Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts

The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P21212 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P21212 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus particle. RNA segments organized about the icosahedral twofold axes were present in crystals grown from ammonium sulfate and sodium chloride, as in the canonical I222 crystals (PDB entry 4oq8), but were not observed in crystals grown from sodium bromide and sodium nitrate. Bromide and nitrate ions generally replaced the RNA phosphates present in the I222 crystals, including the phosphates seen on fivefold axes, and were also found at threefold vertices in both the rhombohedral and cubic forms. An additional anion was also found on the fivefold axis 5 Å from the first anion, and slightly outside the capsid in crystals grown from sodium chloride, sodium bromide and sodium nitrate, suggesting that the path along the symmetry axis might be an ion channel. The electron densities for RNA strands at individual icosahedral dyads, as well as at the amino-terminal peptides of protein subunits, exhibited a diversity of orientations, in particular the residues at the ends.

Marked enhancement of neutralizing antibody and IFN-γ T-cell responses by GX-19N DNA booster in mice primed with inactivated vaccine

In response to the COVID-19 pandemic, an unprecedented level of vaccine development has occurred. As a result, various COVID-19 vaccines have been approved for use. Among these, inactivated virus particle vaccines have been widely used worldwide, but additional vaccination strategies are needed because of the short duration of immune responses elicited by these vaccines. Here, we evaluated homologous and heterologous prime-boost regimens using inactivated virus particle vaccine and GX-19N DNA vaccine for their ability to enhance the protective immune response against SARS-CoV-2. We demonstrated that a heterologous prime-boost regimen with the inactivated virus particle vaccine and GX-19N DNA vaccine resulted in enhanced SRBD- and N-specific antibody responses, compared to the homologous inactivated virus particle vaccine prime-boost vaccination. In addition, the neutralizing antibody response was significantly improved with the heterologous inactivated virus particle prime DNA boost regimen, and the neutralizing antibody induced with the heterologous prime boost regimen did not decrease against the SARS-CoV-2 variant of concern. The heterologous inactivated virus particle prime-DNA boost regimen not only significantly increased S- and N-specific IFN-g T cell responses, but also induced an equivalent level of T cell response against SARS-CoV-2 variant of concerns. Our results provide new insights into prophylactic vaccination strategies for COVID-19 vaccination.

The impact of heating, ventilation, and air conditioning design features on the transmission of viruses, including the 2019 novel coronavirus: a systematic review of ventilation and coronavirus

Aerosol transmission has been a pathway for virus spread for many viruses. Similarly, emerging evidence regarding SARS-CoV-2, and the resulting pandemic as declared by WHO in March 2020, determined aerosol transmission for SARS-CoV-2 to be significant. As such, public health officials and professionals have sought data regarding the effect of Heating, Ventilation, and Air Conditioning (HVAC) features to control and mitigate viruses, particularly coronaviruses. A systematic review was conducted using international standards to identify and comprehensively synthesize research examining the effectiveness of ventilation for mitigating transmission of coronaviruses. The results from 32 relevant studies showed that: increased ventilation rate was associated with decreased transmission, transmission probability/risk, infection probability/risk, droplet persistence, virus concentration, and increased virus removal and virus particle removal efficiency; increased ventilation rate decreased risk at longer exposure times; some ventilation was better than no ventilation; airflow patterns affected transmission; ventilation feature (e.g., supply/exhaust, fans) placement influenced particle distribution. Some studies provided qualitative recommendations; however, few provided specific quantitative ventilation parameters suggesting a significant gap in current research. Adapting HVAC ventilation systems to mitigate virus transmission is not a one-solution-fits-all approach but instead requires consideration of factors such as ventilation rate, airflow patterns, air balancing, occupancy, and feature placement.Practical ImplicationsIncreasing ventilation, whether through ventilation rates (ACH, m3/h, m3/min, L/min) or as determined by CO2 levels (ppm), is associated with decreased transmission, transmission probability/risk, infection probability/risk, droplet persistence, and virus concentration, and increased virus removal and efficiency of virus particle removal. As well, professionals should consider the fact that changing ventilation rate or using mixing ventilation is not always the only way to mitigate and control viruses as varying airflow patterns and the use of ventilation resulted in better outcomes than situations without ventilation. Practitioners also need to consider occupancy, ventilation feature (supply/exhaust and fans) placement, and exposure time in conjunction with both ventilation rates and airflow patterns. Some recommendations with quantified data were made, including using an air change rate of 9 h-1 for a hospital ward; waiting six air changes or 2.5 hours before allowing different individuals into an unfiltered office with ∼2 fresh air changes (FCH) and one air change for a high-efficiency MERV or HEPA filtered laboratory; and using a pressure difference between -2 and -25 Pa in negative pressure isolation spaces. Other recommendations for practice included using or increasing ventilation, introducing fresh air, using maximum supply rates, avoiding poorly ventilated spaces, assessing fan placement and potentially increasing ventilation locations, and employing ventilation testing and air balancing checks.

