Introduction to Medical Virology PDF 2024/2025

BMS 10404: Microbiology and Parasitology for Health Professionals | Academic Session 2024/2025 Introduction to Medical Virology Prof Dr Yeo Chew Chieng...

BMS 10404: Microbiology and Parasitology for Health Professionals | Academic Session 2024/2025 Introduction to Medical Virology Prof Dr Yeo Chew Chieng Faculty of Medicine 1 Learning Outcomes 1. Describe the structure, characteristics and classification of viruses 2. Describe the steps involved in viral replication 3. List common RNA and DNA viruses of clinical significance 4. Name common diseases caused by medically important viruses 5. Describe the chemotherapy of viral infections 2 General Properties of Viruses Viruses are the smallest infectious agents (ranges from 20 – 300 nm in diameter) Contains only one type of nucleic acid (either DNA or RNA) as their genome encased in a protein shell (capsid) Entire infectious unit = virion 3 General Properties of Viruses 4 General Properties of Viruses Viruses are inert in extracellular environment – they replicate only in living cells Viral genome contains information required to program the host cell to synthesize virus- specific macromolecules Viruses are known to infect almost all living organisms The host range for any given virus may be broad or may be extremely limited 5  Viruses are separated into major Taxonomy of Viruses groupings called families based on (i) morphology, (ii) genome structure and (iii) replication strategies Virus family names have the suffix – viridae e.g. Hepadnaviridae, Retroviridae Within each family, subdivisions called genera are based on biological, genomic, physicochemical or serological differences Genus names carry the suffix – virus e.g. Orthohepadnavirus (hepatitis B virus), Lentivirus (human immunodeficiency virus) 6 Structure of Viruses Capsid Protein shell or coat that encloses the nucleic acid genome Nucleocapsid Protein-nucleic acid complex representing packaged form of the viral genome 7 Structure of Viruses Structural proteins that make up the viral capsid have several important functions: 1. Facilitate transfer of viral genome from one host cell to another 2. Serves to protect the viral genome against inactivation by host nucleases 3. Participate in attachment of virus particle to susceptible cell Structural proteins determines the antigenic characteristic of the virus 8 Structure of Viruses Capsomeres Smallest structural components visible in electron microscope images on the surface of icosahedral virus particles Protein subunits that make up the viral capsid – serving as its basic morphological building blocks Capsid – formed by assembly of capsomeres that are arranged in a specific pattern to give the viral capsid its distinct shape 9 Structure of Viruses Envelope Lipid-containing membrane that surrounds some (but not all) virus particles Acquired during viral maturation by budding process through host cell membrane Virus-encoded glycoproteins are exposed on the surface of the envelope Surface glycoproteins attach the virus to the target cell by interacting with specific cellular receptors Glycoproteins are important viral antigens involved in interaction of the enveloped virus with neutralizing antibodies 10 11 Structure of Viruses Virion Complete infectious virus particle In some cases (e.g. papillomaviruses, picornaviruses), virion = nucleocapsid Non-enveloped viruses also known as “naked viruses” In complex virions (herpesviruses, orthomyxoviruses), virion = nucleocapsid + envelope 12 Structure of Viruses: Nucleocapsid Symmetry Nucleocapsids are often constructed in highly symmetrical ways Symmetry refers to the way capsomeres are arranged in the virus capsid Two kinds of symmetry are recognized in viruses Helical symmetry – seen in rod-shaped viruses Icosahedral symmetry – spherical viruses usually arranged in an icosahedral shape Most efficient arrangement of subunits in a closed shell 13 Structure of Viruses: Nucleocapsid Symmetry Some virus particles do not exhibit simple icosahedral or helical symmetry but are more complex in structure, e.g.: Poxviruses are brick-shaped with ridges on the external surface with core and lateral bodies inside Bacterial viruses such as bacteriophage T4 of E. coli have icosahedral heads plus complex tail structure 14  Viruses have either DNA or RNA genomes: single- or double-stranded Viral circular or linear; segmented or non-segmented Some group of viruses use both DNA and RNA as their Genomes genetic material but at different stages of their replication cycle 15 Viral Genomes RNA