Virology Lecture Review: Key Concepts

A set of practice flashcards covering core virology concepts from the lecture, including viral biology, phages, zoonoses, notable viruses, HIV, SARS-CoV-2, and vaccine data.

What defines viruses in terms of their cellular structure and parasitic nature?

Viruses are non-cellular entities, meaning they inherently lack the complex organelles, cytoplasm, and a nucleus characteristic of living cells. They are obligate intracellular parasites, which is a crucial aspect of their lifestyle, as they can only replicate by infecting and exploiting the metabolic and synthetic machinery of a host cell. They cannot perform metabolic functions independently.

How do viruses effectively utilize and manipulate host cells to ensure their survival and reproduction?

To survive and reproduce, viruses infect host cells and commandeering cellular processes. This hijacking involves redirecting the host's existing metabolic pathways, ribosomes, enzymes, and energy resources towards producing viral components (e.g., proteins, nucleic acids). Viruses may also produce their own hydrolytic enzymes and other factors designed to optimize the host's internal environment specifically for viral replication, assembly, and subsequent dissemination to new cells.

What types of genetic material (genomes) can viruses possess?

Yes, viruses possess a genome, which is their genetic blueprint, and it can be remarkably diverse in its composition. Viral genomes are made of nucleic acids and can include:1. Double-stranded DNA (dsDNA)2. Single-stranded DNA (ssDNA)3. Double-stranded RNA (dsRNA)4. Single-stranded RNA (ssRNA), which can be further classified as positive-sense, negative-sense, or ambisense.Some less common references also mention ribosomal RNA genomes, highlighting the vast genetic variability found among viruses.

Define the viral capsid, its composition, and its structural characteristics.

The viral capsid is a protective and robust protein-based shell that encloses and safeguards the viral genetic material (genome). It is primarily constructed from multiple, repeating protein subunits called capsomeres. The specific shape of the capsid—which can range from helical to icosahedral (polyhedral)—and the genes encoding its capsomeres are highly diverse across different virus types, playing a critical role in viral morphology, host recognition, and stability.

What methods are used for the morphological and genetic identification of viruses?

Viruses are typically identified using two primary scientific approaches:1. Morphological Identification (Phenotypic): This involves visualizing the virus's physical structure and overall shape externally, most commonly achieved with high magnification using transmission electron microscopy (TEM).2. Genetic Identification (Genotypic): This method focuses on analyzing the virus's genetic material. It involves sequencing their genomes to study specific genes, such as those encoding capsid proteins, and other unique genetic features, providing precise identification, classification, and understanding of evolutionary relationships.

What is a bacteriophage, and what are its characteristic features?

A bacteriophage (often abbreviated as 'phage') is a distinct type of virus that exclusively infects bacteria. They often exhibit a characteristic structure, which typically includes a protein capsid that encapsulates their genetic material (DNA or RNA). Many bacteriophages also possess an intricate tail structure with tail fibers that enable them to specifically attach to the bacterial surface and facilitate the injection of their genome into the host cell.

Outline the general replication cycle of bacteriophages.

The general replication cycle of bacteriophages typically involves a series of coordinated steps:1. Attachment: The phage uses its tail fibers to specifically attach to receptors on the surface of the bacterial host cell.2. Injection: The phage then injects its genetic material (genome) directly into the bacterial cytoplasm, leaving most of its capsid outside.3. Replication & Synthesis: The viral genes quickly hijack the host's cellular machinery, redirecting it to replicate the viral genome and synthesize viral proteins (capsomeres, enzymes, etc.).4. Assembly: Newly synthesized viral genomes and proteins are then assembled into new, complete phage particles (virions) within the host cell.5. Lysis & Release: The host cell is subsequently lysed (broken open), often by phage-encoded enzymes, which leads to the release of numerous progeny (newly formed) phages into the environment, ready to infect other bacteria.

What structural characteristics of viral capsids are illustrated by the Tobacco Mosaic Virus (TMV)?

The Tobacco Mosaic Virus (TMV) exemplifies a common viral capsid architecture. Its capsid is described as linear, meaning its capsomeres are typically arranged in a rod-like fashion around the viral RNA genome. While the existing description mentions it can form a 'polyhedral shape,' it's important to recognize that viral capsids primarily exhibit either helical symmetry (like rod-shaped TMV) or icosahedral/polyhedral symmetry (roughly spherical). This fundamental protein shell, constructed from repeating capsomere subunits, is a frequent evolutionary design for enclosing and protecting genetic material across a wide range of viruses.

What are the key surface proteins of influenza viruses, and how are they used for classification?

Influenza viruses are critically characterized by two major surface glycoproteins that project from their envelope, crucial for infection and immune evasion:1. Hemagglutinin (H): This protein is essential for the virus's ability to attach to specific sialic acid receptors on the surface of host cells, initiating the infection process.2. Neuraminidase (N): This is an enzyme that plays a vital role in the release of newly formed virions from infected cells by cleaving sialic acid receptors, preventing the virus from clumping and facilitating its spread.The specific types and combinations of these H and N proteins (e.g., H1N1, H3N2) are used as a basis to classify different influenza strains, which is fundamental for epidemiological tracking, vaccine design, and public health responses.

