Viruses and Virions

Viruses and Virions

• Viruses need a host cell and possess a nucleic acid genome for replication.
• A virion is a virus's extracellular form facilitating infection.
• Examples of viruses include Flu Virus, SARS-COV-2, and Zika Virus.

Naked vs. Enveloped Viruses

• Naked viruses consist solely of a nucleocapsid and are common among bacterial viruses.
• Enveloped viruses have a nucleocapsid plus an outer envelope made of proteins and lipids.
• Virion surface proteins are essential for host cell attachment.
• A viral envelope is required to infect host cells, and virus-specific envelope proteins are essential for host attachment and release post-replication.

Capsid and Capsomeres

• The capsid is a protein shell enclosing the viral genome, providing protection outside the host.
• Capsomeres are individual protein units constituting the capsid; most viruses have a single type that aids in self-assembly.

Viral Mutation Rates

• Small viral genomes within RNA viruses exhibit the highest mutation rates, including dsDNA, ssDNA, RNA viruses, and viroids.
• Mutation rates are slower for large viral genomes in higher eukaryotes and prokaryotes.

Viral Classification

• Viruses are classified based on the host they infect and their genome structure.

Baltimore Classification System

• David Baltimore established this system in 1975 for retroviruses and reverse transcriptase.
• Classification is based on the host they infect and their genome structure.

Bacteriophages

• Bacteriophages have lysozyme-like enzymes for infection and release.
• They are enzymes inside virions since viruses lack metabolic processes.

Bacterial Virus Replication Cycle

• A permissive cell supports the virus's full replication cycle.
• Attachment: The virion adsorbs to the host cell.
• Penetration: Viral nucleic acid enters or is injected into the host.
• Synthesis: The host cell synthesizes viral nucleic acid and protein, redirected by the virus.
• Assembly: Capsids are assembled, and viral genomes are packaged into new virions.
• Release: New virions are released from the cell.

Latent Period of Viral Infection

• This is the phase between viral entry and new viral particle release.
• Critical replication steps are undergoing, so infectious virions are undetectable outside the cell.
• Eclipse Phase: The virus attaches to the host and enters, but infectious virus is undetectable because the viral genome is uncoated, and viral mRNA transcription and protein synthesis begin; viral genome replication produces new genetic material for assembly.
• Maturation Phase: New viral components are assembled into virions inside the host, preparing for release via lysis or budding.
• The period ends when assembled virions release into the extracellular environment; it lasts minutes to hours in bacteriophage infections but hours to days in animal viruses.

Viral Attachment and Host Specificity

• Viruses use surface proteins to attach to their host.
• These proteins interact with receptors (proteins, carbohydrates, glycoproteins, lipids, or macromolecules) on the host cell surface.
• Receptors perform normal functions for the cell.

Lytic vs. Lysogenic Viral Infection

• Lytic Infection: The virus redirects the host's metabolism to support replication, destroying the host (e.g., Bacteriophage T4, Influenza, and SARS). ssDNA and RNA bacterial viruses only conduct lytic life cycles.
• Lysogenic Infection: The virus incorporates into the host's genome, waiting for optimal conditions before entering the lytic phase (e.g., HIV, Phage B, and Phage CTX).
• Lytic infections are fast and destructive, while lysogenic infections are dormant and allow long-term survival.
• Lysogenic viruses can switch to lytic, leading to active infection and host destruction, with some viruses having both phases.

Acquisition of New Genetic Information

• During lysogenic infection, bacteriophages can transfer genetic material between bacteria through transduction, leading to the acquisition of new genetic information.
• Temperate phages integrate into the bacterial genome as a prophage during the lysogenic pathway.
• The virus genes are not transcribed, and the viral genome is passed onto daughter cells, giving the host new properties and creating lysogen hosts.
• Bacteriophage lambda integrates into the host chromosome, where a repressor protein keeps it incorporated.
• If the repressor is inactivated, the phage enters the lytic stage, causing cell stress and DNA damage.
• A lytic lifestyle is favored when host cells are plentiful, whereas lysogeny is favored when host cell numbers are low.

Plaque Assay

• It quantifies viral suspension by determining the number of infectious virions per fluid volume, measured in titer units.
• Used for bacteriophages and animal viruses that cause visible cell damage, to isolate genetically identical populations, compare wild-type vs. mutant viruses, and monitor viral replication and vaccine development.

Animal vs. Bacteriophage Infections

• Animal Viruses: The entire virion enters the host cell, replicates in the nucleus of eukaryotic cells, and uses host cell receptors for macromolecules in intercellular communication
• Both: the infection, type of host replication, capsids, and classification by genome structure
• Bacteriophages: Most have head-and-tail structures with dsDNA genomes and overlapping genes.