viral genomes: Positive-sense (e.g., picornaviruses, togaviruses) RNA genomes are infectious → can function as mRNA within infected cell Negative-sense (e.g. orthomyxoviruses, rhabdoviruses) RNA genomes are non- infectious: Virions carry an RNA polymerase that transcribes the genome into complementary RNA molecules that can then function as mRNA 16  The Baltimore classification scheme is based on the type of viral genome, the relationship of The Baltimore the viral genome to its mRNA and its mode of Viral Classification replication Scheme Seven classes of viruses 17  The Baltimore classification scheme is based on the type of viral genome, the relationship of The Baltimore the viral genome to its mRNA and its mode of Viral Classification replication Scheme Seven classes of viruses 18  Viruses multiply only in living cells Host cells provide energy, biosynthetic machinery and precursors required for synthesis of viral proteins and nucleic acids Viral genome contains all the necessary Replication of information to code for viral-specific macromolecules Viruses Viral replication requires host cell to synthesize viral proteins → virus genome must produce a functional mRNA 19 Replication of Viruses The viral replication cycle can generally be divided into six main steps: 1. Attachment (adsorption) of the virion to the host cell 2. Penetration (injection) of the virion or its nucleic acid into the host cell 3. Uncoating occurs for viruses which enter the host cell as a complete nucleocapsid (animal viruses) 4. Replication of viral nucleic acids and proteins by host cell a) Early protein synthesis b) Nucleic acid synthesis c) Late protein synthesis and processing 5. Assembly of capsids and packaging of viral genomes into new virions 6. Release of mature virions from the host cell 20 Replication of Viruses Duration of viral replication cycle varies: 20 – 60 min for most bacterial viruses 8 – 40 h for most animal viruses 21 Replication of Viruses: Attachment First step in viral infection Interaction of virion with specific receptor on the surface of the host cell Receptors can either be surface proteins or oligosaccharides e.g., HIV binds to CD4 and CCR5 receptors of cells of the immune system; SARS-CoV-2 binds to angiotensin converting enzyme 2 (ACE2) receptor Presence or absence of receptors – determines cell tropism and viral pathogenesis 22 Replication of Viruses: After binding to host cell, Penetration the virus particle is taken up inside In some viruses such as HIV, this occurs by fusion of the virion envelope with the plasma membrane of the host cell In other cells, this occurs via receptor-mediated endocytosis → leads to uptake of the ingested virus within endosomes 23  Uncoating occurs along with or shortly after penetration Physical separation of viral genome from outer structural components Infectivity of the virus is lost during uncoating Some enveloped animal viruses are uncoated in the cytoplasm, others (e.g., influenza) are uncoated at the nuclear membrane and the viral genome then enters the nucleus Replication of Viruses: Uncoating Entry of influenza virus into host cell via endocytosis and uncoating within endosomes 24 Replication of Viruses: Synthesis and Assembly Non-enveloped double-stranded DNA viruses: After penetration, viral DNA is uncoated and enters nucleus Viral genes are transcribed into mRNA Viral mRNA translated in cytoplasm; newly synthesized viral proteins enter nucleus Viral DNA is replicated in nucleus Viral DNA and structural proteins assemble in the nucleus → new progeny virions On rare occasions, viral DNA may be incorporated into host cell DNA 25 Replication of Viruses: Synthesis and Assembly Positive-sense single-stranded RNA viruses: Virus enters cell and viral RNA is uncoated ss RNA (+) genome can be directly translated in the cytoplasm producing viral proteins A negative-sense RNA strand is synthesized by viral RNA-dependent RNA polymerase This is used to produce many positive-sense copies Positive-sense RNA molecules assembled with viral structural proteins to produce progeny virions 26 Replication of Viruses: Synthesis and Assembly All RNA viruses require a viral-encoded RNA- dependent RNA polymerase since host cellular RNA polymerase do not catalyze formation of RNA from an RNA template For ss RNA (–) viruses, RNA polymerase will synthesize the (+)strand which will function as mRNA and also as template to make more (–)strand RNA genomes For dsRNA viruses, the RNA polymerase will transcribe the viral genome into functional mRNA 27 Replication of Viruses: Retroviruses Retroviruses