method for the detection of SARS-CoV-2. In summary, FilmArrayTM RP significantly broadens our capability to detect multiple respiratory infections due to viruses and atypical bacteria. It provides a prompt evaluation of pathogens to enhance patient care and clinical selection strategies in emergency departments during the COVID-19 pandemic.
Collapse
|
30
|
Butler KS, Carson BD, Podlevsky JD, Mayes CM, Rowland JM, Campbell D, Ricken JB, Wudiri G, Timlin JA. Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting. Sci Rep 2022; 12:17733. [PMID: 36273023 PMCID: PMC9587995 DOI: 10.1038/s41598-022-22106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/10/2022] [Indexed: 01/18/2023] Open
Abstract
For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.
Collapse
Affiliation(s)
- Kimberly S Butler
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Bryan D Carson
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Joshua D Podlevsky
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Cathryn M Mayes
- WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jessica M Rowland
- Global Chemical and Biological Security, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - DeAnna Campbell
- Biological and Chemical Sensors Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - J Bryce Ricken
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - George Wudiri
- Cooperative Nuclear Counterproliferation, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jerilyn A Timlin
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
- Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
| |
Collapse
|
31
|
Cao G, Huo D, Chen X, Wang X, Zhou S, Zhao S, Luo X, Hou C. Automated, portable, and high-throughput fluorescence analyzer (APHF-analyzer) and lateral flow strip based on CRISPR/Cas13a for sensitive and visual detection of SARS-CoV-2. Talanta 2022; 248:123594. [PMID: 35653961 PMCID: PMC9135497 DOI: 10.1016/j.talanta.2022.123594] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/13/2022] [Accepted: 05/25/2022] [Indexed: 01/17/2023]
Abstract
COVID-19 has erupted and quickly swept across the globe, causing huge losses to human health and wealth. It is of great value to develop a quick, accurate, visual, and high-throughput detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we developed a biosensor based on CRISPR/Cas13a combined with recombinase polymerase amplification (RPA) to detect S and Orf1ab genes of SARS-CoV-2 within 30 min. Most important of all, we developed an automated, portable, and high-throughput fluorescence analyzer (APHF-analyzer) with a 3D-printed microfluidic chip for sensitively detecting SARS-CoV-2, which addressed aerosol contamination issue and provided a more accurate and high-throughput detection during the on-site detection process. The detection limits of S gene and Orf1ab gene were as low as 0.68 fM and 4.16 fM. Furthermore, we used the lateral flow strip to realize visualization and point of care testing (POCT) of SARS-CoV-2. Therefore, profit from the efficient amplification of RPA and the high specificity of CRISPR/Cas13a, APHF-analyzer and the lateral flow strip to simultaneous detection of S gene and Orf1ab gene would be applied as a promising tool in the field of SARS-CoV-2 detection.