Outcomes of Viral Infection in Animal Cells

• Virulent infection results in host cell lysis due to replication.
• Latent infection involves viral DNA without replication, leaving the host unharmed.
• Persistent infection involves slow virion release through budding, potentially without host cell lysis.
• Transformation converts normal cells to tumor cells.

Origin of Viruses and RNA World Hypothesis

• Origin of viruses remains uncertain, with 3 main hypotheses: regressive, progressive and virus-first
• The RNA world hypothesis suggests early life was based on self-replicating RNA molecules.
• RNA viruses may be remnants of this RNA-based world, indicating viruses played a role in early molecular evolution.

Archaeal Viruses

• Negative-strand RNA viruses have complementary mRNA genomes.
• Example: Rabies virus and Influenza virus.

Varicella-Zoster Virus (VZV)

• Chickenpox is highly contagious and spreads through direct contact, droplet transmission, and airborne transmission. It establishes latent infection in root ganglia and can lead to shingles through stress, menstruation, or UV light exposure.
• Shingles is less contagious, occurs only in those previously exposed to chickenpox, and affects nerve bundles, causing sensory issues.

Smallpox and Monkeypox (Mpox)

• In 2024, the WHO states mpox is a public health emergency of international concern and declared smallpox eradicated in 1980.
• Global smallpox eradication used widespread vaccination, which cross-protected against orthopoxviruses like mpox
• As smallpox vaccination ended, mpox emerged and spread because there was a lack of immunity and continued presence of mpox.

Differences between Chickenpox and Shingles

• Chickenpox is highly contagious, spreads easily, and establishes latent infection possibly leading to shingles.
• Shingles is less contagious, occurs only after chickenpox, and affects nerve bundles.

Poliovirus

• Poliovirus uniquely targets human cells, causing irreversible paralysis, is part of the enterovirus family. It is transmitted via the fecal-oral route and specifically infects motor neurons.

Influenza Virus

• Virion Characteristics: It has a negative-sense single-stranded RNA genome, enveloped with hemagglutinin (HA) for host cell binding, and neuraminidase (NA) for virion release, plus a segmented genome that's the core of frequent genetic reassortment.
• Highly contagious, infecting the respiratory tract and causing seasonal epidemics with fever, cough, sore throat, and body aches due to constant mutations.
• The influenza virus vaccine is based on predicted viral strains, but antigenic drift (gradual change) and shift (abrupt change) alter the virus enough to evade the immune system.
• Vaccine effectiveness can be reduced by genetic changes that mismatch circulating strains.
• Antigenic drift causes small changes in HA and NA surface proteins, resulting in seasonal variations and partial unrecognizability and Antigenic shift involves a major change when different strains infect the same host and exchange material, which can lead to new strains.

Coronavirus and Influenza Viruses

• Similarities: Both are RNA viruses, enveloped, and transmitted via aerosols causing respiratory diseases.
• Both have spike proteins, but with different binding mechanisms (ACE2 receptor in coronavirus, hemagglutinin in influenza).
• Differences: Influenza has a segmented RNA genome, whereas coronavirus has a single-stranded RNA genome and they replicate in different parts of the cell; coronaviruses replicate in the cytoplasm, while influenza viruses replicate in the nucleus.
• COVID-19 has a more severe pathogenesis than influenza.

COVID-19 and Influenza

• Viruses share virion characteristics, with both being enveloped RNA viruses, but influenza is segmented while coronavirus is non-segmented.
• Influenza infects the upper respiratory tract, causing seasonal epidemics, while COVID-19 leads to systemic effects with more severe disease. COVID-19 cases have been significantly higher, especially in global pandemics.
• Protection: Various platforms exist for COVID-19 vaccines (mRNA, viral vector), while the flu vaccine is inactivated or subunit-based.

Coronavirus Testing

• The N gene (nucleocapsid protein) and S gene (spike protein) are targeted in PCR tests for SARS-CoV-2 detection.

Coronavirus Attachment

• The coronavirus spike protein (S protein) binds to the ACE2 receptor, with ACE2 receptor expression influencing susceptibility and disease severity.

Diversity Types

• Phylogenetic diversity refers to evolutionary relationships between organisms.
• Metabolic diversity pertains to biochemical processes for energy and carbon fixation.
• Functional diversity is the variety of functions in ecosystems.
• These diversities are connected, with phylogenetic relationships affecting metabolic and functional abilities.

Phototrophs Defined

• Phototrophs get energy from light as the base of the food chain.

