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Describe the biological properties of fungi important for growth in humans and that act as barriers to treatment

1) Eukaryotic - cellular machinery is functionally interchangeable with human cells

2) Thick rigid cell walls - inhibits phagocytosis, drugs from reaching cytoplasm --> human immune defense is via phagocytes i.e. neutrophils --> neutropenic patients susceptible to fungal infections; cell wall contains mannan (human mannose-binding protein sets off complement)

3) Saprophytes - secrete enzymes that break down organic matter and transport back into cell

4) Immunogens - source of allergies

Fungi are not part of normal flora, but infections are not contagious


Describe the fungal life cycles in terms of perfect and imperfect states

1. Imperfect state
Vegetative haploid cells divide via mitosis and produce conidia (asexual spores) --> germinate to produce more haploid vegetative cells

2. Perfect state
Two haploid cells (of different mating types) fuse to form diploid cell --> undergoes meiosis and produces haploid sexual spores --> germinate to form vegetative haploid cells *rarely takes place in mammalian cells/clinical samples*

Sexual structures important for classification but not identification of pathogens


Describe the classification of fungi and the four major groups:
1) Zygomycetes
2) Ascomycetes
3) Basidiomycetes
4) Fungi imperfecti

Classification based on structures in which meiosis occurs - requires starvation in order for meiosis to happen; mycoses = fungi that cause diseases in humans

1) Zygomycetes: sporangium contains many haploid spores formed by meiosis; pathogenic strains include Rhizopus and mucor

2) Ascomycetes: single cells undergo meiosis -- 4 meiotic spores in ascus sac; strains include bread, brewing yeast

3) Basidiomycetes: diploid nuclei in basidium (club-shaped structure) undergo meiosis, haploid spores bud in chains from the top of the; pathogenic strains include Cryptococcus neoformans (heavily encapsulated - causes lung or brain opportunistic infections, diagnose via bronchopulmonary washings, latex agglutination, silver stain, or india ink test)

4) Fungi imperfecti: no meiotic stage known --> Asexual; can have imperfect form of a fungus


How do you ID fungi via culture, colony color, and staining?

1) Culture: non-fastidious Saboraud agar, incubate at 30C (below body temp) and for 30 days since they grow slowly

2) Colony color: pigmented = dematiciaceous vs colorless = hyaline; dark pigment aids virulence

3) Staining: drop of KOH, calcoflour white staining, and silver staining

Serological tests available, but ID depends heavily on morphology


Describe the following fungi growth forms:
1) Yeast
2) Mold
3) Pseudohyphae
4) Chlamydospores
5) Conidia - micro and macro
6) Arthroconidia
7) Phialoconidia

1) Yeast: unicellular, reproduce by budding; colonies are moist or creamy

2) Mold: form elongated filaments called hyphae --> multiple hyphae = mycelium; colonies are fuzzy or powdery; dimorphic forms grow as yeast in rich medium at 37C but as hyphae in poor medium at 30C

3) Pseudohyphae: yeast buds that elongate but do not fully separate

4) Chlamydospores: terminal cell of a hypha differentiates into large, round, thick-walled cell

5) Conidia: asexual spores that bud off hypha, which have septa (cross-walls); micro contain only single cell, macro contain multiple cells

6) Arthroconidia: hyphae break apart at septa so there are only alternate cells

7) Phialoconidia: chains of conidia bud from the tip of a specialized terminal cell of hyphae e.g. penicillium


Describe the type of fungal infections including types of pathogens involved:
1) Superficial
2) Cutaneous
3) Subcutaneous

1) Superficial: outermost layer of skin, nails, and hair without invasion of deeper tissue; produced by fungi of low virulence; ID via hair samples under Wood's IV lamp
Example: piedra - hyphae grow in hair shaft

2) Cutaneous: involve only skin --> lesion with central healing and inflamed rim of active infection, caused by dermatophytes from soil, animals, or humans; infections are called tinea e.g. tinea corporis (ringworm), tinea pedis (athlete's foot)

3) Subcutaneous: fungi introduced by local trauma (thorns, splinters, falls); form localized lesions or mycetoma/"fungus tumor" (mass of fungi surrounded by granulomatous inflammation); can look similar to Gram + actinomyces infection
Example: Sporothrix schenckii (dimorphic fungus found on plants)--> causes sporotrichosis with subcutaneous lesions along lymphatics from initial trauma site


For the 4th type of fungal infection (Systemic) - describe common features, diagnosis, and treatment

Common features:
-endemic to specific areas
-can infect immunocompetents but associated with immunocompromised
-infection initially in lung
-occupational exposure
-little human transmission
-asymptomatic infections
-dimorphic - yeast at 37C in tissue, hyphae in culture at 30C "mold in cold, yeast in heat"

-microscopy to look at morphology
-skin testing
-exoantigen test - react soluble antigens from reference and patient isolates with specific antisera (either urine or serum rapid antigen tests)
-serologically via Ab titers (IgM for recent infection)

-treat local infection with -conazoles
-treat systemic/disseminated infection with amphotericin B


For the 4th type of fungal infection (Systemic) -describe details of the four types incl morphology, geographical distribution, and clinical symptoms:
1) Histoplasma capsulatum
2) Blastomyces dermatitidis
3) Coccidiodes immitis
4) Paracoccidiodes braziliensis

In order of increasing size

1) Histoplasma capsulatum - manifests as intracellular yeast in clinical material, tuberculate conidia (asexual spores) in culture; spread via bats, endemic in midwest and central US, can lead to hepatosplenomegaly

2) Blastomyces dermatitidis - large yeast with broad-based buds; emulsify tissue sample with KOH to destroy everything except fungal cell walls; endemic in wet places e.g. Great Lakes, can affect skin + bones

3) Coccidiodes immitis - manifests as large spherules in lung tissue, arthroconidia (long chain) morphology in culture; endemic in southwestern US, can cause acute pneumonia or disseminate to skin, lungs, meninges

4) Paracoccidiodes braziliensis - yeast with multiple buds radiating from central vacuole --> "ship's wheel"; endemic in South America, can cause mucocutaneous lesions


Describe Candida albicans in terms of morphology and infections caused

Candida albicans - causes majority of opportunistic fungal infections

1. Morphology
-dimorphic but not typical "mold in cold" --> forms pseudohypha/budding yeast at 20C, germ tubes/hyphae mold at 37C or when placed in serum

2. Part of normal flora but can cause:
- vaginal infections with changes in flora (pregnancy, diabetes, antibiotics or birth control use) --> but does not change vaginal pH from ~4
- thrush (oral candidiasis - white fungal patches that can be scraped off) in immunosuppressed or oral steroid users
-candidal esophagitis in AIDS patients (CD4 ~ 100)
- diaper rash in infants

-local infections with -zoles
-nystatin for oral/esophageal candidiasis
-amphotericin B for systemic infections; capsofungin if amphotericin-resistant


Describe the following types of opportunistic fungal pathogens:
1) Aspergillus
2) Zygomyces/mucormycosis
3) Pneumocystis jiroveci
4) Microsporidia

1) Aspergillus: ubiquitous in soil/plants, esp affects neutropenic patients; Clinical: ABPA (type I hypersensitivity), aspergillomas in lung, angioinvasive aspergillosis (systemic w ring enhancing brain lesions, renal failure, endocarditis --> can be fatal); hyphae septated and branch at acute angles; transmitted via inhaled conidiophores

2) Zygomyces e.g. mucor, rhizopus classes --> cause mucormycosis: nasopharyngeal but can be fatal if it penetrates cribriform plate and spreads to the brain; hyphae branch at right angles; transmitted via inhalation of spores; increased susceptibility in diabetics esp DKA

3) Pneumocystis jirovecii: ubiquitous yeast, we all develop Ab in childhood but are asymptomatic in healthy people; common coinfection of AIDS when CD4 less than 200 --> causes PCP (pneumocystic pneumonia) and ground-glass lung appearance but mortality lowered due to AIDS prophylaxis with Bactrim (TMP-SMX); cannot be cultured in lab

4) Microsporidia: transmission via contaminated food/water; spore is infectious form --> eye, GI, systemic infections; AIDS coinfection


Amphotericin B [membrane disrupting antifungal]
1) Structure
2) MOA
3) Clinical uses
4) Resistance
5) Administration/PKA
6) Adverse effects

Amphotericin B [membrane disrupting antifungal]
`1) Structure - macrolide with amphipathic ring, similar to nystatin

2) MOA - nonpolar side binds ergosterol in fungal cell membrane by binding to mycosamine sugar unit, polar side forms pore for ions to leak out --> kills cells

3) Clinical uses - broad anti-fungal spectrum e.g. yeast (candida albicans, cryptococcans neoformans), pathogenic molds; used as initial treatment in critical cases e.g. systemic infections

4) Resistance - no significant problems clinically but include decreased/modified ergosterol (found only in fungi/protozoa)

5) Administration/PKA- insoluble in water, prepared with lipid; limited oral use bc poorly absorbed; widely distributed (except CSF) and excreted slowly

6) Adverse effects - infusion-related toxicity, renal damage; interacts with nephrotoxic drugs (cyclosporine, aminoglycosides)


Flucytosine [nucleic acid inhibitor anti-fungal]
1) Structure
2) MOA
3) Clinical uses
4) Resistance
5) Administration/PKA
6) Adverse effects

Flucytosine [nucleic acid inhibitor]
1) Structure - prodrug 5-FC, taken up fungal cytosine permease

2) MOA - cytosine deaminase (found only in fungal cells) converts to 5-FU --> 5-FUTP (inhibits RNA synthesis) or 5-FdUMP (inhibits DNA synthesis)

3) Clinical uses- limited spectrum - Candida and cryptococcus, given in combo therapy with amphotericin B or itraconazole

4) Resistance - loss of conversion from prodrug 5-FC to active form

5) Administration/PKA - rapidly absorbed from GI and cleared by kidney, well distributed (incl CSF)

6) Adverse effects - leukopenia/thrombocytopenia, rash/GI effects due to conversion to toxic materials by intestinal bacteria


Azoles [membrane disrupting antifungal]
1) Classification - imidazole vs triazole + examples
2) MOA
3) Selectivity
4) Resistance

1) Imidazoles contain 2 Nitrogens in 5 membered rings e.g. ketoconazole, clotrimazole, miconazole; older, have been replaced by triazoles
Triazoles contain 3 Ns in 4 membered rings e.g. itraconazole, fluconazole, voriconazole

2) MOA - inhibit p450 enzyme ERG11 by binding to active site--> block ergosterol biosynthesis + accumulation of toxic methylsterol byproduct that inhibits membrane enzymes

3) Selectivity - binds less effectively to mammalian p450 enzymes

4) Resistance - ERG11 mutation or increased ERG11


For Itraconazole
1) Clinical use
2) Administration
3) Metabolism
4) Toxicity
5) Drug interactions