Collapse
Affiliation(s)
- Gaihua Cao
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China,Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China
| | - Xiaolong Chen
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Xianfeng Wang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Shiying Zhou
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Shixian Zhao
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China,Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, China,Corresponding author. Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, China
| | - Xiaogang Luo
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China,Corresponding author
| | - Changjun Hou
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, PR China,Corresponding author
| |
Collapse
|
32
|
Ellis JE, Guest P, Lawson V, Loecherbach J, Lindner N, McCulloch A. Performance Evaluation of the Microfluidic Antigen LumiraDx SARS-CoV-2 and Flu A/B Test in Diagnosing COVID-19 and Influenza in Patients with Respiratory Symptoms. Infect Dis Ther 2022; 11:2099-2109. [PMID: 36152227 PMCID: PMC9510530 DOI: 10.1007/s40121-022-00696-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) and influenza share similar symptoms, which hampers diagnosis. Given that they require different containment and treatment strategies, fast and accurate distinction between the two infections is needed. This study evaluates the sensitivity and specificity of the microfluidic antigen LumiraDx SARS-CoV-2 and Flu A/B Test for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B from a single nasal swab. Methods Nasal samples were collected from patients as part of the ASPIRE (NCT04557046) and INSPIRE (NCT04288921) studies at point-of-care testing sites in the USA. ASPIRE study participants were included after developing COVID-19 symptoms in the last 14 days or following a positive SARS-CoV-2 test in the last 48 h. INSPIRE study participants were included after developing influenza symptoms in the last 4 days. Samples were extracted into proprietary buffer and analysed using the LumiraDx SARS-CoV-2 and Flu A/B Test. A reference sample was taken from each subject, placed into universal transport medium and tested using reference SARS-CoV-2 and influenza reverse transcription polymerase chain reaction (RT-PCR) tests. The test and reference samples were compared using the positive percent agreement (PPA) and negative percent agreement (NPA), together with their 95% confidence intervals (CIs). Results Analysis of the data from the ASPIRE (N = 124) and INSPIRE (N = 159) studies revealed high levels of agreement between the LumiraDx SARS-CoV-2 and Flu A/B Test and the reference tests in detecting SARS-CoV-2 (PPA = 95.5% [95% CI 84.9%, 98.7%]; NPA = 96.0% [95% CI 90.9%, 98.3%]), influenza A (PPA = 83.3% [95% CI 66.4%, 92.7%]; NPA = 97.7% [95% CI 93.4%, 99.2%]) and influenza B (PPA = 80.0% [95% CI 62.7%, 90.5%]; NPA = 95.3% [95% CI 90.2%, 97.9%]). Conclusions The LumiraDx SARS-CoV-2 and Flu A/B Test shows a high agreement with the reference RT-PCR tests while simultaneously detecting and differentiating between SARS-CoV-2 and influenza A/B. Trial Registration ClinicalTrials.gov identifiers NCT04557046 and NCT04288921. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00696-8.
Collapse
Affiliation(s)
- Jayne E Ellis
- LumiraDx Ltd, Stirling, UK. .,LumiraDx Ltd, 3 More London Riverside, London, SE1 2AQ, UK.
| | | | | | | | | | | |
Collapse
|
33
|
Advances in the Biology, Detection Techniques, and Clinical Applications of Circulating Tumor Cells. JOURNAL OF ONCOLOGY 2022; 2022:7149686. [PMID: 36090904 PMCID: PMC9462976 DOI: 10.1155/2022/7149686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022]
Abstract
Circulating tumor cells (CTCs) play a crucial role in tumor recurrence and metastasis, and their early detection has shown remarkable benefits in clinical theranostics. However, CTCs are extremely rare, thus detecting them in the blood is very challenging. New CTC detection techniques are continuously being developed, enabling deeper analysis of CTC biology and potential clinical application. This article reviews current CTC detection techniques and their clinical application. CTCs have provided, and will continue to provide, important insights into the process of metastasis, which could lead to development of new therapies for different cancers.
Collapse
|
34
|
Lu M, Joung Y, Jeon CS, Kim S, Yong D, Jang H, Pyun SH, Kang T, Choo J. Dual-mode SERS-based lateral flow assay strips for simultaneous diagnosis of SARS-CoV-2 and influenza a virus. NANO CONVERGENCE 2022; 9:39. [PMID: 36063218 PMCID: PMC9441817 DOI: 10.1186/s40580-022-00330-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/15/2022] [Indexed: 05/28/2023]
Abstract
Since COVID-19 and flu have similar symptoms, they are difficult to distinguish without an accurate diagnosis. Therefore, it is critical to quickly and accurately determine which virus was infected and take appropriate treatments when a person has an infection. This study developed a dual-mode surface-enhanced Raman scattering (SERS)-based LFA strip that can diagnose SARS-CoV-2 and influenza A virus with high accuracy to reduce the false-negative problem of the commercial colorimetric LFA strip. Furthermore, using a single strip, it is feasible to detect SARS-CoV-2 and influenza A virus simultaneously. A clinical test was performed on 39 patient samples (28 SARS-CoV-2 positives, 6 influenza A virus positives, and 5 negatives), evaluating the clinical efficacy of the proposed dual-mode SERS-LFA strip. Our assay results for clinical samples show that the dual-mode LFA strip significantly reduced the false-negative rate for both SARS-CoV-2 and influenza A virus.
