Virology

What is a virus?

• Viruses are genetic information enveloped with a protein coat.
• They are obligate intracellular parasites.
• Viruses lack the mechanisms to replicate without a host cell, such as enzymes and energetic pathways.
• It is debated whether viruses are living organisms.

Living Organism Criteria

• Cell: Viruses consist of DNA or RNA with a protein envelope, not cells.
• Reproduction: Viruses reproduce by copying DNA or RNA, but require a host cell.
• Energy Use: Viruses do not use energy outside a cell; they need a host cell.
• Response to Environment: Viruses bind to cell receptors, inject genetic material, and cause immune response activation and evolution, but the response is minimal.

Virus classification

• Viruses are classified based on structure, geographical location, and diseases.
• Structure pertains to genetic information (DNA, RNA), coat (enveloped, unenveloped), and shape (icosahedral, helical).
• Geographical localization can be northern, southern hemisphere, or tropical.
• Diseases caused by viruses are respiratory, GIT, CNS, and skin infections.

Virion Structure

• Naked capsid viruses (non-enveloped) consist of nucleic acid, enzymes, structural proteins, and a nucleocapsid.
• Enveloped viruses have a membrane and glycoproteins.

Virus timeline replication

• The virus timeline includes infection, eclipse, cell burst/virion release, and infection maintenance.
• Log virus concentration changes over time; it increases from the eclipse phase to the infection maintenance phase.

Phases of viral replication

• Initial phases include recognition and attachment to the target cell receptor.
• Viruses then undergo penetration and uncoating.
• Macromolecular synthesis is followed by the release of the viral particles.
• Release of viral particle may occur through cell death (lysis), budding, or active exocytosis.

Intracellular Viral Reproduction

• The viral reproduction cycle include recognition, attachment, penetration, uncoating, transcription, protein synthesis, assembly, envelopment and release
• Different antiviral meds target different stages of this process
• Some major targets include:
  • Nucleotide biosynthesis and mutation: ribavirin,
  • Thymidine kinase (drug activation): acyclovir, penciclovir
  • Neuraminidase: zanamivir, oseltamivir

Protein Synthesis

• Viruses utilize the host cell's components, including ribosomes, tRNA, and mechanisms for post-translational modification.
• Some RNA viruses undergo translation into a single protein, cleaved by proteases.

Papillomaviridae (HPV - Human Papillomaviruses)

• HPV is dsDNA, non-enveloped with 200 known genotypes.
• High-risk HPV can cause malignant proliferation (HPV 16, 18) and low-risk HPV can cause benign lesions (HPV 6, 11).
• Pathogenesis involves infection and replication in the squamous epithelium of the skin and mucosal membranes, such as genital, oral, or conjunctival papillomas.
• Disease progression is from skin or mucosal dysplasia to cancer.
• Prevention is through vaccination (voluntary).
• Transmission is through direct or sexual contact, leading to hand, throat, foot, or cervix papillomas.

Polyomaviridae

• BK virus (renal disease), JC virus (PML).
• The virus is dsDNA, non-enveloped, and has at least 100 types.
• Pathogenesis includes asymptomatic manifestation leading to latent infection.
• Immunocompromised patients may experience progressive multifocal leukoencephalopathy (PML) or renal disease.
• Transmission occurs through aerosol, leading to multiplication in the respiratory tract, viremia, multiplication in the kidney, viruria, hemorrhagic cystitis, and CNS involvement.

Adenoviridae

• Adenovirus is linear, dsDNA, non-enveloped, with over 100 serotypes, most often 1-7.
• Pathogenesis starts with infections of muco-epithelial cells in the respiratory, gastrointestinal tract, conjunctiva, or cornea.
• Diseases include respiratory infections such as acute respiratory disease, laryngitis, croup, and bronchiolitis (AdV-B, C group).
• Other diseases include conjunctivitis, epidemic keratoconjunctivitis (AdV-B, D group), and gastroenteritis, diarrhea (AdV-F, G group).
• Transmission is through direct contact via respiratory droplets or fecal mass, direct contact via hands, and indirect contact via inadequately chlorinated swimming pools, or contaminated items (towels).
• Typical patients are children younger than 14 years old and people in crowded areas.
• Prevention involves vaccination for serotypes AdV-4 and -7 in the military.

Herpesviridae

• Herpesviridae are dsDNA, enveloped viruses causing lifelong infections.

Alpha Herpesviruses

• Includes HHV-1 (Herpes simplex 1), HHV-2 (Herpes simplex 2), and HHV-3 (Varicella-zoster).
• Primary target: Mucoepithelial cells.
• Site of latency: Neuron.
• Transmission is through close contact (STD) for HSV-1/2 and respiratory/close contact for Varicella-zoster.