Itraconazole - most potent azole
1) Clinical use - favored over ketoconazole (imidazole) bc wide spectrum of action and fewer side effects

2) Administration - oral bc well absorbed, widely distributed (except CSF)

3) Metabolism - lipid soluble, metabolized via CYP3A4, long half life

4) Toxicity - minor toxicity incl GI distress, teratogenic

5) Drug interactions - drugs that decrease gastric activity (H2 blockers, PPIs) and drugs metabolized by p450 enzymes (cyclosporine, warfarin)

*Fluconazole is good alternative to intraconazole, no problem with gastric acidity


Echinocandins [Cell wall inhibitor anti-fungal]
1) Structure
2) MOA
3) Clinical uses
4) Resistance
5) Administration/PKA
6) Adverse effects

Echinocandins [Cell wall inhibitor anti-fungal] - newest anti-fungal agents

1) Structure - semi-synthetic lipopeptide derivative; cyclic peptide attached to long FA chain

2) MOA - inhibits FKS1 enzyme responsible for synthesizing key component of cell wall - beta 1,3 glucan

3) Clinical uses - candida, invasive aspergillosis that fails amphotericin B

4) Resistance - mutation in FKS1

5) Administration/PKA - administered parenterally

6) Adverse effects - minor including fever, nausea, vomiting


Terbinafine [systemic drug]
1) Structure
2) MOA
3) Clinical uses
4) Resistance
5) Administration/PKA
6) Adverse effects

Terbinafine [systemic drug]
1) Structure - synthetic allylamine

2) MOA - inhibits squalene epoxidase ERG1 enzyme --> blocks ergosterol biosynthesis + toxic accumulation of sterol squalene

3) Clinical uses - mucocutaneous infections e.g. dermatophyte-caused tinea; accumulates in skin, nails, fat to prevent infections

4) Resistance - N/A

5) Administration/PKA - topical, use continuously until infection cleared; synergistic with triazoles

6) Adverse effects - GI distress and headache, no drug interactions


Nystatin [topical]
1) Structure
2) MOA
3) Clinical uses
4) Administration/PKA

Nystatin [topical]
1) Structure - derivative of amphotericin - macrolide with amphipathic ring

2) MOA - binds selectively to ergosterol in fungal membrane --> forms pores to cause leakage of ions --> cell death

3) Clinical uses - local suppression of candida infections --> oral/esophageal candidiasis

4) Administration/PKA - creams and ointments


What are protozoa?
1. Trophozoite
2. Cyst
3. Definitive vs intermediate host

Protozoa = unicellular eukaryotic organisms; parasitic species found in intestines, blood, tissues

1. Trophozoite: A growing/multiplying form of a parasitic protozoan.
2. Cyst: A non-growing form, specialized for resistance to unfavorable environments and/or for dispersal
3. Definite host - parasite undergoes sexual cycle vs intermediate - parasite multiplies asexually


How are parasitic infections diagnosed?

Microscopic examination is key, culture not commonly used (expensive + laborious)

-direct smears of blood, stool, tissues
-tissue histology
-can also use serological tests or DNA tests (nucleic acid amplification)


Describe the MOA of common anti-protozoal drugs
1. Metronidazole (Flagyl)
2. Eflornithine (Ornidyl)
3. Hydroxychloroquine (Plaquenil)
4. Tinidazole

drugs are often toxic

1. Metronidazole: Inhibit DNA synthesis
2. Eflornithine: inhibit ornithine decarboxylase of
polyamine biosynthesis
3. Hydroxychloroquine: inhibit DNA synthesis
4. Tinidazole: contain nitro group which is reduced to free nitro radical


Giardia lamblia [Flagellate]
1. Disease
2. Life cycle
3. Epi
4. Morphology
5. Treatment/prevention

Giardia lamblia [Flagellate] - backpacker's diarrhea

1. Disease: organisms adhere to brush border (but do not invade) --> impaired absorptive capacity of intestine --> acute, foul-smelling steatorrhea and watery diarrhea (chronic in AIDS patient)

2. Life cycle: ingested as cyst, differentiates into trophozoite and multiplies in intestinal lumen and cells shed in feces; can grow in all mammals, life cycle alternates bw trophozoite and infectious cyst

3. Epi: fecal-oral spread through cysts in contaminated water; widespread in lakes/streams in wilderness US

4. Morphology: two nuclei and "sucker disc" on trophozoite form (which is how they adhere to intestinal mucosa)

5. Treatment/prevention: Treat with metronidazole orally; prevent by boiling, iodine, filtering water


Trichomonas vaginalis [Flagellate]
1. Disease
2. Life cycle
3. Epi
4. Morphology
5. Treatment/prevention

Trichomonas vaginalis [Flagellate] - STD

1. Disease: Trichomoniasis - (women) vaginitis with yellow-green watery discharge or cervicitis "strawberry cervix", (men) urethritis but can ascend to prostate/seminal vesicles

2. Life cycle: multiplies on GI mucosal membrane; diagnose via motile trophozoites on wet mounts

3. Epi: sexually transmitted, more common in women than men; vaginal infections cause pH greater than 4.5

4. Morphology: tufts of flagella at one end and undulating membrane; non-pathogenic version is part of normal flora

5. Treatment/prevention: metronidazole or tinidazole, also treat sexual partners


For hemoflagellates:
1. Transmission
2. Difference trypanosoma and leishmania species
3. Morphology

Hemoflagellates: parasitiz protozoa that lives in the blood
1. Transmission: insect vectors, multiple in vectors and host

2. Trypanosoma multiply outside cells --> blood infections; antigenic phase variation due to variable surface glycoprotein (VSG)
Leishmania multiple in cells --> tissue infections

3. Morphology: You don't want a hemoflagellate as A PET
A. Amastigote: central nucleus and kinetoplast (combo mt + basal body), no flagella; intracellular form
P. Promastigote: anterior kinetoplast, flagellum
E. Epimastigote: central kinetoplast, flagellum + undulating membrane
T. Trypomastigote: posterior kinetoplast, fully undulating membrane + flagellum


Trypanosoma brucei [hemoflagellate]
1. Disease
2. Life cycle
3. Epi
4. Treatment/prevention

Trypanosoma brucei
T. b. brucei - livestock disease; East Africa
T. b. rhodesiense - rapidly progressive in humans; East Africa
T. b. gambesiense - slowly progressive in humans; West Africa

1. Disease: African sleeping sickness w/ 3 stages:
A. Localized inflammatory lesion
B. Acute - disease in bloodstream, chronic inflammation (fever, headache, muscle pain), travels to lymph --> lymphadenopathy
C. Late stage - CNS invasion (stupor, coma, death)

2. Life cycle: epimastigotes multiple in guts and salivary glands of tsetse fly --> fly bite --> trypomastigotes multiply in bloodstream of mammals and are seen in blood smear

3. Epi: vector = tsetse fly; evade immune system through VSG antigenic phase variation --> increased IgM bc of repeated primary immune response

4. Treatment/Prevention: (Early) Treat with pentamidine (late) treat with eflornithine nifurtimox; prevent with control of tsetse flies


Trypanosoma cruzi [hemoflagellate]
1. Disease
2. Life cycle
3. Epi
4. Treatment/prevention

Trypanosoma cruzi [hemoflagellate]

1. Disease: Chagas disease
A. primary lesion at site of infection --> Romana's sign (unilateral eyelid swelling)
B. Acute - fever, lymphadenopathy bc of amastigotes in muscle
C. Late stage - invasion of heart, CNS, abdominal viscera via parasite burrowing--> megacolon, mega-esophagus, dilated cardiomyopathy --> can be fatal

2. Life cycle: promastigates in gut of triatoma bug --> bug bite and feces on skin, introduce via scratching --> amastigotes multiple in muscle --> migrate to other parts of body through bloodstream --> trypomastigote (can see on heart biopsy in cardiac myocytes)

3. Epi: vector is triatoma "kissing bug"; diagnose with seroconversion or muscle biopsy; in Central and South America

4. Treatment/prevention: Treat with Benznidazole, Nifurtimox; no treatment for chronic chagas


Leishmania [hemoflagellate]
1. Disease
2. Life cycle
3. Epi
4. Treatment/prevention

Leishmania [hemoflagellate] - 20/35 species infect humans

1. Disease: Leishmaniasis
A. Visceral - Kala-Aza aka black fever; amastigotes in tissue = LD bodies --> causes pancytopenia when infection spreads to bone marrow and hepatosplenomegaly
B. Cutaneous - ulcerative lesions at back of neck
C. Mucosal

2. Life cycle: promastigotes (infective form) multiply in gut of sandfly --> fly bite --> tranform into amastigotes in humans and multiple intracellularly in macrophages --> released by cell lysis

3. Epi: vector is sandfly, widespread (except Australia) esp in desert

4. Treatment/prevention: sodium stibogluconate for cutaneous, amphitocerin B for visceral


Entamoeba histolytica (amoeba)
1. Disease
2. Life cycle
3. Epi
4. Morphology
5. Treatment/prevention

Entamoeba histolytica (amoeba- protozoa)

1. Disease: infection = amebiasis;
A. Bowel lumen amebiasis - asymptomatic, infectious cysts and non-infectious trophozoites in feces; flask-shaped ulcers in intestinead
B. Tissue-invading invasive amebiasis - amoebic dysentery --> (mild) diarrhea, cramps, vomiting; (severe) bloody stools, dehydration

2. Life cycle: infectious cysts ingested in contaminated water/food --> develop into trophozoites in colon --> trophozoites produce more cysts + invade intestinal wall and liver --> liver abscesses (esp right lobe) + cysts excreted in feces

3. Epi: fecal-oral transmission, also anal-oral (in MSM)

4. Morphology: microscopic examination of stool (stool O&P)--> cysts are round with four nuclei; trophozoites distinguished from commensal amoebae bc larger, have ingested rbcs, and pseudopod

5. Treatment/prevention: (bowel lumen amoebiasis) paromycin or diloxanide furoate (tissue amoebiasis) dehydroemetine, metronidazole, tinidazole (liver abscess) chloroquine


Describe Amoebic Meningoencephalitis including transmission, symptoms, and treatment

Amoebic Meningoencephalitis

Transmission - amoebae in natural waters e.g. Naegleria, Hartmanella, Acanthamoeba --> Spread from sinuses to brain

Symptoms: keratitis, progressive infections, death within a week

Treatment: amphotericin + azoles


Balantidium coli [ciliate]
1. Disease
2. Life cycle
3. Epi
4. Morphology
5. Treatment/prevention

Balantidium coli [ciliate]

1. Disease: only ciliate that causes disease in humans --> blantidiasis (similar to disease of produced by E. histolytica) --> diarrhea, hemorrhage, ulceration

2. Life cycle: Ingestion of cysts, develop into trophozoites, excretion of cysts

3. Epi: diagnosis through organism in stool, fecal oral transmission

4. Morphology: largest parasitic protozoan (both trophozoite and cysts), contain micro and macronucleus

5. Treatment: Tetracyclines, Metronidazole or Iodoquinol


What are Apicomplexa and their life cycle

Apicomplexa = phylum of parasitic protists

Life cycle: Invade cells --> trophozoites grow without cytokinesis to form schizonts (large multinucleate forms)--> cleave into multiple infective progeny --> released when cell lysed


What genus of Aplicomplexa cause malaria? Which 4 species in particular?