Collapse
Affiliation(s)
- Mengdan Lu
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea
| | - Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea
| | - Chang Su Jeon
- R&D Center, Speclipse Inc., Seongnam, 13461, South Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, 52727, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Sung Hyun Pyun
- R&D Center, Speclipse Inc., Seongnam, 13461, South Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul, 06974, South Korea.
| |
Collapse
|
35
|
Filchakova O, Dossym D, Ilyas A, Kuanysheva T, Abdizhamil A, Bukasov R. Review of COVID-19 testing and diagnostic methods. Talanta 2022; 244:123409. [PMID: 35390680 PMCID: PMC8970625 DOI: 10.1016/j.talanta.2022.123409] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/09/2023]
Abstract
More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.
Collapse
Affiliation(s)
- Olena Filchakova
- Biology Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Dina Dossym
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Aisha Ilyas
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Tamila Kuanysheva
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Altynay Abdizhamil
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Rostislav Bukasov
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan.
| |
Collapse
|
36
|
Kim TY, Kim JY, Shim HJ, Yun SA, Jang JH, Huh HJ, Kim JW, Lee NY. Performance Evaluation of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-Time PCR Kit in Comparison with the BioFire Respiratory Panel. Ann Lab Med 2022; 42:473-477. [PMID: 35177568 PMCID: PMC8859561 DOI: 10.3343/alm.2022.42.4.473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/27/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses may pose enormous challenges to our healthcare system. We evaluated the performance of the PowerChek SARS-CoV-2, Influenza A & B Multiplex Real-time PCR Kit (PowerChek; Kogene Biotech, Seoul, Korea) in comparison with the BioFire Respiratory Panels 2 and 2.1 (RP2 and RP2.1; bioMérieux, Marcy l’Étoile, France), using 147 nasopharyngeal swabs. The limit of detection (LOD) of the PowerChek assay was determined using SARS-CoV-2, influenza A, and B RNA standards. The LOD values of the PowerChek assay for SARS-CoV-2 and influenza A and B were 1.12, 1.24, and 0.61 copies/μL, respectively. The positive and negative percent agreements of the PowerChek assay compared with RP2 and RP2.1 were 97.5% (39/40) and 100% (107/107) for SARS-CoV-2; 100% (39/39) and 100% (108/108) for influenza A; and 100% (35/35) and 100% (112/112) for influenza B, respectively. The performance of the PowerChek assay was comparable to that of RP2 and RP2.1 for detecting SARS-CoV-2 and influenza A and B, suggesting its use in diagnosing SARS-CoV-2 and influenza infections.
Collapse
Affiliation(s)
- Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
37
|
Havasi A, Visan S, Cainap C, Cainap SS, Mihaila AA, Pop LA. Influenza A, Influenza B, and SARS-CoV-2 Similarities and Differences – A Focus on Diagnosis. Front Microbiol 2022; 13:908525. [PMID: 35794916 PMCID: PMC9251468 DOI: 10.3389/fmicb.2022.908525] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/23/2022] [Indexed: 12/23/2022] Open
Abstract
In late December 2019, the first cases of viral pneumonia caused by an unidentified pathogen were reported in China. Two years later, SARS-CoV-2 was responsible for almost 450 million cases, claiming more than 6 million lives. The COVID-19 pandemic strained the limits of healthcare systems all across the world. Identifying viral RNA through real-time reverse transcription-polymerase chain reaction remains the gold standard in diagnosing SARS-CoV-2 infection. However, equipment cost, availability, and the need for trained personnel limited testing capacity. Through an unprecedented research effort, new diagnostic techniques such as rapid diagnostic testing, isothermal amplification techniques, and next-generation sequencing were developed, enabling accurate and accessible diagnosis. Influenza viruses are responsible for seasonal outbreaks infecting up to a quarter of the human population worldwide. Influenza and SARS-CoV-2 present with flu-like symptoms, making the differential diagnosis challenging solely on clinical presentation. Healthcare systems are likely to be faced with overlapping SARS-CoV-2 and Influenza outbreaks. This review aims to present the similarities and differences of both infections while focusing on the diagnosis. We discuss the clinical presentation of Influenza and SARS-CoV-2 and techniques available for diagnosis. Furthermore, we summarize available data regarding the multiplex diagnostic assay of both viral infections.