Phototroph Importance

• As the base of the food chain, phototrophs use light, produce food through photosynthesis, and provide energy. They also are essential in producing oxygen and fixing carbon which is a key element to maintaining functioning ecosystems.

Oxygenic vs. Anoxygenic Phototrophs

• Oxygenic phototrophs produce oxygen using water as an electron donor, including plants, algae, and cyanobacteria.
• Examples of anoxygenic species includes purple and green sulfur, and heliobacteria. As they use something other than water they do not produce water as a result.
• Both types use light for photosynthesis and pigments such as chlorophyll, but differ in specific pigments, function, and electron donors.

Habitats of Phototrophs

• Oxygenic phototrophs thrive in sunlight-rich zones like oceans, land, and lakes ecosystems, where water and sunlight are abudnant.
• Anoxygenic phototrophs thrive in environments where oxygen is scarce; or completely absent such as muddy environments, deep water and sulfur-rich seas.

Light-Harvesting Pigments

• These critical compounds capture light energy of photosynthesis and convert it to chemical energy. Their diversification of pigments allows for absorption of a range of light wavelengths boosting maximum energy capture.
• Pigments enable the diversity among species and contribute to a wide range of ecosystems.

Cyanobacteria's Environmental Role

• Cyanobacteria are key primary producers in various ecosystems, supporting oxygen production and contributing to the global food chain. They also are the key oxygenic phototrophs and play a pivotal role especially in the nitrogen cycle.

Naming System of Anoxygenic Phototrophs

• These organisms are named by the electron donor used through photosynthesis, such as in sulfur bacteria.
• This system also highlights preferences in environments with low percentages of Oxygen.

Microbes in Carbon and Nitrogen Cycles

• CO₂ is converted through bacteria into organic matter through photosynthesis and this organic matter is consumed.
• Bacteria convert N2 into NH3 which plants use and convert into nitrate which then becomes nitrogen gas through microbes.

Synergistic Microbe Relationships

• Different bacterium and organisms cycle nutrients within symbiotic practices; decomposers breakdown organic components and transfer back nutrients, and can work as bacteria which transfers nitrogen.

What constitutes 'the built environment'

• Where humans perform all activities and work. This often includes the transportation system, the parks and also homes/buildings in these areas.

Water Quality

• Water quality is the condition of the water; chemical, biological and how suitable it is for a particular task. Some key indicators of water quality include turbidity, presence of solids and saturation of nutrients.

Sources of Contaminants

• Examples of human-related contaminants include nitrates, animal waste, heavy metals, household waste and fertilizer. Some natural ones include salt, radon and heavy metals.

Positives/Negatives of Microbes to Water Quality

• They assist with bioremediation and wastewater treatments, however can also form as a waterborne pathogen.

The Goals of Potable Water

• Drinkable water must not have any pathogens, tastes or odors, and a low level of solids.

Waterborne Pathogens

• An pathogen, originating in a water source, that is causing disease or illness.

Treatment Steps for Potable Water

• Disinfection is a process using chlorine which removes pathogens through disinfection.
• Coagulation is the act of adding ferric chloride or saline in order to facilitate in removing solids during said procedures.
• Flocculation is then mixing the concoction, to improve agglomeration which helps remove more contaminents.
• Water then experiences filtration and sedimentation to remove any additional particles before leaving the facility; all to create potable water from previously unclean water!

Chlorine and Ozone

• Chlorine destroys pathogens, while controlling the color and odor. It helps increase efficiency but it has a transportation safety hazard in addition to being non-effective when concerning cryptosporidium. Another solution therefore is ozone where nearly all waterborne pathogens are eliminated but an extremely expensive and unstable procedure.

Indicators of Water Quality

• The presence, absence or abundance of such quality indicators indicates the potential lack or existance of a certain disease. They determine if more treatment needs to occur.

Key Features of Good Indicators

• Must be heavily present where pathogens exist.

Coliform's Importance

• These organisms, when tested, represent strong fecal contamination as these intestinal carriers are often excreted in large quantities.

The Remediation Effect

• A microbe is able to help clean up toxins in the current environment. All since they resemble familiar material to the organism.

Bacteria Degrading Plastics

• They can remove plastics by creating enzymes, turning polymers into useable molecules.

Pseudmonas Syringae

• Bad since it produces a protein on the outside which forms ice and causes frost damage at roughly -1 C but also helpful since animals often exploit that damage.

Microbial Genetics

• Tree of life used an old version to track genetic material, as opposed to the rRNA sequencing technique.
• Candidate phyla radiation members - or CPR - are bacterium without all known genetic features, which can often make then the minority percentage in tree of life sequencing.

Building Novel Machines

• Biotech benefits from designing machines to have specific functions.