1. Influenza
  2. Retroviruses
  3. HIV


RNA or DNA. Have capsid coat, might have lipid envelope. Helical, icosahedral, or complex shape.
Protein shell enveloping genetic material.
By genomes, capsids, or reproductive strategies.
Baltimore Classification System
Viruses are classified by how mRNA is produced by genes, # of strands, + or - nucleic acids, RNA or DNA.
Intracellular trafficking
Ensures molecules target the correct cell area.
Human viruses
Mostly -RNA.
Plant viruses
Mostly +RNA.
Fungal viruses
Mostly dsRNA.
Mostly tailed dsDNA.
Algae + protozoan viruses
Mostly large dsDNA.


Orthomyxoviridae. Types A, B, C. -ssRNA, enveloped, segmented genome. 8 vRNP (viral ribonucleoprotein segments) in A + B, 7 segments in C. High morbidity and mortality. Must be diagnosed by lab tests.

Type / Town / # of isolates / Year / Major (type of HA + NA). Example: A SINGAPORE 6 66 H1N1.
In humans and swine by respiratory droplets, in birds by fecal-oral.
Fever, headache, sore throat, cough, myalgia, worsen chronic disease, superinfection (bacterial / viral pneumonia), direct rapid progression (severe viral pneumonia).
Because of host resistance (melatonin + Vitamin D), temperature, or changing host behaviour (more time indoors, closer contact).
Genetic drift
Minor HA / NA changes, does not change subtype.
Genetic shift
Major HA / NA changes, can change subtype, from different strains, can cause pandemics.

Types: 16 HA subtypes, 9 NA subtypes. All are in birds. HA 1-3 and NA 1-2 are human flus.

Severe, pandemic, gene shift + drift, treat with Rimantidine and Amantadine.
Less severe, epidemic, gene drift, above antivirals have no effect.
Least severe, gene drift, above antivirals have no effect.


Surface protein that helps attach and penetrate. Binds to sialic acid α2,3 in birds and α2,6 in humans.
Surface protein that helps release from host cell. Cleaves sialic acid and releases. Prevents clumping so that the virus can spread farther.
M2 protein
Endosome acidity helps M2 release vRNP into the cytoplasm which goes into the nucleus to replicate.
M1 protein
Targeting signals to package RNA. Binds to HA + NA.
Suppresses immune system's interferons and prevents activation of Protein Kinase R that would inactivate transcription.


1918 Spanish Flu (H1N1)
Low mortality but widespread. From avian source. Scientists used reverse genetics to remove HA + NA and splice harmless strains. HA + polymerase cause lung damage. Resurrection led to antivirals, vaccines, and discovery that most died from bacterial pneumonia (secondary infection).
Avian flu (H5N1)
Very pathogenic for waterfowl. Can infect mice withhout adaptation. Rarely infects humans but can have high mortality, and cannot transmit from human to human. Difficult to make a vaccine because it evolves continuously, and 2 clades are circulating. More avian flu exists maybe because farms are flu factories. A human was infected aand treated with antivirals in April 2022.
Swine flu (H1N1)
Mild, similar to the flu, has some drug resistance. Filamentous shape. No markers of pathogenicity. Control by hygiene, antivirals, and vaccine (immunoprophylaxis, should not be received if less than 6 months old or have illness with fever). Flu shot (contains 3 inactivated / killed strains). Nasal spray (contains 3 attenuated strains). Quadrivalent (contains 3 strains + another type B virus, egg based or cell / recomb based).


For type A, block viral entry and release
Amantadine, rimantadine. Resistance is a problem. Side effects on nervous system, liver, and kidneys.
For uncomplicated A + B, NA competitive inhibitors
Zanamivir (Relenza), Oseltamivir (Tamiflu), Peramivir (Rapivab, injectable)
Enzyme inhibitors
XOFLUZA (one dose).


Retroviridae. Diploid +ssRNA with polyA tail +5' cap, tRNA primer binding site, some regions of base pairing. Uses DNA intermediates. Icosahedral, enveloped, has tRNA and enzymes. Avian leukemia virus / Rous Sarcoma chicken tumors were discovered. Can infect vertebrates and plants.

Simple: Only make structural genes (gag, pol, env, maybe src) and do not kill cell.

Oncogenic. Leukemia and sarcoma. Example: RSV.
Example: MMTV.
Example: FeLV.

Complex: Make regulatory genes and may kill cell.

Example: HTLV.
Example: HIV.