Collapse
Affiliation(s)
- Andrei Havasi
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, Cluj-Napoca, Romania
| | - Simona Visan
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, Cluj-Napoca, Romania
| | - Calin Cainap
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, Cluj-Napoca, Romania
| | - Simona Sorana Cainap
- Pediatric Clinic No. 2, Department of Pediatric Cardiology, Emergency County Hospital for Children, Cluj-Napoca, Romania
- Department of Mother and Child, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- *Correspondence: Simona Sorana Cainap, ;
| | - Alin Adrian Mihaila
- Faculty of Economics and Business Administration, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Laura-Ancuta Pop
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| |
Collapse
|
38
|
Mouliou DS. Managing Viral Emerging Infectious Diseases via current Molecular Diagnostics in the Emergency Department: the Tricky Cases. Expert Rev Anti Infect Ther 2022; 20:1163-1169. [PMID: 35702989 DOI: 10.1080/14787210.2022.2089653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Emerging infectious diseases' diagnosis has been a major problem in most hospitals and other senior care facilities, especially for the current Coronavirus Disease 2019 (COVID-19). The various clinical manifestations, and the several radiology and laboratory data combined with the misleading test results for identifying the virus, are responsible for certain misdiagnoses, especially for suspected cases that visit the emergency department and require urgent management and further treatment. AREAS COVERED The major challenges for emerging infectious diseases' molecular diagnosis are being described here on a great scale, and, finally, strategies for a precise and on-the-spot molecular diagnosis are thoroughly discussed. Related literature was searched using the PubMed, Science Direct, and EMBASE databases published until May 2022 on the general information for viral infections and relevant false test results. EXPERT OPINION Emerging diseases' molecular diagnosis via current common diagnostic assays seems to be extremely tricky, and front-line physicians and other senior care facilities should be able to recognize some falsely diagnosed cases or even prevent their existence. Further biotechnologic revolution concerning viral molecular diagnostics will be evident in the near future, thus new methods' limitations should be highlighted to physicians from the very beginning of their performances and wide utilization.
Collapse
Affiliation(s)
- Dimitra S Mouliou
- Faculty of Medicine, University of Thessaly, BIOPOLIS, Larisa, Greece
| |
Collapse
|
39
|
Emergency SARS-CoV-2 variants of concern: rapidly direct RT-qPCR detection without RNA extraction, clinical comparison, cost-effective, and high-throughput. Aging (Albany NY) 2022; 14:4624-4633. [PMID: 35657641 PMCID: PMC9217698 DOI: 10.18632/aging.204095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Abstract
Since the late 2020, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern has been characterized by the emergence of spike protein mutations, and these variants have become dominant worldwide. The gold standard SARS-CoV-2 diagnosis protocol requires two complex processes, namely, RNA extraction and real-time reverse transcriptase polymerase chain reaction (RT-PCR). There is a need for a faster, simpler, and more cost-effective detection strategy that can be utilized worldwide, especially in developing countries. We propose the novel use of direct RT-qPCR, which does not require RNA extraction or a preheating step. For the detection, retrospectively, we used 770 clinical nasopharyngeal swabs, including positive and negative samples. The samples were subjected to RT-qPCR in the N1 and E genes using two different thermocyclers. The limit of detection was 30 copies/reaction for N1 and 60 copies/reaction for E. Analytical sensitivity was assessed for the developed direct RT-qPCR; the sensitivity was 95.69%, negative predictive value was 99.9%, accuracy of 99.35%, and area under the curve was 0.978. This novel direct RT-qPCR diagnosis method without RNA extraction is a reliable and high-throughput alternative method that can significantly save cost, labor, and time during the coronavirus disease 2019 pandemic.