Computational investigation for endocytosis of CoVID-19 virus SARS-CoV-2 in cell membrane

CoVID-19 virus SARS-CoV-2 follows the endocytosis process to enter inside a cell to infect it. It is important to study the endocytosis of SARS-CoV-2 in cell membrane to prevent the pandemic of CoVID-19. In this paper we develop a finite element based computational model for endocytosis of SARS-CoV-2 in cell membrane and determine curvature generation on it during the process. The virus SARS-CoV-2 is modeled as a rigid spherical particle and cell membrane as an anisotropic elastic material, while its fluidic nature due to lipid exchange with infinite reservoir is preserved using suitable conditions. With the help of a contact pair created between the virus particle and cell membrane, endocytosis process is computationally studied and the curvature of membrane is evaluated as the time progresses during the endocytosis process. At the tip of the virus particle and half-radius distance from it, the membrane follows the curvature of virus very quickly. However, it takes more time for the membrane point located at a distance equal to the radius of the virus particle. This is compensated by the cytoplasmic peripheral proteins binding onto the inside surface of the cell membrane. The role of cytoplasmic peripheral BAR proteins is investigated by using a linear curvature-coupling model with protein concentrations. It is observed that F-BAR protein is more sensitive to the curvature of virus particle in comparison to the other BAR proteins. The sensitiveness deteriorates as the curvature is increased.

Homology between SARS CoV-2 and human proteins

An extremely high contagiousness of SARS CoV-2 indicates that the virus developed the ability to deceive the innate immune system. The virus could have included in its outer protein domains some motifs that are structurally similar to those that the potential victim's immune system has learned to ignore. The similarity of the primary structures of the viral and human proteins can provoke an autoimmune process. Using an open-access protein database Uniprot, we have compared the SARS CoV-2 proteome with those of other organisms. In the SARS CoV-2 spike (S) protein molecule, we have localized more than two dozen hepta- and octamers homologous to human proteins. They are scattered along the entire length of the S protein molecule, while some of them fuse into sequences of considerable length. Except for one, all these n-mers project from the virus particle and therefore can be involved in providing mimicry and misleading the immune system. All hepta- and octamers of the envelope (E) protein, homologous to human proteins, are located in the viral transmembrane domain and form a 28-mer protein E14-41. The involvement of the protein E in provoking an autoimmune response (after the destruction of the virus particle) seems to be highly likely. Some SARS CoV-2 nonstructural proteins may also be involved in this process, namely ORF3a, ORF7a, ORF7b, ORF8, and ORF9b. It is possible that ORF7b is involved in the dysfunction of olfactory receptors, and the S protein in the dysfunction of taste perception.

