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Diagnostic Methods


SARS-CoV-2 Serum-based Antibody Tests

Study Rationale

  • Accurate serological testing for SARS-CoV-2 exposure is important to assess infection and potential immunity to guide rational clinical and public health policies.

Study Description

  • The performance of different SARS-CoV-2 serological assays was evaluated.

Study Summary

  • 10 immunochromatographic Lateral Flow Assay and 2 ELISA tests evaluated.
  • 80 symptomatic SARS-CoV-2 positive and 108 pre-COVID-19 negative controls.
  • Majority demonstrated 81-100% sensitivity and above 95% specificity.
  • Seropositivity significantly increases after two weeks of symptom presentation and peaks at >20 days.



What is measured and how

IgG/IgM levels during infection

Potential test results





Rapid Testing (RT-PCR)

Study Rationale

  • Lack of rapid, accessible, and accurate SARS-CoV-2 testing hinders public health response. A new CRISPR-Cas12-based lateral flow assay (LFA) has been developed to facilitate the diagnosis.

Study Description

  • The method (DETECTR) was tested on COVID-19 patients and patients with other respiratory infections with a sensitivity of 95% and a specificity of 100%.


Study Summary

  • Total subjects: 36 COVID-19 patients and 42 with other respiratory infections were tested.
  • The method can run in 30-40 min and visualized on an LFA.

Findings

  • Saliva yields greater detection sensitivity and consistency.
  • Less variability in self-sample collection of saliva.
  • Saliva is a viable and more accurate alternative to nasoph and suitable for large scale testing.

 

Endonuclease-Targeted CRISPR Trans Reporter (DETECTR)


DETECTR readout


Requirements

To perform DETECTR protocol upon RNA extraction, minimal lab requirements are needed:

  • test tubes and reagents
  • heat blocks or water baths (37⁰C and 62⁰C)
  • nuclease-free water
  • pipettes and tips
  • lateral flow strips

Positive results and interpretation

The detection of at least one of the two N or E viral genes is considered positive for the presence of SARS-CoV-2:

The results of the lateral flow assay are interpreted following the schema in this table:

SARS-CoV-2 Detection by DETECTR

DETECTR can identify SARS-CoV-2 at a concentration of at least 10 viral copies in 1 µl, while the RT-qPCR method can detect the virus at a concentration as low as 1 copy per 1 µl.

Examination of clinical samples from 41 COVID-19 positives and 42 COVID-19 negatives demonstrated high sensitivity (38 out 40 positive agreement) and perfect specificity (42 out 42 negative agreement).



SARS-CoV-2 RNA in Saliva Samples

Study Rationale

  • Rapid and accurate SARS-CoV-2 diagnostic is important to control the ongoing pandemic. A nasopharengeal swab alternative is needed that is more accessible, reliable, and that is comparable in sensitivity.

Study Description

  • The detection of SARS-CoV-2 in saliva is validated and compared to nasopharengeal swabs.

 

Study Summary

  • Total subjects: 142, of which 62 had paired saliva-nasoph. samples
  • 44 COVID-19 inpatients
  • 98 healthcare workers

Findings

  • Saliva yields greater detection sensitivity and consistency.
  • Less variability in self-sample collection of saliva.
  • Saliva is a viable and more accurate alternative to nasoph. swabs (PBA: However, large volumes collected (~20ml) and only early morninig sampling assessed) and suitable for large scale testing.




SARS-CoV-2 and HLA Binding

Study Rationale

  • Most individuals infected by SARS-CoV-2 develop mild or undetectable symptoms while others suffer severe symptoms. The phenomenon could potentially be explained by genetic differences in the MHC class I genes [HLA-A,-B,-C].

Study Description

  • In silico analysis of viral-peptide-MHC class I binding affinity across HLA-A, -B, -C genotypes for all SARS-CoV-2 peptides was assessed.

Study Summary

  • Binding affinity across 145 HLA-A, -B, -C gentotypes for SARS-CoV-2 peptides.
  • 8- to 12-mers SARS-CoV-2 proteome (48.395 peptides) interogated. 32.257 predicted to be processed MHC class I --> affinity assessed to 145 different HLA types.
  • Global distribution of HLA types with potential epidemiolgical ramifications.

Findings

  • HLA-B*46:01 revealed the fewest predicted binding peptides for SARS-CoV-2.
  • HLA-B*15:03 shows the greatest capacity to present conserved SARS-CoV-2 peptides.

Points to Address

  • Validate findings in SARS-CoV-2 positive subjects with severe and asymptomatic disease.
  • Have countries with a high capacity of HLA presentation suffered less from the pandemic?

 

HLA allele frequencies and their predicted capacity for SARS-CoV-2 presentation

HLA allele frequency distribution for six representative alleles