How can malaria be transmitted?

1. Plasmodium
P. falciparum *most virulent*
P. malariae
P. ovale
P. vivax
*diagnosed by examining morphological characteristics on blood smears*

2. Transmission:
A. Bite of Anopheles mosquito.
B. Blood transfusion.
C. Mother to fetus


1. Describe the malaria life cycle in humans

2. How does the life cycle differ among different plasmodium species?

Mosquito = definitive host, humans = intermediate host

1. Exo-erythrocytic cycle: sporozoites from saliva of mosquito bite --> enter liver and release thousands of merozoites into the bloodstream

Erythrocytic cycle: merozoites infect RBCs --> forms vacuolated ring form --> enlarges into trophozoite --> nuclear division into immature schizont --> cytoplasmic cleavage of schizont --> RBC cell lysis releases many merozoites --> symptoms of disease
*can have multiple rounds of infection in RBCs --> gametocytes produced from merozoites so infected person can transmit plasmodia to mosquitos

2. falciparum and malariae have only one cycle of replication in the liver --> need only suppressive cure;

P. vivax and P. ovale remain in liver as dormant hypnozoites --> need radical cure to prevent relapse


Describe the malaria life cycle in anopheles mosquitos

Gametocytes are infectious for mosquitos

microgametocytes --> meosis to form motile gametes --> fertilize macrogametocytes --> motile zygotes = ookinetes --> invade gut wall and form oocysts --> divides and produces multiple sporozoites


1. Diagnosis
2. Disease process
3. Symptoms

1. Diagnosis: multiple blood smear samples and/or NAAT

2. Disease process: incubation period of 1-4 weeks during hepatic (exo-erythrocytic) cycle + first few erythrocytic cycles as parasite numbers increase

3. Synchronized waves of merozoite release upon maturation and rupture of erythroytic schizont --> periodic fevers, along with headache vomiting + malaise --> sweats as fever relapses
chronic: anemia, cachexia, blackwater fever


Describe the differences in the species that cause malaria
1. Histologically
2. Clinically

1. Histologically
P. vivax - (ring form) dot - nucleus (trophozoite) Shuffner's dots --> granules of malarial pigment since plasmodia ingest hemozoin (schizont) can form bradyzoites
P. ovale - (trophozoite) distorted fimbriated host cell
P. malariae - (trophozoite) classic band appearance
P. falciparum - (ring form) multiple rings per cell; (trophozoites and schizonts) not seen in peripheral blood; (gametocytes) characteristic banana shape

2. Clinically
P. vivax and P. ovale - least severe, benign tertian malaria --> fevers at 48 hr intervals (days 1 and 3), persistence in liver due to hypnozoites
P. malariae - quartan malaria --> fevers at 72 hr intervals (days 1 and 4), persistence in blood
P. falciparum - most severe, malign irregular fever patterns; rbc aggregate and adhere to capillary endothelium --> occlusion and tissue infarcts to brain, kidneys, lungs *sickle cell anemia is protective*


Describe the treatment options for malaria - Drugs:
1. Chloroquine phosphate
2. Quinine and quinidine
3. Mefloquine
4. Primaquine
5. Atovaquone
6. Pyrimethamine and Proguanil
7. Amodiaquine
8. Artemisine

1. Chloroquine - inhibits plasmodium heme polymerase --> prevents polymerization of Hb --> intracellular toxic accumulation of heme; effective in blood>>liver parasites, does not eliminate liver hypnozoites

2. Quinine and quinidine - inhibits heme polymerase --> detoxifies heme produced by plasmodia; effective for blood but not liver; can cause cinchonism (tinnitus + headache)

3. Mefloquine - MOA unknown; for chloroquine-resistant strains of P. falciparum, Strong blood schizonticide against P falciparum and P vivax; not effective for liver; good for prophylaxis in chloroquine resistant areas

4. Primaquine - forms metabolites that act as cellular oxidants; effective against liver stage of all four species of plasmodia, effective for hypnozoites of P vivax and P ovale, Gametocidal against all four species of plasmodia

5. Atovaquone - disrupts mt electron transport; malarone combo for P. falciparum; combo with proguanil for prophylaxis to travelers in chloroquine resistant areas

6. Pyrimethamine and Proguanil - inhibits folate synthesis, effective for blood for all 4 species

7. Amodiaquine - related to chloroquine

8. Artemisinin - converted into free radicals, for chloroquine resistant P. falciparum; IV artesunate for severe infections


Describe the treatment options for malaria - antibiotics

Active against RBC forms of all species, usually for chloroquine resistant strains

- Tetracycline.
- Doxycycline.
- Clindamycin.
- Azithromycin.
- Fluoroquinolones.


Describe immune response to malaria

-both cell mediated and humoral immune system responsible for ultimately clearing organism but takes years AND immunosuppressive (decreased response to antigen,
poor control of viruses --> can promote devlpt of Burkitt's lymphoma)

- premunition – immunity to bloodstream super-infection with same species

-malaria does NOT confer lifelong immunity

-immune response poor where malaria endemic and children have the lowest response and highest mortality rate


Describe the diseases caused by other pathogenic Apicomplexa:
1) Babesia
2) Cryptosporidium
3) Toxoplasma

Intermediate (asexual) and definitive (sexual) hosts

1) Babesia - intermediate host = mammal/bird; definitive host = arthropod (tick-borne); tick borne vector in NE USA, reservoir is dogs/livestock --> malaria-like illness (jaundice, fever)

2) Cryptosporidium Isospora, Cyclospora - humans are intermediate and definitive hosts --> diarrhea, chronic in HIV patients, fecal-oral spread and acid-fast; cyst = 4 motile trophozoites

3) Toxoplasma, Sarcocystis - intermediate host = rodent while humans are "accidental"; definitive host = carnivore --> transmitted cysts through undercooked meat and oocysts through cat feces, also maternal-fetal transmission --> non-specific febrile illness, can cause congenital problems e.g. encephalitis, deafness


1. Disease
2. Life cycle
3. Epi
4. Morphology
5. Treatment/prevention

Species: Encephalitozoon, Enterocytozoon, Nosemia

1. Disease: intestinal, eye, systemic infections

2. Life cycle: Cyst enters host cells through polar filament (hollow tube) --> grow without division in vacuole in host cell --> cleave to produce large numbers of infectious progeny spores

3. Epi: affect immunocompromised, also maternal fetal transmission; diagnosis via stained specimens

4. Morphology: v small, smallest genome

5. Treatment: Albendazole (microtubule inhibitor) and
Fumigillin (methionine aminopeptidase inhibitor)


Describe properties of viruses incl structure and how they differ from other biological entities

-Small, obligate intracellular parasites (smaller than bacteria)
-Structure: nucleic acid covered by protein capsid, can also have protein spikes OR host-derived lipid bilayer envelope + glycoprotein spikes
-all viruses have only one type of nucleic acid in genome
-rapid and unique replication process - virus uncoated/ disassembled, genome separated from nucleocapsid and transcribed/replicated


What are the steps of viral classification?
1. Nucleic acid
2. Nucleocapsid shape
3. Virion envelope

1. Nucleic acid: DNA or RNA?
A. ss or ds?
i. If ss RNA --> (+) or (-) strand? (+) ss RNA means ribosomes in cell recognize as message sense and start making proteins; (-) ss RNA viruses need to be changed to (+) first
B. Circular or linear

2. Shape of nucleocapsid: icosohedral, helical or complex
A. Icosohedral - capsomere (made up of protomer protein subunits), vertices are attachment points
B. Helical - spiral protein core, can be rigid or flexible
C. Complex - doesnt fit into either category e.g. HIV (cone shaped), pox virus (figure 8 shape)

3. Virion (complete viral particle): naked or enveloped?
A. Naked - nucleic acid + protein capsid + protein spikes for attachment to cell receptors
B. Enveloped - outer lipid envelope with glycoprotein spikes for attachment to cell receptors
*spikes are I) antigenic determinants --> neutralizing antibodies attach to spikes to virus cannot be internalized and 2) tissue tropism - tell us which tissues the virus can infect


What are the steps in viral replication?

1. Adsorption - attachment through spikes and receptors on cell surface

2. Entry
A. Receptor mediated endocytosis: invagination of cell wall/membrane --> vesicles with entire virus internalized --> virus breaks out of vesicle
B. Non-endocytic route: envelope viruses enter bc receptor attaches to cell membrane and membranes fuse --> capsid released into cytoplasm

3. Synthesis of non-structural proteins - proteins which make viral RNA or DNA so virus can begin replicating; beginning of eclipse period (infected cell contains no infectious virions)

4. Replication of genome

5. Synthesis of structural proteins - proteins of nucleocapsid and envelope aka "late" proteins, so virus can make new progeny

6. Packaging of genome - assembly of nucleocapsid so new virus particles are created inside the cell

7. Acquisition of envelope (if applicable)

8. Release of virus from cell -- via lysis or budding (take part of cell membrane and become enveloped viruses)


What are the effects of viruses on cells?

- no apparent effect

- kill host cell

- "cytopathic effect" -changes in cell shape e.g. infected cells fuse to form multinucleated giant cells, commonly RNA viruses e.g. paramyxoviruses

- transform cells - become infinitely dividing and long-lived e.g. HPV, tumor viruses


How are viruses detected?

1. Serology - most common approach; Ab against viruses, paired sera - taking samples 2 weeks apart (for epidemiological reasons to compare IgM and IgG) --> 4x increase in titer is diagnostic

2. Viral antigen - fluorescent ab against viruses in samples e.g. to differentiate Influenza A and B

3. PCR - e.g. NAAT, need high level of sample to do PCR

4. Plaque assay - tissue culture e.g. herpes, CMV
-plate dilutions of virus on monolayer of mammalian cells --> virus will kill the cells (clear circles) as a PFU (plaque forming unit) *detects only infectious virions*

5. Hemagglutination - viruses attach to RBCs and form lattice structure; add Ab to neutralize virus and inhibit hemagglutination


What are common features of positive strand RNA viruses?

