Biomechanics Study of SARS-CoV-2 Virus-Like Particles

SARS-CoV-2 is the causative agent of COVID-19, which has emerged as a potent human pathogen in 2019.

The virus particles after secretion are in steady state with their environment and can be viewed as well assembled nano-machines ready to infect their next host.

The viral genome and most of the viral proteins of SARS-CoV-2 are hidden within the lipid envelope of the virus, which forms a sphere of diameter 130 ± 30 nm.

The viral envelope is also home to multiple copies of the spike protein S, which has a molecular weight of ~160kD and is inserted in the membrane with a single membrane spanning helical domain.

The envelope is also underpinned by multiple copies of the M protein of SARS-CoV-2, which is approximately 25kD with triple membrane spanning helical domains.

Together the S, M and the envelope of SARS-CoV-2 provide structural integrity for the virus particles as the particles travel through various environments between hosts.

Utilizing a RAPID NSF award, over the past 6 months the PIs have established the minimal system to harvest SARS-CoV-2 virus like particles (VLPs) and identified regions in S and M proteins where genetic tags can be tolerated without effecting VLP structures.

These VLPs have similar morphology (as well as S and M protein content) as fully infectious virions, but do not package the genome and therefore are not infectious. The PIs will study the mechanics of this viral pathogen.

They will increase the participation of underrepresented groups in the pursuit of basic science at University of Utah and create opportunities for cross-disciplinary training at the university. The PIs will also train students and communicate science with the broader public.

The PIs preliminary data show that the S protein can shed and re-insert back into the viral envelope, in strong contrast with known behavior of other envelope-spanning glycoproteins from other enveloped viruses. The SARS-CoV-2 S protein is a major antigen recognized by the immune system.

Shedding of the S protein is therefore relevant for progression of COVID-19 disease; however the basic physics and stochastic thermodynamics view of the S protein shedding/reinsertion needs to be understood in detail since there are no parallel models of such behavior among other enveloped viruses.

To elucidate the mechanism of S protein shedding/reinsertion and its implication for viral infection the PIs will: (1) Measure the S protein shedding and re-insertion dynamics in single immobilized SARS-CoV-2 VLPs. The biologically active form of the S protein is a protein trimer.

They will utilize single molecule fluorescence as well as force spectroscopy techniques to establish the S protein shedding/re-insertion dynamics.

In addition the PIs will investigate the effects of S protein shedding-re-insertion on formation of trimers and also establish chemical and physical factors which promote and inhibit S protein shedding. (2) Model the effect of the S protein equilibrium on the viral life cycle.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.