Virology Pt. 1

• Viruses are genetic information enveloped in a protein coat from an unknown source.
• Viruses are obligate intracellular parasites.
• Viruses lack mechanisms to replicate themselves, like enzymes or energetic pathways, without a host cell.
• It is debated whether viruses are living organisms.
• A virus is DNA/RNA with a protein envelope and needs a host cell to reproduce and/or use energy.
• A virus's response to the environment is binding to cell receptors, injecting genetic material, and causing immune activation/evolution, but the response is minimal.

Virus Classification

• Viruses are classified by structure, geographical location, and the diseases they cause.
• The structure includes genetic information (DNA, RNA), coat (enveloped/unenveloped), and shape (icosahedral, helical).

Virion Structure: Naked Capsid Virus (Non-Enveloped)

• Naked capsid viruses are more stable and often cause the common cold.
• The structure includes Nucleic acid, with a core of Enzymes and Structural proteins to build the Nucleocapsid

Virion Structure: Enveloped Viruses

• Enveloped viruses consists of a nucleic acid in the nucleocapsid covered by a membrane and glycoproteins.

Virus Timeline Replication

• The virus timeline replication has phases indicating changes in log virus concentration over time:
• Infection introduction: The virus binds to cells.
• Eclipse: Virions penetrate the cells.
• Cell burst/virion release: A large number of virion particles are released.
• Infection maintenance
• The timeline also corresponds to the immune system response and can result in recovery or latent infection.

Phases of Viral Replication

• Viral replication includes these phases:
• Recognition and attachment to a target cell via a receptor.
• Penetration
• Uncoating
• Macromolecular synthesis
• Release of viral particles through cell death (lysis), budding, or active exocytosis.
• Viruses use host cell components such as Ribosomes, tRNA, and mechanisms for post-translation modification

Protein Synthesis

• In some RNA viruses, RNA is translated into a single protein cleaved by proteases.

Special Virology

Papillomaviridae: HPV (Human Papillomaviruses)

• HPV is dsDNA, non-enveloped; there are 200 known genotypes.
• High-risk HPV (HPV 16, 18) causes malignant proliferation.
• Low-risk HPV (HPV 6, 11) causes benign lesions.
• The pathogenesis of HPV involves infection and replication in squamous epithelium of skin and mucosal membranes (genital, oral, conjunctival papillomas).
• The disease associated with HPV progresses from skin or mucosal dysplasia to cancer.
• HPV epidemiology involves direct contact (sexual contact) leading to inoculation of the epithelium and resulting in papillomas of hands, feet, throat, and cervix.
• HPV can be prevented with vaccination (voluntary).

Polyomaviridae: BK (renal disease), JC (PML) virus

• Types of Polyomaviridae are dsDNA, non-enveloped viruses having at least 100 variants.
• Often show asymptomatic manifestation leading to latent infection, but affect immunocompromised patients.
• Infections result in progressive multifocal leukoencephalopathy (PML) or renal disease.
• Polyomaviridae travels though aerosol, resulting in multiplication in the respiratory tract, then viremia.
• Viremia leads to multiplication in the kidney with reactivation leading to viruria, hemorrhagic cystitis, or affecting the central nervous system (CNS).

Adenoviridae: Adenovirus

• Adenovirus is a linear, dsDNA, non-enveloped virus with over 100 serotypes, most often 1-7
• It includes infections of muco-epithelial cells in the respiratory gastrointestinal tract, conjunctiva, or cornea.
• Diseases associated with Adenovirus include Respiratory infections (AdV-B and C group), Conjunctivitis, epidemic keratoconjunctivitis (AdV-B and D group), and gastroenteritis, diarrhea (AdV-F and G group).
• Adenoviridae is transmitted through direct contact via respiratory droplets or fecal mass, and indirect contact (contaminated items), and it typically affects children younger than 14 years or people in crowded areas.
• Prevention of Adenoviridae includes vaccination for serotypes AdV-4 and -7 for those in the armed forces.

