Retrovirus

Retroviral family includes γ-retrovirus and lentivirus. It has ability to reverse transcribe its RNA genome into a cDNA copy, and the cDNA copy can be stably integrated into the host cell genome. Retroviruses are usually divided into two types: simple type (sometimes called oncogenic virus or gamma-retrovirus, such as murine leukemia virus) and complex type (such as lentivirus). The main difference between these subtypes is that complex retroviruses have some accessory genes and regulatory genes, while simple ones do not. Both types of virus particles contain two positive-stranded RNAs with viral reverse transcriptase (RT) attached to the RNA, which are located in the core of the virus. Also located in the core are structural proteins and enzymes, including nucleocapsid (NC), capsid (CA), integrase (IN) and protease (PR). The inner core is surrounded by a layer of peripheral protein, which includes matrix protein (MA). MA is surrounded by the peritoneum, inserted with envelope glycoprotein. The peritoneum is derived from the cell membrane of the host cell.

Figure 1 Simple and complex retroviral particle structure.

Retroviral Genome

• Simple retrovirus (γ-retrovirus, murine leukemia virus)

Both simple and complex retroviruses contain two linear, unsegmented, single-stranded RNAs of 7-12 kb in length, encoding gag, pol and env genes. Gag encodes a polyprotein that is translated from a piece of unspliced mRNA, which is then cleaved by viral protease (PR) into MA, CA, and NC proteins. The Env gene also encodes a polyprotein precursor, which is cleaved by intracellular proteases into surface envelope glycoprotein (SU) gp120 and transmembrane (TM) glycoprotein gp41. Among them, gp120 interacts with cell surface receptors and co-receptors. and gp41 forms a gp120/gp41 complex on the viral membrane, which catalyzes membrane fusion when the virus enters the host cell. Because ribosomal frameshift occurs during translation of Gag mRNA, Pol expresses Gag-Pol polyprotein, which encodes three enzymes: RT, PR and IN. These three proteins are attached to the genome of the virus particle. RT protein has the following three activities: (a) RNA-dependent DNA polymerase activity, responsible for transcribing RNA into cDNA; (b) ribonuclease H activity; (c) DNA-dependent DNA polymerase activity. PR is used to cleave Gag and Gag-Pol polyproteins, leading to the maturation of virus particles and the production of infectious virus particles. IN is responsible for integrating the cDNA of the virus into the genome of the host cell. Once the integration is complete, the viral genome is connected to the host cell chromosome and is called a provirus.

• Complex Retrovirus (Lentivirus)

The main difference between the complex retroviral genome and the simple retroviral genome is that the former has a set of accessory genes, and its products involve transcription regulation, RNA transfer, gene expression and assembly. These include Rev and Tat proteins and accessory proteins such as Vpu, Vif, Vpr, and Nef. Rev is an RNA binding protein that guarantees gene expression in the late stage. It is also very important for the transport of unspliced and single-stranded mRNA, which encodes viral structural proteins. Tat is an RNA-binding protein that enhances transcription. Nef protein inhibits T cell activation. Vpu can enhance the release of the virus from the cell surface to the cytoplasm during the entry process. Vif protein is necessary for lentivirus replication, because it can down-regulate the host's antiviral response.

• Integrated Proviral Genome

The integrated proviral genome has long terminal repeats (LTR) at the 5'and 3'ends respectively. The LTR consists of the following three parts: (a) U3 region, which acts as a promoter and contains transcriptional enhancement elements and A TATA box; (b) R region, the transcription start site; (c) U5 region, involved in reverse transcription, with a tRNA primer binding site. Other important sequence elements in proviruses include the packaging signal (ψ, psi) and the polypurine tract (ppt), the latter is the site where the positive strand DNA starts to be synthesized during the reverse transcription process.

Figure 2 The structure of the complex retroviral genome.