Science of virology

Summary

Virology is a scientific field emphasizing the study of submicroscopic entities known as viruses. Because genetic material within viruses can be easily manipulated and viruses replicate at a relatively rapid rate, research in molecular genetics between the 1940s and 1970s largely consisted of the study of viruses. Scientific application within virology has led to understanding cell processes such as the molecular basis for cancer as well as developments in the field of biotechnology. Genetic engineering, the process of altering the genetic makeup of organisms using viral vectors, has also provided a means for the production of numerous pharmaceuticals.

Definition and Basic Principles

Viruses are intracellular parasites that infect all types of organisms, including bacteria, plants, and animals. Because viruses are commonly associated with human diseases, the public usually views these biological entities only in this context. However, the ability of viruses to infect cells and, in some cases, to integrate within the host genetic material has led to the development of new technologies for insertion or replacement of defective genetic material.

Although all cells can be infected by viruses, viruses often exhibit a specific host range. Bacterial viruses infect only specific strains of bacteria, and animal viruses are usually restricted to a specific species or tissues within the species. Viruses contain surface proteins that determine which cells can be infected. In a manner analogous to a lock and key, viruses attach to specific receptors expressed on the cell's surface. Viral vaccines induce the body to produce neutralizing proteins, or antibodies, which bind to the virus's surface and block its adsorption into the cell.

Background and History

Viral diseases have probably existed since the early years of human civilization, but viruses were not discovered until the late 1800s. The cause of many human diseases was unknown until the development of the germ theory of disease in the mid-nineteenth century. During the golden age of microbiology, from about 1875 to 1900, scientists were able to determine that microorganisms caused certain diseases. French scientist Louis Pasteur and German physician Robert Koch were prominent among these early microbiologists. The work of Pasteur, Koch, and their associates involved isolating and growing bacteria in the laboratory and demonstrating that these organisms were able to cause specific diseases in animals.

Pasteur, working with rabies in the early 1880s, noted that unlike bacteria, the agent that caused rabies did not grow on culture media and was capable of passing through minute filters. The agent was called a virus from the Latin word meaning poison. During the late nineteenth and early twentieth centuries, scientists demonstrated that viruses were capable of replicating, indicating that they were a life-form rather than a poison. A number of human diseases, including smallpox, influenza, and rabies, were shown to be caused by these agents.

The development of the electron microscope during the 1930s allowed viruses to be observed. The first viruses to be extensively studied were bacteriophages, viruses that infect bacteria. Because some bacteriophages kill bacteria, it was at one time thought that they could be used to treat bacterial infections. The plot of Sinclair Lewis's book Arrowsmith (1925), in which physician Martin Arrowsmith used “phage” to deal with an outbreak of plague, was predicated on that idea.

How It Works

Much of the study of viruses has revolved around finding a way to treat viral diseases or prevent them through vaccines. However, as the mechanism by which they infect people became better understood, scientists began to develop ways in which they could use viruses to treat other diseases and conditions.

Viral Vaccines. The first human vaccine against a viral disease was created in the 1790s through a serendipitous discovery by British physician Edward Jenner. He observed that people previously infected with material from lesions on the udders of cattle (cowpox) became immune to smallpox. Although Jenner was unaware of why cowpox provided immunity to smallpox, scientists later determined that the cowpox virus contains proteins that cross-react with those of smallpox and produce immunity in those exposed to it. The process of immunization became known as vaccination, derived from the Latin word vacca, which means cow.

Although the smallpox vaccine uses a naturally cross-reactive virus, modern viral vaccines take advantage of the ability of artificially attenuated or killed viruses to provide immunity. Attenuated viruses, such as those used to immunize against rabies, polio (Sabin vaccine), measles, and mumps, are viruses that have had their disease-causing ability reduced through animal or cell culture passage, and they produce immunity to the disease although they are incapable of causing illness. The Salk vaccine against polio uses a virus that has been killed through chemical treatment.

