Microbiology - Virology

• Obligate intracellular parasite
• Not free living (living?)
• Transferred in the environment from one host to another as an infectious particle
• Nearly completely depend on the host cell

• Depends on host's machinery for replication and energy or proteins
• must use host cell processes to produce their components - viral mRNA, protein, identical copies of the genome
• If the above conditions are not met, viruses must encode any required processes not provided by the cell
• Viral components must self-assemble

• E. coli O157:H7 16
• Vertebrates 1-10
• Human 8
• Corn 60
• Pine tree 90

• Streptococcus pyogenes - hyaluronidase
• Staphylococcus aureus - staphylokinase
• Staphylococcus aureus - TSST
• Corynebacterium diphtheriae - diphtheria toxin
• Shigella dysenteriae - shiga toxin
• Vibrio chloerae - cholera toxin
• Phages facilitate in gene transfer, Hypothesized to be the most significant driver of bacterial evolution

• Nucleic acid
• Capsid
• Envelope
• Viruses can be classified by these characteristics
• Also classified by size, morphology, biochemical characteristics, disease cause, transmission, host range, tissue tropism…

• core: SS/DS linear/circular (+/-/ambisense) DNA/RNA
• proteins
• nucleocapsid/naked capsid virus
• + envelope (glycoprotein & membrane) = enveloped virus

• Rigid in structure - resistance to drying, acid, and detergents, including the acid and bile of the enteric tract
• Assembled from individual proteins that associate in to progressively larger units - Individual structural proteins -> Subunits -> Protomers and capsomeres -> Procapsid or capsid
• Contains viral attachment proteins (VAPs) on the surface allowing interaction with the target cell

• Only maintained in aqueous environments
• Not resistant to drying, acidic conditions, detergents, and solvents
• Must remain wet and transmitted in fluids, respiratory droplets, blood, and tissue
• Components (VAPs) may facilitate binding to permissive host cells

• Nonenveloped: ss or ds
• Enveloped: ALL ss

• Nonenveloped: ss or ds
• Enveloped: ds or partially ds

• 1. Recognition of the target cell
• 2. Attachment
• 3. Penetration
• 4. Uncoating
• 5. Macromolecular synthesis
• a. Early messenger RNA (mRNA) and nonstructural protein synthesis: genes for enzymes and nucleic acid-binding proteins
• b. Replication of genome
• c. Late mRNA and structural protein synthesis
• d. Posttranslational modification of protein
• 6. Assembly of virus
• 7. Budding of enveloped viruses
• 8. Release of virus

• Target tissue
• Portal of entry of virus
• Access to target tissue
• Tissue tropism of virus
• Permissiveness of cells for viral replication
• Pathogenic activity (strain)

• Death; release of virus
• Multiplication and slow release of virus without cell death
• Transformation into tumor cell
• Persistent/Latent infection
• Some viruses can have more than one outcome

• • Lytic infections
• • Lysis -> more viral particles release

• Non-lytic infections
• Virus grows/lives in cell w/o causing damage to cell
• Can emerge later on from latent -> lytic infection when there is a reactivation signal
• Way for virus to hide from immune system - integrate into host genome; hard to target/find infected cells

• Oncogenic viruses
• Tumor cell division
• • Uninhibited cell growth
• • Way to make cell type in lab live for longer than 1-2
• generations

Takes part of host cell membrane with it (i.e. HIV)

• Cytology - microscopy observe changes in cell morphology, cell lysis, vacuolation, syncytia, and inclusion bodies
• Virus isolation and growth - Growth tissue/cell culture; Counting of infectious particles by plaque assay
• Detection of viral proteins (antigens and enzymes) - specific antibodies against proteins; Immunofluorescence, western blotting, and ELISA techniques
• Detection of viral genomes - PCR, RT-PCR, FISH, Southern or Northern blot
• Serology - evaluate the patients immune response

• Pour mixture of molten top agar, bacterial cells, and phage suspension onto nutrient agar plate
• Inspect the phage plaques among the host cell lawn

• Barrier effect of the epithelium
• Openings (orifices) protected by:
• • Ciliated epithelium
• • Mucous
• • Tears
• • Gastric acid and bile
• Antigen-nonspecific antiviral responses
• • Interferon - flu-like systemic symptoms
• • Natural killer cells and macrophages
• Antigen-specific immune responses
• • T-cell responses - cell killing, inflammation
• • Antibody responses - complement, antibody-dependent cellular cytotoxicity, immune complexes
• Other inflammatory responses

