Retroviruses

A retrovirus consists of a lipid envelope surrounding a protein shell called a capsid. The capsid contains viral proteins, enzymes, and a dimeric RNA genome encoding three major protein types: gag proteins forming the core structure, envelope proteins for host cell recognition, and Pol proteins including reverse transcriptase, integrase, and RNase H.

After the retrovirus fuses with the host cell membrane, reverse transcriptase transcribes the viral RNA into single-stranded DNA, forming a DNA/RNA duplex. RNase H then degrades the RNA template, and reverse transcriptase synthesizes the complementary DNA strand, creating double-stranded proviral DNA that integrates into the host genome.

Endogenous retroviruses are non-pathogenic transposable elements that remain dormant in cells; the human genome contains 100–1,000 copies. Exogenous retroviruses are pathogenic pathogens that enter cells and exploit host replication and translation machinery to produce viral copies and proteins, including AIDS virus, T-cell leukemia, and Hepatitis B.

Integrase is a viral enzyme that cleaves host DNA and inserts the proviral DNA into the host genome. This integration allows viral genes to be replicated and translated alongside host genes, enabling the retrovirus to hijack the cell's molecular machinery for producing new viral particles and proteins.

Gag proteins form the core structural scaffold of the viral particle, while envelope proteins are embedded in the lipid bilayer to recognize and bind host cell surface receptors. During assembly, the retroviral mRNA is translated into polyproteins that are processed and packaged with the viral genome into the capsid, which is then enveloped by host cell membrane.

Although retrotransposons can form capsid proteins, they cannot synthesize viral envelopes. Without the lipid envelope and envelope proteins, mature virus particles cannot form, preventing horizontal transfer between cells. This fundamental difference distinguishes retrotransposons from exogenous retroviruses that can spread infection.

Approximately 8% of the human genome contains retroviral elements in a latent state, considered fossils of ancient retroviruses. These sequences are immensely helpful in understanding vertebrate evolution, as retroviruses are proposed to have evolved from ancient foamy viruses captured by retrotransposons encoding envelope proteins.