The theory behind any immunization is that components of the vaccine induce the recipient to produce antibodies, which provide protection against any subsequent exposure to that agent. Viruses have their own means to avoid neutralization by antibodies. Influenza virus is prone to two forms of changeAntigenic drift, mutations in the surface hemagglutinin protein that is the target of the antibody response, and antigenic shift, the recombination of the human strain with animal influenza strains to create an entirely new variety of influenza virus. The 2009 swine flu (H1N1 flu) was the result of such a shift. Rhinoviruses, associated with most cases of the common cold, do not mutate significantly. However, more than one hundred strains of the virus exist, and immunity to one does not confer immunity to the other strains.

Genetic Manipulation. Genetic diseases generally originate from mutations that affect the proper expression of specific genes or the function of the gene product. Although the mutation affects only a single gene in most cases, the effect may be significant because many gene products are pleiotropic, producing multiple effects in the organism. An example is the FBN1 gene, which encodes fibrillin, a protein necessary for proper connective tissue formation. Mutations in the gene result in Marfan syndrome, a weakening in connective tissue throughout the body, which can affect the limbs, aorta, or particular organs.

The principle behind gene therapy is that replacement of the gene containing the mutation with a normal copy may reverse the effects of the genetic error. The idea applies in particular to genetic defects that are associated with a single gene, or monogenic diseases. The challenge has been how to introduce the correct gene into the tissues that are affected in a manner that minimizes side effects yet produces a permanent correction. Viruses are particularly useful in serving as gene vectors because some have the ability to infect multiple cells and multiple types of tissue and, in some cases, integrate into the host genome, becoming a permanent part of the genetic material.

Because viruses by their nature generally alter or kill the cells they infect, they must first be rendered harmless to be used in gene therapy. This is carried out by first deleting the genes necessary for viral replication. For example, to render human adenoviruses harmless, two specific genes, E1 and E3, are deleted to block virus replication. Deletion of an additional gene called F1, which encodes the surface fiber that allows the virus to attach, reduces the danger of inflammation following the virus's introduction into a host. Deletion of the fiber also reduces the host range, limiting the variety of cells that can be infected. Cutting of the deoxyribonucleic acid (DNA) with the proper restriction enzymes allows the desired therapeutic gene to be inserted at the site once occupied by the E1 and E3 genes, creating recombinant DNA. Cell cultures that can provide the necessary functions for duplication of the recombinant DNA are then transfected with the engineered viral DNA.

Anticancer Therapy. The limitation of host range for viral infection has been applied to develop anticancer therapies. The theory posits viruses can infect only certain cells, and therefore, viruses could be altered to express proteins detrimental to the survival of cancer cells. Gene therapy using viruses has taken several approaches. Several clinical trials have involved the introduction into cancer cells of retroviruses carrying genes for cytokines, proteins that stimulate an immune response directed against the neoplasm. A second approach uses viruses that infect only specific types of cells, such as nerve cells. For example, viral agents such as herpesviruses naturally target tissues found in the nervous system. Genetically altered herpesviruses could be used to kill only tumor cells that arise in the brain or spinal cord.

Applications and Products

Gene Introduction and Integration. The ability to insert specific genes into viral vectors provides a mechanism for introducing genetic material into individual cells or tissues within organisms. Several viruses, each with its own advantages and disadvantages, have served as such vectors. These viruses have in common the ability to infect a broad range of hosts, allowing for a wide range of applications in the field of genetic engineering. Replacement of defective genes in human cells remains the goal, but only a few therapies have been developed to the point where they could be tested in clinical trials.

The choice of virus is generally based on the size of the genetic material to be introduced and the likelihood of any immune or inflammatory response. For larger segments of DNA, ranging between 7,500 and 35,000 base pairs, enough to encode a protein or proteins with about 2,500 to 10,000 amino acids, the primary choices as vectors are either vaccinia virus or adenovirus. Vaccinia, a large enveloped double-stranded DNA virus, has previously served a role as the vaccine against smallpox. When vaccinia is used as a vector, viral genes necessary for replication are deleted before inserting the desired genetic material, rendering the virus unable to replicate. Unfortunately, vaccinia frequently elicits a significant inflammatory response, limiting its usefulness.

