Evaluation of SARS-CoV-2 with a biophysical perspective

Figures & data

Table 1. A summary of studies on the electrostatic interaction with the host cell.

Topic	Methods	Results	Conclusion	References
Electrostatic energies and the corresponding osmotic pressures in ssRNA viruses and dsDNA bacteriophages	–	The electrostatic interactions between viral proteins and genome molecule significantly constrain the size and architecture of viruses	Both the replication error rate of a virus; and the physical interactions conducted by the genome molecule limits the genome length.	Siber et al. [41]
C-terminal fragment of Zika Virus (ZIKV) nonstructural protein 1 (NS1): its crystal structure; and differences when compared with West Nile (WNV) and dengue virus (DNV) NS1 structures	–	ZIKV may have altered binding properties of host factors and antibodies to flavivirus NS1due to ZIKV NS1 displaying a loop-surface interface with divergent electrostatic potential	Future vaccine development can benefit from eliciting antibodies against ZIKV NS1	Song et al. [42]
The filtration and surface charge of recombinant Norwalk virus (rNV) particles	–	Pore water pH has a strong influence on the rNV particles’ surface charge and filtration in packed beds of quartz sand, over the range of pH 5-7	Electrostatic interactions between the virus and filter media has a great impact on the physicochemical filtration of rNV	Redman et al. [43]
The importance of the absorption characteristics of viruses and the suspending conditions in retention of enteric viruses by MF membranes	Hydrophobic (GVHP) and hydrophilic (GVWP) 0.22 μm MF membranes were used at different pH levels and with different salts to investigate the retention of bacteriophage MS-2	High retention levels at the iso-electric point of MS-2, pH 3.9 (5 log retention) and pH 7 (4.3 log retention) in the presence of salts and with a hydrophobic membrane	The hydrophobic membrane is superior to a hydrophilic membrane in virus retention. The salt also improves the retention capacity of the membrane.	Voorthuizen et al. [44]
Electrostatic features of currently available COVID-19 coronavirus-related structures	Protein Data Bank (PDB) was scanned	Four COVID-19 Coronavirus-related structures: 6LU7 - The crystal structure of COVID-19 main protease; 6LVN - Structure of the 2019-nCoV HR2 domain; 6LXT - Structure of post fusion core of 2019-nCoV S2 subunit; 6VSB - Prefusion 2019-nCoV spike glycoprotein	SARS-CoV-2 structure and function are better understood	Li et al. [45]
IEP of viruses replicating in hosts of Kingdom Plantae, Bacteria, and Animalia	–	Virus IEPs are in the pH range from 1.9 to 8.4; they are most frequently measured in a band of 3.5 < IEP < 7		Michen et al. [46]
Novel models and techniques to address hydrodynamic and electrostatic properties of microbes	–	The zeta-potential principle is not ideal for examining bioparticles such as bacteria, viruses or yeast cells.	It is necessary to use appropriate electrokinetics along with other physico-chemical measurements and microbiological techniques while studying direct correlation between complex interphase properties of microbes and, their tendency to adhere onto charged surfaces	Duval et al. [47]
The impact of static and ELF EMFs on cellular free radical activities	–	EMF exposure can cause changes in cellular ROS/RNS levels, and endogenous antioxidant enzymes and compounds that maintain physiological free radical concentrations in cells	EMF can have a significant impact on cell proliferation and differentiation by inducing changes in free radicals	Lai [48]
Poliovirus recovery from tap water via Microporous filters	Analysis of ZetaPlus filters that are composed of diatomaceous earth-cellulose-‘charge-modified’ resin mixtures and having a net positive charge of up to pH 5 to 6	Recoveries with Zeta Plus filters averaged %64 and %22.5 for single- and two-stage concentration procedures, respectively, under water quality conditions where poliovirus recoveries from large volumes of water were less than %5 with traditional negatively charged filters and standard methods	Electropositive filters have more advantages for concentrating viruses from water than traditional negatively charged filters	Sobsey et al. [49]

Table 2. A summary of the studies on biophysical characterization.

