CRISPR-based assay reveals SARS-CoV-2 RNA dynamic changes and redistribution patterns in non-human primate model

Area of Science:

• Virology
• Molecular Biology
• Infectious Diseases

Background:

• SARS-CoV-2 infects multiple systemic tissues, but RNA detection in non-respiratory samples is challenging.
• Standard RT-qPCR assays show limited sensitivity and performance with non-respiratory specimens.

Purpose of the Study:

• To evaluate SARS-CoV-2 RNA dynamics in various specimen types using an ultrasensitive CRISPR-RT-PCR assay.
• To compare the performance of CRISPR-RT-PCR with conventional RT-qPCR for detecting SARS-CoV-2 RNA.

Main Methods:

• Longitudinal analysis of mucosal (nasal, buccal, pharyngeal, rectal), plasma, and breath samples from SARS-CoV-2-infected non-human primates (NHPs).
• Utilized an ultrasensitive CRISPR-RT-PCR assay for high-sensitivity detection of SARS-CoV-2 RNA.
• Compared CRISPR-RT-PCR results with standard RT-qPCR.

Main Results:

• CRISPR-RT-PCR consistently detected SARS-CoV-2 RNA in all tested sample types across most time points.
• RT-qPCR showed positive results mainly in nasal, pharyngeal, and rectal swabs, with earlier decreases in detection.
• SARS-CoV-2 RNA was detectable in both pulmonary and extrapulmonary sites from early to late infection stages.

Conclusions:

• Ultrasensitive CRISPR-RT-PCR enhances SARS-CoV-2 RNA detection in diverse specimens, including non-respiratory ones.
• This assay may aid in diagnosing COVID-19 cases missed by standard RT-PCR.
• Monitoring SARS-CoV-2 RNA in alternative specimens can improve evaluation of infection progression and resolution.