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

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

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.

Study Overview

• Status: Completed
• Conditions: Covid19
• Intervention / Treatment: Diagnostic test: RT-PCR; Diagnostic test: LAMP; Diagnostic test: POOL RT-PCR; Diagnostic test: POOL LAMP

• Study Type: Observational
• Enrollment (Actual): 30

Contacts and Locations

Study Locations

• Bolivia
  • Tarija, Bolivia, 00000
    • Universidad Autónoma Juan Misael Saracho

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 21 years to 64 years (Adult)
• Accepts Healthy Volunteers: Yes

• Sampling Method: Non-Probability Sample

Study Population

Validation will be carried out using samples from volunteer adults from the municipality of Tarija, Bolivia, without gender restriction. Samples will be grouped according to the clinical classification determined above. These individuals will need to sign the informed consent form required to agree to be part of the study and provide their complete information or access to their medical history.

Description

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.

Study Plan

How is the study designed?

Number of groups / cohorts

1

Cohorts and Interventions

Group / Cohort

Intervention / Treatment

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

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.; Other Names: Real-Time Polymerase Chain Reaction; 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.; Other Names: Loop-mediated isothermal amplification; 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.; Other Names: Pooled Real-Time Polymerase Chain Reaction; 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; Other Names: Pooled Loop-mediated isothermal amplification

What is the study measuring?

Primary Outcome Measures

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

Secondary Outcome Measures

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

Collaborators and Investigators

• Sponsor: Hunter College of City University of New York
• Collaborators: Universidad Mayor de San Simón; Universidad Autonoma Juan Misael Saracho; Gobierno Autonomo Departamental De Tarija; SEDES - Tarija; CAINCO - Bolivia
• Investigators: Principal Investigator: Kenji Shoji, PhD, Galapagos NV; Study Chair: Rodrigo Arce Cardozo, MD, MPH, City University of New York, School of Public Health

Publications and helpful links

General Publications

• 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. No abstract available.
• 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.
• 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):5380. 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):182. doi: 10.3390/biology9080182.

Helpful Links

• Local Sponsor University Website

Study record dates

Study Major Dates

• Study Start (Actual): October 8, 2020
• Primary Completion (Actual): October 10, 2020
• Study Completion (Actual): October 30, 2020

Study Registration Dates

• First Submitted: October 7, 2020
• First Submitted That Met QC Criteria: October 7, 2020
• First Posted (Actual): October 9, 2020

Study Record Updates

• Last Update Posted (Actual): October 15, 2024
• Last Update Submitted That Met QC Criteria: October 11, 2024
• Last Verified: October 1, 2024

More Information

Terms related to this study

• Keywords: COVID 19; Bolivia; Clinical Laboratory Techniques
• Additional Relevant MeSH Terms: Coronavirus Infections; Coronaviridae Infections; Nidovirales Infections; RNA Virus Infections; Virus Diseases; Infections; Respiratory Tract Infections; Respiratory Tract Diseases; Pneumonia, Viral; Pneumonia; Lung Diseases; COVID-19
• Other Study ID Numbers: PROY - UAJMS001/2020

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: YES
• IPD Plan Description: We will share deidentified data
• IPD Sharing Time Frame: Paper submitted for publication
• IPD Sharing Access Criteria: Open
• IPD Sharing Supporting Information Type: STUDY_PROTOCOL; SAP; ICF; ANALYTIC_CODE; CSR

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No