New Strategies for Detection, Standardization and Isolation of the New SARS-CoV-2 Virus

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Background

The biggest problem during a pandemic due to a new virus is to find fast and effective systems for the detection of the virus itself. The emergency is opposed to a good experimental system and the urgency to get results should not prevail on result accuracy.
To do this, it is necessary to use existing and validated protocols, without losing time to develop new technologies. Furthermore, considering the state of emergency, it is often necessary to use automated procedures to contrast the large numbers of samples that need to be processed. As a consequence of that, an experimental blind situation is created by the simultaneous need to process a huge quantity of samples, without having the time necessary for the experimental validation.
Moreover, during the initial phase of the pandemic the matrices in which the virus is searched are the canonical ones, whereas in the later stages the need for more in-depth studies will lead to the identification of viral RNA in complex matrices such as tears, saliva, feces, and organ tissues. With this in mind, it is therefore necessary to develop biochemical and molecular biology techniques that are increasingly reliable, sensitive and adapted for different heterogeneous matrices.
Reverse transcription quantitative polymerase chain reaction (RT qPCR) is the gold standard method for the diagnosis of COVID 19 infection since all the largest laboratories of the World Health Organization have decided to use this system. Even if this technique, broadly used all over the world, is the preferred one for the virus detection, it shows some drawbacks such as problems of execution, limits and a complex standardization of the results. New extraction, amplification and detection techniques are therefore necessary to overcome the weak points of RT-qPCR.
In addition to that, Realtime PCR, Lamp PCR, ddPCR, Fluorescent fragment analysis, colorimetric assays and direct sequencing, despite being the most used techniques, are also excessively affected by the quality and quantity of the nucleic acid and by the good laboratory practices used. The chemistry of the reagents and the viral isolation capacity are therefore the basis of the success of the amplification reaction.

The goal of this Research Topic is to develop and evaluate new methods for finding SARS-CoV-2, increasing the depth of detection and detection in complex matrices.

We particularly welcome articles on the following areas (but not limited to):
1. Development of new PCR methodologies for the amplification of viral RNA.
2. Development of protocols for the extraction of viral RNA in complex matrices.
3. Development of one step methodologies for the detection of viral RNA.
4. Sensitivity comparison in existing methods such as qRT-PCR Vs LAMP.
5. Alternative methods to the use of fluorescent probes for the detection of viral RNA.
6. Development of protocols for the "selective" extraction of viral RNA.
7. Discrimination between viral viability with respect to the presence of viral RNA.


Dr. Stefano Stracquadanio in the role of Coordinator contributed to developing the Research Topic description.

Topic Editor Prof. Stefani received financial support from Basilea, Correvio, Shionogi, Pfizer, Biosynth, DMG. She is on the scientific board of Pfizer, Biomerieux, Liofilchem, MSD, Shionogi, Correvio, Menarini and she holds a patent. The other Topic Editors declare no competing interests with regard to the Research Topic subject.





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Keywords: Realtime PCR, Lamp PCR, ddPCR, Fluorescent fragment analysis, colorimetric assays, SARS-CoV-2 Virus, Detection, Isolation

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