Reverse transcription-polymerase chain reaction (RT-PCR) is the standard method of diagnosing COVID-19.  An inconclusive test result occurs when 1 RT-PCR target is positive for SARS-CoV-2 and 1 RT-PCR target is negative for SARS-CoV-2 within the same sample.  To understand the role of subgenomic RNA transcripts in discordant results from RT-PCR tests for COVID-19.


 This study showed that a greater copy number of N-gene relative to E-gene and ORF1 transcripts could potentially explain inconclusive results for some RT-PCR tests on low viral load samples.  The use of N-gene RT-PCR target(s) as opposed to ORF1 targets for routine testing is supported by these data.
RT-PCR
A panel of 6 droplet digital PCR assays was designed to quantify the ORF1, E-gene, and N-gene of SARS-CoV-2. 
droplet digital PCR