• target viral-encoded enzymes or viral structures that are important for replication
• Classic biochemical inhibitors of viral-encoded enzymes
• stimulators of host innate immune protective responses

• Enveloped viruses are susceptible to lipid and detergent-like agents; Disperse or disrupt the envelope membrane prevent acquisition of the virus
• Nonoxynol-9 -> inactivate herpes simplex virus (HSV) and HIV and prevent sexual acquisition of the viruses
• Rhinoviruses (naked) are susceptible to acid, and citric acid can be incorporated into facial tissues to block transmission

• Receptor agonists
• Block cell surface receptor of VAP with neutralizing Ab
• Administration of specific Ab (passive immunization) is the oldest form of antiviral therapy
• Peptide or sugar analogues of the cell receptor or the VAP, eg. HIV treatment
• Acidic polysaccharides (heparan and dextran sulfate) interfere with viral binding for HIV, HSV, and others

• necessary steps to deliver the viral genome
• Uncoating of small RNA viruses (picornaviruses) is blocked when the drugs sits in capsid receptor binding area and prevents disassembly - Arildone, disoxaril, pleconaril, and other methylisoxazole
• Viruses that enter through endocytic vesicles, uncoating may be triggered by conformational changes in the pH of the environment
• - Amantadine, rimantadine -> influenza A
• - Tromantadine -> HSV

• Hydrophobic amine (weak organic bases) that neutralizes the pH of the endocytic vesicle
• Prevents hydrogen ion (H+) influx by binding and blocking the viral H+ channel
• No uncoating so no movement of the nucleocapsid to the nucleus, transcription, and replication are prevented
• Blocking the pore also disrupts the processing of the hemagglutinin

• • Most antiviral drugs are nucleoside analogues
• (modifications of the base, sugar, or both)
• • Selectively inhibit viral polymerases (less accurate
• than host cell enzymes)
• • Prevent chain elongation
• • Alter recognition and base pairing inducing inactivating mutations

• Inhibits herpes DNA polymerase
• Viral thymidine kinase activates ACV by phosphorylation, and host completes to triphosphate form
• The triphosphate causes termination of the growing viral DNA chain
• No initial phosphorylation in uninfected cells, there is no active drug to inhibit cellular DNA synthesis or to cause toxicity.

• Inhibits reverse transcriptase
• Effective against HIV
• AZT must be phosphorylated by host cell enzymes
• It lacks the 3′-hydroxyl necessary for DNA chain elongation and prevents complementary DNA synthesis
• Problems with resistance through mutations from the HIV polymerase
• Need to use in combination with other therapies

• Pyrophosphate-like compounds inhibit replication by preventing nucleotide binding by binding to the pyrophosphate-binding site of the DNA polymerase
• - Foscarnet (PFA) and phosphonoacetic acid (PAA) useful against herpes viruses and the HIV
• Reverse transcriptase noncompetitive inhibitor, Mechanisms differ from nucleoside analogues, good for combination therapy
• - Nevirapine, delavirdine, efavirenz, and other no nucleoside for HIV infection

• Protease inhibitors
• • Saquinavir, ritonavir, and indinavir - HIV therapy; Computer-assisted modeling
• • Bocepravir and telaprevir - hepatitis C virus
• Enzyme inhibitors
• • Zanamivir (Relenza) and oseltamivir (Tamiflu) - inhibit neuraminidase of influenza A and B.

• Small
• Naked
• circular dsDNA
• Encodes proteins that cause cell growth
• • Facilitates lytic viral replication in permissive cell
• • In non-permissive cells can be oncogenic
• Acquired by close contact or the mixing and matching of mucous membranes
• • Skin to skin contact
• • Considered an STD
• Tissue tropism depends on virus type - > 100 types
• Induces epithelial proliferation

• Innate and cell-mediated immunity are important
• HPV can suppress or hide from protective immune responses
• In addition to very low levels of antigen expression, the keratinocyte is immunologically privileged for replication.
• Inflammatory responses are required to activate protective cytolytic responses and promote resolution of warts.
• Immunosuppressed persons have recurrences and more severe infections.

