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Generalov V, Cheremiskina A, Glukhov A, Grabezhova V, Kruchinina M, Safatov A. Investigation of Limitations in the Detection of Antibody + Antigen Complexes Using the Silicon-on-Insulator Field-Effect Transistor Biosensor. SENSORS (BASEL, SWITZERLAND) 2023; 23:7490. [PMID: 37687945 PMCID: PMC10490761 DOI: 10.3390/s23177490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
The SOI-FET biosensor (silicon-on-insulator field-effect transistor) for virus detection is a promising device in the fields of medicine, virology, biotechnology, and the environment. However, the applications of modern biosensors face numerous problems and require improvement. Some of these problems can be attributed to sensor design, while others can be attributed to technological limitations. The aim of this work is to conduct a theoretical investigation of the "antibody + antigen" complex (AB + AG) detection processes of a SOI-FET biosensor, which may also solve some of the aforementioned problems. Our investigation concentrates on the analysis of the probability of AB + AG complex detection and evaluation. Poisson probability density distribution was used to estimate the probability of the adsorption of the target molecules on the biosensor's surface and, consequently, to obtain correct detection results. Many implicit and unexpected causes of error detection have been identified for AB + AG complexes using SOI-FET biosensors. We showed that accuracy and time of detection depend on the number of SOI-FET biosensors on a crystal.
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Affiliation(s)
- Vladimir Generalov
- Federal State Research Institution State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia; (A.C.); (A.S.)
- Faculty of Automation and Computer Engineering, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Anastasia Cheremiskina
- Federal State Research Institution State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia; (A.C.); (A.S.)
| | - Alexander Glukhov
- Design Center of Bio-Microelectronic Technology Vega, 630082 Novosibirsk, Russia; (A.G.); (V.G.)
| | - Victoria Grabezhova
- Design Center of Bio-Microelectronic Technology Vega, 630082 Novosibirsk, Russia; (A.G.); (V.G.)
| | - Margarita Kruchinina
- Research Institute of Internal and Preventive Medicine—Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630089 Novosibirsk, Russia;
| | - Alexander Safatov
- Federal State Research Institution State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia; (A.C.); (A.S.)
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Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida. Viruses 2023; 15:v15030593. [PMID: 36992302 PMCID: PMC10059866 DOI: 10.3390/v15030593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Over the course of the COVID-19 pandemic, SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and immune escape capabilities, such as Delta and Omicron, have triggered waves of new COVID-19 infections worldwide, and Omicron subvariants continue to represent a global health concern. Tracking the prevalence and dynamics of VOCs has clinical and epidemiological significance and is essential for modeling the progression and evolution of the COVID-19 pandemic. Next generation sequencing (NGS) is recognized as the gold standard for genomic characterization of SARS-CoV-2 variants, but it is labor and cost intensive and not amenable to rapid lineage identification. Here we describe a two-pronged approach for rapid, cost-effective surveillance of SARS-CoV-2 VOCs by combining reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and periodic NGS with the ARTIC sequencing method. Variant surveillance by RT-qPCR included the commercially available TaqPath COVID-19 Combo Kit to track S-gene target failure (SGTF) associated with the spike protein deletion H69-V70, as well as two internally designed and validated RT-qPCR assays targeting two N-terminal-domain (NTD) spike gene deletions, NTD156-7 and NTD25-7. The NTD156-7 RT-qPCR assay facilitated tracking of the Delta variant, while the NTD25-7 RT-qPCR assay was used for tracking Omicron variants, including the BA.2, BA.4, and BA.5 lineages. In silico validation of the NTD156-7 and NTD25-7 primers and probes compared with publicly available SARS-CoV-2 genome databases showed low variability in regions corresponding to oligonucleotide binding sites. Similarly, in vitro validation with NGS-confirmed samples showed excellent correlation. RT-qPCR assays allow for near-real-time monitoring of circulating and emerging variants allowing for ongoing surveillance of variant dynamics in a local population. By performing periodic sequencing of variant surveillance by RT-qPCR methods, we were able to provide ongoing validation of the results obtained by RT-qPCR screening. Rapid SARS-CoV-2 variant identification and surveillance by this combined approach served to inform clinical decisions in a timely manner and permitted better utilization of sequencing resources.