Collapse
|
40
|
Comparative Performance Evaluation of FilmArray BioFire RP2.1 and MAScIR 2.0 Assays for SARS-CoV-2 Detection. Adv Virol 2022; 2022:4510900. [PMID: 35693128 PMCID: PMC9177333 DOI: 10.1155/2022/4510900] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022] Open
Abstract
Background RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory's reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit. Results Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations. Conclusion The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory's reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.
Collapse
|
41
|
Hartnett J, Donga P, Ispas G, Vandendijck Y, Anderson D, House S, Suner S. Risk factors and medical resource utilization in US adults hospitalized with influenza or respiratory syncytial virus in the Hospitalized Acute Respiratory Tract Infection study. Influenza Other Respir Viruses 2022; 16:906-915. [PMID: 35474419 PMCID: PMC9343339 DOI: 10.1111/irv.12994] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 12/02/2022] Open
Abstract
Background Influenza and respiratory syncytial virus (RSV) are associated with substantial morbidity and mortality in the United States. We assessed risk factors for severe disease and medical resource utilization (MRU) among US adults hospitalized with influenza or RSV in the Hospitalized Acute Respiratory Tract Infection (HARTI) study. Methods HARTI was a prospective global (40 centers, 12 countries) epidemiological study of adults hospitalized with acute respiratory tract infections conducted across the 2017–2019 epidemic seasons. Patients with confirmed influenza or RSV were followed up to 3 months post‐discharge. Baseline characteristics, prevalence of core risk factors (CRFs) for severe disease (age ≥65 years, chronic heart or renal disease, chronic obstructive pulmonary disease, or asthma), and MRU were summarized descriptively. Results The US cohort included 280 influenza‐positive and 120 RSV‐positive patients. RSV patients were older (mean: 63.1 vs. 59.7 years) and a higher proportion had CRFs (87.5% vs. 81.4%). Among those with CRFs (influenza, n = 153; RSV, n = 99), RSV patients required longer hospitalizations (median length of stay: 4.5 days) and a greater proportion (79.8%) required oxygen supplementation during hospitalization compared with influenza patients (4.0 days and 59.5%, respectively). At 3 months post‐discharge, a greater proportion of RSV patients with CRFs reported use of antibiotics, antitussives, bronchodilators, and inhaled and systemic steroids versus those with influenza and CRFs. Many patients with CRFs reported hospital readmission at 3 months post‐discharge (RSV: 13.4%; influenza: 11.9%). Conclusions MRU during and post‐hospitalization due to RSV in adults is similar to or greater than that of influenza. Enhanced RSV surveillance and preventive and therapeutic interventions are needed.