Herpesviridae

• Herpesviridae are dsDNA enveloped viruses that can cause lifelong infections.
• Alpha Subfamily: Herpes simplex 1 (HHV-1) and 2 (HHV-2), varicella-zoster (HHV-3)
• Gamma Subfamily: Epstein-Barr (HHV-4).
• Beta Subfamily: cytomegalovirus (HHV-5).
• Herpes-simplex virus 1 and 2 (HSV-1, HSV-2) spread through close contact, STD resulting in gingivostomatitis herpetica which reactivates as Herpes labialis and herpes genitalis.
• Complications can include:
• Respiratory system: herpes pharyngitis, tracheobronchitis
• Eye: herpetic keratitis
• Skin: eczema herpeticum, herpetic whitlow, herpes gladiatorum
• Herpes encephalitis and meningitis
• Herpes neonatorum
• Organ dissemination in immunocompromised patients
• Herpes-simplex virus 1 and 2 (HSV-1, HSV-2) include treatment with Acyclovir, Valacyclovir, Penciclovir, and Famciclovir

Herpesviridae: Varicella-Zoster Virus (VZV)

• VZV primoinfection causes chickenpox while reactivation causes herpes zoster.
• Spread is through air (droplets), close contact.
• Chickenpox includes classic childhood exanthems, primary infection more severe in adults (interstitial pneumonia).
• Herpes zoster occurs with immunodeficiency.
• Complications: interstitial pneumonia, postherpetic neuralgia (HZ effect), neonatal varicella (teratogenic effect)
• VZV Can be prevented though vaccination (voluntary)

Herpesviridae: Epstein-Barr Virus (EBV)

• EBV causes B lymphocyte persistence, spread via saliva and is spread though close contact (kissing).
• It causes infectious mononucleosis ("kissing disease").
• Its primoinfection is mostly asymptomatic in children, while symptomatic adolescents (mononucleosis) may experience high fever, tonsillitis, lymphadenopathy, (hepato)splenomegaly, leukocytosis, atypical lymphocytes, heterophile antibodies.
• EBV reactivation is asymptomatic or symptomatic.
• EBV-induced oncogenic effects causes Lymphoproliferative diseases, oral hairy leukoplakia, endemic Burkitt lymphoma, nasopharyngeal carcinoma, and Hodgkin lymphoma,

Herpesviridae: Cytomegalovirus (CMV)

• CMV causes cell inclusion (cytomegalia) and is spread via saliva, close contact, STD, transfusion, or tissue transplantation.
• Its primoinfection is mostly asymptomatic ,but causes reactivation (symptomatic).
• Infections causes the following in immunocompromised patients: pneumonia, retinitis, colitis, esophagitis, and failure of many kidney transplants
• Congenital infection results in congenital cytomegalic inclusion disease because of mother's primoinfection during pregnancy.
• The fetus may experience signs of infection when including small size, thrombocytopenia, microcephaly rash, hepatosplenomegaly, icterus, hearing and vision impairment, and more.
• CMV is treated with Ganciclovir, Valganciclovir, Cidofovir, or Foscarnet.

Poxviridae

• Poxviridae are complex large viruses containing DNA.
• Its pathogenesis includes first replication in the upper respiratory tract that spreads dissemination to internal and dermal tissues
• Variola major (20-40% mortality), variola minor (mortality 1%) for smallpox was eradicated in 1977 with a vaccination.
• Poxviridae also includes a disease Molluscum contagiosum which causes being skin lesions more often in children.
• Smallpox was prevalent in 18th century England, accounting for 7-12% of all deaths and 30% of childhood deaths however, In 1796 the first vaccine was created which lead to its eradication in 1980

Picornaviridae

Includes

• Small RNA viruses with a naked capsid
• Enteroviruses
• Rhinoviruses
• Hepatitis A virus

Picornaviridae – Enteroviruses

• A range of Enteroviruses can cause infections:
• Poliovirus
• Coxackie viruses (A and B)
• Echoviruses
• Pathogenesis occurs by fecal-oral route, upper respiratory tract, oropharynx, and intestinal tract as entry points, followed by viremia, and attacking different cell types.
• Disease includes:
• Upper respiratory infections, rash, meningitis, encephalitis, myocarditis (caused by Coxackie and echoviruses).
• Poliomyelitis which only effected less than 2% of those infected
• Polio eradicated in Europe 2002, but the are sporadic cases in the USA (import) and it is endemic in Africa, and the Near and Middle East
• Prevention (CZ mandatory)
• Inactivated polio vaccine (IPV)
• Live attenuated oral polio vaccine (OPV) reported mutations to wild-type polio

