1
|
Omar RF, Boissinot M, Huletsky A, Bergeron MG. Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention. Infect Dis Rep 2024; 16:216-227. [PMID: 38525764 PMCID: PMC10961803 DOI: 10.3390/idr16020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.
Collapse
Affiliation(s)
- Rabeea F. Omar
- Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (M.B.); (A.H.); (M.G.B.)
| | | | | | | |
Collapse
|
2
|
Krause E, Michel J, Puyskens A, Hofmann N, Rinner T, Biere B, Dorner BG, Skiba M, Schaade L, Nitsche A. Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic. Virol J 2023; 20:139. [PMID: 37408040 DOI: 10.1186/s12985-023-02088-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. METHODS We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. RESULTS All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. CONCLUSION Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.
Collapse
Affiliation(s)
- Eva Krause
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany.
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Puyskens
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Natalie Hofmann
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Barbara Biere
- Department for Infectious Diseases, Unit Influenza and Other Respiratory Viruses (FG 17), Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Martin Skiba
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| |
Collapse
|
3
|
Supplisson O, Charmet T, Galmiche S, Schaeffer L, Chény O, Lévy A, Jeandet N, Omar F, David C, Mailles A, Fontanet A. SARS-CoV-2 self-test uptake and factors associated with self-testing during Omicron BA.1 and BA.2 waves in France, January to May 2022. Euro Surveill 2023; 28:2200781. [PMID: 37140451 PMCID: PMC10161682 DOI: 10.2807/1560-7917.es.2023.28.18.2200781] [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: 09/28/2022] [Accepted: 03/03/2023] [Indexed: 05/05/2023] Open
Abstract
BackgroundFollowing the SARS-CoV-2 Omicron variant spread, the use of unsupervised antigenic rapid diagnostic tests (self-tests) increased.AimThis study aimed to measure self-test uptake and factors associated with self-testing.MethodsIn this cross-sectional study from 20 January to 2 May 2022, the case series from a case-control study on factors associated with SARS-CoV-2 infection were used to analyse self-testing habits in France. A multivariable quasi-Poisson regression was used to explore the variables associated with self-testing among symptomatic cases who were not contacts of another infected individual. The control series from the same study was used as a proxy for the self-test background rate in the non-infected population of France.ResultsDuring the study period, 179,165 cases who tested positive through supervised tests were recruited. Of these, 64.7% had performed a self-test in the 3 days preceding this supervised test, of which 79,038 (68.2%) were positive. The most frequently reported reason for self-testing was the presence of symptoms (64.6%). Among symptomatic cases who were not aware of being contacts of another case, self-testing was positively associated with being female, higher education, household size, being a teacher and negatively associated with older age, not French by birth, healthcare-related work and immunosuppression. Among the control series, 12% self-tested during the 8 days preceding questionnaire filling, with temporal heterogeneity.ConclusionThe analysis showed high self-test uptake in France with some inequalities which must be addressed through education and facilitated access (cost and availability) for making it a more efficient epidemic control tool.
Collapse
Affiliation(s)
- Olivier Supplisson
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Center for Interdisciplinary Research in Biology, Ecology and Evolution of Health team (Collège de France, CNRS/UMR 7241, Inserm U1050), Paris, France
- Sorbonne Université, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Simon Galmiche
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Sorbonne Université, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Clinical Operation Coordination Office, Paris, France
| | - Anne Lévy
- Caisse Nationale d'Assurance Maladie, Paris, France
| | | | | | | | | | - Arnaud Fontanet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Conservatoire National des Arts et Métiers, unité PACRI, Paris, France
| |
Collapse
|
4
|
Quantification of a COVID-19 Antibody Assay Using a Lateral Flow Test and a Cell Phone. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although several biomedical assays have been developed to screen for antibodies against SARS-CoV-2, very few can be completed without drawing blood. We developed a rapid lateral flow screening tool that used saliva samples and yielded rapid results that could be quantified using a cell phone. This assay provided the sensitive detection of IgG antibodies against SARS-CoV-2 within 10 min. We started by synthesising, modifying, and characterising gold nanoparticles. Using these particles as a coloured label, we developed a lateral flow strip made of nitrocellulose, glass fibre, and cellulose material. We quantified our visual results using pictures acquired with a cell phone and calculated a limit of detection of 4 ng/mL of antibodies against the SARS-CoV-2 spike protein.
Collapse
|