Collapse
Affiliation(s)
| | - Prina Donga
- Janssen Scientific Affairs, LLC, Titusville, New Jersey, USA
| | | | | | - David Anderson
- Janssen Scientific Affairs, LLC, Titusville, New Jersey, USA
| | - Stacey House
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Selim Suner
- Department of Emergency Medicine, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| |
Collapse
|
42
|
Mathematical Model and Optimization Methods of Wide-Scale Pooled Sample Testing for COVID-19. MATHEMATICS 2022. [DOI: 10.3390/math10071183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, coronavirus disease 2019 (COVID-19) has become the most severe infectious disease affecting the world, which has spread around the world to more than 200 countries in 2020. Until the number of COVID-19 vaccines is insufficient, nucleic acid testing is considered as an effective way to screen virus carriers and control the spread of the virus. Considering that the medical resources and infection rates are different across various countries and regions, if all infected areas adopt the traditional individual nucleic acid testing method, the workload will be heavy and time-consuming. Therefore, this will not lead to the control of the pandemic. After Wuhan completed a citywide nucleic acid testing in May 2020, China basically controlled the spread of COVID-19 and entered the post-epidemic period. Since then, although some cities in China, such as Qingdao, Xinjiang, Beijing, and Dalian, have experienced a local epidemic resurgence, the pandemic was quickly suppressed through wide-scale pooled nucleic acid testing methods. Combined with the successful experience of mass nucleic acid testing in China, this study introduces two main pooled testing methods used in two cities with a population of more than ten million people, Wuhan’s “five-in-one” and Qingdao’s “ten-in-one” rapid pooled testing methods. This study proposes an improved method for optimising the second round of “ten-in-one” pooled testing, known as “the pentagram mini-pooled testing method”, which speeds up the testing process (as a result of reducing the numbers of testing by 40%) and significantly reduces the cost. Qingdao’s optimised “ten-in-one” pooled testing method quickly screens out the infections by running fewer testing samples. This study also mathematically examines the probabilistic principles and applicability conditions for pooled testing of COVID-19. Herein, the study theoretically determines the optimal number of samples that could successfully be combined into a pool under different infection rates. Then, it quantitatively discusses the applicability and principles for choosing the pooled testing instead of individual testing. Overall, this research offers a reference for other countries with different infection rates to help them in implementing the mass testing for COVID-19 to reduce the spread of coronavirus.
Collapse
|
43
|
Özdemir Ö, Dikici Ü. Coinfection between SARS‐CoV‐2 and other respiratory tract viruses. J Clin Lab Anal 2022; 36:e24365. [PMID: 35373384 PMCID: PMC9110981 DOI: 10.1002/jcla.24365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Öner Özdemir
- Division of Allergy and Immunology Department of Pediatrics Faculty of Medicine Research and Training Hospital of Sakarya University Sakarya University Sakarya Turkey
| | - Ümmügülsüm Dikici
- Division of Allergy and Immunology Department of Pediatrics Faculty of Medicine Research and Training Hospital of Sakarya University Sakarya University Sakarya Turkey
| |
Collapse
|
44
|
Chen H, Park SK, Joung Y, Kang T, Lee MK, Choo J. SERS-based dual-mode DNA aptasensors for rapid classification of SARS-CoV-2 and influenza A/H1N1 infection. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 355:131324. [PMID: 34987275 PMCID: PMC8716169 DOI: 10.1016/j.snb.2021.131324] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 05/02/2023]
Abstract
We developed a dual-mode surface-enhanced Raman scattering (SERS)-based aptasensor that can accurately diagnose and distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/H1N1 at the same time. Herein, DNA aptamers that selectively bind to SARS-CoV-2 and influenza A/H1N1 were immobilized together on Au nanopopcorn substrate. Raman reporters (Cy3 and RRX), attached to the terminal of DNA aptamers, could generate strong SERS signals in the nanogap of the Au nanopopcorn substrate. Additionally, the internal standard Raman reporter (4-MBA) was immobilized on the Au nanopopcorn substrate along with aptamer DNAs to reduce errors caused by changes in the measurement environment. When SARS-CoV-2 or influenza A virus approaches the Au nanopopcorn substrate, the corresponding DNA aptamer selectively detaches from the substrate due to the significant binding affinity between the corresponding DNA aptamer and the virus. As a result, the related SERS intensity decreases with increasing target virus concentration. Thus, it is possible to determine whether a suspected patient is infected with SARS-CoV-2 or influenza A using this SERS-based DNA aptasensor. Furthermore, this sensor enables a quantitative evaluation of the target virus concentration with high sensitivity without being affected by cross-reactivity. Therefore, this SERS-based diagnostic platform is considered a conceptually new diagnostic tool that rapidly discriminates against these two respiratory diseases to prevent their spread.