Gamma Herpesviruses

• Includes HHV-4 (Epstein Barr).
• Primary target: B cells and epithelial cells.
• Site of latency: B cells.
• Transmission is through saliva.

Beta Herpesviruses

• Includes HHV-5 (Cytomegalovirus).
• Primary target: Monocytes, granulocytes, lymphocytes, and epithelial cells.
• Site of latency: Myeloid cell lineage.
• Transmissin is through close contact, transfusions, and tissue transplantation.

Herpes-simplex virus (type 1 and 2)

• Is transmitted through close contact, STD
• It causes Gingivostomatitis herpetica which reactivates into Herpes labialis (HSV-1) and herpes genitalis (HSV-2).
• It caused cause the following complications:
  • Herpes pharyngitis, tracheobronchitis
  • herpetic keratitis
  • eczema herpeticum, herpetic whitlow (fingers), herpes gladiatorum (infection of the body)
  • Herpes encephalitis (90 % HSV-1) and meningitis (often HSV-2)
  • Herpes neonatorum (mostly HSV-2) – during childbirth
  • organ dissemination in immunocompromised patients

Herpes-simplex virus (type 1 and 2) Treatment

• The main treatments are Acyclovir, Valacyclovir, Penciclovir, Famciclovir

Varicella-Zoster virus (VZV)

• Varicella-Zoster virus is transferred through The air (droplets), close contact
• The primoinfection causes chickenpox (varicella), reactivation becomes Herpes zoster
• Chickenpox causes classic childhood exanthems
• Herpes zoster causes Immunodeficiency
• Complications include interstitial pneumonia, postherpetic neuralgia, and neonatal varicella (teratogenic effect) neonatal varicella
• This infection has preventable through vaccination

Epstein-Barr Virus (EBV)

• The Epstein-Barr Virus affects B lymphocytes
• It spreads through saliva, close contact, commonly referred to as "kissing disease"
• The primoinfection its mostly asymptomatic in children but symptomatic in adolescents (mononucleosis)
• It can cause High fever, tonsillitis, lymphadenopathy, heterophile antibodies (only 1st month)
• Can be Reactivated as asymptomatic or symptomatic
• EBV has an oncogenic effect causing EBV-Induced Lymphoproliferative diseases

Cytomegalovirus (CMV)

• Cytomegalovirus causes cell inclusion and cytomegalia
• Spreads through saliva, close contact, STD, transfusion, tissue transplantation
• Primoinfection is mostly asymptomatic which can reactivated and become symptomatic
• infection in the immunocompromised patient has specific symptoms like pneumonia or retinitis
• congenital cytomegalic inclusion disease may be transfered through mothers primoinfection causing: fetus small size, thrombocytopenia, microcephaly, rash, hepatosplenomegaly, icterus, hearing and vision impairment
• The infections can be treated with Ganciclovir, Valganciclovir, Cidofovir, Foscarnet

Poxviridae

• Poxviridae are complex large viruses made of DNA
• Pathogenesis starts from the upper respiratory tract then disseminate to internal and dermal tissues
• Can cause diseases such as Smallpox, variola (Orthopoxvirus) or Molluscum contagiosum (Molluscipoxvirus)
• Smallpox has two types: variola major (20-40% mortality) and variola minor (mortality 1%). It was eradicated in 1977 (vaccination)
• Molluscum contagiosum creates benign skin lesions more often in children

Poxviridae, Smallpox specifics

• Causes between 7-12% of all deaths in England (18th century) and 30% of those deaths were children
• The first ever vaccine was created to treat smallpox
• It was eradicated from all countries by 1977

Picornaviridae

• This virus is a small RNA virus with a naked capsid
• The enter related viruses are Enteroviruses, rhinoviruses or Hepatitis A virus
• Pathogenesis: Its transmitted through the fecal-oral or upper respiratory tract where it contaminates the oropharynx, intestinal tract with the viruses (its spread through viremia)
• Can cause: paralysis, rash, meningitis, encephalitis, myocardium or a viral infection to the respiratory tract

Picornaviridae - Enteroviruses specifics

• Polio was eradicated in 2002 in Europe
• USA still has sporadic cases of imports
• Africa or the middleeast are still endemic
• (CE) Preventable with inactivated polio vaccine (IPV) or live attenuated oral polio vaccine (OPV)

Picornaviridae - Rhinovirus specifics

• There are >170 serotypes which are split into 3 groups that have no memory
• It causes the common cold
• The virus can be found year round with main spikes in Autumn Spring
• can cause Bronchiolitis

Paramyxoviridae

• Paramxyoviridae are negative-sense ssRNA with envelope
• Specific species include Measles, mumps, Respiratory syncytial virus, Human metapneumovirus and Nipah Virus (zoonosis, encephilitis)