1. replicate in cytoplasm
2. genomic RNA serves as message and is translated
3. genomic RNA is infectious -- > ribosomes can make viral proteins right away once virus enters cell
4. virions do not contain any enzymes (no need for them - uses host RNA polymerase)
5. viral proteins translated as long polyproteins --> then processed by proteases to give smaller active proteins

*some are enveloped, some are not
*retroviruses are positive strand but grouped separately


Poliovirus [Prototype Picornavirus]
1. Structure
2. Features of genome
3. Replication

1. Structure - small, naked icosahedral (+) strand RNA virus; contains 4 proteins - VP1-3 on outside, VP4 internal; 3 serological types (so could make vaccine)

2. Features of genome - (+) sense non-segmented RNA genome; encoded 3' polyA but not 5' cap (instead there is VPg peptide); 5' IRES --> captures ribosomes without the need of 5' cap

3. Replication: Entry via receptor-mediated endocytosis --> viral RNA in cytosol attaches to ribosomes at IRES --> makes long viral polyprotein via replication complex of (+) and (-) strand RNA--> cleaved by proteases into smaller viral proteins N-P1-P2-P3-C--> packaged into particles and released upon cell lysis
-P1 gives non-structural proteins (VP1-4) and P2 + P3 give structural proteins
-viral protein that inhibits host cell initiation complex by cleaving 5' cap--> poliovirus takes over all protein synthesis
-RNA dependent RNA polymerase --> makes anti-genome e.g. (-) strand to replicate the viral RNA


Poliovirus [Picornavirus]
1. Infection/symptoms
2. Transmission
3. Diagnosis
4. Prevention

1. Infection: Enters GI tract --> multiplies in epithelial cells --> goes to lymph nodes (e.g. Peyer's patches)--> blood stream --> anterior horn spinal cord neurons --> asymmetric flaccid paralysis
-Symptoms: mostly asymptomatic or restricted to GI tract --> minor illness (GI upset, flu-like symptoms)
-respiratory insufficiency -can be fatal
-1% --> goes to CNS (meningitis, flaccid paralysis)

2. Transmission: fecal-oral --> feces, fingers, flies, food, water; polio paradox --> increased polio cases with industrialization bc babies werent exposed young when they still had maternal Ab
*digestive or respiratory tract*

3. Diagnosis: virus isolation via throat swab, stool, CSF, Ab titer

4. Prevention: Salk vaccine (killed), Sabin vaccine (live attenuated), elPV (enhanced IPV)
-vaccines must immunize against all 3 serotypes
-Sabin is more dangerous (can revert to virus through mutation) but cheaper, more stable, and easier to administer
*no treatment available*


Describe symptoms/diseases caused by the following types of non-polio enteroviruses:
1. Coxsackievirus
2. Echovirus
3. Enterovirus

Describe symptoms/diseases caused by following type of (+) strand RNA virus:
4. Calicivirus

Enterovirus - type of Picornavirus (in addn to Hep A and h) - non-enveloped/naked icosahedral nucleocapsid (+) strand RNA
*Usually not fatal but immunosuppressed can get severe disease from these viruses e.g. most common cause of aseptic meningitis

1. Coxsackievirus - v common
Type A - causes hand foot mouth disease, red vesicular rash, conjunctivitis, and rarely meningitis
Type B- dilated cardiomyopathy, pleurodynia (sharp chest pain)
2. Echovirus - conjunctivitis, febrile rash, diarrhea, rarely meningitis
3. Enterovirus - just GI symptoms

4. Calicivirus - also naked (+) strand RNA virus
-most common is Norovirus/Norwalk virus
-responsible for illness in cruise ships, also daycares/schools
-associated with consumption of shellfish
-causes explosive watery diarrhea


What are common features between the enveloped icosahedral (+) strand RNA virus families: togaviridae and flaviviridae

What are the differences in replication between the two families?

1. Common features:
-non-segmented (+) strand RNA genome
-replicate in cytoplasm
-arthropod-borne (mosquitoes or ticks)
-enter cell via receptor mediated endocytosis

2. Differences in replication:
-Flavivirus: one reading frame --> one polyprotein; structural genes at 5' end
-Togavirus: two messages --> both polyproteins; structural genes at 3' end; (-) strand is template for 2 (+) strand RNAs --> control over relative amounts of structural vs non-structural proteins made


Describe the Alphavirus and Rubivirus genera of the Togaviridae family

Togavirus - enveloped icosahedral (+) strand non-segmented RNA viruses

Alphavirus genus aka Arbovirus (arthropod-borne virus) - 28 viruses with mosquito transmission
A. chikungunya virus - like arthritis, endemic in Africa
B. equine encephalitis (bc all cause this disease in horses)
i. Eastern (more severe, less common) + Western (less severe, more common) --> humans and horses are accidental, dead-end hosts bw mosquitoes and birds --> causes encephalitis in humans
ii. Venezuelan --> from rodents and mosquitoes, causes influenza-like disease in humans

Rubivirus genus - 1 virus
A. Rubella i.e. German measles (respiratory transmission)
i. Childhood rubella - lymphadenopathy, fever, maculopapular rash starts at head and moves fast downwards
ii. Congenital - malformations incl patent ductus arteriosus, deafness, cataracts, blueberry muffin rash, jaundice
iii. Adult - fever, arthritis, myalgia
- MMR vaccine - live attenuated (so do NOT give to pregnant women or immunocompromised)


Describe the diseases in the flavivirus genus of the Flaviviridae family:
1. West Nile
2. Dengue
3. Yellow fever
4. Zika

Flavirus genus - enveloped icosahedral (+) strand non-segmented RNA viruses
1. West Nile - birds are reservoirs, vector is mosquitos and humans are dead-end host; majority asymptomatic, symptoms include enchephalitis, fatigue, Guillan Barre/flaccid paralysis, seizures/coma

2. Dengue - humans are natural hosts, vector is aedes egyptei mosquito; self-limiting but debilitating, symptoms include severe chronic bone and joint pain --> "break bone fever", small % cases fatal due to shock/hemorrhagic fever bc of Ab to different serotypes

3. Yellow fever - closely related to dengue; vector = Aedes mosquitoes transmit to monkeys and humans; virus spreads to all organs --> jaundice, fever, shock, backache, bloody stools/GI bleeds --> high mortality rate
A. jungle yellow fevers - bw monkeys, humans accidental host
B. urban yellow fever - humans are reservoir

4. Zika - transmitted via Aedes mosquito; asymptomatic or mild symptoms but can cause microcephaly if pregnant woman is infected


Describe Coronavirus in the Coronaviridae family

Enveloped (+) strand ssRNA virus with helical nucleocapsid

-Structure: glycoprotein spikes that look like a crown
-majority of infections are asymptomatic --> cause of common cold
-SARS is a coronavirus --> aerosol transmission with rapid spread --> acute bronchitis --> Acute respiratory distress syndrome
-MERS - middle eastern variant --> v similar with higher fatality rate


Describe the Influenza virus genus in the Orthomyxoviridae family [negative strand RNA virus]
1. Structure
2. Life cycle
3. Reservoir/transmission
4. Disease caused
5. Treatment/prevention

Influenza A, B, C
1. Structure:
A. envelope with 2 glycoprotein spikes - hemagglutinin (main antigenic determinant; attaches to sialic acid receptors on human cells and causes RBC clumping) and neuraminidase (cleaves sialic acid receptors --> prevents viruses from entering already infected cells; Ab prevent cell-to-cell spread)
B. 2 matrix proteins - M1 gives stability to spikes, M2 is ion channel protein that creates pH for viral uncoating
C. helical nucleocapsid - segmented genome (8 RNA molecules) + associated proteins incl RNA dependent RNA polymerase (transcribes (-) sense into (+) sense mRNA intermediate which is used to make more (-) RNA)

2. Life cycle: receptor mediated endocytosis --> fusion of viral enveloped w vesicle through M2 proteins --> nucleocapsid freed and goes to nucleus --> steals 5' caps in nucleus --> 8 viral proteins made --> new virus buds off with nucleocapsid + glycoprotein spikes (embedded proteins)

3. Reservoir/transmission: respiratory transmission, waterfowl are reservoirs and infects swine, humans, avian

4. Diseases: destroy ciliated cells --> sequelae bacterial infections e.g. pneumonia (staph aureus or strep pneumo); can cause viremia or Guillan Barre (Ascending paralysis)
- Reye's syndrome - liver dysfunction and acute brain damage in kids due to taking aspirin, MOA unknown

5. Treatment/prevention: IgA in nasal secretions (Via live attenuated nasal spray vaccine), IgG in serum (ramped up with killed vaccine - trivalent or quadrivalent); drugs available but do NOT replace vaccines


What are the types of viral mutations that affect HA and NA subtypes of Influenza? [negative strand RNA virus, Orthomyxoviridae family]

1. Antigenic drift - minor changes e.g. point mutations in viral RNA (N, H, or both) that accumulate slowly--> annual seasonal epidemics

2. Antigenic shifts *Influenza A only*- major antigenic changes e.g. recombination of N and H subtypes that occur faster --> new HN subtype formed --> pandemics every 8-10 years

-1918 flu epidemic was so deadly bc of new subtypes from avian and human strains, which share common sialic acid-galactose receptors with swine flu


For the Paramyxoviridae family [negative strand RNA virus]
1. Structure
2. Replication

Paramyxoviridae family
1. Structure:
A. Spherical enveloped with 3 glycoprotein spike - HA, N, and F (for fusion)
-F glycoprotein responsible for fusion of infected cells --> syncytia aka multi-nucleated giant cells
-Inclusion bodies - in cytoplasm, site of viral replication
B. Helical nucleocapsid with non-segmented genome

2. Replication: Fusion of envelope with cell membrane via F glycoprotein --> capsid liberated and stays in cytoplasm --> new glycoprotein embed in cell membrane --> new particles bud off


Describe the diseases caused by the viruses in the Paramyxoviridae family [negative strand RNA virus]:
1. Parainfluenza
2. Mumps
3. Measles
4. RSV

Paramyxoviridae family - all spread via respiratory droplets/secretions

1. Parainfluenza - due to human PIV 1-4; causes croup --> seal-bark cough and inspiratory stridor; has all 3 virulence factors (NA, HA, fusion protein)
-more common in children and most severe in elderly, immunocompromised (esp with pneumonia)
-limited to respiratory tract

2. Mumps - has all 3 virulence factors; primary URT, can spread beyond respiratory tract --> viremia --> salivary gland swelling (parotitis) and other organs e.g. gonads (unilateral orchitis), kidneys, heart, CNS (meningitis); deafness sequelae

3. Measles=Rubeola - one of the most infectious (only need few particles), particles live on fomites so can survive for hours; winter and spring epidemics, no neuraminidase activity but have HA and fusion proteins
i. Symptoms: 4 C's (Cough, coryza/runny nose, conjunctivitis, Koplik's spots - on buccal mucosa); primary RT but can spread --> viremia via blood, where second viral multiplication occurs --> maculopapular rash (starts on head and moves downwards)
ii. Complications: keratitis (w/ Vit A deficiency), bacterial infections, mortality, SSPE (subacute sclerosing panencephalitis - happens years after when virus is not cleared from neural cells), giant cell pneumonia