Increased capsid oligomerization is deleterious to dengue virus particle production

The capsid protein (C) of dengue virus is required for viral infectivity as it packages viral RNA genome into infectious particles. C exists as a homodimer that forms via hydrophobic interactions between the α2 and α4 helices of monomers. To identify C region(s) important for virus particle production, a complementation system was employed in which single-round infectious particles are generated by trans-encapsidation of a viral C-deleted genome by recombinant C expressed in mosquito cells. Mutants harbouring a complete α3 deletion, or a dual Ile65-/Trp69-to-Ala substitution in the α3 helix, exhibited reduced production of infectious virus. Unexpectedly, higher proportions of oligomeric C were detected in cells expressing both mutated forms as compared with the wild-type counterpart, indicating that the α3 helix, through its internal hydrophobic residues, may down-modulate oligomerization of C during particle formation. Compared with wild-type C, the double Ile65-/Trp69 to Ala mutations appeared to hamper viral infectivity but not C and genomic RNA incorporation into the pseudo-infectious virus particles, suggesting that increased C oligomerization may impair DENV replication at the cell entry step.

Identification of One Critical Amino Acid Residue of the Nucleoprotein as a Determinant for in vitro Viral Replication Fitness of Influenza D Virus

The newly identified influenza D virus (IDV) of the Orthomyxoviridae family has a wide host range with broad geographical distribution. Despite the first appearance in U.S. pig herds in 2011, subsequent studies demonstrate that IDV is widespread in global cattle populations, supporting a theory that IDV utilizes bovines as a primary reservoir. Our investigation of the two reference influenza D viruses, D/swine/Oklahoma/1334/2011 (OK/11) isolated from swine and D/Bovine/Oklahoma/660/2013 (660/13) from cattle, revealed that 660/13 replicated to titers approximately 100-fold higher than those for OK/11 in multiple cell lines. By using a recently developed IDV reverse genetics system derived from low-titer OK/11, we generated recombinant chimeric OK/11 viruses in that one of the seven genome segments was replaced with its counterpart from high-titer 660/13 virus. Further characterization demonstrated that the replication level of the chimeric OK/11 virus was significantly increased only when harboring the 660/13 nucleoprotein (NP) segment. Finally, through both gain-of-function and loss-of-function experiments, we identified that one amino acid residue at position 381, located in the body domain of NP protein, was a key determinant for the replication difference between the low-titer OK/11 virus and the high-titer 660/13 virus. Taken together, our findings provide important insight into IDV replication fitness mediated by the NP protein, which should facilitate future study of infectious virus particle production mechanism of IDV. IMPORTANCE Little is known about virus infection and production mechanism for newly discovered influenza D virus (IDV) that utilizes bovines as a primary reservoir with frequent spillover to new hosts including swine. In this study, we showed that two well-characterized IDVs, 660/13 replicated more efficiently (approximately 100-fold higher) than OK/11. Using a recently developed IDV reverse genetics system, we identified viral nucleoprotein (NP) as a primary determinant of the different replication capacity observed between these two nearly identical viruses. Mechanistic investigation further revealed that a mutation at NP position 381 evidently modulated virus fitness. Taken together, these observations indicate that IDV NP protein performs a critical role in infectious virus particle production. Our study thus illustrates a NP-based mechanism for efficient IDV infection and production in vitro .

Experimental Evaluation of an Interferometric Light Microscopy Particle Counter for Titering and Characterization of Virus Preparations

Virus particle concentration is a critical piece of information for virology, viral vaccines and gene therapy research. We tested a novel nanoparticle counting device, “Videodrop”, for its efficacy in titering and characterization of virus particles. The Videodrop nanoparticle counter is based on interferometric light microscopy (ILM). The method allows the detection of particles under the diffraction limit capabilities of conventional light microscopy. We analyzed lenti-, adeno-, and baculovirus samples in different concentrations and compared the readings against traditional titering and characterization methods. The tested Videodrop particle counter is especially useful when measuring high-concentration purified virus preparations. Certain non-purified sample types or small viruses may be impossible to characterize or may require the use of standard curve or background subtraction methods, which increases the duration of the analysis. Together, our testing shows that Videodrop is a reasonable option for virus particle counting in situations where a moderate number of samples need to be analyzed quickly.