BIOl204-M4L23

What is a virus?

an obligate intracellular parasite that relies on a host for most machinery

Defining characteristics of viruses

• not made of cells

• no metabolism

• rely on hosts for replication

• have genomes

• evolve rapidly

• enclosed in a protein shell (capsid)

Why are viruses considered obligate intracellular parasites that occupy a gray area between living and non-living systems

they are considered obligate intracellular parasites because they rely on host cells for replication and a lot of other machinery, but occupy a grey area because they still evolve, have genetic material, but lack cells, metabolisms, and rely on hosts for such things (have both living and non-living characteristics)

Virions

viruses out of host cells (infectious particles) and cannot replicate in this state

• virion is a shuttle to transmit genetic material from one host cell to another

Why do we study viruses?

• medically important: kill humans, other animals, plants, and have a large-scale impact (epidemics, pandemics)

Features that oppose that viruses are living

• not made of cells

• can’t produce their own ATP

• no ribosomes

• no metabolism

• no independent transcription or translation

• can’t replicate independently

they rely on host cells for all of these processes

Virus abundance

• they are extremely small and highly abundant

• most abundant biological identities

Evolutionary importance of viruses

• agents of natural selection: host immune system will evolve defenses and then viruses will evolve counter defenses

• rapid evolution: they have high mutation rates and short generation times, and LTG helps, allowing them to quickly adapt to new environments and antivirals

• help shape genomes by transferring genes between organisms or incorporating their own genes into hosts—this can lead to genetic variation which natural selection can then act on

Viruses and genetics

• they can introduce foreign genes into cellular genomes through lateral gene transfer (shuttling the genes from one organism to another)

• they can contribute their own genetic material into host cells (8% of human genome is virus gene remnants)

• these allow traits to appear faster than with mutation alone

• some viral genes are important: a protein coded by an abandoned viral gene is essential for proper development of the placenta 

Population level affects of viruses

• epidemic: disease that rapidly affects many individuals over a widening area (region)

• pandemic: epidemic on a worldwide scope

• both cause sharp drops in life expectancy, deaths, and affect the immune system, rapid adaptations (arms race), genetic influence

Naked viruses

enclosed by just a capsid (shell of protein)

• only use capsid to protect genetic material

Enveloped viruses

enclosed by both a capsid and one or more membranous envelopes

• envelope contains embedded viral proteins and is derived from a lipid bilayer of a host cell

• bilayer functional consequence: aid in entry to hosts by those membrane proteins binding host receptors but this leads to vulnerability because detergents like soaps can be harmful to these viruses

Capsid function

protects the genome while outside the host and releases the genome when virus infects a new cell

How do viruses infect host cells?

• replicative growth: actively replicate to produce next generation of viruses and often kills host cell

• dormancy: growth cycle that temporarily suspends production of virions and allows viral genome to coexist with host genome for period of time

Transmission mechanisms of viruses to new hosts

• through the body: via bloodstream or lymphatic system

• between organisms: through respiratory droplets, bodily fluids, vectors of disease

Ecological connection of viruses

new host to viruses represents an unexploited habitat with abundant resources–transmission is essentially dispersal

How can viruses co-exist in host cells?

when transmitting and existing within hosts they have different dormant states that they can enter to coexist in host cell

• dormancy meaning they arrest the replicative cycle

• lysogeny or latency

Lysogeny

• used by bacteriophages (viruses that infect bacteria)

• molecular cues trigger the stop of the viruses replicative cycle and instead the viral DNA incorporates into the hosts chromosomes

• the host's DNA polymerase continues to replicate the viral DNA each time the cell divides (so each daughter cell now has the dormant viral DNA)

• host stress (UV light, temperature) can lead to re-activation of the viral DNA and re-entry into replicative growth cycle

Latency

• occurs in viruses that affect animal cells

• the virus remains dormant (arrest replicative growth) in the host cell without usually incorporating itself into the hosts DNA—not immediately producing new virions

• they do this to avoid immune response and detection

• they rely on host cell machinery to survive, live in, and eventually re-activate

Hypotheses for origin of viruses

• escaped gene hypothesis

• degeneration hypothesis

• RNA-world hypothesis

• conclusion of all hypotheses is that viruses likely originated multiple times

Escaped gene hypothesis

viruses originated from mobile genetic elements (plasmids/transposons) that "escaped" from cells; then those escaped gene sets took on a parasitic mobile existence (viruses)

• Support: strong similarities between mobile genetic elements and viruses

• researchers would need to discover a virus that had recently derived from prokaryotic or eukaryotic genes and the viral genome has to strongly resemble sequence of those genes for supporting evidence

Degeneration hypothesis

viruses descended from parasitic cells; the cellular ancestors degenerated into viruses by gradually losing certain genes for ribosome, ATP, and nucleotide synthesis, becoming viruses

• Support: some giant viruses have unusually large genomes that were previously thought to exist only cells 

• Shortfalls: could represent possible intermediate state between cells and viruses but we don't know what the intermediate state would truly look like

RNA-world hypothesis

RNA viruses are descendants of the earliest RNA molecules that predated DNA-based life

support:

• ribosomes show RNA can act like enzymes (early life relied on RNA instead of DNA)

• RNA viruses use RNA dependent RNA polymerases which is rare in cells

• some viral replication strategies are fundamentally different from cellular life

Emerging viruses

 a new illness infecting humans for the first time that suddenly affects significant numbers of individuals in a host population

• Ex. when viruses jump from their natural species (animals) to their host (humans)

• difficult to understand because figuring out what they're targeting between humans and other animals

• new illness means no original immunity (natural selection, arms race)

Viral phylogenies

can show that an emerging virus has jumped to a new host and can help reveal virus reservoirs; can help identify future risks

• Ex. HIV has  multiple independent jumps from primates to humans 

Ecological role of viruses

• regulate populations, benefitting the environment and maintaining a stable ecosystem through nutrient cycling

Host-range specificity

host range refers to the variety of species or cell types a virus can infect

• viruses can be limited to a certain species

• must over-come hosts immune defenses

• viruses can occasionally cross species barriers and jump from one species to another

• the host cell must provide the necessary machinery

Factors that can cause pandemics or epidemics

• the viruses is new and the population affected by it lacks immunity

• high evolutionary and replication rates and ability to transmit before symptoms appear

• contact between species like humans and animals which may be virus reservoirs

Why are viruses able to evolve rapidly?

• high mutation rates

• short generation times

• genetic exchange is a major driver of rapid evolution, allowing viruses to adapt to new hosts, evade immune systems, and develop drug resistance

Why did viruses likely originate multiple times?

because no one hypothesis explains all viruses, some support each individual hypothesis so they likely originated multiple times

How does viruses transferring genes between hosts benefit the virus?

• gene exchange allows viruses to adapt to new host species or environments

• viruses can acquire host genes that mimic immune-regulating proteins, allowing them to hide from the host's immune response

How do viruses act as agents of evolution

• natural selection

• transferring genes

• influencing host genomes