*MMR live attenuated vaccine for Measles, Mumps, Rubella - lasts for 10-15 years

4. RSV (Respiratory syncytial virus) - most common cause of LRT disease (pneumonia, bronchitis) in infants less than 6 months old
-multinucleated giant cells due to fusion protein virulence factor; NO HA or NA activity or glycoprotein spikes
-treatment: IM injectable monoclonal antibody


Describe the structure, diseases caused, and treatment of viruses in following families [negative strand ssRNA viruses]:
1. Arenavirus

2. Bunyavirus

3. Filovirus

1. Arenavirus: enveloped helical nucleocapsid with bisegmented RNA (L and S) --> negative strand BUT ambisense --> message transcribed from both (-) and (+) sense RNA --> 2x genes on same genome; T-shaped glycoproteins GP1 and GP2
A. Transmission: via rodent hosts
B. Diseases: Lymphocytic choriomeningitis virus (LCV), lassa fever --> can escalate to hemorrhagic fevers, shock, and death
C. Treatment: treat with ribavirin, prevent with rodent control

2. Bunyavirus: envelope from host cell Golgi body, genome with 3 RNA segments, transmitted via rodent feces/urine, deer mouse hosts
A. Diseases: CNS (La Crosse virus), hemorrhagic fevers (Hanta virus pulmonary disease), cardiac disease (Sin Nombre virus), GI (Heartland virus)

3. Filovirus: unsegmented RNA in helical nucleocapsid but pleimorphic (many possible shapes)
A. Ebola: VL4 disease --> need isolation/containment/barrier nursing --> bc vector, transmission, reservoir unknown + no cure
i. Clinical: Flu-like symptoms, petechial rash--> hemorrhagic fever, hypovolemic shock --> end-organ failure within days
ii. Epidemic in Guinea, Sierra Leone, and Liberia


Respiratory Enteric Orphan Virus [double stranded RNA virus]
1. Structure
2. Replication
3. Diseases

REO Virus family
1. Structure: no envelope/naked but icosahedral double protein capsid- outer shell has glycoproteins and inner shell has dsRNA of 10-12 segments --> both (+) and (-) sense
*dsRNA is red flag to immune system*

2. Replication: Receptor mediated endocytosis --> outer capsid degrades --> dsRNA remains in inner capsule to hide from immune system; RNA dependent RNA polymerase in inner capsule transcribes message --> translated in cytoplasm --> positive strand is encapsulated in protein capsule --> polymerase goes inside capsule and makes the double strand --> second capsule forms --> released from cell by lysis
-cytoplasmic inclusion bodies with virus particles being formed

3. Disease: Rotavirus - most common GI virus for infants and children
-NSP4 enterotoxin --> increases Cl- permeability --> secretory watery diarrhea
-Transmission: fecal-oral, respiratory secretions, fomites; seasonal (wintertime)
-Prevention: 2 live attenuated oral viruses; cause side effect of intussusception (telescoping of the bowel)


What are the different replication strategies based on DNA virus size?

Smallest (parvoviruses) - only replicate in dividing cells

Medium (papovaviruses)- drive cells into division

Large (herpes and adenoviruses)- make own enzymes incl polymerases, can replicate in non-dividing cells

Largest (pox viruses) - makes all its own replication enzymes, doesnt need cell at all and can replicate in the cytoplasm


1. Morphology
2. Life cycle
3. Epi
4. Disease
5. Treatment/prevention

Parvovirus - smallest pathogenic viruses

1. Morphology: icosahedral nucleocapsids, non-enveloped/naked with linear (-) ssDNA genome that encodes 2 proteins *ONLY single stranded DNA virus*

2. Life cycle: replicates in nucleus, only in dividing cells (needs host cell proteins)

3. Epi: only human pathogen is B-19; transmitted via blood transfusion, respiratory, or maternal-fetal; v common and most people have Ab

4. Disease: "Fifth disease" bc fifth childhood infection with fever and then rash ("slapped-cheek" rash on face that spreads as lacy rash to trunk/arms)
*as opposed to Sixths disease (rash starts on trunk, does not affect face)*
-transient aplastic anemia in sickle cell patients
-hydrops fetalis --> spontaneous abortions in fetuses

5. Treatment/prevention: usually self-limiting


Papovaviruses [DNA virus]
1. Morphology
2. Life cycle
3. Epi
4. Disease
5. Treatment/prevention

Papovaviruses [DNA virus]

1. Morphology: icosahedral, non-enveloped/naked nucleocapsids with dsDNA genome

2. Life cycle: replicates in nucleus of epithelial cells, viral proteins keep cells in division (needs host cell replication machinery) --> virus kills infected cells and releases new viral particles (necrosis shows as warts/condylomata)

3. Epi: 3 different families --> A) Papilloma - warts, B) polyoma - animal tumors, and C) simian vacuolating virus 40 - only cytopathic in cells

4. Disease: HPV
- major risk factor for cervical/anogenital cancer --> results from abortive infection: viral DNA fragment integrated into host DNA --> early viral proteins E6 and E7 expressed --> E6 inhibits p53; E7 binds Rb so it cant requester elongation factor E2 --> cell driven to continuous division --> late proteins not made so viral particles not released/cell is not lysed --> sets stage for genetic changes --> neoplasia and cancer
-HSV 1-4 cause cutaneous common warts (in children)
-HSV 6 and 11 cause anogenital warts (from sexual transmission)

5. Treatment/prevention: Gardasil (inactivated subunit vaccine) - only covers HPV 6, 11, 16, 18
-diagnose via pap smear


Adenoviruses [DNA virus]
1. Morphology
2. Life cycle
3. Epi
4. Disease
5. Treatment/prevention

Adenoviruses [DNA virus]

1. Morphology: icosahedral nucleocapsid, non-enveloped/naked

2. Life cycle: Drive infected cells to division through early viral proteins --> E1A binds and inhibits Rb and E1B binds and inhibits p53

3. Epi: transform cell cultures but no link to human cancers; 40+ types; fecal-oral or respiratory transmission; common in children, military recruits

4. Disease: self-limiting infections --> tonsillitis/adenitis, gastroenteritis/diarrhea, febrile pharyngitis / respiratory disease, epidemic conjunctivitis

5. Treatment/prevention: oral live vaccine to prevent epidemic respiratory disease in military recruits


Poxviruses [DNA virus]
1. Morphology
2. Life cycle
3. Epi
4. Disease
5. Treatment/prevention

Poxviruses [DNA virus]

1. Morphology: largest and most complex human viruses; brick-shaped, enveloped virions with cytoplasmic inclusion bodies (sites of viral replication); DNA containing core flanked by two lateral bodies

2. Life cycle: ONLY DNA viruses which replicate in the cytoplasm bc they have all the enzymes they need e.g. DNA dependent RNA polymerase --> new virions exocytosed

3. Epi: contain genes that are homologous to host immune system --> downregulate host immune, complement, and interferon systems

4. Disease
A. Molluscum contagiosum virus - little warts on trunk, common in children, not dangerous but last for a while
B. Smallpox (variola virus) - highly contagious and 30% fatality, respiratory transmission, spread through body via macrophages
i. Variola major - severe and most common --> high fever and rash on face/extremities (macules --> papules --> vesicles --> pustules --> scab --> scar)
*Lesions are ALL at the same stage (unlike chicken pox)
ii. Variola minor - less severe and common --> gives you lifelong immunity
C. Cowpox - how smallpox vaccine was developed

5. Treatment/prevention: immunization no longer given bc it has been eradicated


Herpesviruses family [DNA virus]
1. Shared biological properties
2. Morphology
3. Replication
4. Protein synthesis cascade

Herpesviruses [DNA virus]
1. Shared properties:
-virus remains latent in host lifelong - latent cells make anti-sense transcripts
-encodes many types of enzymes
-viral DNA synthesis and capsid assembly in nucleus

2. Morphology:
-envelope with lipoproteins + glycoprotein spikes
-icosahedral capsid with core of linear dsDNA and proteins in toroid shape
-tegument - amorphous area bw envelope and capsid that has various proteins and mRNA

3. Replication: viral envelope fusion --> virion uncoating --> linear DNA goes into the nucleus and forms closed circle--> immediate early genes transcribed --> mRNA in cytoplasm translated into protein --> proteins come in and cause delayed early genes to be transcribed/translated --> proteins come in and cause late genes to be transcribed/translated --> structural proteins package the replicated DNA --> buds out of nuclear membrane (becomes the envelope) and makes its way out of the cell

4. Protein synthesis cascade:
-Immediate early IE genes (turn off host systems and induce DE) -->
-Delayed early DE genes (replication of viral DNA and induce late) -->
-Late genes (Structural genes that form new virions)


Compare and contrast general features of subfamilies in the Herpesvirus family:
1. Alphaherpes
2. Betaherpes
3. Gammaherpes

4. How do herpesviruses evade the immune system?

1. Alpha herpes - destruction of infected cells leads to warts/sores; short reproductive cycle but large host range and rapid spread; latent in sensory ganglia

2. Beta herpes - long reproductive cycle but restricted host range and slow infectivity; latent in monocytes; infected cells become v large syncytia

3. Gamma herpes - infection specific to B or T cells; latent in lymph tissue

4. Evading immune system:
-No T cell response --> Decrease MHC Class 1 activity by removal or endocytosis of Class I chains, inhibiting antigen presentation, etc.
-cytokine and interferon homologs that bind receptors but not elicit immune response --> shut down immune system
-block apoptosis
-hinder macrophage activation


Describe the following genera in the Alphaherpes subfamily [Herpes DNA virus family]:
1. HSV
2. VZV

1. HSV: linear, enveloped dsDNA virus
-transmission through sex, saliva, and vertical (TORCH infection)
-virus multiples locally, travels along neurons adjacent to primary infection, and establishes latent infection in single sensory ganglia
-Pathology - focal necrosis, multinucleated giant cells, intra-nuclear inclusion bodies (Cowdry bodies)
-free virus only during initial infection (so Ab wont help) --> cell-mediated immunity (via CTLs) is main defense and recognizes glycoprotein spikes
-latency associated mRNA transcript (LAT) hybridize to viral gene ICPO --> keeps virus latent until person is stressed/immunosuppressed --> Recurrence with viral multiplication

A. HSV1 - latent in trigeminal ganglia
i. Herpetic gingivostomatitis - asymptomatic but can present with cold sores and fever blisters on mouth
ii. Herpetic keratoconjunctivitis - swelling and inflammation of superficial tissue of anterior eye
iii. Herpes simplex encephalitis - v dangerous with personality changes --> coma/death, more common in infants/immunosuppressed