which has a diploid ss RNA (+) genome (i.e., 2 copies of ssRNA) replicates through a dsDNA intermediate: Viral reverse transcriptase catalyzes the synthesis of DNA from the ss RNA (+) genome The dsDNA is then integrated into host DNA (“provirus” stage) and subsequently used as a template by the host cell machinery to synthesize mRNA for translation of viral proteins 28 Replication of Viruses: Release In general, non-enveloped viruses accumulate in infected cells, and the cells eventually lyse and release the virus particles Enveloped viruses mature by budding process Virus-specific glycoproteins are inserted into the cell membrane Viral nucleocapsids then bud through the membrane at these modified sites → acquisition of the viral envelope Enveloped viruses are not infectious until they acquire their envelopes 29 30 Cultivation of Viruses Cultivation of Viruses Bacteriophages (bacterial viruses): Grown in bacterial cell culture Animal/Human viruses: Living animals Mice, rabbits, guinea pigs Chicken embryos (eggs) Used to be the most common method to grow viruses Convenient and inexpensive Death of the embryo, embryo cell damage, lesions on egg membrane Cell culture Most common method to grow viruses today 32 Cultivation of Viruses For animal viruses, plaques may be observed using cultured animal cells as hosts Monolayer of cultured animal cells prepared on a plate or flat bottle Virus suspension is overlaid Plaques are revealed by zones of destruction of the animal cells Estimation of the virus titer can be made by counting the number of plaques produced (plaque-forming units/PFUs) 33 Cultivation of Viruses When using cell cultures for animal viruses, viral multiplication could be monitored by observing for cytopathic effects (i.e., morphological changes in the infected cells) Cell lysis or necrosis, inclusion formation, giant cell formation, cytoplasmic vacuolization 34  DNA Viruses Viruses of Clinical Importance RNA Viruses DNA Viruses 36 DNA Viruses: Adenoviridae (Adenoviruses) Non-enveloped, icosahedral viruses with fibers protruding from the vertex capsomeres Genome: linear dsDNA, 26 – 45 kbp in size At least 67 different types of adenoviruses infect humans, especially the mucous membranes Causes acute respiratory diseases (Group C adenoviruses), conjunctivitis (types 8, 19 and 37) and gastroenteritis (types 40 and 41) No specific treatment available for adenovirus infections Adenoviruses are being used as delivery vehicles for vaccines (including for SARS-CoV2: University of Oxford-Astra-Zeneca, Johnson & Johnson’s, CanSino Biologics, Russia’s Sputnik V vaccines) and for experimental gene therapy 37 DNA Viruses: Papilomaviridae (Papilomaviruses) Non-enveloped, icosahedral viruses Genome: circular dsDNA – 8 kbp in size Causes infections at cutaneous and mucosal sites leading to development of different kinds of warts and cancers Human papilomavirus (HPV) is known causative agent for genital cancers (e.g., cervical cancers) HPV genital infections are sexually transmitted HPV – most common viral infection of the reproductive tract (estimated 400 million people worldwide have HPV infections) HPV-16 and HPV-18 responsible for >70% cervical cancers Vaccines against common types of HPV available since 2006 38 DNA Viruses: Herpesviridae (Herpesviruses) Enveloped, icosahedral-shaped viruses Genome: linear dsDNA of 125 – 240 kbp in size Characterized by latent infections for life – usually in ganglial or lymphoblastoid cells Human herpesviruses: Herpes simplex types 1 and 2 (HSV-1 and HSV-2) – causes oral and genital lesions Varicella-zoster virus (chickenpox and shingles) Cytomegalovirus Epstein-Barr virus (infectious mononucleosis, associated with human neoplasms) Human herpesviruses 6 and 7 (T lymphotropic) Human herpesvirus 8 (associated with Kaposi’s sarcoma) 39 DNA Viruses: Large, brick-shaped enveloped viruses Poxviridae (Poxviruses) Genome: linear, dsDNA of 130 – 375 kbp in size All poxviruses tend to produce skin lesions Human pathogens: variola (smallpox), vaccinia, molluscum contagiosum Animal pathogens such as cowpox and monkeypox can infect humans Smallpox declared eradicated by WHO in 1980 – successful mass vaccination campaign that was started in 1967 40 DNA Viruses: Hepadnaviridae (Hepadnaviruses) Typified by the Hepatitis B virus (HBV) Enveloped viruses Pleomorphic with three main morphologies: Spherical (majority), tubular and filamentous Genome: circular dsDNA of 3.2 kbp in size Viral replication occurs primarily in the liver and is shed into the bloodstream Can cause acute and chronic