Picornaviridae: Rhinovirus

• Rhinovirus has >170 serotypes into 3 groups (A, B, C), but has no immune memory.
• Rhinovirus is the most often cause of the common cold.
• There is evidence that it infects year- round, with main activity in the spring in autumn and can cause bronchiolitis.
• Inhalation Sodium Chloride 3-5% has shown treatment

Paramyxoviridae

• This family Includes negative-sense ssRNA enveloped viruses
• Measles virus
• Mumps virus
• Respiratory syncytial virus (RSV)
• Human metapneumovirus
• Nipah Virus, Hendra virus severe encephalitis and are zoonosis
• Measles (Morbillivirus) is indicated by maculopapular rash, cough, conjunctivitis, fever, and photophobia while those infected experience lifelong immunity.
• Complications can include bronchopneumonia, otitis media, post-infectious encephalitis (1:2000), and subacute sclerosing panencephalitis (1:100 000).
• Parainfluenza viruses 1-4 infection has a pathogenesis that causes infection of epithelial cells of the upper respiratory tract.
• Parainfluenza is a ubiquitous virus that causes common infection manifested in mild, cold-like upper respiratory tract infections, bronchiolitis, or pneumonia.
• Mumps (Parotitis) affect the gonads, causing pancreatitis, meningitis, and inner ear effect (deafness), almost 40 % are asymptomatic and have swelling of the parotid glands.
• All are preventable though mandatory vaccination

Paramyxoviridae: Respiratory Syncytial Virus (RSV)

• RSV is a respiratory syncytial virus; mild common cold, otitis media, severe pneumonia are all caused by respiratory syncytial virus.
• Prevention is passive immunization with antibodies and vaccination and is especially dangerous for infants less than 1 year, and immunocompromised

Orthomyxoviridae

• This family of viruses Includes negative-sense RNA enveloped viruses.
• Orthomyxoviridae can be further classified:
• Influenza A virus
• Influenza B virus
• Influenza C virus
• Its pathogenesis includes establishing a local upper respiratory tract infection when invading mucus-secreting and ciliated cells. Then In the case of infestation of lower respiratory tract, the virus can cause serious desquamation of bronchial and alveolar epithelium, resulting in low level viremia. the virus can rarely infected other organs then lung
• The envelope includes hemagglutinin (HA, H) (H1-H16 H1-H3), neuraminidase (NA, N) (N1-N9 N1-N2), and matrix membrane proteins (M1, M2).
• the core has eight different helical nucleocapsid segments (nucleoprotein and transcriptase). Replication occurs in the nucleus of host cell.
• The most common strains include:
• "Spanish flu" HswN1 (1918)
• H1N1 (1947)
• H2N2 (1957)
• H3N2 (1968)
• H1N1 (1977)
• Clinical manifestation is highly variable, however most report mild to severe cases, fever, malaise, myalgia, sore throat, nonproductive cough, gastrointestinal symptoms, and otitis media.
  • Viral pneumonia
  • Bacterial pneumonia (superinfection)
  • Myositis
  • Encephalitis
• Prevention includes vaccination (2023/2024 season tetravalent vaccine):
  • A Victoria/4897/2022 (H1N1)pdm09
  • A/Darwin/9/2021 (H3N2)
  • B/Austria/1359417/2021
  • B/Phuket/3073/2013

Rhabdoviridae

• Rhabdoviridae is a negative-sense RNA enveloped virus.
• The rabies virus infection is incurable and spread by bite of a rabid animal (zoonosis).
• Pathogenesis includes replication in the muscle causing a minimum symptoms, then spreading of infection up from the along peripheral nerves to the brain, resulting death without counter measures.
• Vaccination is inactivated and is administered to travelers, hunters, farmers, and anyone working with animals (every 5 years)

Filoviridae

• Filoviridae is a negative-sense RNA and enveloped virus that can cause disease.
• Marburg Virus
• Ebola virus , ... are included
• It causes severe or fatal hemorrhagic fevers that are spread by infected body fluids.