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Kwok HF. The significance of advanced COVID-19 diagnostic testing in pandemic control measures. Int J Biol Sci 2022; 18:4610-4617. [PMID: 35874951 PMCID: PMC9305263 DOI: 10.7150/ijbs.72837] [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: 03/13/2022] [Accepted: 05/02/2022] [Indexed: 12/11/2022] Open
Abstract
During the 2 years since the start of the novel coronavirus disease 2019 (COVID-19) pandemic, the scientific world made an enormous effort to fight against this disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has high transmissibility. Advancements in vaccine and treatment strategies have reduced both the hospitalization and mortality rates. However, the virus has shown its ability to evolve and evade from our COVID-19 combating armamentaria by the most common evolution mechanism—mutation. Diagnostic testing has been the first line of defense following the identification of the causative agent. Ever since, the scientific community has developed nuclei acid-based, antigen-based, and antibody-based diagnostic tests, and these testing methodologies are still playing a central role in slowing down viral transmission. These testing methods have different sensitivity and specificity and could be optimally used in areas facing different challenges owing to different level and conditions of COVID-19 outbreak. In this review, we discuss these testing methodologies as well as the considerations on how to apply these diagnostic tests optimally in the community to cope with the ever-changing pandemic conditions.
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Affiliation(s)
- Hang Fai Kwok
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR
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Tekin AB, Yassa M, Birol İlter P, Yavuz E, Önden B, Usta C, Budak D, Günkaya OS, Çavuşoğlu G, Taymur BD, Tuğ N. COVID-19 related maternal mortality cases in associated with Delta and Omicron waves and the role of lung ultrasound. Turk J Obstet Gynecol 2022; 19:88-97. [PMID: 35770508 PMCID: PMC9249361 DOI: 10.4274/tjod.galenos.2022.36937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/23/2022] [Indexed: 12/21/2022] Open
Abstract
Objective To present coronavirus disease-2019 (COVID-19) related maternal mortality in relation to Delta and Omicron waves and to investigate the role of lung ultrasound (LUS) in estimating mortality. Materials and Methods This retrospective cohort study was conducted in the obstetrics and gynecology clinic of a tertiary pandemic hospital between March 2020 and January 2022. The hospitalized pregnant women with COVID-19 diagnosis and maternal deaths were studied in relation with Delta and Omicron waves. The relationship between LUS scores of hospitalized patients and maternal mortality was explored. Results Thousand and sixty-five pregnant women were hospitalized because of COVID-19 infection. Fifty-one (4.79%) of these patients had critical sickness, 96 (9.01%) of them had severe illness, 62 (5.82%) of them were admitted to the intensive care unit and 28 (2.63%) of all hospitalized pregnant women had died. Of the 1.065 patients, 783 (73.5%) were hospitalized before the Delta wave and the maternal mortality rate was 1.28% (10/783), 243 (22.8%) were hospitalized during the Delta wave and the maternal mortality rate was 7% (17/243) [relative risk (RR)=5.478, 95% confidence interval (CI) (2.54-11.8), z=4.342, p<0.001]. During the Omicron wave 39 (3.66%) patients were hospitalized and the maternal mortality rate was 2.56% (1/39). Maternal mortality rates, according to LUS scores, were 0.37% (1/273) for LUS 0, 0.72% (2/277) for LUS 1, 2.58% (10/387) for LUS 2 and 11.72% (15/128) for LUS 3 respectively (LUS 3 vs. others; maternal mortality: RR=8.447, 95% CI (4.11-17.34), z=5.814, p<0.0001). There were no vaccinated patients in the study cohort. Conclusion The maternal mortality rate was relatively high, particularly during the Delta wave at our referral center. The Delta wave, delayed vaccination and vaccine hesitancy of pregnant women might have important roles in maternal mortality. Higher LUS scores should warn clinicians of an increased risk of maternal death.
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Affiliation(s)
- Arzu Bilge Tekin
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Murat Yassa
- Bahçeşehir University, VM Medical Park Maltepe Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Pınar Birol İlter
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Emre Yavuz
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Betül Önden
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Canberk Usta
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Doğuş Budak
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Osman Samet Günkaya
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Gül Çavuşoğlu
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Bilge Doğan Taymur
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
| | - Niyazi Tuğ
- University of Health Sciences Turkey, Şehit Prof. Dr. İlhan Varank Sancaktepe Training and Research Hospital, Clinic of Obstetrics and Gynecology, İstanbul, Turkey
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Borro M, Salerno G, Montori A, Petrucca A, Anibaldi P, Marcolongo A, Bonfini R, Simmaco M, Santino I. SARS-CoV-2 Transmission Control Measures in the Emergency Department: The Role of Rapid Antigenic Testing in Asymptomatic Subjects. Healthcare (Basel) 2022; 10:healthcare10050790. [PMID: 35627926 PMCID: PMC9140606 DOI: 10.3390/healthcare10050790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022] Open
Abstract
Limiting transmission of SARS-CoV-2 from asymptomatic people assumes the paramount importance of keeping fragile subjects protected. We evaluated the utility of rapid SARS-CoV-2 antigen testing in asymptomatic subjects attending emergency departments in non-COVID-19 areas, using a single nasopharyngeal swab specimen collected in universal transport medium to perform both rapid antigen testing and rRT-PCR (used as reference standard) in a cohort of 899 patients. In the overall sample, the rapid antigen test had 43.9% sensitivity, 100% specificity, 100% positive predictive value, 93.6% negative predictive value. Considering subjects with rRT-PCR cycle threshold ≤30, the test had 80.4% sensitivity, 100% specificity, 100% positive predictive value, 98.8% negative predictive value. Considering subjects with rRT-PCR cycle threshold ≤25, the test had 94.7% sensitivity, 100% specificity, 100% positive predictive value and 99.7% negative predictive value. Despite low sensitivity, routine application of rapid antigen testing in the emergency department can lead to isolation in less than 30 min of about a half of asymptomatic COVID-19 subjects assigned to non-COVID-19 areas by clinical triage. The rapid test correctly identified 94.7% of asymptomatic patients with cycle threshold ≤ 25 that are supposed to be more infective; thus, it could be a useful measure to contain viral transmission in non-COVID-19 areas.