• Infects and replicates in squamous epithelium of skin - warts
• Self limiting
• Incubation period of 3-4 months

• The virus promotes outgrowth of the basal cell layer increasing the number of prickle cells
• Cause the skin to thicken and produce keratin -> epithelial spikes
• Virus is produced in the granulosum layer

• Infects and replicates in mucous membranes - genital, oral, conjunctival papillomas
• Benign head and neck tumors
• Oral papillomas - the most prevalent benign epithelial tumors that can be removed surgically and rarely recur
• Cervical dysplasia and neoplasia

• Types 16/18 cause cervical papillomas and dysplasias
• Virus integrates in human genome, encoding two oncogenic proteins E6 and E7 which bind and inactivate cell growth suppressors - p53 and p105 (Retinobastoma gene protein (RB)), respectively
• > 85% of cervical carcinomas have integrated HPV DNA
• HPV infects/replicates in cervical epithelial cells, maturing and releasing virus as cells progress through terminal differentiation
• Growth stimulation of the basal cells produces a wart
• In some cells, viral genome integrates into host chromosomes with silencing of viral genes necessary for replication, expression of the other genes stimulates growth of the cells and possible progression to neoplasia
• Cervical cancer Can be detected in pap smear
• Can be transmitted via direct contact through small
• breaks in the skin During sexual contact or to a newborn in the birth canal
• Cervical cancer vaccine for girls starting at age 11
• • Gardasil against HPV 6/11/16/18
• • Cervarix against HPV 16/18

• Warts usually regress but can be removed by cryotherapy, chemically or surgically - stripping off duct tape
• Stimulation of innate and inflammatory responses
• • imiquimod (Aldara), interferon
• Topical or intralesional delivery of cidofovir
• • Cidofovir induces apoptosis by inhibiting the host cell DNA polymerase - selectively killing infected cells
• HPV vaccine

• • Herpes simplex viruses (HSV) 1 and 2
• • Varicella Zoster virus (VZV)
• • Epstein Barr Virus (EBV)
• • Cytomegalovirus (CMV)
• • HHV 6, 7, 8
• ds linear DNA
• enveloped - glycoprotein
• Ubiquitous (except for HHV 8) and common
• encode many proteins that manipulate the host cell and immune response
• Cell-mediated immunity is required for control

• Very common
• Transmission via vesicle fluid, saliva, vaginal secretions
• Causes oral and genital lesions
• HSV-1 common oral contact
• HSV-2 sexual contact or mother to infant at birth
• • Can cause severe brain infection in the baby
• Lytic infection of fibroblasts and epithelial cells
• Latent infection in neurons
• • no detectable damage
• • Recurrence activated by stress, trauma, UV (UVB) light
• • Virus travels down nerve to initial site of infection -> blisters/sores
• • Happens in same place - initial site of infection
• Persistent infection in lymphocytes and macrophages

• Oral Herpes - Primary herpetic gingivostomatitis
• Children HSV-1
• Adults HSV-1 and 2
• Start as clear vesicles, proceed to rapid ulceration (cold sores/fever blisters)
• Primary infection worse, recurrent less severe

• Transport along periphery sensory nerves
• Site of latency - trigeminal ganglia
• Site of lesion - replicate in epithelium

• Herpetic keratitis
• • Infection of eye
• • Can cause blindness
• Herpes gladitorium
• • Infection of the body
• • Seen in rugby players or wrestlers
• Genital herpes
• • HSV-2
• • Most primary infections asymptomatic
• • Can transmit without knowing
• Herpes Whitlow
• • Infection of finger
• • Can occur in dentists

• 1. suppress amount of virus made in active infection or virus in blood
• 2. prevents or shortens the course of primary or recurrent disease
• Cannot eliminate latent infection

• • Acyclovir and Pencyclovir
• • Nucleoside analogs that inhibit viral polymerase (competes with GTP)

• Chicken pox or varicella
• Upon reactivation can cause herpes zoster or shingles
• • Older patients (60+)
• Transmitted through droplets infects respiratory tract, viremia, then lesions on skin
• Becomes latent in dorsal root ganglion or cranial nerve ganglion

• Vaccine available
• • Live attenuated - children after 2 years old
• • Shingles vaccine - after age 60
• Drugs to target viral DNA polymerase with nucleoside analogs - Acyclovir and Famciclovir
• Varicella-zoster immune globulin
• Zoster immune plasma - Generally for immunocompromised

• Ultimate B cell parasite
• Very limited host range
• Tissue tropism - cells w/ recognized receptor; B cells and some epithelial cells of the oropharynx and nasopharynx
• Potential outcomes:
• 1. replicate in permissive B cells or epithelial cells
• 2. cause latent infection of memory B cells in the presence of competent T cells
• 3. stimulate and immortalize B cells

