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Applied Sciences
Volume 13
Issue 18
10.3390/app131810431
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Communication

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

by
Dominik Hadzega
1,*,
Klaudia Babisová
1,
Michaela Hyblová
1,
Nikola Janostiaková
2,
Peter Sabaka
3,
Pavol Janega
1 and
Gabriel Minarik
1
1
Medirex Group Academy, n.o. Novozámocká 67, 949 05 Nitra, Slovakia
2
Institute of Medical Biology, Genetics and Clinical Genetics, Medical Faculty, Comenius University in Bratislava, Špitálska 24, 811 08 Bratislava, Slovakia
3
Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, 833 05 Bratislava, Slovakia
*
Author to whom correspondence should be addressed.
Appl. Sci. 2023, 13(18), 10431; https://doi.org/10.3390/app131810431
Submission received: 27 June 2023 / Revised: 13 September 2023 / Accepted: 15 September 2023 / Published: 18 September 2023
(This article belongs to the Collection BioMEMS)
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The results of the study can be applied in choosing the correct RNA-sequencing strategy for the purpose of SARS-CoV-2 genome assembly.

Abstract

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).
Keywords: SARS-CoV-2; RNA genome assembly; RT-qPCR; SPAdes SARS-CoV-2; RNA genome assembly; RT-qPCR; SPAdes

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MDPI and ACS Style

Hadzega, D.; Babisová, K.; Hyblová, M.; Janostiaková, N.; Sabaka, P.; Janega, P.; Minarik, G. Ct Value from RT-qPCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success. Appl. Sci. 2023, 13, 10431. https://doi.org/10.3390/app131810431

AMA Style

Hadzega D, Babisová K, Hyblová M, Janostiaková N, Sabaka P, Janega P, Minarik G. Ct Value from RT-qPCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success. Applied Sciences. 2023; 13(18):10431. https://doi.org/10.3390/app131810431

Chicago/Turabian Style

Hadzega, Dominik, Klaudia Babisová, Michaela Hyblová, Nikola Janostiaková, Peter Sabaka, Pavol Janega, and Gabriel Minarik. 2023. "Ct Value from RT-qPCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success" Applied Sciences 13, no. 18: 10431. https://doi.org/10.3390/app131810431

APA Style

Hadzega, D., Babisová, K., Hyblová, M., Janostiaková, N., Sabaka, P., Janega, P., & Minarik, G. (2023). Ct Value from RT-qPCR Can Predict SARS-CoV-2 Virus Assembly and Lineage Assignment Success. Applied Sciences, 13(18), 10431. https://doi.org/10.3390/app131810431

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