Viral Replication & PCR

• The vast number of viruses, estimated to be around 10 nonillion, highlights their incredible diversity and significant role in ecosystems and human health.

Vastness of Virus Quantities

• The sheer volume of viruses present on Earth is staggering, with estimates suggesting that there are approximately 10 nonillion individual viral entities inhabiting various environments, from deep oceans to the human gut.

• In terms of comparison, this quantity far surpasses the total number of stars that can be found in the observable universe, making viruses one of the most abundant biological entities on the planet.

• To comprehend this scale, it is noteworthy that assigning one virus to every star would still leave an overwhelming surplus, with an estimate suggesting that there would be enough viruses to circulate through each of the 100 million stars multiple times.

• To illustrate the enormity of a nonillion, it is important to recognize that it represents the figure 1 followed by 30 zeros (1,000,000,000,000,000,000,000,000,000,000), a number that is practically unimaginable in everyday scenarios.

• This diversity of viruses includes a wide variety of types, some of which play critical roles in ecological processes, while others can influence human health either positively or negatively. Understanding these quantities allows scientists to appreciate their impact on both natural and human-engineered systems.

• There are more viruses than stars in the universe

• It is estimated that there are 10 nonillion viruses on the planet

• Equals enough viruses to assign one to every star in the universe 100 million times over

• A nonillion equals 1 followed by 30 zeros.

• Viruses are constantly falling from the sky and circulating Earth's atmosphere

Why do you need a virus?

• If all viruses were eliminated, organisms would probably die in about 2 days
• Most are not pathogenic to humans
• Viruses help with ecosystems, fungi, and plants
• Bacteriophages keep bacteria from taking over
• Some viruses kill bacteria in the oceans allowing Plankton to survive to produce more oxygen
• Oncolytic viruses exist

Viruses vs Prokaryotes

• Viruses do not consist of cells
• Viruses do not metabolize
• Viruses do not respond to stimuli
• Viruses do multiply if they have access to a living cell

Properties of Viruses

• Viruses must be infectious to endure in nature
• They must use host cell processes to produce viral messenger RNA, proteins, and identical copies of the genome
• Viruses must encode any required processes not provided by the cell, and must self-assemble

Viral Structure

• Knowledge of structural and genetic features gives insight into how the viruses replicate, spread, and cause disease
• Nucleic acid is protected by a capsid
• Structures could be a naked icosahedral capsid virus or enveloped viruses with a nucleocapsid
• Helical nucleocapsids are mostly enveloped for human viruses
• DNA or RNA and structural proteins = nucleocapsid, and a capsid virus = delivery system/payload

Capsid Morphology and Envelopes

• Capsids are single or double layer protein shells that surround viral nucleic acid
• Nucleic acid and capsid = nucleocapsid
• Icosahedral capsids have 20 triangular faces and 12 vertices subunits
• Helical capsids have varied subunits and spherical core tight with specific viral capsid proteins
• Viral Envelopes are membranes consisting of lipids, proteins, and glycoproteins
• Nonenveloped viruses are relatively stable and resistant to temperature, acids, proteases detergents, and drying
• Enveloped viruses are more fragile and susceptible to heat, acids, detergents, and drying

Virus Transmission

• Enveloped viruses must remain wet and generally transmitted in fluids.
• Virus-specific envelope glycoproteins protrude from the outer surface of the envelope
• Virus particles= virion

Virus Classification

• Occurs by size, morphology, and nucleic acid
• Biochemical characteristics: structure and mode of replication
• Diseases can be classified as encephalitis and hepatitis viruses, for example
• Means of Transmission: arbovirus spread by insects
• Host cell/range: animal, plant, bacteria
• Tissue Tropism (organ): adenovirus, enterovirus

Glycoproteins

• Most Viral Glycoproteins have asparagine-linked carbohydrates which extend through the envelope away from the virion
• "Spike Glycoproteins elicit immunity VAPs (virus-associated pyramids) bind structures on target cells
• Hemagglutinins (HAs) bind to erythrocytes
• Neuraminidase (NA; influenza), Fc receptor & C3b receptor (HSV) are types of glycoproteins
• Naked viruses express glycoproteins on Capsid i.e. adenoviruses

Main Groups of Viruses

• Human viruses may contain DNA or RNA, be enveloped or non-enveloped
• RNA viruses may be Astroviruses, Caliciviruses, Picornaviruses, Toga-, Flavi-, Corona-, Rhabdo, Paramyxo-, Orthomyxo-, Bunya-, Arena-viruses, or Reoviruses and Retroviruses
• DNA viruses may be Parvo-, Adeno-, Papilloma-, Herpes-, Pox-, and Hepadna-viruses

The Six basic Stages of Viral Infection

• Encounter(entry), Spread, Damage, Multiplication, Outcome, and Recovery

Viral Entry Protocols

• Compare/contrast viral entry protocols
• Four main routes: respiratory, gastrointestinal, transcutaneous, sexual
• Most viral diseases are exogenous
• Endogenous happens from reactivation of a latent virus from within a host cell like herpes zoster (HZV) shingles

