Pathogenesis is disease. Normal flora are part of host’s normal microbial community. Primary pathogens infect healthy hosts. Opportunistic pathogens infect compromised hosts. Virulence is a quantifiable measure of pathogenicity. Parasites do not kill the host. Parasite: consume host resources at host expense. A parasite is an organism that lives in or on the living tissue of a host organism at the expense of that host, but without immediately killing the host. The biological interaction between the host and the parasite is called parasitism. Parasitism is a type of symbiosis, by one definition, although another definition of symbiosis excludes parasitism, since certain types of DNA, such as transposable elements and B chromosomes, may also be considered as parasites of the host genome.
Some organisms are parasitic only during a part of their lifecycle. Many cuckoos, for example, are brood parasites: their young are parasitic on the host species, but adult cuckoos fend for themselves.

Salmonella is a gram-negative intracellular pathogen

T breakthru host immunse system and cause diseaseExposure to host, adherence to host titissue & recognize it carbo, lipd etc, invasion host cell invsaion/nucleus/organelles/tissues, growth and disseminationFirulence factors…act directly on host tissues or indirect: produce ppooclined by it
Virulence factors…host cell damage host defenses: physical like pH, skin or immune system innate and adaptive

Parasites do not kill the host.

1) exposure
2) adherence
3) invasion
4) growth and dissemination
5) virulence factors
6) host cell damage
7) evade host defenses

As with bacterial colonies, it is easy to screen for presence of a virus. When overlaid onto a bacterial lawn, a single virion will create a visible clearing in the lawn. These clearings are called viral plaques, and the virion responsible is called a plaque forming unit (pfu). A large percentage of virions produced will not be capable of infection. Therefore, is important to determine particles per pfu. For example, if for every pfu there are 100 ineffective virions, then particles per pfu = 100.

The following experiment shows the growth pattern of a virus. The methodology is as follows:

• Prepare a bacterial culture in exponential growth.
• Add 10⁴/mL virions.
• Incubate, removing 100µL every 2 minutes.
• Dilute each aliquot 10⁶χ
• Overlay each aliquot onto a bacterial lawn.
• Incubate overnight
• Repeat this experiment, except add chloroform (CH₃Cl) to each aliquot before dilution.

The chloroform will dissolve cytoplasmic membranes, lysing the cells, but the virions will remain unharmed. The following graph shows the results. The y-axis represents pfu/mL, and the x-axis represents time. Solid is without chloroform, dotted is with chloroform.

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|                    ....__.__.__.__.__.__.__
|                   .   /
|                  .   /
|                 .   /
|                .   /
|               .   /
|______________.___/
| .           .
|  .         .
|   .       .
|    .     .
|     .   .
|      ...
|_____________________________________________

Notice there are two differences between pfu/mL with and without chloroform:

• With chloroform, there is a dip. This is because the viable viruses infect cells and degenerate, causing a temporary decrease in pfu.
• With chloroform, the graph peaks sooner. While usually it takes a while for the viruses to lyse the host cell, that phase is eliminated because the lipid bilayer is dissolved by chloroform.

Viruses have three major differences from bacteria: their genome organization, characteristic mode of replication, and effect on host cell (either death, fusion, or transformation). Viruses are not alive in and of themselves. Instead, they are obligate intracellular parasites capable of replication and reproducing within living cells. A complete virus particle or virion may be regarded as a block of genetic material (nucleic acid) surrounded by proteins (capsid) to protect the nucleic acid. In some viruses, the nucleocapsid (nucleic acid and capsid) is surrounded by an envelope (made of lipids, proteins and glycoproteins). In addition, most viruses are much smaller than bacteria. However, the largest viruses are the same size as the smallest bacteria.

Virus multiply in particular host cells. This is defined by the host cell range of the virus. In transfection, entry does not depend on specific receptors. That is why transfection can be performed on a large host cell range. Host cell range is determined by:

• Specificity of attachment (receptor on cell surface)
• Availability of cellular factors required for viral replication

Breakdown of Events in Viral Life Cycle

1. Attachment or adsoprtion: viruses bind to cells via specific receptor on the surface of the cell. htese are generally proteins or glycoprtoeins. cells naturally lacking poliovirus receptors or in which ireceptor for influenza viruss are enzymatically destroyed are resistant to infection from these viruses….for some viruses use both receptor and coreceptor.
2. Penetration…viruses generally penetrate thoruhg one of the following means: direct fusion with cell membrane releaseing content of virus into cell, by being enveloped into a coated pit which is a vesicle whose outer walls are coated with protein clathrin.
3. Uncoated and elcipse…within the cell, the coated pit will fuse wiht lysosomes, and the lower pH inside the lysosome results in: (i) fusion of the viral emmbrane to the mebrane of the lysosome and (ii) partial uncoating of the capsid. the viral nucleocapsid is then released intot he cytoplasm of the cell. it may remain here for some viruses (cytoplasmic viruses) or migrate into the nucleus for tohers (nuclear viruses). Uncoating of the virion results in eclipse or loss of inefectivityy (failure to recover infectious virus from infected cell).
4. synthetic phase…review of gene expression..DNA replication, transcription, splicing and translation. In order to complete their replication, all viruses must accomplish a common series of events…(i) synthesis of mRNA (ii) translation of mRNA to virus-specific proeins (iii) replciation of viral genome….ss and dsDNA viruses replicate their DNA in a manner similar to ellular DNA replication semi-conservative…
5. Release of progeny virion. Capsid protein and nucleic acids are assembled into virion particles. There are 2 ways the virions can be released:
   • Lysis of cells. For some viruses primarily the non-enveloped and POX viruses, infected cells are lysed by a viral proces to liberate viral progeny.
   • Budding: Enveloped viruses are released by a process known as budding through the cell membrane. viral envelope proteins are incorporated into specific regions of host cell membranes. the assembled nucleocapsid ithen buds though these patches containing viral envelope proteins, possibly some cellular proteins and lipids and becomes enveloped by them. thus budding forms viral envelope.

There are 5 common ways to assay viruses:

There are 3 common ways to combat viruses: