COVID-19 in Baselland: Validation of Simple and Accurate Tests for COVID-19 Detection, Monitoring and Tracing (ACCURATE-BL-COVID-19)

Study Overview
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Brief Summary
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This study is to establish an accurate, robust and easily scalable COVID-19 viral nucleic acid analysis platform from, but not limited to, saliva to help enable and support contact tracing in the canton of Baselland/ Switzerland. To achieve this, crude ribonucleotide acid (RNA) extraction from saliva is validated in combination with next-generation sequencing (NGS) diagnostics and loop mediated amplification (LAMP) assays as well as point of care test (POCT) for rapid detection of viral antigens on patients' samples.

Official Title
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COVID-19 in Baselland: Validation of Simple and Accurate Tests for COVID-19 Detection, Monitoring and Tracing (ACCURATE-BL-COVID-19)

Conditions
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Coronavirus Infectious Disease 2019 (COVID-19)

Intervention / Treatment
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* Other: Saliva based assay: crude RNA extraction
* Other: Validation of the NGS method
* Other: Validation of the LAMP assays
* Other: Validation of the POCT Antigen and Antibody tests


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: symptomatic patients getting tested for COVID-19 Exclusion Criteria: mentally incompetent adults

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Intervention/Treatment |
| --- |
|Other: Saliva based assay: crude RNA extraction|Crude RNA extraction to inactivate the virus and stabilize the RNA for transport at room temperature. Validation of the crude RNA extraction from saliva in combination with NGS diagnostics and LAMP assays and point of care test (POCT) for rapid detection of viral antigens on patients' samples.|
|Other: Validation of the NGS method|Compare the results obtained with the next-generation sequencing (NGS) method to the nasopharyngeal swabs analysed in a FAMH certified lab.|
|Other: Validation of the LAMP assays|The RNA will be analyzed onsite using the loop mediated amplification (LAMP) assay.|
|Other: Validation of the POCT Antigen and Antibody tests|Rapid point of care tests (POCT) detecting viral protein antigens (Ag) and antibodies (Ab) on patients' samples. POCT are often employed in low income countries, but for COVID-19 they are not yet characterized. Their performance is to be characterized that they can be used as a safe guard if the lab diagnostics fail.|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| qualitative method validation of the crude extraction in combination with the LAMP or the NGS (count values for detection) | For all qualitative method validation, the qualitative and quantitative result of the Foederatio Analyticorum Medicinalium Helveticorum (FAMH) performed RT-PCR (patient does / does not have SARS-Cov-2 and if yes, how many ct values for detection) is considered as the gold standard against which the crude extraction in combination with the LAMP or the NGS method using univariate measures is compared. | single point assessment at baseline | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay, point of care tests (POCT), next-generation sequencing (NGS) method, contact tracing, transmission chains, crude RNA extraction from saliva, loop mediated amplification (LAMP) assay, viral nucleic acid analysis platform