WBCs review

T cells
Lymphocyte from thymus. T helper (CD4. TH1 secretes IFN that activates macrophages, TH2 stimulates T cells and makes B cells become plasma cells that secrete antibodies) or Cytotoxic (CD8, recognize infected cells). Recognize antigen from APCs. Divide rapidly and become memory cells.
Dendritic cells
APCs, can take virus as trojan horse. In blood, lymph(oid tissue), skin, tissue mucosa.

Structural genes and proteins

Capsid proteins MA (matrix), CA (capsid), NC (nucleocapsid).
Polymerase (p6), RT (with RNase H activities), protease (pr, cuts gag and helps maturation), integrase (in).
Envelope, glycoproteins / peplomer proteins (gp120 + gp41 = gp160) that attach to receptors, transmembrane protein (TM). Makes it hard to make vaccines.

Regulatory genes and proteins

Transactivator. Extends transcription, binds to TAR (transactivating response region) to phosphorylate RNA poly II.
Activates nuclear export of unspliced RNA with RRE. Binds to RRE (unspliced or singly spliced) in env.

Accessory genes + oncogene products

Viral infectivity factor. Needed for continual replication and transmission.
Viral protein replication. Assembly and release of virus, gets viral DNA into nucleus. Promotes G2/M arrest, infects macrophages.
Viral protein u. Promotes budding and release by enhancing Tetherin. Lowers CD4, surrounds nucleus.
Negative factor. Lowers CD4, makes HIV and SIV more pathogenic. Regulatory.

Genome regions

Repeated on both ends. Transcription start site, polyA, TAR.
Unique to 5'. Primer binding site for tRNA / replication.
Primer binding site.
Psi / DLs
Packaging signal / Dimer linkage site.
Unique to 3'. Transcription factors Sp1, TATA, NF-kB.
Polypurine site.


  1. Binding / absorption (bind to receptors)
  2. Fusion / penetration (release viral core into cytoplasm)
  3. RT (+RNA -> -ssDNA -> +dsDNA)
  4. Transport (+dsDNA in cytoplasm -> nucleus)
  5. Integration
  6. Transcription / translation
  7. Assembly
  8. Budding / Release (from plasma membrane)
  9. Maturation (HIV protease cleaves gag / gag/pol polyproteins into individual proteins)


Lentiretroviridae. Diploid +ssRNA, enveloped. Structural, regulatory, and accessory genes. Long incubation period (30 years), Causes AIDS and Kaposi's Sarcoma. Lowers T cells and increases opportunistic infections.


Deltaretrovirus. Same as ATLV. Human T cell lymphoma virus, infects CD4 and causes leukemia.
Infects CD8 and causes a less aggressive leukemia.
"Gallo's virus" / HTLV-III in early 1980s America. Originated from primates. Lower T cell count and opportunistic infections. Later known as LAV in France. Both later called HIV-I
Slower and less infectous. Mostly in W Africa.

mRNA splicing

30 alternative mRNAs, many polycistronic (many ORFs, single gene product is cleaved into different products).

Unspliced (9-kb)
Produce (structural) gag / gag/pol proteins. From late transcription + translation.
Incomplete / singly (4-kb)
Encode (envelope + acc) env, vif, vpr, or vpu.
Fully / doubly (2-kb)
Encode (regulatory + acc) tat, rev, nef. From early transcription + translation.


By body fluids and prenatally. Must overcome physical barrier by abrasions, ulcers, inflammation, or using dendritic cells as trojan horse.
Genes are not expressed, T cells not activated.
Brain (HIV dementia), gut (wasting), heart (cardiomyopathy).
Measure progression
By CD4 count and blood viral load.
Opportunistic infections
CMV, Mycobacterium, Pneumocystis pneumonia, toxoplasmosis of brain, Kaposi's Sarcoma, thrush, yeast, TB, syphillis.
Avoids immune system
By going latent, antigenic changes, fusion of T cells to form syncytium or polykaryocyte, destroying immune system.
By massive production, gp binding to CD4, forming cyncytia, apoptosis, lysing cells by complement system, by AIDS in 2 years without treatment.
AZT, combination therapy, protease / RT / first entry inhibitor. Might be toxic or cause resistance. Difficult to target.


  1. Acute infection: increasing viral load, can be rapid / slow / longterm nonprogressive.
  2. Seroconversion: developing antibodies.
  3. Asymptomatic: immune system controls virus, mononucleosis symptoms may develop.
  4. Symptomatic: physical signs.
  5. AIDS: opportunistic infections, end stage.

Natural immunity

Deficient viruses
Less nef or vpr.
CCR5 polymorphism
1% of Caucasians have this base pair mutation.
CXCR4 3' UTR mutation
1% of Caucasians have this point mutation that delays disease / death.


Living with HIV
37.7 million. 1/2 women.
Newly infected
1.5 million.
Deaths in 2020