Genetics and Evolution

Molecular Basis of Inheritance

Genome Organization in Viruses

---

Viruses: An Introduction

• Non-living infectious agents
• Consist of genetic material (DNA or RNA) surrounded by a protein coat
• Cannot replicate on their own, require host cells for replication
• Can infect different species of organisms

---

Genome Organization in Viruses

Viruses have different types of genome organization:

1. DNA Viruses: Have DNA as their genetic material

   • Can be single-stranded (ssDNA) or double-stranded (dsDNA)

2. RNA Viruses: Have RNA as their genetic material

   • Can be single-stranded (ssRNA) or double-stranded (dsRNA)

3. Retroviruses: Have RNA as their genetic material, but replicate via reverse transcription (RNA → DNA)

   • Example: HIV

---

Types of DNA Viruses

1. Single-stranded DNA (ssDNA) Viruses:

   • Example: Parvovirus

2. Double-stranded DNA (dsDNA) Viruses:

   • Example: Adenovirus, Herpesvirus

---

Types of RNA Viruses

1. Single-stranded RNA (ssRNA) Viruses:

   • Positive-sense ssRNA viruses (direct mRNA)
     • Example: Rhinovirus, Zika virus
   • Negative-sense ssRNA viruses (complementary to mRNA)
     • Example: Influenza virus, Measles virus

2. Double-stranded RNA (dsRNA) Viruses:

   • Example: Reovirus

---

Genome Organization in Different Viruses

1. Linear Genome:

   • Genetic material in a linear arrangement
   • Example: Poliovirus

2. Circular Genome:

   • Genetic material in a circular arrangement
   • Example: Papillomavirus

3. Segmented Genome:

   • Genetic material divided into separate pieces (segments)
   • Example: Influenza virus

---

Types of Genetic Material in Viruses

1. Non-segmented Genomes:

   • Genetic material not divided into segments
   • Example: HIV, Hepatitis B virus

2. Segmented Genomes:

   • Genetic material divided into multiple segments
   • Example: Influenza virus

---

Non-segmented Genomes

• Non-segmented genomes can be either:

  1. Monopartite:

     • Entire genetic material present in a single piece
     • Example: HIV

  2. Dipartite:

     • Genetic material divided into two separate pieces
     • Example: Hepatitis B virus

---

Segmented Genomes

• Segmented genomes consist of separate pieces of genetic material called segments
• Each segment can encode different functional units or genes
• Example: Influenza virus has 8 separate RNA segments

---

Importance of Genome Organization in Viruses

• Genome organization affects various aspects of viral biology, including:
  • Replication and transcription processes
  • Genetic variability and evolution
  • Interaction with host immune system
  • Potential for recombination and reassortment

====

Replication in DNA Viruses

• DNA synthesis occurs within the infected host cell.
• The viral DNA serves as a template for the synthesis of new viral DNA.
• This process is carried out by viral enzymes.
• Example: Adenovirus uses the host DNA polymerase for replication.

Replication in RNA Viruses

• RNA synthesis can occur within the viral capsid or in the host cell’s cytoplasm.
• Viral RNA polymerase catalyzes the synthesis of viral RNA from a template.
• Positive-sense RNA viruses can directly produce viral proteins, acting as mRNA.
• Negative-sense RNA viruses require the synthesis of complementary mRNA strands.
• Example: Influenza virus uses its RNA polymerase for replication.

Genetic Variability in Viruses

• Viruses show high genetic variability due to:
  • High mutation rates during replication
  • Recombination events between different strains
  • Reassortment of genetic material in segmented genomes
• This helps viruses adapt to changing environments and evade host immune responses.
• Example: Influenza virus mutates rapidly, leading to the emergence of new strains.

Genetic Variation and Evolution

• Genetic variations in viruses can lead to the emergence of new strains.
• Selection pressures, such as host immune responses, drive the evolution of viral strains.
• Evolutionary processes in viruses include:
  • Mutation: Random changes in the viral genome
  • Recombination: Exchange of genetic material between different viral strains
  • Natural selection: Favoring of beneficial genetic variations
• Example: SARS-CoV-2 has undergone mutations, leading to the emergence of new variants.

Host Immune Response to Viral Infections

• Innate immune response:
  • Activation of immune cells to mount a rapid defense against viruses
  • Release of cytokines and chemokines to recruit immune cells
• Adaptive immune response:
  • Specific response against viral antigens by B and T cells
  • Production of antibodies targeting viral proteins
  • T cell-mediated destruction of infected cells
• Example: Interferons released by infected cells help in limiting viral spread.

Viral Evasion of host Immune Responses

• Viruses have evolved various mechanisms to evade host immune responses:
  • Mutations in viral proteins to avoid recognition by antibodies
  • Downregulation of major histocompatibility complex (MHC) molecules
  • Inhibition of interferon production or response
• Example: HIV evades immune responses through high mutation rates and evasion of antibody recognition.

Recombination in Viruses

• Recombination occurs when two genetically distinct viruses infect the same host cell.
• Exchange of genetic material can occur, leading to the creation of novel viral strains.
• Recombination is more common in viruses with segmented genomes.
• Example: Hepatitis C virus undergoes frequent recombination events.

Antiviral Therapy

• Antiviral drugs target specific steps in the viral life cycle, such as:
  • Inhibiting viral replication or transcription
  • Blocking viral entry into host cells
  • Impeding viral protein synthesis
  • Halting viral assembly or release
• Example: Oseltamivir (Tamiflu) is used to treat influenza virus infections.

