1
|
Purcell‐Wiltz A, Zamuner FT, Caraballo K, De Jesus L, Miranda Y, Ortiz D, Negrón AG, Ortiz AC, Baez A, Romaguera J, Jiménez I, Ortiz A, Acevedo J, Viera L, Sidransky D, Guerrero‐Preston R. Evaluation of self-collected nasal, urine, and saliva samples for molecular detection of SARS-CoV-2 using an EUA approved RT-PCR assay and a laboratory developed LAMP SARS-CoV-2 test. Immun Inflamm Dis 2024; 12:e1285. [PMID: 38888444 PMCID: PMC11184932 DOI: 10.1002/iid3.1285] [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: 07/18/2023] [Revised: 04/23/2024] [Accepted: 05/12/2024] [Indexed: 06/20/2024] Open
Abstract
As the SARS-CoV-2 virus spread throughout the world, millions of positive cases of COVID-19 were registered and, even though there are millions of people already vaccinated against SARS-CoV-2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS-CoV-2 molecular testing availability, we evaluated the diagnostic accuracy of self-collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT-PCR) COVID-19 kit to detect SARS-CoV-2. We also created a colorimetric loop-mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS-CoV-2, as another strategy to increase the availability of molecular testing in community-based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS-CoV-2 on the 7500 Fast Dx RT-PCR using the TaqPath RT-PCR COVID-19 molecular test. Data was interpreted by the COVID-19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene-Biomarks' SARS-CoV-2 Rapid Colorimetric LAMP LDT and the TaqPath RT-PCR COVID-19 test. Our results suggest that self-collected saliva is superior to nasal and urine samples for COVID-19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT-PCR tests for the detection of SARS-CoV-2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.
Collapse
Affiliation(s)
- Ana Purcell‐Wiltz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
- Internal Medicine DepartmentSan Juan Bautista School of MedicineCaguasPuerto Rico
| | - Fernando Tadeu Zamuner
- Otolaryngology Department, Head and Neck Cancer Research DivisionJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | - Karem Caraballo
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Lorena De Jesus
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Yaima Miranda
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Denise Ortiz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Amanda García Negrón
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Andrea Cortés Ortiz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
- Internal Medicine DepartmentSan Juan Bautista School of MedicineCaguasPuerto Rico
| | - Adriana Baez
- Otolaryngology DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Josefina Romaguera
- Obstetrics and Gynecology DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Ivonne Jiménez
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Alberto Ortiz
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Jorge Acevedo
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Liliana Viera
- Department of SurgeryUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - David Sidransky
- Otolaryngology Department, Head and Neck Cancer Research DivisionJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | | |
Collapse
|
2
|
Inward RP, Jackson F, Dasgupta A, Lee G, Battle AL, Parag KV, Kraemer MU. Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates. Epidemics 2022; 41:100627. [PMID: 36099708 PMCID: PMC9443927 DOI: 10.1016/j.epidem.2022.100627] [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: 03/31/2022] [Revised: 08/04/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 case data are primary sources for estimating epidemiological parameters and for modelling the dynamics of outbreaks. Understanding biases within case-based data sources used in epidemiological analyses is important as they can detract from the value of these rich datasets. This raises questions of how variations in surveillance can affect the estimation of epidemiological parameters such as the case growth rates. We use standardised line list data of COVID-19 from Argentina, Brazil, Mexico and Colombia to estimate delay distributions of symptom-onset-to-confirmation, -hospitalisation and -death as well as hospitalisation-to-death at high spatial resolutions and throughout time. Using these estimates, we model the biases introduced by the delay from symptom-onset-to-confirmation on national and state level case growth rates (rt) using an adaptation of the Richardson-Lucy deconvolution algorithm. We find significant heterogeneities in the estimation of delay distributions through time and space with delay difference of up to 19 days between epochs at the state level. Further, we find that by changing the spatial scale, estimates of case growth rate can vary by up to 0.13 d-1. Lastly, we find that states with a high variance and/or mean delay in symptom-onset-to-diagnosis also have the largest difference between the rt estimated from raw and deconvolved case counts at the state level. We highlight the importance of high-resolution case-based data in understanding biases in disease reporting and how these biases can be avoided by adjusting case numbers based on empirical delay distributions. Code and openly accessible data to reproduce analyses presented here are available.