B. HSV2 - latent in sacral ganglia
i. Genital herpes - painful genital sores and pustules
ii. Neonatal herpes --> growth and cognitive problems, meningitis, can be fatal

2. Varicella Zoster virus - latent in multiple sensory ganglia
-respiratory transmission or direct contact, also vertical transmission (TORCH infection)
-spread through blood via infected WBCs (systemic) --> goes to organs --> lesions over body (trunk to extremities) in DIFFERENT stages of healing
A. Chicken pox - vesicular rash that itches but not painful (unlike HSV and shingles) --> assists in reinoculation
B. Congenital varicella syndrome- scarring and blindness
C. Herpes Zoster/Shingles - reactivation in elderly, immunocompromised --> painful rash, encephalitis, pneumonia
-live attenuated vaccine for both chicken pox + shingles
-treatment with acyclovir


Describe the following genera in the Betaherpes subfamily [Herpes DNA virus family]:
1. CMV (HHV4)
2. HHV6
3. HHV7

1. Cytomegalovirus CMV:
-slow infectious cycle
-no destruction of infected cells --> cytomegaly (multinucleated giant cells)
-infects WBCs and epithelial cells; latent in mononuclear WBCs (B/T cells, macrophages) but spreads to all organs
-transmission via blood, sexual contact, urine, saliva
A. asymptomatic infection or mono-like disease (fatigue, sore throat) like in EBV, but Monospot test negative
B. congenital CMV (TORCH infection): majority asymptomatic but can lead to jaundice, blueberry muffin rash, hearing loss, mental retardation, hearing loss; hydrops fetalis
C. severe infection in immunosuppressed e.g. retinitis, esophagitis, colitis in AIDS, pneumonia in organ transplant

2. HHV6 aka Sixth disease aka Roseola (self-limiting, spontaneously resolves)
-most common in infants 6 mos-2 yrs
-high fever (can have febrile seizures) for 4 days
-post fever, diffuse lacy rash begins on trunk and spreads to extremities but does NOT affect face, palm/soles

3. HHV7 - crossreactive with 6, common since 90% ppl have Ab, but not linked to any disease


Describe the following genera in the Gammaherpes subfamily [Herpes DNA virus family]:
1. EBV
2. HHV8

1. Epstein-Barr virus EBV:
-transmission via respiratory secretions --> saliva, repeated exposure "kissing disease"
-infects epithelial cells in mouth/local lymph tissues, latent in B cells which produce viral proteins which keep cell alive and maintains viral DNA in quiescent state
-carriers shed virus for lifetime
-most common in adolescents --> asymptomatic or infectious mononucleosis with fever, pharyngitis BUT no cytopathic effects (inclusion bodies, no cell death, etc)
-associated with cancers: African/endemic Burkitt's lymphoma (also connected to malaria), Hodgkin's, nasopharyngeal carcinoma (Asian patients)

-immune response - infected B cells produce nonspecific immunoglobulins (called heterophile antibodies) which agglutinate RBC--> diagnose via Monospot test
-stimulated active CD8 T cells called atypical lymphocytes or Downey cells and seen on blood smear --> proliferate and kill infected B cells --> splenomegaly

-Serology - look for anti-viral capsid antigen (VCA) or anti-EBV nuclear antigen (EBVNA) month post-infection
----> high anti-VCA and no anti-EBVNA = acute
----> high anti-VCA and high anti-EBVNA = past infection

2. HHV8 - Kaposi's sarcoma
-AIDS-defining illness
-dysregulation of VEGF --> angiogenesis --> violaceous lesions on nose, extremities, membranes of GI tract, and on hard palate
-can cause B cell lymphoma


1. What are the clinical features of neurodegenerative diseases caused by prions?

2. What are the 3 modes of transmission of prion diseases + examples of diseases that result

1. Features:
-long incubation period
-CNS degeneration --> Ataxia, dementia, death
-brain histopathology: amyloid deposits, vacuolar degeneration of tissue
-brain tissue is infectious
-no inflammation bc no immune response

2. Modes:
A. Infection (oral) - transmitted to CNS via macrophages
i. Creutzfeldt-Jakob disease - tissue transplant
ii. Scrapie/BSE/Mad Cow - consuming contaminated meat (called vCJD)
B. Inheritance (autosomal dominant)
i. Familial fatal insomnia
ii. Inherited Creutzfeldt-Jakob disease
C. Spontaneously (sporadic)
i. Creutzfeldt-Jakob disease (most common form of CJD), mean age is 65


Describe the structures and features of prions

What is the prion hypothesis?

1. Prions = proteinaceous infectious agent
-little/no nucleic acid --> contains mostly/only protein
-prion protein PrPc is glycoprotein found on extracellular face of neuron plasma membranes
-v stable, but infectious tissue cannot been cultured
-prions from diseased brain PrPsc are rich beta sheets, resistant to proteases, make up the amyloid deposits

2. Prion hypothesis - prion proteins PrPc are normal components (encoded by host genome) --> PrPc spontaneously convert to pathogenic version PrPsc, which continue process via autocatalysis
A. Infective disease via introduction of PrPsc from exogenous source (transplant, meat)
B. Inherited disease via mutations in prion protein gene
C. Sporadic disease via spontaneous conversion of PrPc --> PrPsc


Hepatitis C [Hepacivirus genus, Flaviviridae family]
1. Viral characteristics
2. Epidemiology
3. Clinical characteristics
4. Diagnosis
5. Treatment/Prevention

Clinical hepatitis - refers to elevations of AST/ALT and/or bilirubin; can be caused by HepA, HepB, HepC, CMB, EBV, etc.

Hepatitis C
1. Viral characteristics: (+) strand non-segmented enveloped ssRNA genome; structural proteins for core + envelope and non-structural proteins for viral replication *targets for drugs*
- high replication rate and genetic variability due to lack of 3'--> 5' exonuclease proofreading activity
-6 major genotypes --> new antiviral drugs are reactive for some genotypes but not others

2. Epidemiology: transmission via blood (IV drug use), sex, maternal-child transmission; cause of death from liver disease

3. Clinical:
A. Acute - mostly asymptomatic, symptoms more common in infants and women (who are more likely to clear virus before chronic infection); Ab take while to develop; increase then decrease in ALT; 20% recover and 80% move to chronic
B. Chronic - asymptomatic/fatigue, AST/ALT normal, 25% progress to liver disease, cirrhosis
C. Complications - glomerulonephritis, neuropathy, lymphoma, cirrhosis, hepatocellular carcinoma (Hep A not associated with carcinoma, not chronic)

4. Diagnosis: antibody test OraQuick, PCR to measure viral load; blood tests + liver ultrasound

5. Treatment: goal is to eradicate (cannot eradicate HepB)
-check viral load through sustained virologic response (SVR)
-used to use interferon alpha + ribavarin
-new standard is protease inhibitors or polymerase inhibitors - target non-structural proteins


Hepatitis B [Orthohepadnaviridae genus, Hepadnaviridae family]
1. Viral characteristics
2. Epidemiology
3. Clinical characteristics
4. Diagnosis
5. Treatment/Prevention

Hepatitis B

1. Viral characteristics: icosahedral nucleocapsid contains partially-dsDNA circular genome --> viral reverse transcriptase takes partial dsDNA --> ssRNA --> dsDNA (happens after assembly but before release of progeny virions); intranuclear AND cytoplasmic replication; cell tropism - replicates only in differentiated hepatocytes

2. Epidemiology: 2B with serological evidence, 400M chronic carriers; transmission via maternal-fetal, blood (IV drug, transfusion), sex; infection does not kill cells but immune response does; Delta agent (Hep D) --> dependent on HBV for replication

3. Clinical: acute, self-limited, with or without symptoms
-Symptoms: cirrhosis, hepatocellular carcinoma, co-infection with HIV, HepC
-Complication: fulminant hepatitis -- high mortality

4. Diagnosis: serological markers are HBsAg surface antigen marker --> active infection, HBeAg --> only in infectious virions; anti-HBs antibodies --> immunity from vaccine or recovery from acute infection; anti-HBcore IgM --> acute infection or flare; anti-HBcore IgG --> lifelong marker of infection

5. Treatment: intramuscular vaccine available, antivirals (tenofovir and entecavir)--> goal is to suppress, not cure; therapy for co-infections, immunosuppression, pregnancy, drug resistance, and advanced liver disease


Describe the stages of chronic Hepatitis B (HBV) that is transferred perinatally:
1. Immune tolerance
2. Immune clearance (Replicative)
3. Non-replicative

What are treatment goals of HBV?

1. Immune tolerant (birth to 20) - asymptomatic, normal ALT, positive HBeAg, high HBV DNA levels and Anti-HBc IgG, no change in liver biopsy

2. Immune clearance - replicative phase with acute liver disease; AST/ALT elevated, high HBV DNA and Anti-HBc IgG levels, positive HBsAg and HBeAg, conversion of HBeAg --> anti-HBe, can progress to cirrhosis, males higher risk

3. Non-replicative phase - HBeAg negative, HBsAg positive, HBV low, Anti-HBc IgG high, ALT normal/mildly high, may have already developed cirrhosis so should be followed

4. Treatment goals - remission of liver disease, prevent cirrhosis, hepatic failure + carcinoma; sustained virologic response (low HBV DNA), HBeAg seroconversion, reduction of ALT/AST


Hepatitis A [Hepatovirus genus, Picornavirus family]
1. Viral characteristics
2. Epidemiology
3. Clinical characteristics
4. Diagnosis
5. Treatment/Prevention

Hepatitis A
1. Viral: small, naked icosahedral with (+) strand RNA genome; single serotype

2. Epi: fecal-oral transmission (person to person contact, contaminated food esp shellfish, contaminated water in developing countries); contagious during incubation phase before symptoms develop and 1 week after jaundice

3. Clinical: asymptomatic in children; symptoms include acute hepatitis (not chronic) and jaundice, no association with liver cancer
-only in liver - no cytopathic effect, self-limiting, NO carrier state
-immune-mediated injury
-smokers can develop aversion to smoking

4. Diagnosis: no commercial assay for PCR; virus in blood first --> then stool --> symptoms --> IgM anti-HAV to measure acute HAV infection

5. Prevention: 2 doses of culture-derived inactive vaccine; humans only known HAV reservoir


Define retroviruses and describe the morphology and genome organization

Retrovirus - RNA viruses that replicate through DNA intermediate

Morphology: lipid envelope with glycoprotein spikes, HIV-1 virion has conical structure

Genome: virion is diploid, contains 2 (+) sense ssRNA molecules;
proviral genome is integrated dsDNA : 5' LTR, gag, pol, env, 3' LTR
-gag and env encode structural proteins (gag --> p24 --> capsule for RNA strands; env --> gp41 transmembrane and gp120 outer glycoprotein)
-pol gene encodes replication proteins - reverse transcriptase, integrase, protease
-each LTR contains U3, R, and U5 segments - transcription by cellular RNA pol II starts at 5' U3-R border and polyadenylation occurs at 3' LTR R-U5 border


