CCR5 is necessary for HIV entry into the host cell. CCR5 is expressed by macrophages, dendritic cells, and CD4 T cells. It is thought to be the major co-receptor for establishing primary infection, since individuals who are homozygous for a mutation in CCR5 appear to be resistant to infection by HIV. For example, the CCR5-Delta32 deletion mutation seems to confer resistance against HIV-1 by blocking its attachment to CCR5 so that HIV cannot gain entry to the cell. Development of drugs directed at chemokine receptors is thus an active area of research.

On the other hand, CXCR4 is the other major co-receptor for HIV. Lymphotropic HIV uses CXCR4 found on T cells and requires a high density of CD4 on the cell surface. CXCR4 also binds the CXC-chemokine stromal-derived factor-1 (SDF-1) as a co-receptor. Both co-receptors are G-coupled proteins with 7 transmembrane spanning domains. Mac-1, also called CD11b/CD18, is stored in specific granules that are shuttled to the granulocyte surface. It exists as a chemoattractant activation-dependent molecule that undergoes a conformational change upon stimulation. Until stimulation occurs, it remains in a resting, non-adhesive state. Mac-1 is a β2 integrin. SDF-1 is a small chemokine of the CXC subfamily that is produced constitutively by bone marrow stromal cells and has an important role in early stages of B cell development. It is a growth factor for B cell progenitors and a chemotactic factor for T cells, monocytes, CD34+ hematopoietic progenitor cells, mature megakaryocytes, and dendritic cells. Interleukin-8 or IL-8, a CXC chemokine, is an 11-kDa homodimer of 99 amino acids that is also known as monocyte-derived neutrophil chemotactic factor (MDNCF). It is an important mediator of neutrophil, lymphocyte, and basophil chemotaxis and activation. It is released from several cell types in response to an inflammatory response.

The flu virus can be either live attenuated or inactivated. The center for disease control and prevention (CDC) recommends giving the flu virus annually to healthy adults, pregnant women, and children older than 6 months of age. The virus is different from year to year, and the vaccine each year represents the most common active forms of the virus. Vaccination is a type of primary prevention.

Viral replication takes place in several stages. Once the virus recognizes the target cell, it binds to the cell. The viral attachment protein present on the surface of virion interacts with the cell receptor. Following attachment the virus can penetrate the cell by process of endocytosis or fusion. In the step of uncoating the capsid the envelope is removed and viral nucleic acid is released inside the host cell, so the viral genes become available for transcription.

In the protein synthesis step the process differs according to type of virus and the structure of genome. RNA virus mostly replicates in the cytoplasm. Plus-strand RNA viruses initiate protein synthesis. Minus-strand RNA virus, double-stranded RNA viruses, and DNA viruses initiate nucleic acid synthesis. Protein synthesis in DNA virus replication is divided into early phase and late phase. Once the replication is over the newly synthesized viral protein and nucleic acid is assembled inside the cells. The capsomers are self assembled into capsid. In enveloped virus the viral envelope is added from the cell membrane and becomes associated with nucleocapsid. The newly assembled virus is released from the cell by budding or cell lysis.

Aspergillus flavus is a mold species commonly found in peanut butter and many other foods. It produces aflatoxin, a toxin linked to increased risk of liver cell cancer. The other mold species listed are not considered to be related to liver cancer. Cladosporium species are rarely harmful to humans. Penicillium species produce antibiotics, which we commonly use to treat infections. Mucor species cannot grow in warm temperatures, and are unable to infect humans, with the exception of certain heat-tolerant strains, which may cause some zygomycosis.

Candida albicans is a fungus present in the normal flora of humans. An overgrowth of this fungus may cause yeast infections of the skin, vagina, or mouth. After a child receives antibiotics, they may contract a mycotic diaper rash due to Candida albicans overgrowth since the normal bacterial flora have been eliminated by the antibiotics. Pneumocystis jirovecii may cause pneumocystis pneumonia. Blastomyces dermatitidis and Aspergillus fumigatus may cause lung infection if the spores are inhaled. Lastly, Sporothrix schenckii may cause a skin infection called Sporotrichosis after it enters through a break in skin integrity.

Prions are infectious protein particles that affect proteins, misfolding them and causing loss of function. They are most commonly found in the brain. Prion diseases are also called transmissible spongiform encephalopathies (TSEs) and include diseases such as mad cow disease and Creutzfeldt-Jakob disease.

Fungi are similar to plants in that they both have cell walls (fungi have chitin cell walls and plants have cellulose cell walls) but they do not contain chlorophyll. Fungi such as Candida albicans are present in the normal flora of the human body. An overgrowth of fungi can cause mycotic infections such as a vaginal yeast infection, or orally as in thrush.

A retrovirus is an infectious particle consisting of an RNA genome packaged in a protein capsid, surrounded by a lipid envelope. This lipid envelope contains polypeptide chains, including receptor-binding proteins that link to the membrane receptors of the host cell, initiating the process of infection. In order to replicate, its genetic material (RNA) must first be converted to a DNA molecule by the enzyme reverse transcriptase. This enzyme, which is found in the virus particle, is a DNA polymerase that uses an RNA molecule as a template to synthesize DNA, resulting in an RNA/DNA double helix.

Further enzyme action leads to the synthesis of a DNA double helix using the RNA/DNA template. This DNA helix can then integrate into the host chromosome and be transcribed into RNA molecules coding for capsid proteins, envelope proteins, and the reverse transcriptase. This integration into the host DNA is carried out by the viral integrase. Integration into the host chromosome is required for the synthesis of new viral RNA molecules. A host cell RNA polymerase is responsible for this transcription. Many new virus particles are then assembled containing the RNA molecule and the enzyme reverse transcriptase.

Mononuclear phagocytes (MNPs), which consist of blood monocytes, tissue macrophages, and dendritic cells, are the main cellular elements responsible for elimination of viral pathogens. At the same time, MNPs are the targets and reservoirs for many viruses. Most noteworthy, the MNPs utilize phagocytosis as the first battle armament against the onslaught. This greatly diminishes the quantity of virus until other aspects of the immune system can be activated.

Utilizing a number of antimicrobial mechanisms, macrophages can prevent infection or replication of the virus in other cells, representing an additional protection mechanism. Antibodies produced in response to viral infection may lead to either neutralization or lysis of the target cells. This is partially governed by the macrophage, functioning nonspecifically as an effector cell for antibody dependent cellular cytotoxicity. In addition, both macrophages and monocytes can either activate or be activated upon by cytokines to further increase their antiviral vigilance.

The uptake, processing, and delivery of viral antigens to T cells in the lymph nodes referred to as antigen presentation rounds out the defense mechanisms utilized by macrophages. Monocytes and dendritic cells also function as antigen presenting cells.