Spread and Multiplication Process

• Can happen via vertical or horizontal spread
• Vertical occurs from fetus infected in-utero
• Horizontal occurs between members of susceptible host population
• Can happen via Neural spread through nerves, or Hematogenous carried in the blood if high titer viremia exist
• Incubation Period is the period between exposure and symptoms

Damage Inflicted

• Signs and symptoms of viral disease involves a series of interactions between the virus and host
• Intrinsic protective mechanisms: apoptosis and autophagy
• Extrinsic protective mechanisms: Barriers and innate immune responses
• Adaptive Immune response uses neutralizing antibodies, or antibody dependent cell mediated cytotoxicity that lyse viral infections
• Toll-like receptors are pattern recognition receptors that identify conserved patterns in pathogens
• Interferon inhibit virus replication by inducing cellular proteins

The Outcome

• Acute occurs when the virus undergoes multiple rounds of replication which results in death of host cell OR host successfully controls
• Chronic: viral particles continue shedding without host death; host does not successfully control
• Latent viruses do not result in the production of progeny viruses and the host may or may not have "controlled" the virus
• latent viruses can reactivate or cause cellular transformation into cancer

Methods to prevent infection

• Wash hands, cover coughs, wear masks, and stay home when sick
• Getting vaccinated is the best way

Viral Life Cycle

• The life cycle includes attachment, entry, uncoating, synthesis of protein and nucleic acid, assembly, and release

Attachment, Entry and Uncoating Details

• Attachment happens when the virus attaches to host cell adhesion receptors on the surface of the cell
• Enveloped viruses use surface spike proteins and Naked viruses surface-exposed capsid regions mediate attachment
• Tissue tropism happens is related to binding to a specific receptor or receptors. Entry
• Virion moves along host cell surface and encounters entry receptors (aka co-receptors)
• Membrane fusion happens via the hosts membrane with nucleocapsid release
• Endocytosis occurs as the virus in uncoated inside the cell

RNA & DNA Synthesis

• Synthesis depends on if the virus is single / double stranded and DNA/RNA

Viral Nucleic Acids

• This includes the senses for transcription, genome replication, and show that assembly leads to the formation of the nucleocapsid
• DNA viruses will move to the nucleus for genome replication

RNA Replication

• RNA Viruses mostly replicate in the cytoplasm with influenza and retroviruses having exceptions
• The virus is only encoded by the RNA-dependent RNA Polymerases and includes the enzymes needed for viral mRNA processing.
• Assembly of the genome and proteins produced is a self assembly
• Classified according to the polarity of RNA

Viral Genetics

• Viral Genetics include recombination, reassortment, complement action, and phenotypic mixing.
• Recombination involves genetic information exchanged
• Reassortment is when segmented genomes create a hybrid strain, which leads to antigenic shift
• .Complementation : mutations from viruses get complemented by another virus as a product
• Phenotypic mixing makes virus combine to be coated with surface proteins

Viral Release protocols

• Nonenveloped viruses cause cell lysis or bursting to release
• Lysogenic viruses get incorporated into host genomes
• Enveloped viruses release via budding and exocytosis, reverse phagocytosis, and these can also can sometimes trigger apoptosis

Antiviral Agents

• It is best to choose drugs that don't cause damage since viruses use host cells
• Drugs that are virustatic only act on replicating viruses

Recognition Of drugs

• First you need to recognize the target cell
• Tissue tropism is important as you have to bind that specific receptor
• Enveloped viruses use surface proteins and naked exposed capsid regions mediate

What Are the Steps to Replication?

• The process to replication involves uncoating, interfering with replication, and blocking replication
• Then the release is blocked via non competitive enzymes, and prevents expression for mRNA
• This process relies on host machinery for viral infections

History of Viral Approvals

• There have been increasing approvals between January 1959 ans April 2016 with HIV, HCV, and HVS being at the top
• Acyclovir and other similar antiviral drugs, came into effect later
• You can disrupt the ability to take infect or kill

Ways to disrupt Virions

• You can disrupt them with detergents, acids, lipids that disrupt some surfaces and may prevent rhinovirus transmission by killing the agent

Methods of Testing and Diagnosing

• Methods to select appropriate diagnostic tests include rapid antibody, rapid antigen, culture, PCR, and serology
• Rapid antibody and specific antigens used to capture antibody
• ELISA testing for OR antibody in solution
• Culture uses samples and then tests to identify viral DNA through PCR

The Best Prevention Approach

• Getting vaccinated should be the first approach before the virus infects

The Four Phases

Early phase, Late phase, Eclipse period, Latent period stages.

Good luck With your studies!

Explore viral replication stages, PCR function, and antiviral agents. Learn about the eclipse and latent periods, along with the characteristics of naked viruses. Understand the role of transcription, translation, and replication in viral infections.