List the steps in the retroviral life cycle

Life cycle:
1. surface subunit of viral envelope (gp120) binds to target cell receptor (CD4) + co-receptor (CCR5)-->
2. virus enters cells via membrane fusion-->
3. uncoating of ssRNA and reverse transcription -->
4. dsDNA is pre-integration complex and imported into nucleus -->
5. provirus integrated at cis-attachment sites into host DNA by viral integrase (2 nucleotides lost from end of viral DNA, and 5 bp of host cell DNA replicated) -->
6. transcribed by host cell RNA pol II and processed/ spliced (can make different transcripts based on splicing patterns) -->
7. transported out of cell to be translated, processed* -->
8. gag and RNA packaged
9. particles assembled at inner cell membrane -->
10. bud out of the cell as immature virions -->
11. become mature virions when viral protease processes Gag and Gag-pol polyproteins

*Env (envelope) polyprotein glycosylated in secretory pathway (protects virus from host immune system), processed in ER and Golgi by cellular protease into SU (surface) and TM (transmembrane) subunits, Gag and Gag-pol (made bc of frameshifting at slippery site) polyproteins processed by viral protease upon budding


How are retroviruses used in gene therapy?

make transducing vector which contains cis-acting sequences (covalently linked to viral genome for replication to occur) and removes the trans-acting sequences (which encode the viral proteins)

Transducing vector introduced to packaging cell --> vector virus RNA transcribed and packaged into virions --> buds from packaging cell and targets cells of interest -- vector integrates into genome of host target cell but does not produce progeny virions which would be harmful to the host


How is HIV transmitted and diagnosed?

Transmission: contact with infected bodily fluids
-blood (transfusion, IV drug use)
-maternal-child (perinatal, primary during delivery or via breast milk)

-screening: ELISA (Ab test to screen blood supply), PCR
-follow-up with Western blot
-test upon clinical suspicion or volunteer routine testing of everyone 13-64 at least once


What is the viral latent stage of HIV infection and its implication

latent stage - provirus integrated into host genome but not expressed --> produce no viral antigens so not sensitive to antiviral drugs or immune response, BUT may become activated and produce virus later on (due to tat, rev, NF-kB --> HIV promoter binds NF-kB --> links viral transcription to T cell activation since T cells cant be stimulated to fight HIV without stimulating replication)

implication: need to be on antiretroviral therapy lifelong


1. Compare/contrast HIV DNA from that of other retroviruses.
2. Describe the functions of the add'l regulatory proteins:
A. tat
B. rev
C. nef
D. vif
E. vpu
F. vpr

1. All retroviruses have LTRs and genome that encodes gag, pol, and env

2. HIV DNA and other lentiviruses are complex and has 6 add'l proteins:
A. tat - activates HIV transcription --> binds to 5' tar RNA --> creates stem loop --> recruits cell proteins e.g. protein kinase, RNA pol II
B. rev - prevents splicing of HIV mRNA transcripts by binding to RRE in env RNA region --> switches translation from early regulatory (tat, rev, nef) to late structural proteins (Gag, pol, env)
C. nef - stimulates HIV replication --> increases infectivity and inhibits anti-HIV immune response by downregulating MHC1
D. vif = viral infectivity factor - required for infectivity --> degrades cytosine deaminase (innate cellular defense that damages reverse transcripts)
E. vpu - stimulates viral budding and release --> delivers CD4 to proteasome and reduces tetherin (inhibitor of budding)
F. vpr - aids in transport of viral core to nucleus


Describe the effect of HIV infection of target cells (CD4 is main receptor)
1. CD4+ T cells
2. Monocytes and macrophages
3. Dendritic cells of epithelia

1. CD4+ T cells - infected by both CCR5 and CXCR4 tropic viruses
-preferential infection of activated T cells --> more targets (CCR5, increased division, more transcription factors like NF-kB)
-HIV is cytotoxic --> direct killing by viral cytopathic infection, apoptosis, immune destruction of infected cells by CTLs, death of bystander cells

2. Monocytes - M-tropic CCR5 (predominate in early infection)
-first step of mucosal infections --> infection of monocytic cells in submucosa
-important in pathogenesis of HIV encephalopathy
-less infection of circulating monocytes i.e. macrophages

3. Dendritic cells
-can be productively infected or transfer HIV to CD4 T cells via DC-SIGN surface protein
-infection of mucosal dendritic cells can transport virus to lymphoid tissue


Describe the stages in HIV pathogenesis:
1. Acute initial infection
2. Asymptomatic period (clinical latency)
3. Late-stage symptomatic HIV disease

1. Acute initial infection: 1-2 mos post HIV exposure; in 50% patients; experience non-specific mono-like symptoms e.g. fever, rash + high levels of HIV particles in blood (Viremia)
-site of early HIV replication is gut lymphoid tissue, which is destroyed
-massive depletion of memory CD4+CCR5+ T cells (via direct killing + bystander effects) --> holes in the immune repertoire
-Initial immune response: anti-HIV CD8 response + Ab produced via seroconversion 2 mos post infection

2. Asymptomatic latent period: anti-HIV Ab bind virus particles --> low plasma viral load --> few symptoms
-clinically latent but NOT virally latent -> HIV replication and CD4 T cell destruction persists in secondary lymphoid tissues
-slow but steady decline of immune system --> CD4:CD8 ratio decreases, failure of anti-HIV CTL response

3. Late-stage symptomatic HIV disease: late stage triggered by co-infections, immune escape, low CD4+ numbers, and transition to CXCR4
-AIDS-related complex - fever, lymphadenopathy, weight loss, diarrhea, Candida infections
-immune escape - loss of effective immune response due to viral variability (resistance to neutralizing Ab, CTLs)
-transition to CXCR4 receptor and just T cell tropism --> fast/high level of replication + more cytopathic

4. AIDS: rapid decline of CD4+ lymphocytes to be less than 200 (+loss of immune response), rapid increase in plasma viremia, and development of opportunistic infections (PCP, Kaposi's sarcoma, CMV, Cryptosporidium, Cryptococcus)


Summarize HIV effects on immune organs by stage:
1. Early
2. Intermediate
3. Late

1. Early
-immune stimulation
-follicular dendritic cells can trap HIV
-lymph nodes hyperplastic
-massive HIV replication in GALT

2. Intermediate
-HIV replication in secondary lymphoid organs

3. Late
-immune defects --> can cause diffuse, large B cell lymphoma
-loss of follicular dendritic cells
-lymph nodes are fibrotic, cell-depleted
-failure of immune control to stop viral replication


Describe the clinical status associated with the following CD4+ lymphocyte counts

I. CD4 Counts --> current stage of disease
(viral load in peripheral blood --> predictor of future course of disease)

>500- risk of disease low, responds to immunization/TB testing

500-200- lymphadenopathy, risk of TB or candidiasis ("thrush")

200-50- officially diagnosed as AIDS; risk of opportunistic infections

when CD4+ numbers are low enough --> immunity cannot be maintained --> high level viral multiplication


Describe the features and problems of the different vaccine types:
1. Killed virus/purified antigens
2. Live attenuated virus
3. Recombinant (viral vector + cloned HIV genes)

4. What are ways HIV evades immune response?

1. Killed virus/purified antigens
A. Features: response to diversity of epitopes
B. Problems: plasma Ab only; may not prevent establishment of infection in mucosa

2. Live attenuated virus
A. Features: provides plasma/mucosal Ab and CTL
B. Problems: reversion to virulence

3. Recombinant (viral vector + cloned HIV genes)
A. Features: same as live attenuated
B. Problems: restricted epitope variety

-HIV antigenic diversity
-SU protein heavily glycosylated --> Ab shield
-first prime (immunize with killed-virus vaccine) then boost with live vaccine --> mucosal immunity + CTL


1. Describe the entry of HIV-1 retrovirus into the cell

Describe the following fusion inhibitors [antiretroviral drugs]
2. Enfuvirtide
3. Maraviroc

1. Entry:
-gp120 (SU surface protein of viral envelope) is stripped off by CD4 receptor and CCR5 (or CXCR4) coreceptor on cell
-naked gp41 (TM transmembrane protein of viral envelope) uncoils and exposes hydrophobic fusion peptide, which inserts into cell membrane
-gp41 folds back on itself due to association of alpha helices into helix bundle--> reels virus onto surface of cell
-membrane fusion

2. Enfuvirtide inhibits viral fusion (only in HIV-1)
-synthetic 36AA, digested quickly by the cell
-binds to gp41 and prevents it from folding on top of itself
-requires subcutaneous injections 2x day, can get skin rxns at site

3. Maraviroc inhibits viral fusion (only in CCR5 tropic cells)
-binds CCR5 and blocks gp41 binding and HIV entry
*unusual bc it targets human and not viral protein *
-need to test HIV tropism before giving drug (only 50% patients eligible); metabolized by p450
- orally BID, can get mild adverse effects


1. Describe conversion of RNA genome to DNA copy by HIV

Describe the following RT inhibitors:
2. Nucleoside:
A. Emtricitabine
B. tenofovir
i. tenofovir disproxil fumarate
ii. tenofovir alafenamide fumarate
*A and Bi coformulated as Truvada
*A and Bii coformulated as Descovy

3. Non-nucleoside:
A. efavirenz
B. etravirine

1. Reverse transcriptase enzyme
-starts at free 3' OH of tRNA
-polymerizes first DNA strand and degrades RNA transcript in the process
-little bit of RNA left over --> used as primer for second DNA strand
-dsDNA integrated into the host genome
-crystal structure resembles hand with finger/thumb domains

2. Nucleoside RT inhibitors NRTIs e.g. AZT, 3TC: look like dNTPs used by viral RTs but missing 3' OH --> incorporated and are chain terminators/suicide substrates for viral chains
-selective bc not taken up by DNA polymerases, but sometimes taken up by mt polymerases --> lactic acid buildup --> sore muscles
-prodrugs so it can get into cell- need to be phosphorylated and activated
-taken orally, prevent acute infection but no effect on already infected cells (once virus is integrated)

A. Emtricitabine: fluorinated analog of older NRTI (lamivudine) --> longer half life --> take as pill 1xday (qd) + no p450/ drug-drug interactions
B. tenofovir (2 forms)
i. tenofovir disproxil fumarate: put the first phosphate on to overcome RLS, Pi is protected by disproxil fumarate protection group, which comes off in the plasma --> nephrotoxicity
ii. tenofovir alafenamide fumarate: deprotected only in end target lymphocytes (more stable in plasma)--> reduces levels of drug and less toxicity