Adenoviruses are relatively large nonenveloped DNA viruses with a protein capsid. Spikes or fibers attached to the capsid determine the host range for infection. There are about fifty serotypes of adenoviruses, some of which are associated with human respiratory and gastrointestinal infections. The most commonly used adenovirus strain for genetic studies is serotype 5. Recombinant adenovirus DNA has been used in limited clinical trials to treat patients with cystic fibrosis and ornithine transcarbamylase (OTC) deficiency. Cystic fibrosis, the most common inherited genetic disease in the West, is associated with a mutation in the gene that encodes a regulator protein necessary for proper transport of ions in and out of cells. OTC deficiency is a metabolic disorder in which urea metabolism is affected. About 25 percent of clinical trials using a viral vector have used adenoviruses.

Lentiviruses such as human immunodeficiency virus (HIV) have a vector capacity significantly smaller than that of adenoviruses, but they have the ability to integrate into the host genome, resulting in the recombinant gene becoming part of the host genetic material. In animal trials, lentiviruses have introduced growth factor genes into mouse cells as well as the gene encoding Factor VIII, which is lacking in the most common forms of human hemophilia. Preclinical trials have demonstrated that recombinant HIV can be used to replace defective genes in diseases such as cystic fibrosis and muscular dystrophy. About 25 percent of clinical trials have used retroviruses as the vector, including most of the original clinical trials that used viral vectors.

The ability of lentiviruses to integrate into the host genetic material, one of the desirable features of such viruses, does have its drawbacks. Integration is not random and frequently takes place within the introns (DNA regions in a gene that is not translated into protein) of preexisting genes, some of which are necessary for proper cell function. This can produce severe side effects, such as those that occurred during trials in France that attempted to insert an adenosine deaminase gene to cure a form of severe combined immunodeficiency syndrome (SCID). Although nine patients did show improved immune function, three developed T-cell leukemia, and one person died. On the other hand, in 2021, researchers used lentiviruses as vectors to treat children with the condition adenosine deaminase deficiency SCID (ADA-SCID) that leads to improper functioning of the immune system due to mutations in the ADA gene. They transferred the vector-treated ADA genes to the affected stem cells that normally form blood and immune cells, and the treatment was successful in forty-eight out of the fifty patients treated.

Adeno-associated viruses are naturally defective viruses that require a helper adenovirus to replicate normally. However, they can infect a range of cells and integrate at specific sites in human chromatin. Adeno-associated viruses have been used experimentally to kill certain forms of breast, cervical, and prostate cancer cells. As viral vectors, they have been used to introduce a gene for the production of insulin and the genes for both Factor VIII and Factor IX, lacking in humans with certain forms of hemophilia (hemophilia A and B, respectively), into mice genes that encode erythropoietin. This glycoprotein induces the bone marrow to increase red blood cell production.

Adeno-associated viruses have been associated with only a small proportion of all clinical trials. Other vectors have used naked plasmid DNA, vaccinia, and other poxviruses, as well as other types of viruses.

Careers and Course Work

Because virology is a biological science, students wishing to pursue a career in the field should emphasize undergraduate work in biology, working toward a bachelor of science degree. Undergraduate students should elect coursework in general biology and chemistry, with advanced courses in cell biology, microbiology, and biochemistry. If available, students should also enroll in virology and molecular biology.

Obtaining a graduate degree, such as a master's in biochemistry or biological science, is highly recommended. Graduate work should emphasize the molecular biology of viruses, and the student should seek to gain experience in molecular cloning or genetic engineering. A master's degree is adequate for performing laboratory work. However, a medical degree or a doctorate is required to propose or direct clinical trials. Much of the basic research in virology is carried out in university settings, although researchers with advanced degrees are also part of hospital or medical school staff.

Vaccines or other virus-related treatments are usually tested first on animals to determine any obvious safety problems and to measure the treatment's efficacy. The treatments are then tested on humans in clinical trials, usually carried out by physicians associated with university or hospital health centers. The director of a trial, in conjunction with any associates, obtains the necessary approval of the appropriate government agency. Funding may be provided by either a government agency or a private source. The phase or level of the clinical trial reflects the number of patients involved in the trial. Phase I trials involve fewer than one hundred volunteers, and Phase II trials involve upward of several hundred. Aspirants can work in companies such as GlaxoSmithKline, BridgeBio, Procter and Gamble, and Gilead Sciences.