• replicate in permissive oral epithelial cells
• Transmission through the virus shed in saliva
• • “kissing disease”
• • general malaise not fatal
• • Virus spread to B cells in lymphatics
• • See increase in mononuclear cells (lymphocytosis)
• • Activation of T cells
• • Persists in B cells then shed in saliva when activated
• • 70% of population infected by age 30

• • Infection of epithelial cells characterized by lesions in the mouth
• • Virus infects cell and turns off anti-tumor gene can lead to uncontrollable replication and malignancy

• Such as Non-Hodgkin B cell lymphoma
• • infects cell -> turns off anti tumor factors or tumor suppressor genes -> cells become immortalized
• • up regulate tumor regulation genes in host cell -> uncontrolled replication

• No effective treatment or vaccine
• Infection leads to immunity
• • Best means of preventing infectious mononucleosis is exposure to the virus early in life because the disease is more benign in children

• Most prevalent viral cause of congenital disease - 0.5-2.5% of newborns in US infected with CMV
• 50% of adult population infected
• Asymptomatic in immunocompetent
• Serious disease in neonates and HIV patients
• Treatment is the nucleoside analog, Ganciclovir

• Lymphotropic and ubiquitous
• 45% seropositive by 2 years, nearly 100% by adult (HHV6)
• Causes roseola - high fever followed by rash
• Latent infection in T cells controlled by cell mediated immunity
• Reactivated in immunosuppressed - AIDS

• DNA isolated from Karposi sarcoma specimens
• (Karposi sarcoma associated with AIDS)
• Targets B cells
• Geographically limited - Italy, Greece and Africa

• Largest family of viruses
• ss +RNA, similar to an mRNA molecule - The genome is sufficient to cause infection if microinjected into the cell
• Non-enveloped icosahedron
• Capsids very resistant to harsh environmental conditions, chemicals and drying
• Most are cytolytic

• Enterovirus
• • Polio virus
• • Coxsackie virus A (hand-foot-and-mouth disease)
• • Coxsackie virus B
• • Echovirus
• Hepatitis A virus
• Rhinovirus

• Transmitted by fecal-oral route - impervious to stomach acid, proteases, and bile
• Diseases determined by specific tissue tropisms and infected person’s age
• Infection often asymptomatic with viral shedding

• Three types of polio virus
• 4 outcomes when infected:
• 1. Asymptomatic illness
• 2. Abortive poliomyelitis
• 3. Nonparalytic poliomyelitis or aseptic meningitis
• 4. Paralytic polio

Infection limited to the oropharynx and the gut; 90% of poliovirus infections are asymptomatic

• Minor, nonspecific febrile illness - Fever, headache, malaise, sore throat, vomiting
• 5% of infected people

• 1% to 2% of patients with infections
• Virus progresses into the CNS and the meninges
• Back pain and muscle spasms plus symptoms of the minor illness

• The major illness
• Occurs in 0.1% to 2.0% of infected persons and is the most severe outcome
• 3-4 d after the minor illness - biphasic illness
• Viral spread -> blood to the anterior horn cells of the spinal cord and motor cortex of the brain
• Severity depends on number and which neurons affected
• 1. Spinal paralysis of one or more limbs
• 2. Bulbar (cranial) paralysis may involve a combination of cranial nerves and even the medullary respiratory center - 75% fatal

• Poliomyelitis in 20% to 80% of the original victims 30 to 40 years later
• Deterioration of the originally affected muscles
• Poliovirus is not present
• • from the loss of neurons in the initially affected nerves

• The antiviral drug, Pleconaril, inhibits picornaviruses from entering cell
• Trivalent Vaccines:
• - Inactivated (IPV)
• • Salk
• • Good for immunocompromised and older patients
• - Live attenuated oral vaccine (OPV)
• • Cheaper
• • Easier to give
• • Lifelong mucosal immunity

• Hand-foot-mouth disease
• Vesicles on hands, feet, mouth and tongue
• Herpangina
• • fever, sore throat, vesicles on soft palate and uvula

• Can cause pericarditis, myocarditis, encephalitis and meningitis
• Most serious in neonate--high mortality
• Can cause rash and cold-like symptoms
• Virus infection of pancreas suspected of causing insulin dependent diabetes

• Enteric cytopathic human orphan virus
• Can cause rash and cold-like symptoms
• Can cause meningitis, encephalitis, paralysis and carditis
• Most serious disease with neonates

• Target organ is the liver
• Types A, B, C, D, E and G
• Different virus families but all are infections of the liver