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Affiliation(s)
- Marina Borro
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Sapienza University, Via di Grottarossa 1035/1039, 00189 Rome, Italy; (M.S.); (I.S.)
- Laboratory of Clinical Biochemistry, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
- Correspondence: (M.B.); (G.S.)
| | - Gerardo Salerno
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Sapienza University, Via di Grottarossa 1035/1039, 00189 Rome, Italy; (M.S.); (I.S.)
- Laboratory of Clinical Biochemistry, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
- Correspondence: (M.B.); (G.S.)
| | - Andrea Montori
- Microbiology Unit, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Andrea Petrucca
- Laboratory of Clinical Biochemistry, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Paolo Anibaldi
- Medical Direction, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Adriano Marcolongo
- General Direction, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Rita Bonfini
- Emergency Department Unit, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Maurizio Simmaco
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Sapienza University, Via di Grottarossa 1035/1039, 00189 Rome, Italy; (M.S.); (I.S.)
- Laboratory of Clinical Biochemistry, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
| | - Iolanda Santino
- Department of Neurosciences, Mental Health and Sensory Organs (NESMOS), Sapienza University, Via di Grottarossa 1035/1039, 00189 Rome, Italy; (M.S.); (I.S.)
- Microbiology Unit, Sant’Andrea University Hospital, Via di Grottarossa 1035, 00189 Rome, Italy;
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Instrum RS, Koch RW, Rocha T, Rohani SA, Ladak H, Agrawal SK, Sowerby LJ. Improving Nasopharyngeal Swab Technique via Simulation for Frontline Workers. Laryngoscope 2022; 133:38-42. [PMID: 35102548 PMCID: PMC9015425 DOI: 10.1002/lary.30034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVES/HYPOTHESIS Nasopharyngeal swabs currently remain the gold standard for COVID-19 sample collection. A surge in testing volume has resulted in a large number of health care workers who are unfamiliar with nasal anatomy performing this test, which can lead to improper collection practices culminating in false-negative results and complications. Therefore, we aimed to assess the accuracy and educational potential of a realistic 3D-printed nasal swab simulator to expedite health care workers' skill acquisition. STUDY DESIGN Prospective pre-post interventional study. METHODS A nasal swab task trainer (NSTT) was developed to scale from computed tomography data with a deviated septum. Frontline workers at COVID-19 testing sites in Ontario, Canada, were recruited to use the NSTT for nasopharyngeal swab training. Integrated video recording capability allowed participants to self-evaluate procedure accuracy. A five-point Likert scale was collected regarding the NSTT's educational value and procedural fidelity. RESULTS Sixty-two frontline workers included in the study were primarily registered nurses (52%) or paramedics (16%). Following simulator use, self-assessed accuracy improved in 77% of all participants and 100% of participants who expressed low confidence before training. Ninety-four percent reported that the NSTT provided a complete educational experience, and 82% regarded the system as a more effective training approach than what is currently available. Eighty-one indicated that the simulator should be used at all COVID-19 testing sites, with 77% stating province-wide implementation was warranted. CONCLUSIONS The nasal swab task trainer is an effective educational tool that appears well-suited for improved skill acquisition in COVID-19 testing and may be useful for training other nasal swab applications. LEVEL OF EVIDENCE 3 Laryngoscope, 133:38-42, 2023.
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Affiliation(s)
- Ryan S. Instrum
- Department of Otolaryngology–Head and Neck Surgery, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
| | - Robert W. Koch
- School of Biomedical EngineeringWestern UniversityLondonOntarioCanada
| | - Taciano Rocha
- Department of Otolaryngology–Head and Neck Surgery, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
| | - Seyed Alizera Rohani
- Department of Otolaryngology–Head and Neck Surgery, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
| | - Hanif Ladak
- Department of Electrical and Computer EngineeringWestern UniversityLondonOntarioCanada
| | - Sumit K. Agrawal
- Department of Otolaryngology–Head and Neck Surgery, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
| | - Leigh J Sowerby
- Department of Otolaryngology–Head and Neck Surgery, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
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