Collapse
Affiliation(s)
- Rhys P.D. Inward
- Department of Biology, University of Oxford, United Kingdom,Corresponding author
| | - Felix Jackson
- Department of Biology, University of Oxford, United Kingdom,Department of Computer Science, University of Oxford, United Kingdom
| | - Abhishek Dasgupta
- Department of Biology, University of Oxford, United Kingdom,Department of Computer Science, University of Oxford, United Kingdom
| | - Graham Lee
- Department of Biology, University of Oxford, United Kingdom,Department of Computer Science, University of Oxford, United Kingdom
| | | | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom,NIHR Health Protection Research Unit in Behavioural Science and Evaluation, University of Bristol, Bristol, United Kingdom
| | - Moritz U.G. Kraemer
- Department of Biology, University of Oxford, United Kingdom,Reuben College, University of Oxford, United Kingdom,Corresponding author at: Department of Biology, University of Oxford, United Kingdom
| | | |
Collapse
|
3
|
Berrig C, Andreasen V, Frost Nielsen B. Heterogeneity in testing for infectious diseases. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220129. [PMID: 35600424 PMCID: PMC9114977 DOI: 10.1098/rsos.220129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/28/2022] [Indexed: 05/03/2023]
Abstract
Testing strategies have varied widely between nation states during the COVID-19 pandemic, in intensity as well as methodology. Some countries have mainly performed diagnostic testing while others have opted for mass-screening for the presence of SARS-CoV-2 as well. COVID passport solutions have been introduced, in which access to several aspects of public life requires either testing, proof of vaccination or a combination thereof. This creates a coupling between personal activity levels and testing behaviour which, as we show in a mathematical model, leverages heterogeneous behaviours in a population and turns this heterogeneity from a disadvantage to an advantage for epidemic control.
Collapse
Affiliation(s)
- Christian Berrig
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Viggo Andreasen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Bjarke Frost Nielsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| |
Collapse
|
4
|
Feitelson E, Plaut P, Salzberger E, Shmueli D, Altshuler A, Amir S, Ben-Gal M. Learning from Others' Disasters? A Comparative Study of SARS/MERS and COVID-19 Responses in Five Polities. INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION : IJDRR 2022; 74:102913. [PMID: 35368429 PMCID: PMC8956342 DOI: 10.1016/j.ijdrr.2022.102913] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The ability to successfully manage disasters is a function of the extent to which lessons are learned from prior experience. We focus on the extent to which lessons from SARS/MERS have been learned and implemented during the first wave of COVID-19, and the extent to which the source affects governance learning: from a polity's own experience in previous episodes of the same disaster type; from the experience of other polities with regard to the same disaster type; or by cross-hazard learning - transferring lessons learned from experience with other types of disasters. To assess which types of governance learning occurred we analyze the experience of four East Asian polities that were previously affected by SARS/MERS: South Korea, Taiwan, Singapore and Hong-Kong. Their experience is compared with that of Israel. Having faced other emergencies but not a pandemic, Israel could have potentially learned from its experience with other emergencies, or from the experience of others with regard to pandemics before the onset of COVID-19. We find that governance learning occurred in the polities that experienced either SARS or MERS, but not cross-hazard or cross-polity learning. The consequences in the 5 polities at the end of the first six months of Covid-19, reflected by the numbers of infected and deaths, on one hand, and by the level of disruption to normal life, on the other, verifies these findings. Research insights point to the importance of modifying governance structures to establish effective emergency institutions and necessary legislation as critical preparation for future unknown emergencies.
Collapse
Affiliation(s)
- Eran Feitelson
- Department of Geography, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pnina Plaut
- Faculty of Architecture and Town Planning, Technion, Haifa, Israel
| | | | - Deborah Shmueli
- Department of Geography and Environmental Studies, University of Haifa, Haifa, Israel
| | | | - Smadar Amir
- National Knowledge and Research Center for Emergency Readiness, University of Haifa, Haifa, Israel
| | - Michal Ben-Gal
- National Knowledge and Research Center for Emergency Readiness, University of Haifa, Haifa, Israel
| |
Collapse
|
5
|
Re: Subramanian and Kumar. Vaccination rates and COVID-19 cases. Eur J Epidemiol 2021; 36:1243-1244. [PMID: 34951674 PMCID: PMC8703206 DOI: 10.1007/s10654-021-00817-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/04/2022]
|