Molecular Evolution: Genetic Change and Variability

• Molecular Evolution covers an introduction with practical applications.
• Learning outcomes include reviewing evolution basics, influenza dangers, COVID-19's problematic nature, superbug causes, and inevitable genetic changes leading to evolution.

Basic Concepts of Evolution

• Fitness (selection) and reproductive success are crucial for evolution.
• Population is the unit of evolution.
• Diversity serves as the genetic toolbox.
• Genotypes increase over time due to environmental pressures.

Foundation of Genetic Change: Mutations

• Mutations are transmissible changes to the genetic material, usually DNA or RNA, within a cell/virion.
• These mutations occur in germ line tissues, not somatic cells

Genetic Variability

• Genetic variability drives molecular evolution.
• Populations can adapt, providing a "menu" for the fittest to out-multiply the less fit.
• Fitness relates to reproductive success via viable offspring that can reproduce.
• Darwin's concept: "Descent with modifications," progeny with genetic variation.

Descent with Modifications

• Modification occurs in genes and genetic material.
• Populations evolve, not individuals
• Evolution involves changes in gene/allele frequencies over generations.
• The smallest unit of evolution is a population.
• Changes occur due to changes in gene frequencies.

Viruses and Microbes

• Many generations can be observed quickly.
• "Evolution in progress" is studied in viruses, bacteria, and fast-generation eukaryotes.

Natural Selection

• Evolution is "blind" and selection is tied to fitness.
• Reproductive success equals fitness
• If some are not "selected," others have a chance to increase in numbers.
• Resources are not unlimited, leading to competition.

Genetic Diversity

• Mutations, or changes in RNA or DNA sequences, cause genetic diversity.
• Insertions, deletions, and nucleotide substitutions are types of Mutations.
• Viruses can form quasispecies, like in HIV, with a population of viruses sharing a common ancestor but having many genetic variants.
• Viral quasispecies have increased mutation rates.
• Over time, genes are selected to promote adaptation to alternative hosts.

Recombination

• Recombination in RNA viruses requires co-infections and template switching.
• Template switching could happen when co-infection present
• Bacteria use recombination and other mechanisms to repair chromosomes.
• Eukaryotes exhibit meiosis where homologous chromosomes pair and recombine during prophase I.

Reassortment

• Reassortment applies to viruses with segmented genomes.
• Reassortment leads to "antigenic shift" and needs co-infections.
• An example of viruses with segmented genomes is influenza.
• Eukaryotes undergo meiosis with independent assortment, resulting in genetic diversity.
• Meiosis I and II involve first homologs, then sister chromatids.
• Occurs during Antigenic shift and helps avoid immune system

Descent with Modifications

• Populations must change with environmental conditions to survive.
• Mechanisms are essential that allow for genetic diversity.
• Diversity must be inheritable, involving genetics.

Influenza

• Influenza types A, B, and C differ in host range, epidemiology, and clinical features

Influenza A

• Influenza A is also known as Bird flu.
• It is a segmented single-stranded RNA virus with 8 ssRNA molecules.
• Minus means it needs an RNA polymerase to generate mRNAs because it cannot be directly translated
• It infects humans, swine, horses, birds, and aquatic mammals.

Influenza A: Molecular Components

• HA (hemagglutinin) is needed to gain entry into a cell
• NA (neuraminidase) is used to get out of cell, proteins end up in the viruses envelope

Influenza A: Subtypes

• Classified by two envelope antigens: H (hemagglutinin) and N (neuraminidase).
• H helps get "into" cells.
• N helps get "out" of cells.

Human Influenza A Forms

• Human influenza A forms include N1, N2, H1, H2, and H3.
• H1N1 caused the 1918 Spanish flu pandemic.
• The 1968 Hong Kong Flu was H3N2.
• H3N2 and H1N1 are common.
• Mutations in H and N genes yield new strains yearly.
• Co-infections of two strains yield new strains via recombination and reassortment.

Bird Flu

• Birds act as reservoirs for flu viruses.
• Bird flu, H5N1, is highly pathogenic to avian species.
• Humans lack immunity to H5.
• Identifying avian influenza viruses in pigs is significant.

Influenza A: Pandemic Potential

• A virus has to get in, multiply, get out, and be transmitted from individual to individual
• H5N1 does not easily transfer from human to human.
• Reassortment could lead to H5 types that transfer efficiently in humans, leading to a pandemic.

Influenza: Genetic Diversity (The “Genetic Toolbox")

• Mutation, recombination, and reassortment apply to influenza.
• Applies from bird to human as zoonosis

Mechanisms of a Pandemic Engine

• Mutations
• Recombination and reassortment can also yield new strains

Influenza A: Point Mutations and Antigenic Shift

• Drift: Variants due to point mutations and recombination.
• Antigenic shift: A dramatic change, results from recombination and reassortment allowing more efficient transfer to new hosts.

Influenza A type viruses

• Human, swine, & bird strains can result in new strains via zoonosis:
• Occurs via a "pool of genetic diversity"

Other types of Influenza:

• H1N1 human/swine flu viruses: variants derived in Thailand
• Mexico 2009 (April) H1N1 type: Efficient human-to-human transmission.
• Three swine influenza subtypes: H1N1, H3N2, H1N2

Bats

• Excellent hosts for viruses that can cross to humans via domestic animals/intermediate hosts.

Molecular Evolution in progress: Covid-19

• Caused by a single-stranded RNA virus.
• Viral RNA polymerase has high error rates
• Mutations in spike protein generate new variants
• Spike protein helps to get into mammals immune systems
• Covid-19 is a zoonotic disease: (SARS-CoV-2) i.e., Covid-19 [zoonotic origin]
• • (sense) single stranded RNA virus (~30 000 bases)
• One linear "chromosome” (i.e., not segmented)
• Spike protein interacts with TMPRSS2 and ACE2 - cell surface proteins to enter animal cells
• May require some or all to enter, replicate and be virulent

Analysis of Covid-19 genome

• L Lineage - S ancestral - more aggressive
• L more widespread,
• There are more lineages recorded since the paper was published.

Tissues attacked during Covid-19

• Affects testes, hear, kidney, intestine, lungs
• TMPRSS2 and ACE2 - cell surface proteins needed for Covid-19 "entry"
• Covid transmission is more efficient and aggressive than previous coronavirus epidemics

Antibiotic Resistance and "Superbugs"

• Antibiotic resistance (ABR) is usually a rare trait
• ABR traits can undergo positive selection in hospital settings (antibiotic treatments)
• Community-based ABR is a major concern.
• ABR occurs from mutations and acquired genes from plasmids and mobile elements.
• Many bacteria found in nature
• Superbugs could be next pandemic at ten million deaths per year.

How microbes develop antibiotic resistance?

Resistance

SOS DNA repair system

• Can also promote Antibiotic Resistance
• Disinfectants and UV lights increase mutation rates (survivors become AB resistance)

Acquiring Genes

• Plasmids cam move easily creating Transduction, Transformation or Congugation
• Plasmids can transform the virulence quickly making them very dangerous and difficult to treat

Gene Transfer

• Mobile elements
• Conjugation - genetic material exchange
• Many ABR genes on mobile elements like Tn, plasmids and R factors

Summary: Commensal reservoir that can develop Ab resistance traits

– particular trait under certain conditions gives an advantage