Abstract
As we reach the first anniversary of the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is overwhelming to reflect on all that has happened, and continues to happen, in the world since the first reports of COVID-19. For some time now, the biggest question on most of our minds has been whether the recently approved COVID-19 vaccines will work as well in the real world as they did in clinical trials. Unfortunately, SARS-CoV-2 has been a moving target from day one, and even now as we write this piece, the new variant of SARS-CoV-2 (B.1.1.7), first reported in the United Kingdom, is showing its face in other countries, which was inevitable. The development of COVID-19 vaccines broke all previous records for time to development and approval, and we knew from the start there was a chance that these vaccines might not be effective by the fall of 2021 if the virus mutated significantly enough to facilitate immune escape. However, the virus apparently did not wait until the next year to find out; it had already mutated significantly by the end of 2020. So the new question even the general public is asking is whether or not the currently approved vaccines will work against the rapidly spreading SARS-CoV-2 B.1.1.7 variant. The answer to this question is buried in the structure. Neutralizing antibody studies are undoubtedly already underway to determine whether or not antibodies generated against the original vaccines will also recognize B.1.1.7 Spike protein. This, of course, will depend on whether the mutations in B.1.1.7 affect the structure of important epitopes within the Spike protein, and if so, whether such putative structural changes will facilitate immune escape.
The timing of this special issue, edited by Dr. Reza Khayat from The City College of New York, is rather serendipitous considering the terms “SARS-CoV-2” and “COVID-19” did not exist when this special issue on structural virology was originally planned. However, structural virology is more important now than it has been in the past 100 years. In relation to this timely topic, we have assembled a collection of interesting articles dealing with aspects of structural virology in the context of a number of important viruses. For example, Emmanuel et al. discuss the structures of ∼30 antibodies in complex with different members of the parvovirus family to provide a comprehensive understanding of how antibodies recognize antigens. Parvoviridae is the sole taxon in the order Quintoviricetes. Members of this family are nonenveloped T = 1 icosahedral capsids (18–26 nm) that enclose linear single-stranded DNA (ssDNA) genomes (4–6 knt). Although some members of this family are pathogenic, the review concentrates on antibodies generated against the apathogenic members that are used for gene therapy. Antibodies generated against these gene delivery vehicles are detrimental to the development and use of this technology, as the antibodies serve to neutralize and eliminate the delivery vehicle before it can deliver its therapeutic payload to the host. Thus, understanding how antibodies can neutralize these vehicles, and how we may be able to design vehicles capable of evading these antibodies is essential for the continued development of parvovirus capsids as gene delivery vectors. A structural understanding of how antibodies neutralize pathogens is essential in the design of antigens for vaccine development. Indeed, the recent and rapid development of vaccines for SARS-CoV-2 directly benefited from the structural studies performed on the spike protein. Moreover, structures of neutralizing antibodies in complex with viral proteins can help predict viral escape mutants that are themselves immune to the host's immune response. Ultimately, the use of structural biology in studying how the immune system neutralizes pathogens will guide the engineering of universal vaccines for the ever-changing pathogens (e.g., HIV and influenza virus).
On the topic of respiratory viruses, Cao and Liang discuss Pneumoviridae, which are members of the Mononegavirales order. Members of this order are enveloped, encode for linear single-stranded negative-sense RNA genomes that range from 11 to 19 knt. These viral polymerases use the genomes as templates for synthesizing mRNA (transcription) for subsequent protein synthesis (translation). During this process, the polymerase encounters a number of essential RNA cis-acting signals that require its activities for proper mRNA synthesis. These multifunctional enzymes are composed of a large (L) protein (250 kDa) possessing RNA polymerization, RNA capping (Cap), and methylation of the Cap activities, and a tetrameric phosphoprotein (9 kDa each) responsible for regulating the activities of L. The review discusses the structural similarities and differences between the human respiratory syncytial virus (HRSV) and human metapneumovirus polymerases that are responsible for delineating the mechanisms of their functions. Moreover, these structures provide a framework for the development of therapeutics against these polymerases, which are responsible for the replication of significant human pathogens that include rabies virus, Ebola virus, and HRSV.
