🦠Virology Unit 1 – Virology Basics: Virus Types & Classification

What Are Viruses?

• Viruses are microscopic infectious agents that can only replicate inside the living cells of other organisms (host cells)
• Consist of genetic material (DNA or RNA) encased in a protein coat called a capsid
  • Some viruses also have an outer lipid envelope derived from the host cell membrane
• Viruses are obligate intracellular parasites meaning they require host cells to reproduce and cannot replicate on their own
• Exist in a wide variety of shapes and sizes ranging from simple helical and icosahedral forms to more complex structures
• Viruses are not considered living organisms as they lack the ability to carry out metabolic processes and reproduce independently
• Infect all types of life forms including animals, plants, bacteria, and archaea
• Viral infections can lead to various diseases in humans such as influenza, COVID-19, HIV/AIDS, and Ebola

Virus Structure and Components

• Viruses have a simple structure consisting of two or three main components: genetic material, a protein capsid, and sometimes an envelope
• Genetic material can be either DNA or RNA, which carries the viral genome and the instructions for replicating the virus
  • Viral genomes can be single-stranded or double-stranded, linear or circular
• The protein capsid surrounds and protects the genetic material
  • Capsids are composed of multiple copies of one or a few different proteins that self-assemble to form the structure
  • Capsids can have helical symmetry (rod-shaped) or icosahedral symmetry (spherical)
• Some viruses have an additional lipid envelope surrounding the capsid
  • The envelope is derived from the host cell membrane during the process of viral budding
  • Envelope contains viral glycoproteins that aid in attachment and entry into host cells
• Viruses may also have accessory structures such as matrix proteins, tegument, and viral enzymes packaged within the capsid

Viral Replication Cycle

• The viral replication cycle is the process by which viruses produce new infectious particles within a host cell
• The replication cycle can be divided into several stages: attachment, entry, uncoating, replication, assembly, and release
• Attachment: Viruses bind to specific receptors on the host cell surface using viral surface proteins
• Entry: Viruses enter the host cell through endocytosis or membrane fusion
  • Enveloped viruses fuse their envelope with the host cell membrane to release the capsid into the cytoplasm
  • Non-enveloped viruses are internalized by endocytosis and then escape from the endosome
• Uncoating: The viral capsid is disassembled, releasing the viral genome into the host cell cytoplasm or nucleus
• Replication: The viral genome is replicated using host cell machinery and viral enzymes
  • DNA viruses typically replicate in the nucleus, while RNA viruses replicate in the cytoplasm
• Assembly: New viral particles are assembled from the replicated genetic material and newly synthesized viral proteins
• Release: Mature viruses are released from the host cell by lysis (cell rupture) or budding through the cell membrane

Types of Viruses

• Viruses can be classified based on various characteristics such as genetic material, capsid symmetry, presence of an envelope, and host range
• DNA viruses contain DNA as their genetic material and can be either single-stranded (ssDNA) or double-stranded (dsDNA)
  • Examples of DNA viruses include herpesviruses, poxviruses, and adenoviruses
• RNA viruses contain RNA as their genetic material and can be either single-stranded (ssRNA) or double-stranded (dsRNA)
  • ssRNA viruses can be further classified as positive-sense (+ssRNA) or negative-sense (-ssRNA)
  • Examples of RNA viruses include coronaviruses, influenza viruses, and retroviruses (HIV)
• Reverse transcribing viruses have RNA genomes that are converted into DNA during the replication cycle using the enzyme reverse transcriptase
  • Retroviruses (HIV) and hepadnaviruses (Hepatitis B virus) are examples of reverse transcribing viruses
• Viruses can also be classified based on their host range as animal viruses, plant viruses, bacteriophages (viruses that infect bacteria), and archaeal viruses

