SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in China in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome length RNA replication as well as transcription of genome length and leader containing subgenomic RNAs. Although not fully understood, both replication and transcription are thought to take place in so-called double-membrane vesicles in the cytoplasm of infected cells. We here describe detection of SARS-CoV-2 subgenomic RNAs in diagnostic samples up to 17 days after initial detection of infection, provide evidence for their nuclease resistance and likely protection by cellular membranes consistent with being part of virus-induced replication organelles. Furthermore, we show that the ratios of genomic to subgenomic RNA as well as the ratios of plus to negative strand RNA of genomic and subgenomic RNA are consistent with what have been detected for other coronaviruses in cell culture; albeit with the caveat that in vivo diagnostic samples, even in relatively early infection, the ratios of these RNAs are most reminiscent of late culture, semi-purified virus preparations shown to have a relatively constant ratio of genomic to subgenomic RNAs of around 5-10 or higher, while the ratios of positive to negative strands are more than 100 for the genomic RNA and around 20 for the subgenomic RNAs. Overall, our results may help explain the extended PCR positivity of some samples, and may also, at least in part, help explain discrepancies in results of different diagnostic PCR methods described by others; in particular for samples with a low virus load or of poor quality. Overall, we present evidence that subgenomic RNAs may not be an indicator of active coronavirus replication/infection, but that these RNAs, similar to the virus genome RNA, may be rather stable, and thus detectable for an extended period, most likely due to their close association with cellular membranes.