Topic	Methods	Results	Conclusion	References
The biophysical characteristics of the nucleocapsid protein from a highly virulent North American strain of porcine reproductive and respiratory syndrome virus	Cloning of the N gene into the pTriEx1.1Neo vector. Analytical gel filtration chromatography Protein purification	The formation of disulfide bridges plays a key role in RNA binding	Infectious viruses cannot be rescued if cysteine residues are mutated because the disruptions in RNA binding are caused by defects in the formation of disulfide bridges.	Jourden et al. [51]
Airborne virus capture and inactivation	Use of aerosolized bacteriophages T3 and MS2 −10 to +10 kV voltage Application Samples Plaque assays qPCR assays	More virus particles were captured from the air at higher applied voltages Maximum log reductions of 6.8 and 6.3 for the plaque assay and 4.2 and 3.5 for the qPCR assay of −10 kV for T3 and MS2, respectively.	There is a significant potential for virus capture and inactivation through continual ion and reactive species bombardment.	Kettleson et al. [52]
Na/K pump’s autoregulation and its role in metabolic control of semipermeable properties and excitability of neuronal membrane	–	The conductive membrane theory of Hodgkin-Huxley-Katz is not satisfactory in elucidating the role of electrogenic Na/K pump in regulation of semipermeable properties of cell membrane	Na/K pump and the neuronal membrane have enormous roles in regulating each other	Ayrapetyan [53]

Table 3. A summary of the studies on UVC and antimicrobial properties.

Topic	Methods	Results	References
UV inactivation rate constant for RNA and DNA viruses	Base counting software	UV susceptibility (D90) was correlated with the genomic model and produced the R2 values for viruses and bacteria.	Kowalksi et al. [55]
UVC-LED in water disinfection on Bacillus species	UVC-LED	268 nm is more effective for TRB and TRG treatment.	Shen et al. [57]
Viral removal by ultrafiltration membranes	Ultrafiltration membranes	MS2 bacteriophage was removed better. uX174 bacteriophage removal decreased as the pH of the feed solution increased	Elhadidy et al. [58]
UV-C LED disinfection and potential dual-wavelength synergy	Dual wavelength UVC-LED unit	Must reach efficiencies of 25–39% to match the electrical efficiency per order of log reduction of conventional LP UV sources. Unable to detect dual wavelength synergies for microbial inactivation.	Beck et al. [59]
Far-UVC light to control the spread of airborne-mediated microbial diseases	Far-UVC light	Far UVC can inactivate more than 95% of aerosolized H1N1 influenza virus at a very low dose of 2 mJ/cm^2 of 222 nm light.	Welch et al. [60]
Inactivation of 3 emerging viruses (SARS-CoV, CCHFV, NiV)	UVC light for viruses in platelet concentrates Methylene blue plus visible light for viruses in plasma	Both inactivation systems effectively reduced the infectivity of the viruses	Eickmann et al. [61]
Efficiency of UVC irradiation with air filtration in reducing airborne microorganism	UVC-sustained recirculating air filtration	Recirculating air filtration combined with UVC efficiently reduced the airborne pathogens in the barn compared to the reference barn.	Eisenlöffel et al. [62]
UV decontamination of H5N1, H5N, H1N1, H7N9, MERS-CoV, SARS-CoV	UV decontamination	1 J/cm^2 for UV decontamination made the viruses non-viable	Heimbuch et al. [64]
UV germicidal irradiation of influenza contaminated N95 respirators	UVGI dose optimization	The minimum UVGI dose for > 3-log reduction in viable H1N1 influenza was 1 J/cm^2	Mills et al. [65]

Table 4. A summary of the articles focused on relation between trace element and SARS-CoV-2.

	Zinc	Selenium	Iron	Copper	Na	K	Ca	Mg
Taheri et al. [66]	Zinc inhibits the activity of RNA-dependent RNA polymerase of coronavirus, and therefore compound both of zinc and CQ/HCQ could be useful for COVID-19 treatment	High selenium intake causes better and more immune responses	High level of iron may increase viral infections, although it has reported that COVID-19 patients have low serum level of iron	Copper deficiency can reduce human immune system response. However, serum copper in COVID-19 patients is still unknown	Sodium in patients with pneumonia infected by SARS-CoV-2 is lower than in non-pneumonia patients	Hypokalemia is a high prevalence condition among COVID-19 patients	SARS-CoV entry into some cell lines decreases when intracellular calcium decreases
Lippi et al. [67]					Lower serum concentrations of sodium	Lower serum concentrations of potassium. 93% of acute and seriously ill patients with COVID-19 have hypokalemia and hypokalemia is a widespread outcome in cases with hypomagnesemia	Lower serum concentrations of calcium
Chams et al. [69]	Zinc supplementation may be of potential benefit for prophylaxis and treatment of COVID-19
Rahman and Idid [70]	Zinc supplementation could play an important role to treat COVID-19 patients
Hiffler and Rakatoambinina [71]		Selenium might reduce the effect of SARS-CoV-2 on vascular endothelial cells and aggregation of platelets
Tang et al. [72]								Magnesium supplementation is expected to play an active role in clinical practice in the prevention and treatment of COVID-19
Zhang et al. [73]		Redox-active selenium species formed from high selenium intake might hypothetically inhibit SARS-CoV-2 proteases

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