hepatitis; persistent infections associated with high risk of developing liver cancer Vaccine against HBV available since 1982 – effective to prevent HBV infections 41 RNA Viruses 42 RNA Viruses: dsRNA: Reoviridae (Reoviruses) Reoviruses are non-enveloped with icosahedral symmetry Particles have two or three protein shells with short spikes extending from the virion surface Genome: linear, double-stranded, segmented RNA (10 – 12 segments), 18 – 30 kbp Viral RNA transcriptase transcribes mRNA from the (-) strand of each segment of the dsRNA genome 4 of the 15 genera in the family Reoviridae are human pathogens: Orthoreovirus, Rotavirus, Coltivirus (Colorado tick fever virus) and Orbivirus Rotaviruses are a major cause of diarrhoeal illness in humans (as well as animals) 43 RNA Viruses: ssRNA(+): Coronaviridae (Coronaviruses) Enveloped viruses, helical symmetry with petal-shaped projections on the outer surface suggestive of solar corona Single-stranded positive-sense RNA, 27 – 32 kbp in size, largest RNA virus genome Coronaviruses exhibit tropism for epithelial cells of the respiratory and GI tract Divided into four distinct genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus Human coronaviruses cause common colds, may cause lower respiratory tract infections and implicated in gastroenteritis in infants Novel coronaviruses causes severe acute respiratory syndrome (SARS) (SARS-CoV), COVID-19 (SARS-CoV-2) and Middle East respiratory syndrome (MERS) (MERS-CoV) – all are in the genus Betacoronavirus 44 RNA Viruses: ssRNA(+): Coronaviridae (Coronaviruses) SARS-CoV Causes severe respiratory disease, mortality rate about 10% First outbreak of SARS in Southern China in late 2002 – spread to 19 countries Outbreak waned by mid-2003 – more than 8,000 infected with 800 deaths Zoonotic, originated likely in bats, amplified in palm civets and transmitted to humans in live animal markets in southern China MERS-CoV Causes mild to severe respiratory illness in children and adults; patients with comorbidities are more severely affected, as are the elderly First identified in Saudi Arabia in 2012 and spread to 27 countries Relatively inefficient transmission compared to SARS-CoV but higher mortality rate of up to 35% Also zoonotic with camels identified as the intermediate host 45 RNA Viruses: ssRNA(+): Coronaviridae (Coronaviruses) SARS-CoV-2 Emerged in Wuhan, China in December 2019 with patients showing atypical pneumonia By January 2020, China has obtained and shared the full genome sequence of the novel coronavirus International Committee on the Taxonomy of Viruses designated the novel coronavirus as SARS-CoV-2 while the World Health Organisation (WHO) named the disease COVID-19 SARS-CoV-2 has emerged as one of the most notorious pandemics in human history SARS-CoV-2 is also zoonotic but its origins are still inconclusive although very similar viruses have been found in bats and pangolins ACE-2 serves as the receptor for both SARS-CoV and SARS-CoV-2 46 RNA Viruses: ssRNA(+): Picornaviridae (Picornaviruses) Small, non-enveloped, icosahedral viruses Genome: single-stranded positive-sense RNA, 7.2 – 8.4 kb in size Large family of viruses with many major human pathogens: Polioviruses, Coxsackieviruses, Rhinoviruses and other Enteroviruses Hepatovirus (Hepatitis A virus) Poliomyelitis Mouth is the portal of entry – primary viral multiplication in oropharynx and intestine Poliovirus spread along axons of peripheral nerves → CNS (involves spinal cord/brain) Poliovirus invades certain nerve cells – damage or complete destruction of these cells Although most infection results in mild disease, it can lead to paralytic poliomyelitis – flaccid paralysis resulting from lower motor neuron damage WHO launched a campaign in 1988 to eradicate poliovirus through mass oral vaccination (containing live attenuated virus) programme 47 RNA Viruses: ssRNA(+): Picornaviridae (Picornaviruses) Coxsackievirus Can cause a variety of illnesses including hand-foot and mouth disease (HFMD, which is also associated with enterovirus 71), aseptic meningitis and myocarditis (coxsackievirus primary cause of viral-associated myocarditis) Rhinovirus Common cold virus; enters via the respiratory tract More than 150 types are known Hepatovirus (Hepatitis A virus) Infection route – predominantly fecal-oral Onset of disease tend to occur abruptly (within 24 hrs) in contrast to more insidious/slower onset for HBV and HCV Often cause outbreaks of disease (largest outbreak in Shanghai 1988 where 300,000 cases of hepatitis A attributed to uncooked clams in polluted waters) Vaccine