Collapse
Affiliation(s)
- Hao Chen
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Sung-Kyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon 51508, South Korea
| | - Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul 06973, South Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| |
Collapse
|
45
|
Gard L, Fliss M, Bosma F, ter Veen D, Niesters H. Validation and verification of the GeneFinder™ COVID-19 Plus RealAmp kit on the ELITe InGenius® instrument. J Virol Methods 2022; 300:114378. [PMID: 34838535 PMCID: PMC8611827 DOI: 10.1016/j.jviromet.2021.114378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 02/09/2023]
Abstract
BACKGROUND Throughout the SARS-CoV-2 pandemic, a rapid identification of the virus was essential to quickly recognize positive cases and limit further spread by applying appropriate infection prevention. Many diagnostic laboratories use a multiplex Real-Time PCR assay, as they are not only highly sensitive but also specific. Currently, there are several assays and platforms in the market available which target different SARS-CoV-2 genes. The aim of this study was to validate and verify the GeneFinder™ COVID-19 PLUS RealAmp kit on the ELITe InGenius® instrument and compare to the national reference method. METHODS GeneFinder™ COVID-19 PLUS RealAmp kit was evaluated against the routine WHO in- house Real-Time PCR assay, which is also the national reference method in the Netherlands and used in our laboratory. The sensitivity was tested using the analytical panel from Qnostics (Glasgow, United Kingdom) and the specificity was tested with patient material comprising of other seasonal respiratory viruses. In addition, 96 clinical samples initially analyzed by routine Real-Time PCR were tested using the GeneFinder™ COVID-19 PLUS RealAmp kit on the ELITe InGenius® instrument. RESULTS The GeneFinder™ COVID-19 PLUS RealAmp kit had a similar performance compared to routine in-house testing, with a limit of detection of 500 dC/mL for the RdRp-gene and E gene. Meanwhile, the N gene showed a limit of detection of 50 dC/mL. The SARS-CoV-2 test was highly specific and detected no other respiratory viruses. The results of the clinical samples were comparable between both assays with similar Ct values observed for the in-house Real-Time-PCR and the GeneFinder™ COVID-19 PLUS RealAmp kit for the N gene. CONCLUSION The GeneFinder™ COVID-19 PLUS RealAmp kit on the ELITe InGenius® instrument had an appropriate sensitivity and specificity that could be used in small scale laboratories or during night shifts where accurate diagnostics are crucial.
Collapse
Affiliation(s)
- L. Gard
- Corresponding author at: Department of Medical Microbiology & Infection Prevention, Unit Molecular & Serology, The University of Groningen, University Medical Centre Groningen, MVC Building, Room 67.1.35, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands
| | | | | | | | | |
Collapse
|
46
|
Renaud C, Kollef MH. Classical and Molecular Techniques to Diagnose HAP/VAP. Semin Respir Crit Care Med 2022; 43:219-228. [PMID: 35042263 DOI: 10.1055/s-0041-1739359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nosocomial pneumonia, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), are the most common nosocomial infections occurring in critically ill patients requiring intensive care. However, challenges exist in making a timely and accurate diagnosis of HAP and VAP. Under diagnosis of HAP and VAP can result in greater mortality risk, especially if accompanied by delays in the administration of appropriate antimicrobial treatment. Over diagnosis of HAP and VAP results in the unnecessary administration of broad spectrum antibiotics that can lead to further escalation of antibiotic resistance. Optimal diagnosis and management of HAP and VAP require a systematic approach that combines clinical and radiographic assessments along with proper microbiologic techniques. The use of more invasive sampling methods (bronchoalveolar lavage and protected specimen brush) may enhance specimen collection resulting in more specific diagnoses to limit unnecessary antibiotic exposure. Molecular techniques, currently in use and investigational technique, may improve the diagnosis of HAP and VAP by allowing more rapid identification of offending pathogens, if present, thus increasing both appropriate antibiotic treatment and avoiding unnecessary drug exposure.
Collapse
Affiliation(s)
- Cherie Renaud
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
47
|
Mboumba Bouassa RS, Tonen-Wolyec S, Veyer D, Péré H, Bélec L. Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens. PLoS One 2022; 17:e0262258. [PMID: 34986156 PMCID: PMC8730414 DOI: 10.1371/journal.pone.0262258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.