Vaccines and Viral Infections

• Vaccines help prevent viral infections by inducing immunity against specific viruses.
• Types of vaccines include:
  • Inactivated or attenuated viral vaccines
  • Subunit vaccines containing viral proteins
  • mRNA vaccines encoding viral antigens
• Example: The polio vaccine is an inactivated viral vaccine.

Viral Zoonosis and Emergence of Pandemics

• Zoonotic viruses are those that can be transmitted between animals and humans.
• Cross-species transmission can lead to the emergence of pandemics.
• Factors contributing to viral zoonosis include:
  • Changes in land use and animal-human interactions
  • Wildlife trade and consumption of exotic animals
• Examples: SARS-CoV-2 (COVID-19) originated from animals, as did Ebola and Zika viruses.

Here are slides 21 to 30 on the topic “Genetics and Evolution - Molecular Basis of Inheritance - Genome organization in viruses”:

---

Modes of Viral Transmission

Viruses can be transmitted through various routes:

• Direct contact transmission:

  • Physical contact with an infected individual or their bodily fluids
  • Example: Influenza virus spreads through respiratory droplets.

• Indirect contact transmission:

  • Touching surfaces contaminated with the virus
  • Example: Norovirus can be transmitted through contaminated food or water.

• Vector-borne transmission:

  • Transmission through the bite of arthropod vectors, such as mosquitoes or ticks
  • Example: Dengue virus is transmitted by Aedes mosquitoes.

• Airborne transmission:

  • Inhalation of infectious airborne particles
  • Example: Measles virus can be transmitted through airborne droplets.

• Vertical transmission:

  • Passage of the virus from mother to fetus during pregnancy, or from parent to offspring
  • Example: Rubella virus can be transmitted from a pregnant woman to her unborn baby.

---

Host Range of Viruses

• Viruses have specific host ranges, which determine the species they can infect.

• Tissue tropism: Specific tissues or organs targeted by a particular virus.

• Cell tropism: Specific types of host cells infected by a virus.

• Example: Human Immunodeficiency Virus (HIV) mainly infects CD4+ T cells.

• Zoonotic viruses: Viruses that can be transmitted between animals and humans.

• Example: Avian Influenza viruses can infect both birds and humans.

---

Factors Influencing Viral Host Range

Several factors can influence the host range of viruses:

• Viral Attachment Proteins: Viral proteins that determine the attachment or entry into host cells.
• Cell Receptor Availability: Presence or absence of cellular receptors required for viral entry.
• Host Factors: Availability of host factors necessary for viral replication or immune response.
• Host Defense Mechanisms: Ability of the host immune system to recognize and eliminate viruses.

---

Factors Influencing Viral Transmission

Various factors can influence viral transmission:

• Environmental Factors: Climate, temperature, humidity, and ecology of the habitat.
• Host Behavior: Human activities impacting contact with infected individuals or vectors.
• Immune Status: Immunocompromised individuals are more susceptible to viral infections.
• Viral Stability: How long a virus can survive outside a host or in different environmental conditions.

---

Viral Replication Cycles

Viral replication involves several stages:

1. Attachment: Virus attaches to specific receptors on the host cell surface.
2. Entry: Virus enters the host cell, releasing genetic material into the cell.
3. Replication: Viral genetic material replicates using host cell machinery.
4. Assembly: Newly synthesized viral components assemble to form mature virions.
5. Release: Mature virions are released from the host cell to infect other cells or hosts.

---

Viral Latency and Integration

• Some viruses can establish a latent infection, remaining dormant within host cells.
• Latent viruses can reactivate later to cause disease.
• Examples:
  • Herpesviruses establish latency in nerve cells, causing recurrent outbreaks.
  • Human Immunodeficiency Virus (HIV) can integrate its genetic material into the host genome and remain latent in immune cells.

---

Major Viral Diseases

Several well-known viral diseases affect humans:

• Influenza: Caused by the Orthomyxovirus family, leads to respiratory illness.
• HIV/AIDS: Caused by Human Immunodeficiency Virus, leads to the progressive breakdown of the immune system.
• Hepatitis: Caused by Hepatitis viruses (A, B, C, D, E), leads to inflammation of the liver.
• Ebola: Caused by Ebola virus, leads to severe hemorrhagic fever.

---

Importance of Viruses

Viruses play significant roles in:

• Evolution: Contributing to genetic diversity and shaping the genomes of organisms.
• Medicine: Development of vaccines, antiviral drugs, and gene therapy techniques.
• Biotechnology: Viral vectors used in gene transfer and genetic engineering.
• Ecology: Impacting ecosystems through interactions with host organisms.

---

Virus Detection and Diagnosis

Methods used for virus detection and diagnosis:

• Molecular Methods: PCR, RT-PCR, nucleic acid sequencing to detect viral genetic material.
• Serological Methods: ELISA, Western blotting to detect viral antigens or antibodies.
• Cultivation Methods: Growing viruses in cell cultures or animal models.
• Microscopy: Electron microscopy for visualizing viral particles.

---

Conclusion

• Viruses have diverse genome organizations and modes of replication.
• Genetic variations and evolution drive the emergence of new viral strains.
• Viruses interact with host immune responses and can evade or subvert them.
• Understanding viral host range, transmission, and replication cycles is crucial for managing viral diseases.

---

These are the main concepts regarding “Genetics and Evolution - Molecular Basis of Inheritance - Genome organization in viruses”.