3. Non-nucleoside RT inhibitors (non-NRTIs)
-MOA: allosteric inhibitors that bind to pocket of RT adjacent to active site --> induce conformational change --> prevent RT domains from coming together
-does not require phosphorylation/activation
-selective for HIV-1 (not HIV-2)
-oral, diffuses into cells
-downside is they interact with p450

A. efavirenz
-adverse effect: false positive cannabis test
B. etravirine - also binds pocket but has strategic flexibility -> can accommodate mutations in the binding pocket --> wiggle and jiggle
-reserved for patients who are are non-NRTI resistance


1. Describe HIV virus integration

2. Describe viral integrase inhibitors (INSTI)
A. Raltegravir
B. Elvitegravir
C. Dolutegravir

1. Viral integration
-HIV viral integrase processes ends of the dsDNA by cleaving off 2 nucleotides from each 3' end
-makes cuts in host DNA --> fuses nucleophilic 3' OH groups to the nicks in the DNA
-host cell machinery fixes the nicks in the DNA

2. Viral integrase strand transfer inhibitor (INSTI)
-MOA: binds Mg at the active site of integrase-DNA complex --> kicks 3' OH ends that need to be integrated out of the active site pocket
A. Raltegravir: first INSTI, potent first line therapy; does not interact with p450 and low toxicity
B. Elvitegravir
-approved as Stribild = 4 drug combo pill (elvitegravir/cobicistat/emtricitabine/tenofovir)
-p450 interactions, inhibited by addn of cobicistat to the combo (has no antiviral activity)
C. Dolutegravir
-use for patients resistant to other INSTIs
-does not require cobicistat boosting


1. Describe the function of HIV proteases

2. Describe protease inhibitors
A. ritonavir
B. atazanavir
C. darunavir

1. HIV protease cleaves gag-pol protein into active enzymes from pol gene (RT, integrase, protease) and structural proteins from gag (p7, 9, 17, 24)
-aspartic acid protease dimer carries out rxn; selectivity from human aspartic acid proteases which are monomers

2. Protease inhibitors: transition state analog (tetrahedral with 2 OHs) that binds reversibly *first use of rational-based drug design*
-v effective but side effects which include hyperlipidemia, hyperglycemia, and pseudo-Cushing's syndrome
-metabolized by p450 - affects levels of rifampin, ketoconazole

A. ritonavir - one of the first drugs, peptido-mimetic which resembled cleavage site
B. tazanavir - distinct structure and resistance profile --> can be taken 1xday and lower side effects
C. darunavir - newest, active against HIV isolates resistant to other protease inhibitors, has strategic flexibility


1. What factors need to be taken into account when making combo pill formulation?

2. Describe the makeup of the following coformulations:
A. Truvada
B. Descovy
C. Triumeq
D. Stribild
E. Genvoya

1. Similar half-lives/pharmacokinetics, varied side effects and resistance mechanisms

2. Coformulations
A. Truvada = Emtricitabine + tenofovir disproxil fumarate [NRTIs]
B. Descovy = Emtricitabine + tenofovir alafenamide fumarate [NRTIs]
C. Triumeq = Dolutegravir [INSTI] + abacavir [NRTI] + lamivudine [NRTI]
D. Stribild = elvitegravir [INSTI] + cobicistat [booster] + emtricitabine [NRTI] + tenofovir disproxil fumarate [NRTI]
E. Genvoya = elvitegravir [INSTI] + cobicistat [booster] + emtricitabine [NRTI] + tenofovir alafenamide fumarate [NRTI]


1. Describe the current guidelines for HIV treatment.
A. Protease inhibitor based
B. Integrase inhibitor based

2. When should you start treatment and why?

3. What are issues with HIV treatment?

4. What do you do when drugs fail?

1. Multidrug therapy - since resistance to single drug will arise rapidly due to high mutation rate of HIV virus
A. Protease inhibitor based: ritonavir-boosted darunavir + tenofovir/emtricitabine
B. Integrase inhibitor based:
-Stribild or Genvoya combo pills
-dolutegravir + tenofovir/emtricitabine
-raltegravir + tenofovir/emtricitabine

2. Start ART upon diagnosis with HIV regardless of viral load or CD4 count
-drugs are better - lower toxicity, less resistance, better dosing --> higher compliance
-early treatment associated with better outcomes
-ART can prevent transmission of HIV

3. Issues:
-Compliance - even occasional lapses cuts efficacy from 95% to 60%
-Community-acquired resistance (different from resistance that emerges during treatment)

5. Figure out why drugs failed (intolerance, compliance, etc)
-add 2 new drugs
-drug susceptibility testing
-take cross-resistance into consideration when switching drugs
-consult expert


Describe HIV prophylaxis strategies for different situations
1. pre exposure
2. HIV positive pregnancy
3. Infants with HIV positive mothers
4. healthcare workers post-exposure

1. PrEp (pre exposure prophylaxis) - Truvada approved for non-infected high-risk individuals

2. HIV positive women during pregnancy - to prevent MCT
-AZT(zidovudine)/3TC (lamivudine) [NRTIs] + lopinavir [protease inhibitor]

3. Infant prophylaxis - oral 3TC (lamivudine) for 6 weeks, no breastfeeding

4. healthcare workers post-exposure - 2 NRTIs or ART if exposure was severe


Describe nucleoside analogs [antiviral drugs] for herpes (HSV, CMV)
1. Acyclovir
2. Cidofovir
3. Topicals

Describe non-nucleoside analog
4. Foscarnet

Nucleoside analogs - inhibit viral DNA replication by competing for binding with viral DNA polymerase --> chain termination
-prodrug - need to be triphosphorylated (trapped in cells once they are)
1. Acyclovir - requires HSV viral thymidine kinase for the first phosphate --> not activated in uninfected cells
-oral, topical, IV formulations
-generally well tolerated but can get GI upset
2. Cidofovir - comes with first Pi
-long half-life --> infrequent dosing
-can cause nephrotoxicity
3. Topicals - trifluridine and vidarabine
-too toxic, only topical use

4. Foscarnet - blocks viral DNA polymerase, RNA polymerase, HIV RT
-selective for viral over host enzymes
-activity against cidofovir-resistant strains
-nephrotoxicity and CNS toxicities


Describe targets of anti-influenza drugs and MOA
1. viral entry inhibitors
A. Amantidine
B. Rimantidine

2. Viral exit inhibitors
A. Zanamivir
B. Oseltamivir

Give anti-influenza drugs early on (within 48 hours) or in at-risk population (65, pregnant, hospitalized) --> reduces duration symptoms, risk of complications

1. viral entry inhibitors - virus enters via endocytosis --> acidified --> activates M2 ion channel pore protein to create proper acidic pH --> virus uncoats
-only effective against influenza A (B lacks M2 protein)
A. Amantidine
B. Rimantidine

2. Viral exit inhibitors - inhibit neuraminidase --> prevent cleaving of sialic acid receptors that would allow virus to leave the cell; works on influenza A and B
A. Zanamivir
-inhaled bc of low oral bioavailability
B. Oseltamivir (Tamiflu)
-oral prodrug activated by esterases in liver/GI
-take for 5 days


What is SVR and its use

Describe vaccination options for Hepatitis B and C

SVR = Sustained virologic response --> benchmark for therapy

Hepatitis B - vaccine available, DNA virus that passes through RNA pre-genomic intermediate
-most common cause of hepatocellular carcinoma

Hepatitis C - no vaccine available, RNA virus
-often asymptomatic, progresses slowly
-6 major genotypes


Describe treatment options for Hepatitis C (HCV):
1. Sofosbuvir
2. Ribavirin
3. Simiprevir/grazoprevir
4. Ledipasvir
5. Viekira Pak

1. Sofosbuvir - nucleotide analog --> chain terminator for RNA dependent RNA polymerase
-combo with ribavarin was first oral treatment for HCV
-prodrug that has first Pi
-doesnt induce p450, oral pill 1xday
2. Ribavirin - nucleoside analog that lowers GTP levels, mRNA capping, RNA viral replication
-dose-dependent hemolytic anemia
-teratogenic in animals --> keep away from pregnant women

3. Simiprevir/grazoprevir - viral protease inhibitors
-Simiprevir + IFN has 80% SVR
-Grazoprevir approved in 2016

4. Ledipasvir - inhibits HCV structural protein NS5A --> blocks viral RNA replication and packaging
-broad spectrum --> use against all genotypes
-Harvoni = ledipasvir + sofosbuvir --> 90% SVR
-also daclatasvir, elbasvir --> new and potent

5. Viekira Pak - all oral multi-drug treatment
-contains protease inhibitor, NS5A inhibitor, and dasabuvir (non-nucleoside inhibitor of HCV RNA dependent RNA polymerase)
-can cause liver damage


Describe interferons and use as antiviral agents against hepatitis

Interferons - human proteins that trigger endogenous antiviral activity through JAK-STAT pathway
-many activities incl inhibition of transcription, translation, protein processing, viral maturation
-PEGylated to increase half-life
-administered as injection, but effective only in 50% patients
-bad side effects --> neurotoxicity, hepatotoxicity, psychiatric disorders (1/3 patients have to stop early)


Describe treatment options for Hepatitis B (HBV)
1. Entecavir
2. Truvada
3. Adefovir
4. Telbivudine

PEG-IFN is first line treatment for HBV, less drug devlpt
unusual replication - DNA virus with RNA intermediate

1. Entecavir - nucleoside analog - chain terminator for HBV RT
-has 3' OH --> more bases can be added but distorts DNA --> terminates chain
-selective for HBV only --> treatment for life and rebounding effect
-not a lot of resistance bc requires 2 mutations

2. Truvada = embtricitabine + tenofovir disproxil fumarate (both are nucleoside RT inhibitors); also used for HIV PrEp

3. Adefovir - second line bc of side effects
-nucleoside analog (NRTI)
-effective despite lamivudine resistance and entecavir cross-resistance

4. Telbivudine - thymidine analog active against HBV only
-works for adefovir resistant mutations
-better than lamivudine


Describe the structure, diseases caused, and treatment of viruses in Rhabdovirus

Rhabdovirus: (-) sense unsegmented, enveloped ssRNA virus

1. Rhabdovirus: helical nucleocapsid that is rigid and bullet shaped with unsegmented RNA; G glycoprotein spike on envelope that binds to nicotinic acetylcholine receptors of neurons in post-synaptic motor endplate
-diagnose via Negri (cytoplasmic inclusion) bodies in Purkinje cells
A. Rabies: killed vaccine (active) + anti-rabies immunoglobulin (passive for post-exposure prophylaxis)
i. Prodromal phase - long incubation period where virus migrates slowly retrograde along skeletal muscle until it reaches CNS --> flu-like symptoms
ii. Acute neurological - fear of water bc of throat spasms, paralysis, agitation
iii. Coma --> Death due to respiratory arrest (~100% fatality)