Paramyxoviridae - Measles

• Its characteristic signs are fever, rash, coughs and light sensitivity (photophobia)
• infection grants life long imunity
• Complications can include; pneumonia, Otitis media, or infections in the encephalon

Paramyxoviridae - Parainfluenza

• Affects the epithelial cells in the upper respiration tract
• It is also ubiquitous
• Manifests as regular cold (upper Resp. infection, Bronchiolitis, Pneumonia

Paramyxoviridae - Mumps

• Symptoms are (almost 40% asymptomatic, the other have affected/swollen parotid glands and gonads, pancreatitis, meningitis, inner ear deafness

Paramyxoviridae - RSV (respiratory)

• Manifest as the common cold, otitis media, and pneumonia
• very dangelrous with infants, and patients with immunodeficiency
• The treatments involves mandatory vaccines against Measles and Mumps and optional vaccine for RSV

Orthomyxoviridae

• This family of virus affects RNA
• The virions are enveloped
• The family inclue influenza variants A,B, and C
• Pathogenesis: the upper respiratory tract has an infection, and may damage mucus secrating cells
• There is low virimia
• rarely infects the lungs instead of the rest of the body

Orthomyxoviridae - Influenza (structure)

• The virus is made with 8 helix of nuclecapsid and the genetic code is copied in the nucleus

Orthomyxoviridae - Influenza

• Clinical manifestations include mild to severe cases
• Fever, cough or fatigue
• Gastro and abdominal symptoms
• Possible for oitis to occur
• Complications: Viral/Bacterial pneumonia or an infection to the encephalon

Orthomyxoviridae - Influenza vaccines

• Treatment involves tetravilent vaccines
• strains change over time and are resistant to existing anti biotics
• strains can emerge through antigenic, genetic or recombination

Rhabdoviridae, Rabies virus

• Is a negative sense, encapsulated RNA virus
• it is not curable
• Pathogenesis: It transferred animal bites (zoonosis), replicates muscles then spread through the periphernal nerves and into the brain, killing the host when death occurs
• preventative treamtent is possible with regular, every 5 year inactivated shots

Filoviridae

• Has an enveloped core and is negative stranded RNA virus
• Marburg and Ebola virus are main examples of this family
• Infection can result in fatal fever

Reoviridae

• The virions are non encapsulated and have dsRNA
• Rotaviruses is an specific type of viridae that causes infants to have diarrhea

Caliciviridae

• This virions are non encapsulated and use ssRNA
• Norovirus is a specific viridae that can cause diarrhea
• The prevention is optional injections of rotavirus

Togaviridae and Flaviviridae

• Use positive sense RNA
• Arboviruses, Rubella virus, Hepatitis C virus are the main family viruses
• Zoonatic diseases
• The hosts are mosquitos (vectors)
• Can manifest as encephalitis like Dengue or Yellow Fever

Togaviridae, Rubella

• Is one of many classic exanthem childhood diseases
• Complication include arrhythmia
• Congenital defects can occur between the weeks 1 & 20
• vaccination is manditory

Bunyaviridae - Arenaviridae

• Negative Strand of RNA that is also enveloped
• Bunyavius, Phelebovirus and hantavirus and speciric variants
• Manifest as encephalitis or a respitory illness

Detection of Virus

• Direct detection focus on diagnosing specific illnesses
• Indirect detection on antibody and how the hosts respond to infection

Limits of the method

• Direct method can lack in specificity, due to the agent not being present during the test
• Indirect shows the patient is infected, but may not explain where or what has happened

Detection of Virus

• Direct treatments focus and aim toward PCR or antibody usage to find
• Indirect tests focus mostly on finding the anti bodies

Detection of Virus - Tools (PCR tests)

• To run PCR tests, first you need to isolate DNA or RNA from the host
• Amplify strands (with a transcription)
• To see the result

Detection of Virus - Tools (Multiplex Pannels)

• Tool that test for more specific genetic information
• Use film array for multiple virus detections

Detection of Virus - Tools (Immunofluorescence direct methods)

• Immunolfuorescence requires the signal of a Indicator (anti-antibody that can be detected with microscope)
• second antibody (will attach to the anti gen)
• viral antigen (to be identified, attaches to bottom by)
• Capture antibody

Detection of Virus - Tools (Cultivation)

• Involve treating the virus as a single culture sample inside a lab
• Process is time consuming

Detection of Virus - Tools (microscopy)

• Involve looking for virusies using a strong microscope
• Its able to determine specific virus types

Immunological detection - Techniques

• Many techniques from basic sciences are applicable to immuno virus testing
• These include: Precipitation, Agglutination, Complement-fixation, Neutralization, ELISA, Blotting

Immunological methods

• Analyte levels rise to detect
• RNA test will peak faster than antigen tests
• Immunoglobins will react a little later but can test past the RNA or AG test ranges