Ct Value from RT-qPCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success

Featured Application: The results of the study can be applied in choosing the correct RNA-sequencing strategy for the purpose of SARS-CoV-2 genome assembly. During the recent pandemics of COVID-19, sequencing technics became a powerful tool for gaining information about the SARS-CoV-2 virus and using this knowledge to our advantage. Thanks to this advantage, scientists all over the world were able to search for emerging variations, watching the virus evolve in real time. Assembly of the virus genomes is a crucial part of obtaining this kind of useful information. In our study, we sequenced 79 samples from nasopharyngeal swabs of COVID-19 patients. Positivity to disease was evaluated using RT-qPCR. In this work, we described the relationship between RT-qPCR Ct value and genome construction success (plus genome lineage assignment). The specific value of this study is that this relationship was described for data from metatranscriptomic sequencing of human tissue, while there was no step of viral RNA isolation (usual for genome assembly procedure). RT-qPCR Ct value and assembly quality metric NG50 were correlated. We observed that the RT-qPCR Ct value threshold of the certain success of genome assembly (Ct value < 25) and certain failure (Ct value > 30) could be drawn, while results varied for values between (with completed, completed with lower quality, and failed assemblies).

Automated summary

This study investigates the relationship between RT-qPCR Ct values and the success rate of SARS-CoV-2 genome assembly, describing it using metatranscriptomic sequencing data from human tissue without viral RNA isolation.