Collapse
Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Serge Tonen-Wolyec
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Faculty of Medicine and Pharmacy, University of Kisangani, Kisangani, The Democratic Republic of the Congo
| | - David Veyer
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
48
|
Lapa SA, Miftakhov RA, Klochikhina ES, Ammur YI, Blagodatskikh SA, Shershov VE, Zasedatelev AS, Chudinov AV. Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens. Mol Biol 2021; 55:828-838. [PMID: 34955557 PMCID: PMC8682033 DOI: 10.1134/s0026893321040063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]
Abstract
A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.
Collapse
Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Yu I Ammur
- Mechnikov Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - S A Blagodatskikh
- Scientific Center of Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - V E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
49
|
Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Chang FY, Hung KS, Chen ES, Yang MH, Shang HS. Multicenter study evaluating one multiplex RT-PCR assay to detect SARS-CoV-2, influenza A/B, and respiratory syncytia virus using the LabTurbo AIO open platform: epidemiological features, automated sample-to-result, and high-throughput testing. Aging (Albany NY) 2021; 13:24931-24942. [PMID: 34897035 PMCID: PMC8714143 DOI: 10.18632/aging.203761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/23/2021] [Indexed: 04/20/2023]
Abstract
Since the Coronavirus 19 (COVID-19) pandemic, several SARS-CoV-2 variants of concern (SARS-CoV-2 VOC) have been reported. The B.1.1.7 variant has been associated with increased mortality and transmission risk. Furthermore, cluster and possible co-infection cases could occur in the next influenza season or COVID-19 pandemic wave, warranting efficient diagnosis and treatment decision making. Here, we aimed to detect SARS-CoV-2 and other common respiratory viruses using multiplex RT-PCR developed on the LabTurbo AIO 48 open system. We performed a multicenter study to evaluate the performance and analytical sensitivity of the LabTurbo AIO 48 system for SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) using 652 nasopharyngeal swab clinical samples from patients. The LabTurbo AIO 48 system demonstrated a sensitivity of 9.4 copies/per PCR for N2 of SARS-CoV-2; 24 copies/per PCR for M of influenza A and B; and 24 copies/per PCR for N of RSV. The assay presented consistent performance in the multicenter study. The multiplex RT-PCR applied on the LabTurbo AIO 48 open platform provided highly sensitive, robust, and accurate results and enabled high-throughput detection of B.1.1.7, influenza A/B, and RSV with short turnaround times. Therefore, this automated molecular diagnostic assay could enable streamlined testing if COVID-19 becomes a seasonal disease.
Collapse
Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - En-Sung Chen
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan, ROC
| | - Mei-Hsiu Yang
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| |
Collapse
|
50
|
Manzanas C, Alam MM, Loeb JC, Lednicky JA, Wu CY, Fan ZH. A Valve-Enabled Sample Preparation Device with Isothermal Amplification for Multiplexed Virus Detection at the Point-of-Care. ACS Sens 2021; 6:4176-4184. [PMID: 34767357 PMCID: PMC8609915 DOI: 10.1021/acssensors.1c01718] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses at the point-of-care is crucial for reducing disease transmission during the current pandemic and future flu seasons. To prepare for potential cocirculation of these two viruses, we report a valve-enabled, paper-based sample preparation device integrated with isothermal amplification for their simultaneous detection. The device incorporates (1) virus lysis and RNA enrichment, enabled by ball-based valves for sequential delivery of reagents with no pipet requirement, (2) reverse transcription loop-mediated isothermal amplification, carried out in a coffee mug, and (3) colorimetric detection. We have used the device for simultaneously detecting inactivated SARS-CoV-2 and influenza A H1N1 viruses in 50 min, with limits of detection at 2 and 6 genome equivalents, respectively. The device was further demonstrated to detect both viruses in environmental samples.
Collapse
Affiliation(s)
- Carlos Manzanas
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P. O. Box 116250, Gainesville, Florida 32611, United States
| | - Md Mahbubul Alam
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Julia C Loeb
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - John A Lednicky
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Chang-Yu Wu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P. O. Box 116250, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|