• Picornavirus
• RNA virus (+ssRNA)
• Naked icosahedral capsid
• Transmission: Fecal-oral route
• Consumption of contaminated water or shellfish
• Rarely fatal, food poison-like disease
• Not cytolytic
• • Does not kill the cell
• • Released by endocytosis
• spread in contaminated water, food, & by dirty hands
• resistant to detergents, acid (pH of 1), and temperatures as high as 60° C, can survive for many months in fresh water and salt water
• Chlorine can be used to treat contaminated water
• Prevention through good hygiene
• Liver pathology caused by immune system not virus
• Does not cause chronic infection
• Not associated with hepatic cancer
• Vaccine available for high risk population
• Natural infection provides lifelong immunity

• Hepadnavirus
• strict tissue tropism to the liver
• Circular DNA, partly DS, partly SS
• - Encodes a reverse transcriptase and has RNA intermediate for replication
• - genome can integrate into the host chromosome
• Enveloped
• • Dane particle
• • Stable, can resist ether, low pH, freezing, moderate heating, despite envelope!
• • produces HBsAg particles
•     • Glycoproteins that lack DNA
•     • overwhelm the immune system and viral particle can escape because decoys bind antibodies and titrate them out

• 1.Enter and uncoat nucleocapsid into the hepatocyte
• 2.The partially ds DNA genome is completed by enzymes in the core and delivered to the nucleus
• 3.Transcription of the genome produces mRNAs
• 4.mRNA then moves to the cytoplasm and is translated into protein
• 5.Core proteins assemble around the mRNA, and (-) DNA is synthesized by a RT activity in the core
• 6.RNA is degraded, (+) DNA is made
• 7.The core is enveloped and released by exocytosis

• Major source is blood
• Spreads by needle sticks with healthcare workers
• Transmitted to babies through blood at childbirth and through milk

• Dependent on the immune system
• CMI and inflammation are responsible for causing the symptoms and resolution

• Integrates in genome--latent infection--can reactivate. Chronic infections in 5-10% of patients. Cause of cirrhosis or liver cancer. 80% of Primary Hepatic carcinoma is result of chronic HBV infections
• • Cancer is usually fatal

• Cancer promoted by the liver’s attempt to repair tissue
• • repair and cell growth (mutation occurs -> uncontrolled growth)
• Virus may integrate in region of DNA that turns on growth factors
• • GF up regulated by strong viral promoters -> lots of
• transcription

• Hepatitis B immune globulin
• • Infants of HBsAg+ mothers
• Chronic HBV
• • Drugs that target the polymerase - Lamivudine
• • Nucleoside analogs - Adefovir, dipivoxil, and famciclovir
• • Interferon
• Vaccine
• • Derived from the HBsAg
• • Recommended at birth or those at risk

• Delta agent, circular ssRNA, enveloped
• Genome surrounded by the delta antigen core, which is surrounded by an HBsAg-containing envelope
• The delta agent increases the severity of HBV infections
• • only in people with active HBV infections
• • co-infection with HBV
• • Super-infection of chronic HBV

• non-A, non-B hepatitis virus
• Flaviviridae
• +RNA virus, enveloped
• Multiple genotypes that vary by geography-complicates universal vaccine development and drug treatments
• Cannot be grown in tissue culture and few animal models exist
• • Hard to identify/study
• • Can see effects of virus and can see in sections from
• patients
• Transmitted primarily in infected blood and sexually
• The high incidence of chronic asymptomatic infections promotes the spread of the virus in the population

• Acute infection
• • 15% recovery and clearance of virus
• • 85% persistent infection
• • Leads to chronic infection
• Chronic infection
• • liver failure, or cirrhosis or hepatic carcinoma
• Treatment
• • Interferon alpha and Ribavirin (nucleoside analog)
• - • 50% recovery with the two
• • Protease inhibitors - Boceprevir, telaprevir, sofosbuvir

• HGV also known as GB virus-C [GBV-C]
• Similar to HCV in many ways
• • flavivirus
• • transmitted in blood
• • Tends to cause chronic hepatitis infection

• +ssRNA, non-enveloped, Hepeviridae
• Usually self-limiting but may develop into fulminant hepatitis (acute liver failure)
• Fecal-oral route:
• • Via contaminated water
• • foodborne transmission from ingestion of products derived from infected animals
• • transfusion of infected blood products
• • vertical transmission from pregnant woman to fetus
• Found worldwide, but the prevalence is highest in East and South Asia
• China has vaccine