Reoviridae and Caliciviridae

• They includes ds RNA with a non-enveloped virus.
• Rotaviruses cause infantile diarrhea.
• Its pathogenesis comes from replication in the epithelial cell of the small intestine.
• Caliciviridae has ss RNA, a non-enveloped virus:
• Norovirus causes diarrhea + vomiting.
• Rotavirus includes vaccination as prevention.

Togaviridae and Flaviviridae

• Togaviridae and Flaviviridae are related in that they have a positive-sense RNA
• Arboviruses
• Rubella virus
• Hepatitis C virus
• Infections typically present zoonotic diseases caused by vectors (mosquitoes or ticks).
• Arboviruses are often indicated by Equine encephalitis, and mild systemic disease.
• Flaviviruses are often contracted though Encephalitis, fever (i.e. Dengue , Yellow fever, or West-Nile Encephalitis).
• Rubella virus (Rubivirus) is represented by classic childhood exanthems (with roseola, fifth disease – parvo B19, measles, and chickenpox) with complications related to arthralgia, arthritis, and rarely causing post-infection encephalitis. And Severe congenital defects can be induced during the 1st – 2nd trimmest (until 20th week of pregnancy), and its most observable symptoms are ocular defects, hearth defects, deafness, microcephaly, and mental retardation Prevention includes vaccination (mandatory)

Bunyaviridae and Arenaviridae

• Bunyaviridae and Arenaviridae are related in that they have a negative-strand RNA and are enveloped.
• These include for example Bunyavirus, and Phlebovirus however these agents all follow more or the less same transmission and pathogenesis.
• Infection often presents zoonotic diseases caused by vectors (mosquitoes or ticks), or other direct transmission with the environment.
• Infections can cause hemorrhaging, a high temperature and even Encephalitis.

Detection of Viruses

Direct & Indirect Diagnostics

• Direct detection involves identifying the pathogen or its components via cultivation, microscopy, antigen detection, or PCR.
• Indirect detection involves detection of the host's immune response by identifying antibody production and its dynamics, identifying immune cells, or identifying their stimulation

Limitations of Methods

Direct methods can be limited by the following:

• Infectious agents must be present in a clinical specimen.
• Sometimes, the tests have a low sensitivity.
• Tests require proper collection of clinical specimen

Indirect methods can be limited when:

• There can be low or no immune response (e.g., start of the infection, immunosuppressed patients)
• The dynamics of the antibodies should be usually checked.
• Cross-reactions can be observed.
• Identified changes can be physiological, so the real infectious agent can be missed.

Methods For the Detection Of Viruses

• Direct methods include PCR diagnostics (RT-PCR for RNA viruses), immunological methods to detect antigens, cultivation of viruses, and electron microscopy.
• Indirect methods: Immunological diagnostics (antibody detection)

PCR Diagnostics

• PCR diagnostics includes steps for proper clinical specimen collection, isolation of DNA/RNA, PCR amplification (with or without reverse transcription), and detection of PCR product (typically real-time).
• Multiplex include detection of more different agents for syndrome-based diagnostics

Immunological Direct Methods

• Immunological direct methods rely on Immunofluorescence or ELISA.
• Cultivation of Virus occurs in tissue cultures by taking a small volume an allowing it to multiply.
• Identification occurs by cytopathic which depends of time and has to be very carefully worked out
• Electron Microscopy
• Electron gun sends High voltage electrons though condenser lenses which uses beam of light and Fluorescent screen. Used to determine different features the body or to make other tests
• Immunological Methods Include:

Basic immuno methods

• Precipitation
• Agglutination
• Complement-fixation
• Neutralization ELISA (https://www.youtube.com/watch?v=0c2FdQH33hk) Blotting techniques

Antibody Detection

• Antibody detection occurs through methods that include direct/indirect and can show the presnece on viral RNA and Viral Antigens, with Antibodies IgM (early stages) and IgG (later stages).