available 48 RNA Viruses: ssRNA(+): Flaviviridae (Flaviviruses) Enveloped, icosahedral viruses Genome: single-stranded, positive-sense, size: 9.5 – 12.5 kbp Most flaviviruses that are human pathogens involved arthropods as vectors for transmission to humans Dengue virus – vector: Aedes aegypti West Nile virus – vector: Culex, Anopheles, Aedes Yellow fever virus – vector: Aedes aegypti Zika virus – vector: Aedes Exception: hepatitis C virus – no known vector Transmitted primarily through direct percutaneous exposure to blood (e.g., drug-abusers, hemodialysis patients, etc.); mother- to-child transmission can occur but less frequently compared to hepatitis B virus 49 RNA Viruses: ssRNA(-): Orthomyxoviridae (Orthomyxoviruses) Influenza viruses that infect humans and animals Three immunologic types: types A, B and C Enveloped, usually spherical-shaped, helical symmetry with surface projections containing hemagglutinin and neuraminidase activity Genome: linear, segmented, negative-sense single-stranded RNA (total genome size: 10 – 13.6 kb) Influenza A and B contain 8 segments; influenza C contain 7 segments Sudden changes in surface antigens – epidemiologic features of influenza; also problems in vaccine development 50  Segmented nature of the genome enables RNA Viruses: genetic reassortment when a cell is co- infected with two influenza viruses of a given ssRNA(-): Orthomyxoviridae type → mixtures of parental gene segments (Orthomyxoviruses) assembled into progeny virions 51 RNA Viruses: ssRNA(-): Paramyxoviridae (Paramyxoviruses) Pleomorphic, enveloped viruses Genome: linear, non-segmented negative-sense single-stranded RNA, size 16 – 20 kbp In contrast to influenza viruses, paramyxoviruses are genetically more stable Human pathogens: mumps, measles, parainfluenza and respiratory syncytial virus, also Nipah virus and Hendra virus Nipah virus caused an outbreak of severe encephalitis in Malaysia in 1998 – 1999; high mortality rate (>35%) among more than 250 cases Nipah virus infection occurred by direct transmission from pigs to humans (zoonotic) Hendra virus is an equine virus that caused human cases of encephalitis in Australia Fruit bats are natural hosts for both Nipah and Hendra viruses 52 RNA Viruses: ssRNA(-): Filoviridae (Filoviruses) Enveloped, pleomorphic viruses that usually appear very long and threadlike Genome: linear, non-segmented, negative-sense single-stranded RNA, 19 kb in size Marburg and Ebola viruses – severe hemorrhagic fever Highly virulent in humans and non-human primates (Biosafety Level 4) Both causes severe acute disease characterized by fever, headache, sore throat, muscle pain followed by abdominal pain, vomiting, diarrhea and rash with internal and external bleeding, often leading to shock and death Highest mortality rate (25 – 90%) of all viral hemorrhagic fevers Natural reservoirs of Marburg and Ebola viruses are still unknown No specific antiviral therapies available for these viruses 53 RNA Viruses: Retroviridae (Retroviruses) Spherical, enveloped viruses Genome: two copies of linear, positive-sense single-stranded RNA; each RNA 7 – 11 kbp in size Unique replication via reverse transcriptase that produces a DNA copy of the RNA genome → DNA circularizes and integrate into host chromosome Virus replicate from integrated “provirus” DNA copy Assembly of virion occurs by budding through plasma membrane Hosts remain chronically infected Human and other animal genomes contains endogenous proviruses resulting from ancient infections of germ cells → transmitted as inherited genes in most species Includes: leukemia and sarcoma viruses of animals and humans, also lentiviruses (human immunodeficiency virus/HIV) 54 RNA Viruses: Retroviridae (Retroviruses) HIV is a member of the Lentivirus genus of retroviruses HIV, the etiologic agent for AIDS, is derived from primate lentiviruses Acquired Immunodeficiency Syndrome (AIDS) was first described in 1981 and HIV-1 was isolated end of 1983 Since then, AIDS has become a worldwide epidemic, infecting millions Once infected, individuals remain infected for life 55 RNA Viruses: Retroviridae (Retroviruses) Two distinct types of AIDS virus: HIV-1 and HIV-2 Distinguished on the basis of genome organization and evolutionary relationship with primate lentiviruses All primate lentiviruses use the CD4 molecule expressed on macrophages and T lymphocytes as receptor Main feature of HIV infection is depletion of T helper-induced lymphocytes – resulting from HIV replication in this population of lymphocytes Leads to pronounced suppression of the immune system 56