virology unit 17 study guides

Key Concepts and Definitions

• Viral evolution involves changes in the genetic makeup of viruses over time, driven by mutations, recombination, and reassortment
• Molecular epidemiology studies the genetic and molecular factors influencing the spread and distribution of viral diseases in populations
• Genetic diversity refers to the variety of different genetic sequences present within a viral population
• Mutation rate quantifies the frequency at which genetic changes occur in a viral genome per replication cycle
• Selective pressure encompasses environmental factors that favor certain viral variants over others, shaping the course of viral evolution
• Phylogenetics analyzes the evolutionary relationships among viral strains or species based on their genetic similarities and differences
• Zoonotic transmission involves the transfer of viruses from animal reservoirs to human populations, potentially leading to new viral outbreaks

Viral Genetic Diversity and Mutation

• Viruses exhibit high genetic diversity due to their large population sizes, short generation times, and error-prone replication
• Point mutations, including substitutions, insertions, and deletions, introduce small-scale changes in the viral genome
• Recombination occurs when genetic material is exchanged between different viral strains or species during co-infection of a host cell
  • Can lead to the emergence of novel viral strains with altered properties (increased virulence or drug resistance)
• Reassortment involves the exchange of entire gene segments between viruses with segmented genomes (influenza viruses)
• Viral quasispecies are closely related viral variants that arise due to the accumulation of mutations within a viral population
• Genetic bottlenecks, such as transmission events or antiviral treatment, can reduce viral diversity and influence evolutionary trajectories
• Viral mutation rates are generally higher than those of their hosts, allowing viruses to rapidly adapt to changing environments

Mechanisms of Viral Evolution

• Natural selection acts on viral populations, favoring variants with increased fitness in a given environment
• Antigenic drift refers to gradual changes in viral surface proteins due to point mutations, allowing viruses to evade pre-existing host immunity
  • Occurs continuously in influenza viruses, necessitating annual updates of flu vaccines
• Antigenic shift is a major change in viral surface proteins resulting from reassortment between different viral strains or species
  • Can lead to the emergence of pandemic influenza strains (1918 Spanish flu, 2009 H1N1 swine flu)
• Coevolution occurs when viruses and their hosts exert reciprocal evolutionary pressures on each other over time
• Positive selection favors viral variants with beneficial mutations that increase their fitness and prevalence in the population
• Purifying selection removes deleterious mutations from the viral population, maintaining the functionality of essential viral proteins
• Genetic drift involves random changes in allele frequencies within a viral population, particularly in small populations or during transmission bottlenecks

Molecular Techniques in Viral Epidemiology

• Polymerase chain reaction (PCR) amplifies specific viral genetic sequences for detection and characterization
• Reverse transcription PCR (RT-PCR) is used to detect and quantify RNA viruses by converting viral RNA into complementary DNA (cDNA)
• Quantitative PCR (qPCR) measures the amount of viral genetic material in a sample, enabling viral load monitoring and disease progression studies
• Sanger sequencing determines the nucleotide sequence of viral genomes or specific regions of interest
  • Used for identifying mutations, genotyping, and studying viral evolution
• Next-generation sequencing (NGS) technologies enable high-throughput sequencing of viral genomes, providing a comprehensive view of viral genetic diversity
• Metagenomics allows the characterization of viral communities in environmental or clinical samples without prior knowledge of the viral species present
• Serological assays detect virus-specific antibodies in host serum, indicating past or current viral infection

Phylogenetic Analysis and Viral Lineages

• Phylogenetic trees represent the evolutionary relationships among viral strains or species based on genetic similarities
• Maximum likelihood and Bayesian methods are commonly used to infer phylogenetic trees from viral sequence data
• Bootstrap analysis assesses the statistical support for the branching patterns in a phylogenetic tree
• Molecular clock analysis estimates the rate of viral evolution and the timing of important evolutionary events (emergence of new strains or zoonotic transmissions)
• Phylogeography studies the geographical distribution and spread of viral lineages over time
  • Helps track the origin and transmission routes of viral outbreaks (SARS-CoV-2 pandemic)
• Phylodynamics integrates viral phylogenetic analysis with epidemiological and immunological data to understand viral evolution and transmission dynamics
• Viral lineages are distinct genetic variants of a virus that share a common ancestor and have diverged over time

Host-Pathogen Interactions and Evolutionary Pressure

• Host immune responses exert selective pressure on viral populations, driving the evolution of immune escape variants
• Antigenic variation allows viruses to evade host antibody responses by altering their surface proteins
  • Occurs in HIV, influenza viruses, and hepatitis C virus (HCV)
• Receptor binding specificity influences viral host range and tissue tropism, shaping viral evolution and emergence
• Viral immune evasion strategies, such as interferon antagonism and T cell epitope mutation, promote viral persistence and evolutionary success
• Virus-host coevolution can lead to the adaptation of viruses to new host species, potentially resulting in zoonotic spillover events
• Evolutionary arms race between viruses and their hosts drives the continuous adaptation and counter-adaptation of both parties
• Host genetic variation, including polymorphisms in immune system genes, can influence susceptibility to viral infections and shape viral evolution

Case Studies and Real-World Applications

• HIV evolution and the development of antiretroviral drug resistance demonstrate the impact of viral evolution on treatment outcomes
• Influenza virus surveillance and vaccine strain selection rely on understanding viral evolution and antigenic drift
• Tracking the evolution and spread of SARS-CoV-2 variants (Alpha, Delta, Omicron) informs public health measures and vaccine development
• Studying the evolutionary origins of zoonotic viruses (Ebola, MERS-CoV) helps identify potential animal reservoirs and prevent future spillover events
• Molecular epidemiology has been crucial in investigating nosocomial outbreaks and tracing transmission chains (hospital-acquired infections)
• Evolutionary analysis of hepatitis B virus (HBV) and HCV has guided the development of antiviral therapies and vaccination strategies
• Understanding the evolution of mosquito-borne viruses (dengue, Zika) informs vector control measures and disease prevention efforts

Future Directions and Emerging Technologies

• Single-cell sequencing technologies enable the study of viral evolution and genetic diversity at the individual cell level
• Nanopore sequencing allows real-time, portable sequencing of viral genomes, facilitating rapid outbreak response and surveillance
• Machine learning and artificial intelligence approaches can help predict viral evolution and identify potential vaccine and drug targets
• Integrating viral evolutionary analysis with structural biology and protein engineering can guide the rational design of antiviral therapeutics
• Developing more accurate and computationally efficient methods for reconstructing viral evolutionary histories and transmission networks
• Investigating the role of the microbiome in shaping viral evolution and host susceptibility to infections
• Studying the evolutionary dynamics of viruses in reservoir species to better understand and predict zoonotic emergence events
• Harnessing viral evolution for the development of novel viral vectors for gene therapy and vaccine delivery