In a review by Xian et al., the topic of virion structure in large DNA viruses is tackled. The authors focus on the role of the minor tape measure protein (TmP) and discuss the mechanism of capsid assembly for a subset of nucleocytoplasmic large DNA viruses (NCLDVs). These viruses are grouped together because of similarities in their genomic content; however, the viruses have different sizes and shapes. Similarly, their genomes also vary in configuration (linear or circular dsDNA) and size (100 kb–2.5 Mbp). The review concentrates on icosahedral NCLDVs and proposes an intriguing spiral mechanism of capsid assembly that involves a complex dance between the major capsid proteins responsible for forming the capsomers and icosahedral capsid shell and the minor capsid proteins (TmP) responsible for establishing the frame of the capsid. The spiral mechanism proposes that capsid assembly initiates at an icosahedral vertex and grows continuously with the addition of capsomers and TmPs to generate the icosahedral shell. However, one wonders how assembly continues properly from the initiating vertex to the neighboring vertex given that the vertices are located far apart and thus unaware of one another's influence? The answer to this question is the TmP, which stretches from one vertex to the next while intimately interacting with the capsomers responsible for making the ginormous capsids.
Finally, Dr. Jade Forwood's group at Charles Sturt University provides two reviews, one on Henipaviruses and another on Circoviruses. The first review by Donnelly et al. discusses the multifunctional roles of the matrix (M) protein. The Henipavirus genus belongs to a family of viruses, Paramyoxiviridae, that cause minor to significant human diseases, in some cases with high mortality rates. These enveloped viruses are pleomorphic and possess a negative-sense RNA genome that is <16 knt. The M protein is a structural component of the virion and is responsible for modulating the host's innate immune response, nuclear import of viral proteins for viral replication, driving viral assembly, and recruitment of the endosomal trafficking system for targeting proteins to the plasma membrane for viral assembly and budding. Given the multiple essential functions of this protein in the virus life cycle, it is anticipated that small molecules that inhibit any of its functions might be a therapeutic against Henipavirus replication.
In a second review from the Forwood group, Nath et al. review recent structural studies from proteins encoded by beak feather disease virus (BFDV) and porcine circovirus 2 (PCV2). BFDV and PCV2 are members of the Circoviridae family of the Circovirus genus. These viruses are widely distributed, and can infect avian, terrestrial, and marine animals. Both BFDV and PCV2 cause lymphoid depletion and immunosuppression of their host, leading to death through secondary infections. The pathogenic nature of these viruses causes significant economic burden globally. These viruses are nonenveloped icosahedral (T = 1) viruses ∼21 nm in size, possessing circular ssDNA genomes <2.4 knt in size. The small genome encodes at least two proteins: a replicase responsible for rolling-circle replication (RCR) of the viral genome, and a capsid protein responsible for the enclosure and transport of the genome from one cell to another. Additional proteins are encoded within the genome; however, the exact mechanism of these proteins remains to be determined. The review discusses how studies focused on the N-terminal structure of the PCV2 replicase have provided insight into the initial stages of RCR genome replication. The authors also discuss how the structures of the BFDV and PCV2 capsid protein in complex with nucleic acid have provided insight into capsid assembly, how the structure of the PCV2 capsid in complex with heparin has provided insight into cellular recognition and attachment, and how biochemical studies of the PCV2 capsid have provided insight into how PCV2 may escape from endosomes after endocytosis by the cell.
In closing, the field of structural virology has always been a fascinating area of research that assembles chemistry, physics, and biochemistry, and now, as we move into the second year of the COVID-19 pandemic, structural virology will become even more relevant to the field of viral immunology and the fight against SARS-CoV-2. Despite the tragic and uncertain times we are living in, it is encouraging from a research perspective to reflect on how much we learned in 2020, and exciting to look forward to what we will know by the end of 2021.