SARS-CoV-2 Detection in Nasopharyngeal Samples

Deep nasal cavity swab (nasopharyngeal) samples were collected from patients, and viral RNA was extracted by using “FavorPrep™ Viral Nucleic Acid Extraction Kit” and “Systaaq Diagnostic Products SuperExract 32 instrument” according to the manufacturer’s instructions. SARS‐CoV‐2 was detected by RT‐PCR assay using commercially available “Sansure; Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit” and “Systaaq Diagnostic Products AB QuantGene instrument” according to the manufacturer’s protocol. This kit include primers/probes that are specific for the open reading frame of 1ab (ORF1ab) gene (probe labeled 2 with FAM) and nucleocapsid protein (N) gene (probe labeled with VIC) of SARS-CoV-2. In addition, the kit also contain primers and a probe (labeled with CY5) for the human RNase P gene as an endogenous internal control for specimen integrity, nucleic acid isolation, amplification, and detection. This assay includes Ct values for the Orf1ab and N gene obtained from Sansure Biotech kit, and the Ct value <40 was used for this analysis.

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Shoaib N., Iqbal A., Shah F.A., Zainab W., Qasim M., Zerqoon N., Naseem M.O., Munir R, & Zaidi N. (2023). Population-level median cycle threshold (Ct) values for asymptomatic COVID-19 cases can predict the trajectory of future cases. PLOS ONE, 18(3), e0281899.

Publication 2023

Assay Diagnostic Gene Gene control Human Isolation Nasal cavity Nasopharyngeal Nucleic acid Nucleocapsid protein Patients Primers Rnase p Rt pcr Sars cov 2 Viral rna

Corresponding Organization : University of Health Sciences Lahore

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Variable analysis

independent variables

Sample collection method (deep nasal cavity swab/nasopharyngeal)

dependent variables

SARS-CoV-2 detection by RT-PCR assay
Ct values for the Orf1ab and N gene

control variables

Viral RNA extraction using FavorPrep™ Viral Nucleic Acid Extraction Kit
Viral RNA extraction using Systaaq Diagnostic Products SuperExract 32 instrument
RT-PCR assay using Sansure Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit
RT-PCR assay using Systaaq Diagnostic Products AB QuantGene instrument
Primers/probes specific for Orf1ab and N genes of SARS-CoV-2
Primers/probe for human RNase P gene as internal control

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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