Virus Classification Systems

• Viruses are classified using a hierarchical system developed by the International Committee on Taxonomy of Viruses (ICTV)
• The ICTV classification system groups viruses into orders, families, subfamilies, genera, and species based on their genetic and structural properties
• The Baltimore classification system categorizes viruses into seven groups based on their genome type and replication strategy
  • Group I: dsDNA viruses (e.g., herpesviruses, poxviruses)
  • Group II: ssDNA viruses (e.g., parvoviruses)
  • Group III: dsRNA viruses (e.g., reoviruses)
  • Group IV: (+)ssRNA viruses (e.g., coronaviruses, picornaviruses)
  • Group V: (-)ssRNA viruses (e.g., influenza viruses, rhabdoviruses)
  • Group VI: ssRNA-RT viruses (e.g., retroviruses)
  • Group VII: dsDNA-RT viruses (e.g., hepadnaviruses)
• Other classification systems include the Holmes classification, which is based on virion morphology, and the LHT System, which considers host range, virion morphology, and genome type

Key Viral Families

• Herpesviridae: dsDNA viruses that cause latent infections (e.g., herpes simplex virus, varicella-zoster virus, Epstein-Barr virus)
• Poxviridae: large dsDNA viruses that replicate in the cytoplasm (e.g., smallpox virus, vaccinia virus)
• Adenoviridae: non-enveloped dsDNA viruses that cause respiratory, gastrointestinal, and eye infections
• Picornaviridae: small, non-enveloped +ssRNA viruses (e.g., poliovirus, rhinovirus, hepatitis A virus)
• Orthomyxoviridae: -ssRNA viruses with a segmented genome (e.g., influenza viruses)
• Paramyxoviridae: -ssRNA viruses that cause respiratory infections (e.g., measles virus, mumps virus, respiratory syncytial virus)
• Retroviridae: ssRNA-RT viruses that integrate their genome into the host cell DNA (e.g., human immunodeficiency virus (HIV))
• Coronaviridae: large, enveloped +ssRNA viruses that cause respiratory infections (e.g., SARS-CoV, MERS-CoV, SARS-CoV-2)

Viral Diseases and Transmission

• Viruses are responsible for a wide range of human diseases affecting various organ systems
• Respiratory viral infections include influenza, common cold (rhinovirus), measles, and COVID-19 (SARS-CoV-2)
  • These viruses are typically transmitted through respiratory droplets or aerosols
• Gastrointestinal viral infections include rotavirus, norovirus, and hepatitis A virus
  • Transmission occurs through the fecal-oral route, contaminated food or water, or close contact with an infected person
• Sexually transmitted viral infections include HIV, human papillomavirus (HPV), and herpes simplex virus (HSV)
  • Transmission occurs through sexual contact with an infected person
• Blood-borne viral infections include hepatitis B virus (HBV), hepatitis C virus (HCV), and HIV
  • Transmission occurs through exposure to infected blood, such as through sharing needles or blood transfusions
• Vector-borne viral infections include dengue fever, yellow fever, and Zika virus
  • These viruses are transmitted to humans through the bite of an infected arthropod vector, such as mosquitoes or ticks

Studying Viruses: Methods and Tools

• Virus isolation: Viruses can be isolated from clinical samples by inoculating them into cell cultures, embryonated eggs, or laboratory animals
• Electron microscopy: Used to visualize the morphology and ultrastructure of viruses
  • Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) are commonly used
• Serological assays: Detect the presence of virus-specific antibodies in patient serum
  • Examples include enzyme-linked immunosorbent assay (ELISA), neutralization tests, and hemagglutination inhibition assays
• Molecular techniques: Used to detect and characterize viral genetic material
  • Polymerase chain reaction (PCR) amplifies viral DNA or RNA for detection and sequencing
  • Reverse transcription-PCR (RT-PCR) is used for RNA viruses, converting RNA to cDNA before amplification
• Next-generation sequencing (NGS): High-throughput sequencing methods that allow for rapid sequencing of viral genomes
  • Used for virus discovery, epidemiological studies, and monitoring viral evolution
• Antiviral drug screening: In vitro and in vivo assays to identify compounds with antiviral activity
  • High-throughput screening methods can test large numbers of compounds for their ability to inhibit viral replication
• Animal models: Used to study viral pathogenesis, immune responses, and the efficacy of antiviral drugs and vaccines
  • Examples include mice, ferrets, and non-human primates