What distinct structural features differentiate bacteriophages from many animal viruses?

A primary structural distinction is that bacteriophages frequently possess a more complex and specialized morphology, including a distinct tail structure and tail fibers. These components are specifically adapted for attaching to the rigid cell walls of bacterial hosts and for the precise and efficient injection of their genetic material (DNA or RNA) into the bacterial cytoplasm. In contrast, many animal viruses typically lack such tail structures and usually enter host cells via mechanisms like endocytosis or membrane fusion.

Explain phage therapy and describe the role of the 'c phages' program.

Phage therapy is a rapidly evolving medical strategy that employs bacteriophages to specifically target, infect, and lyse pathogenic bacteria responsible for infections. This approach is gaining particular interest for treating antibiotic-resistant bacterial infections.The 'c phages' program, notably from the University of Pittsburgh, plays a pivotal role in this field by:1. Managing and maintaining a comprehensive library of diverse phages, characterized for their host specificity.2. Actively pursuing emergency FDA authorizations in specific, urgent clinical scenarios. This allows for the compassionate use of carefully selected phages as an experimental therapeutic option for patients with life-threatening bacterial infections who have exhausted conventional treatments.

How is the host range of a bacteriophage determined, and what factors influence it?

The host range of a bacteriophage refers to the specific bacterial species or strains that it is capable of infecting. This specificity is primarily determined by:1. Specific Recognition and Binding: The phage's ability to precisely recognize and bind to particular molecules (e.g., proteins, polysaccharides) or structures present exclusively on the surface of its target host bacterial cells.2. Genome Information and Compatibility: Detailed genomic sequencing of phages provides crucial information about genes encoding host-binding proteins, replication enzymes, and other factors that dictate the phage's ability to not only attach but also successfully replicate within a specific host. Knowledge of this allows researchers to identify which hosts each phage can infect.

Provide an example of a significant bacteriophage host group discussed in the context.

A particularly notable example of a bacteriophage host group highlighted in the context is Mycobacterium phages. These are bacteriophages that have evolved to specifically infect members of the Mycobacterium genus, which includes notorious bacterial pathogens. This group is significant because it includes phages that can infect species related to Mycobacterium leprae, the bacterium responsible for Hansen's disease (leprosy), underscoring their potential for therapeutic or research applications against these challenging pathogens.

Define a zoonotic virus and explain its significance in the context of influenza.

A zoonotic virus is a type of virus that naturally circulates within animal populations but possesses the capacity to 'jump' or transmit to humans. This cross-species transmission event is known as zoonosis. For influenza viruses, their zoonotic potential is profoundly significant because:1. Novel Strains: Animal reservoirs (such as wild birds and pigs) can harbor influenza virus strains that human immune systems have never encountered, meaning humans lack pre-existing immunity.2. Pandemic Potential: When these novel animal-origin strains acquire mutations that enable efficient and sustained human-to-human transmission, they can swiftly lead to widespread and devastating pandemics or epidemics, due to a lack of population immunity and potentially differences in virulence or transmissibility.

Explain the concept of the 'virulence vs. transmission trade-off' in viral evolution.

The virulence vs. transmission trade-off describes a fundamental evolutionary dilemma for many viruses:1. High Virulence: Viruses that are highly virulent often cause severe illness or rapidly kill their host. This can limit the host's social interactions and mobility, thereby reducing opportunities for the virus to transmit efficiently to new hosts.2. High Transmissibility: Conversely, viruses that evolve to be highly transmissible often induce milder symptoms, allowing the infected host to remain mobile and interact with a greater number of individuals for longer durations, thereby increasing the potential for viral spread.Achieving both extremely high virulence and high transmission simultaneously is often difficult from an evolutionary standpoint. Historical pandemics, however, have shown that external factors like increased human movement (e.g., troop movements during wartime) or dense populations can independently boost transmission rates, sometimes decoupling this natural trade-off.

Summarize the debate regarding the geographical origin and naming of the 1918 'Spanish Flu.'

The 1918 'Spanish Flu' pandemic, despite its name, has an debated origin. The term 'Spanish Flu' became commonplace because Spain, a neutral country during World War I, was one of the few nations whose media openly and freely reported on the devastating scale of the pandemic. In contrast, combatant nations (like the U.S., UK, France, Germany) imposed strict wartime censorship, downplaying or suppressing reports of illness to maintain public morale. Consequently, although evidence suggests the virus likely originated elsewhere (e.g., potentially the United States), Spain's transparency led to the misleading geographical designation of the flu.

Define HIV, explain its primary target, and describe the significance of HAART.

HIV (Human Immunodeficiency Virus) is a specific type of retrovirus, characterized by its ability to reverse-transcribe its RNA genome into DNA and integrate it into the host's chromosome. HIV primarily targets and destroys CD4 T cells, which are crucial white blood cells that play a central role in coordinating the human immune response. The progressive depletion of these cells leads to AIDS (Acquired Immunodeficiency Syndrome), rendering individuals highly vulnerable to opportunistic infections and certain cancers. The advent of HAART (Highly Active Antiretroviral Therapy) revolutionized HIV treatment. It involves a cocktail of multiple antiretroviral drugs used simultaneously, which significantly prevents the virus from developing resistance, effectively reducing viral load, stopping disease progression, and allowing individuals to live longer, healthier lives by transforming HIV into a manageable chronic condition.

Explain the rationale behind using multiple drugs simultaneously in HIV treatment.

HIV treatments employ multiple drugs simultaneously (HAART) as a critical strategy to combat the virus's inherent high mutation rate and rapid development of drug resistance. HIV reverse transcriptase is prone to errors, generating many different viral variants. If only a single drug were used, the virus could quickly mutate around that drug's target, rendering the treatment ineffective. By administering a cocktail of drugs that each target different stages of the viral life cycle or distinct viral proteins, it becomes exponentially more difficult for the virus to develop simultaneous resistance to all drugs. This multi-pronged attack effectively slows or prevents the emergence of 'escape mutations,' thereby maintaining therapeutic efficacy and preventing disease progression.

Discuss the known or suspected origins of SARS-CoV-1 and SARS-CoV-2, focusing on their zoonotic nature.

SARS-CoV-1 (the virus responsible for the 2002-2003 SARS outbreak) and SARS-CoV-2 (the virus causing COVID-19) are both zoonotic coronaviruses that are widely accepted to have originated within bat populations.1. SARS-CoV-1: This virus predominantly spread in Asia during 2002–2003, with strong evidence suggesting that civet cats served as an intermediate host, facilitating the jump and transmission of the virus from bats to humans.2. SARS-CoV-2: This virus emerged in late 2019 and rapidly led to a global pandemic. While its ultimate origin is traced back to bats, research indicates the possible involvement of intermediate hosts, such as pangolins or raccoon dogs, which may have acted as a 'bridge' for zoonotic spillover to humans, potentially in settings like Wuhan live animal markets. Crucially, extensive scientific review has found no solid evidence to support claims of genetic manipulation or a laboratory origin for either virus.

What specific lines of evidence have been presented concerning the origin of SARS-CoV-2?

Several key lines of scientific evidence have been presented regarding the origin of SARS-CoV-2:1. Genome Sequencing Similarity: Comprehensive analysis of the viral genome has shown a high degree of similarity to coronaviruses found in bats, strongly indicating a natural bat reservoir as the ultimate source.2. Intermediate Hosts: Investigations suggest the possible involvement of intermediate animal hosts, such as pangolins or raccoon dogs. These animals could have acquired the virus from bats and then transmitted it to humans, potentially in environments like the Wuhan live animal markets, which may have acted as an early amplification site.3. Lack of Genetic Manipulation Evidence: Extensive scientific scrutiny of the SARS-CoV-2 genome has found no conclusive evidence consistent with genetic manipulation or a laboratory origin. The genomic features are consistent with natural evolutionary processes.

What were the key findings from Kaiser Permanente data regarding COVID-19 vaccination and mortality rates?

Data from Kaiser Permanente concerning COVID-19 vaccination outcomes clearly demonstrated a substantially lower mortality rate among vaccinated individuals compared to unvaccinated individuals. Specifically, the data showed:1. Pfizer-BioNTech vaccine: Approximately 4.2 deaths per 1,000 vaccinated individuals, significantly lower than approximately 11 deaths per 1,000 for unvaccinated individuals.2. Moderna vaccine: Exhibited similar protective efficacy and low mortality rates.3. Johnson & Johnson (J&J) vaccine: Showed approximately 8.4 deaths per 1,000 vaccinated individuals.These findings consistently underscored the significant protective effect of initial vaccination and subsequent booster doses in markedly reducing the risk of severe illness, hospitalization, and death due to COVID-19.

What common vaccine adverse events are noted?

While COVID-19 vaccines are generally safe and effective, some specific adverse events have been noted:1. Anaphylaxis: A severe, systemic allergic reaction, which is extremely rare but treatable with immediate medical attention.2. Myocarditis and Pericarditis: Inflammation of the heart muscle or the outer lining of the heart. This risk is a particular concern, mainly for younger men and adolescents, but it remains a rare complication, typically mild, self-limiting, and resolving quickly.3. Thrombosis with Thrombocytopenia Syndrome (TTS): A rare but serious condition involving blood clots combined with low platelet counts, specifically noted with the Johnson & Johnson (J&J) viral vector vaccine.Despite these rare adverse events, the overall risk-benefit analysis overwhelmingly favors vaccination, as the risks of severe illness, hospitalization, and death from the viral infection itself are substantially higher than the risks associated with vaccine adverse events.

Do mRNA vaccines permanently alter or integrate into human DNA?

No, mRNA vaccines do not permanently alter or integrate into human DNA. Messenger RNA (mRNA) functions exclusively in the cell's cytoplasm, where it provides temporary instructions to produce a harmless viral spike protein, which then triggers an immune response. Crucially, mRNA does not enter the cell's nucleus, which is where human DNA is stored. Furthermore, mRNA is naturally fragile and rapidly degraded by the body's cellular enzymes within a short period, making any permanent genetic modification impossible.