Social Context and Future Prospects

Researchers who attempt to control viral disease must address the evolving nature of viruses and the new or unusual viral diseases that develop. Many viruses, including influenza and HIV, mutate at a rapid rate. New viruses emerge and rise to prominence as well. Ebola, for example, increased in prevalence in the twenty-first century, with West Africa suffering from an Ebola epidemic from 2013 to 2016, in which 28,616 people were infected and 11,310 died. Ebola was once considered not worth studying because outbreaks were sporadic and isolated. However, as outbreak frequency increased, it became a major concern for virologists. Another major outbreak was reported in 2018 in the Democratic Republic of Congo and Uganda, with around 3,500 cases and fatalities of more than 2,000 people. In 2019, the FDA approved the first vaccine for the disease. However, it was only proven effective on one of the six ebola types. Another emerging virus, Zika virus, also drew virologists' attention. An mRNA vaccine for the Zika virus reached the clinical trial phase in the late 2010s but failed to gain approval.

Influenza and HIV provide particular challenges. The potential virulence of influenza was demonstrated during the 1918 worldwide pandemic, during which an estimated 50 million people died. Any influenza vaccine that would provide protection against multiple strains would have to address the problems of both genetic drift and genetic shift. The inability to grow the virus in anything but embryonated chicken eggs rather than cell culture also significantly increases the lead time necessary for large-scale vaccine production.

HIV, the etiological agent for AIDS (acquired immunodeficiency syndrome), provides its challenges. HIV mutates at a high rate immediately following infection of human lymphocytes, producing dozens of varieties in weeks. The high rate of mutation is the primary reason that no AIDS vaccine has thus far proven effective. In the early twenty-first century, researchers were trying to find an HIV vaccine that could be effective against its two strains, HIV-1 and HIV-2, which have only 55 percent identical genetic sequence. However, the development of HIV vaccines using mRNA, viral vectors, and broadly neutralizing antibodies (bNAbs) was still under research.

The disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread throughout the world in a devastating pandemic beginning in 2020, killing more than 4 million people. Research related to vaccines accelerated during the COVID-19 pandemic in 2020. In record time, COVID-19 vaccines containing genetic material from messenger ribonucleic acid (mRNA) were developed that could produce antibodies more efficiently after antigen recognition by the immune system.

Bibliography

Allen, Arthur. Vaccine. W. W. Norton, 2007.

Bamford, Dennis H., and Mark Zuckerman. Encyclopedia of Virology. 4th ed., Elsevier, 2021.

Bech, Nicolai S. Encyclopedia of Virology: New Research. Nova Science, 2020.

Cann, Alan J. Principles of Molecular Virology. 6th ed., Elsevier, 2015.

"Gene Therapy Offers Potential Cure to Children Born without an Immune System." UCLA Health, 11 May 2021, www.uclahealth.org/news/gene-therapy-offers-potential-cure-to-children-born-without-an-immune-system. Accessed 11 Jul. 2021.

Hagan, Michael F., et al. "Overview of the 2023 Physical Virology Gordon Research Conference—Viruses at Multiple Levels of Complexity." Viruses, vol. 16, no. 6, 2024. MDPI, doi.org/10.3390/v16060895.

Kent, Chloe. "Will There Ever Be an HIV Vaccine?" Pharmaceutical Technology, Verdict Media, 1 Dec. 2020, www.pharmaceutical-technology.com/features/will-there-ever-be-an-hiv-vaccine. Accessed 11 July 2021.

Madigan, Michael, et al. Brock Biology of Microorganisms. 16th ed., Pearson Benjamin Cummings, 2022.

Orenstein, Walter A., et al. Plotkin’s Vaccines. 8th ed., Elsevier, 2024.

Pierson, Theodore C., and Michael S. Diamond. "The Emergence of Zika Virus and Its New Clinical Syndromes." Nature, vol. 560, 2018, pp. 573–81.

Zuo, Kunlan, et al. “Evolution of Virology: Science History through Milestones and Technological Advancements.” Viruses, vol. 16, no. 3, 28 Feb. 2024. MDPI, doi.org/10.3390/v16030374.