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HuluFISH Probe for All SARS-CoV-2 Strains

Updated: May 21, 2020

At PixelBiotech, we are deeply concerned about the COVID-19 pandemic. Therefore we are developing a new research tool for COVID-19 with our HuluFISH technology. HuluFISH technology is customizable for any gene in any organism, allowing scientists to detect their genes of interest at the single-molecule single-cell level. This means that new strains of the virus or other new viruses can be detected easily by designing new probes.

The key component of this tool is the HuluFISH smFISH probe set against all publicly available strains of the SARS-CoV-2 virus. The SARS-CoV-2 RNA can be visualized under fluorescence microscopy with single-molecule precision and analyzed by our FREE AI image analysis service HuluREAD. It will serve as a new tool for research in disease mechanism, vaccine and drug development for COVID-19.

Normally, a minimal 200bp target sequence is sufficient for custom HuluFISH probe design. SARS-CoV-2 ( is a positive-sense RNA virus with a size of 29,903 bp, which is more than enough for us to design the optimal HuluFISH probe. Specifically, we find the spike glycoprotein, which is roughly 3800bp sized, ideal for our HuluFISH probe design (

We studied the complete sequences of 51 spike glycoprotein variants from GenBank and narrowed down the regions with the highest coverage. We used this region as the target for our HuluFISH probe.

Alignment of spike glycoprotein sequences from 51 strains.

We then designed HuluFISH probes based on the consensus sequence, which yielded a HuluFISH probe set of 34 oligos that detect the spike glycoprotein mRNA of SARS-CoV-2. The probe set can be used to detect SARS-CoV-2 in a fixed tissue sample, infected host cells, or spike protein expressing stable cell lines, and so on. Meanwhile, we also designed a HuluFISH probe set to detect the Human ACE2 mRNA, which is the receptor of the SARS-CoV-2, for simultaneous detection with the SARS-CoV-2 spike glycoprotein mRNA.

SARS-CoV-2 HuluFISH probe set sequences.

We are confident that our HuluFISH probe can accelerate the development of drugs and vaccines by enabling the detection of SARS-CoV-2 and its receptor ACE2 mRNA at the single-cell single-molecule level.

In light of the current situation, we strive to coordinate our supply and logistics in order to fulfill the demands for our HuluFISH probe for everyone who is interested. Please drop us an email at if you have more questions or ideas about the SARS-CoV-2 HuluFISH probes.

Together, we will prevail over the COVID-19 pandemic!

Update 19/05/2020:

We have been notified by Dr. Davide Mazza at IRCCS that our HuluFISH probe for SARS-CoV-2 is specifically detecting the SARS-CoV-2 infection in the Vero cell even just after 8 hours. It is amazing to see how this probe can show the replication dynamics of the SARS-CoV-2 virus inside the host cell.

SARS-CoV-2 infection in Vero cells.

#hulufish #covid19

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