Validation of Laboratory Techniques, Strategies, and Types of Samples for Epidemiological Control in the Covid-19 Pandemic

Overview

This is a study of validation for diagnostic techniques used on epidemiological control in the COVID-19 pandemic. It will be carried out in accredited public, private and university clinical laboratories of the collaborator institutions of the project based in Tarija, Bolivia. It is designed as a sectional validation study, using samples from specific groups of participants from the municipality of Tarija grouped according to their category with respect to symptoms and viral load of COVID-19. The sample is selected for convenience.

Full Title of Study: “Validation of Laboratory Techniques, Strategies, and Types of Samples for Epidemiological Control in the Covid-19 Pandemic, Tarija-Bolivia”

Study Type

  • Study Type: Observational
  • Study Design
    • Time Perspective: Cross-Sectional
  • Study Primary Completion Date: October 31, 2020

Interventions

  • Diagnostic Test: RT-PCR
    • RT-PCR (Gold standard): Real-time PCR testing with reverse transcriptase (RT-PCR). The test consists of a polymerase chain reaction that has previously had a reverse transcription phase, RT. This test allows the cADN (complementary DNA) to be obtained from a RNA chain. This technique allows the detection and amplification of a sequence from a strand of RNA.
  • Diagnostic Test: LAMP
    • LAMP: The LAMP technique, like PCR, has the ability to amplify specific DNA fragments (target sequence), allowing for highly sensitive detection of pathogens. Unlike pcr, LAMP requires between 4 and 6 feeders, external F3 and B3 feeders, which hybridte with the outer regions of the target sequence, while the internal FIP and BIP have sequences in both ways that allow the formation of a loop. The LAMP reaction is isothermal, i.e. it takes place at a single temperature. LAMP has been successfully used to detect viral diseases as well as viral pathogens such as West Nile virus, TMR-1, Norovirus, avian influenza, foot-and-mouth disease, classical swine fever, among others.
  • Diagnostic Test: POOL RT-PCR
    • POOL RT-PCR: This test aims to mix in a single sample the extractions obtained from several people. The joint sample is evaluated and, if negative, it is understood that all are free of COVID-19; if it is positive, an array system is used to detect the affected person. That is, a single PCR (polymerase chain reaction), the diagnostic test used to detect the virus pathogen is applied to a group and repeated individually if positive.
  • Diagnostic Test: POOL LAMP
    • POOL LAMP: Like the RT-PCR pool test. This test essentially involves mixing in a single sample the extractions obtained from several people. This joint sample is tested and, if it is negative, it is understood that everyone is free of COVID-19; if it is positive, an array system is used to detect the affected person. That is: a single LAMP applies to a group

Arms, Groups and Cohorts

  • Volunteer participants
    • Samples of volunteer participants will be collected after informed consent and classified as symptomatic, asymptomatic and negative.

Clinical Trial Outcome Measures

Primary Measures

  • Validation
    • Time Frame: 1 month
    • Validate different molecular tests and sampling and sample type strategies used in epidemiological control of COVID-19 diagnosis in Tarija, Bolivia.

Secondary Measures

  • RT- PCR (Saliva)
    • Time Frame: 1 week
    • Validate the use of molecular testing based on the PCR method using Saliva samples
  • LAMP
    • Time Frame: 1 week
    • Validate the use of the molecular test based on the LAMP method using saliva and nasopharyngeal samples
  • POOL PCR
    • Time Frame: 1 week
    • Validate the use of molecular tests with Pool PCR strategy using saliva samples
  • POOL LAMP
    • Time Frame: 1 week
    • Validate the use of molecular tests with Pool LAMP strategy using saliva samples

Participating in This Clinical Trial

Inclusion Criteria

  • Symptomatic: Subjects with signs and symptoms of respiratory infection less than or equal to 3 days, preferably with clinical and molecular diagnosis compatible with Covid-19. – Asymptomatics: Subjects who have had direct contact with people infected and who have not shown any symptoms related to Covid-19. – Negative: Individuals with negative RT-PCR testing for SARS-CoV-2 (reference test) who have not manifested any symptoms seven days prior to sampling. Exclusion criteria:
  • Adults under the age of 21 or over 65 – Subjects with a clinical history of autoimmune disease or chemotherapy treatments. – Subjects who have received transfusions or convalescent plasma in the last month prior to enrollment. – Subjects with prior diagnosis of other infectious diseases such as, but not limited to AIDS, Hepatitis B or C, Tuberculosis, or any other ongoing or unresolved diseases. – Subjects with malformation or oncological pathology of the upper respiratory track that may hinder sample collection, including but not limited to deviated septum, allergic rhinitis. – Subjects who have not signed or can not sign the informed consent form – Subjects not able to provide their complete information or access to their clinical history.
  • Gender Eligibility: All

    Minimum Age: 21 Years

    Maximum Age: 64 Years

    Are Healthy Volunteers Accepted: Accepts Healthy Volunteers

    Investigator Details

    • Lead Sponsor
      • Hunter College of City University of New York
    • Collaborator
      • Universidad Autonoma Juan Misael Saracho
    • Provider of Information About this Clinical Study
      • Principal Investigator: Rodrigo Arce Cardozo, Adjunct Assistant Professor – Hunter College of City University of New York
    • Overall Official(s)
      • Kenji Shoji, PhD, Principal Investigator, Galapagos NV
      • Rodrigo Arce Cardozo, MD, MPH, Study Chair, City University of New York, School of Public Health
    • Overall Contact(s)
      • Rodrigo Arce Cardozo, MD,MPH, +19173620995, rodrigokarce@gmail.com

    References

    Yu L, Wu S, Hao X, Dong X, Mao L, Pelechano V, Chen WH, Yin X. Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform. Clin Chem. 2020 Jul 1;66(7):975-977. doi: 10.1093/clinchem/hvaa102.

    Kashir J, Yaqinuddin A. Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19. Med Hypotheses. 2020 Aug;141:109786. doi: 10.1016/j.mehy.2020.109786. Epub 2020 Apr 25.

    Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA. 2020 Jul;26(7):771-783. doi: 10.1261/rna.076232.120. Epub 2020 May 1. Review.

    Chow FW, Chan TT, Tam AR, Zhao S, Yao W, Fung J, Cheng FK, Lo GC, Chu S, Aw-Yong KL, Tang JY, Tsang CC, Luk HK, Wong AC, Li KS, Zhu L, He Z, Tam EWT, Chung TW, Wong SCY, Que TL, Fung KS, Lung DC, Wu AK, Hung IF, Woo PC, Lau SK. A Rapid, Simple, Inexpensive, and Mobile Colorimetric Assay COVID-19-LAMP for Mass On-Site Screening of COVID-19. Int J Mol Sci. 2020 Jul 29;21(15). pii: E5380. doi: 10.3390/ijms21155380.

    Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, Thakor AS. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic. Biology (Basel). 2020 Jul 22;9(8). pii: E182. doi: 10.3390/biology9080182. Review.

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