# Retroviruses - Özgün Doğa Aşık

Retroviruses have contributed significantly to the advancement of molecular biology and modern virology. Furthermore, ever since discovering of HIV, they have always been at the focus among all biomedical study.


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> **FIGURE 17.1 The virion structure of retrovirus.**

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**Discovery**
- An avian virus which produces tumors in chickens was the very first retrovirus found.
- Since the discovery of Rous sarcoma virus (RSV), retroviruses have been found in a wide range of species, including mice, rats, and primates.
- Just a few years after the discovery of human T-lymphotropic virus (HTLV-1), HIV was discovered as an etiological agent of acquired immunodeficiency syndrome (AIDS).

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**Classification**
- Simple and complex retroviruses are the two major types of retroviruses. The first encodes three polyproteins, called Gag, Pol, and Env, while the second encodes six accessory proteins as well as these polyproteins.


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> **FIGURE 17.2 The RNA genome structure of retrovirus. Retroviral genome is a single-strand RNA of 8-10 kb in length. The ORFs for Gag, Pol, and Env are denoted by constituent viral proteins. Three cis-acting elements in the 5' noncoding region (ie, R, U5, and PBS), and three cis-acting ele- ments in the 3' noncoding region (ie, PPT, U3, and R) are denoted. The 5' and 3' splice sites (SS) are denoted, respectively. ψ for packaging signal.**

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# **THE LIFE CYCLE OF RETROVIRUS**


> FIGURE 17.3 shows that direct fusion allows the retrovirus to enter the cell.

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1. During viral entrance, reverse transcription (RT) takes place in the cytoplasm.
2. PIC (duplex DNA) enters the nucleus and is placed into the chromosome, transforming the cell into a “pro-virus” condition.
3. Two viral RNAs are transcribed (genomic and subgenomic).
4. Env proteins (such as SU and TM) are translated in the ER/Golgi and then delivered to the plasma membrane.
5. Gag recognizes and packages two genomic RNA mole- cules.
6. Capsid assembly proceeds in tandem with budding at the plasma membrane.

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***Reverse Transcription:***

- During the reverse transcription entrance phase, viral DNA is synthesized in the cytoplasm. Inside the capsid, reverse transcription, that transforms RNA to double-strand DNA, is performed by RT, that has reverse transcriptase activity. Reverse transcription yields a double-stranded DNA strand that is linear.

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# Attachment and Entry

- When the nuclear membrane is disrupted during the M phase of the cell cycle, PIC, a precursor for chromosomal integration, accesses the nucleus. As a result, retrovirus infection is limited to cells that are dividing and in the M phase of the cell cycle. In reality, basic retroviruses are incapable of infecting dormant cells.

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> FIGURE 17.4 Model for HIV entry via direct fusion.

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The gp120 envelope glycoprotein of HIV particles binds to the CD4 molecule expressed on the plasma membrane of CD41 T lymphocyte. The gp120-CD4 binding induces the conformational changes in gp120, which allows coreceptor (CCR5 or CXCR4) binding of gp120. As a result of the interaction between gp120 and the coreceptor, the “fusion peptide” embedded in gp41 (TM) becomes exposed, and is inserted into the plasma membrane, thereby triggering the membrane fusion. Consequently, the viral capsid penetrates into cytoplasm via direct fusion.

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***Integration:*** PIC, a chromosomal integration precursor, reaches the nucleus, and DNA is integrated into the chromosome. When it comes to the chromosomal site, integration happens at random, but it happens properly when it comes to the viral sequence (Fig. 17.5). During integration, the nucleotide sequence at the very end of the LTR is retained. The implanted viral DNA is referred to as a "provirus" which refers to a virus's predecessor.


> FIGURE 17.5 The structure of DNA genome.

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# Transcription

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- The provirus, which is a chromosomal duplicate of the viral DNA, produces retroviral RNAs. The U3 element at 5' LTR serves as a promoter for RNA polymerase II transcription. As a result, viral RNAs have a 5' cap on one end and a poly tail on the other. The viral RNAs are spliced into a subgenomic RNA by alternative splicing.

- The total genomic RNA has two functions. It functions as both an mRNA for GagPol polyprotein translation and an RNA template for viral reverse transcription. The spliced subgenomic RNA, on the other hand, functions as mRNA for Env polyprotein translation.

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# Translation

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- Retroviruses essentially have three polyproteins in common (ie, Gag, Pol, and Env). Indeed, GagPol and Gag polyprotein are both translated from genomic RNA. The second ORF, Pol, is produced as a GagPol fusion protein, which is then processed into Gag and Pol polyprotein.

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**Here's a video about Retrovirus transcription and translation cycle:**

{%youtube eS1GODinO8w%}

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# Packaging and Assembly


> FIGURE 17.10 The capsid assembly and release.

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- The Gag attaches to the genomic RNA in the cytoplasm and starts the retroviral assembly process.
- The Gag/RNA complex is directed to the plasma membrane, where it is assembled into capsids. (Fig. 17.10)
- The NC domain of Gag recognizes the packaging signal and initiates RNA genome packaging.
- Subgenomic RNA is excluded from packaging as the packaging signal is spliced out. (Fig. 17.2)
- Ultimately, Gag recognizes and packages the dimeric RNA genome.

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# Release

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* The Env polyprotein is glycosylated and processed into the SU and TM proteins, that are then transported to the plasma membrane.
* The modified Gag proteins are attracted to the plasma membrane.
* The envelopment of the capsid is aided by TM-Gag interaction at plasma membrane. In other words, the capsid assembly and the envelopment are related.

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***Maturation:*** After the virion is released, the virion is triggered by the activation of PR protease and maturation is initiated by the activation of PR protease. It is accompanied by morphological changes such as capsid condensation.

*Source: [Maturation of Retroviruses](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6730672/)*

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# HIV (Human Immunodeficiency Virus)

HIV is a virus that attacks cells that help the human body fight infection, making the person more sensitive to several other diseases and infections.
*Source: [What is HIV?](https://www.hiv.gov/hiv-basics/overview/about-hiv-and-aids/what-are-hiv-and-aids)*



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HIV's virion structure is similar to that of basic retroviruses. The spike is on the viral envelope (Fig. 17.11). However, there are a few noticeable variances. The HIV capsid, unlike basic retroviruses, is cone-shaped. It's a spherical icosahedral capsid with an extended deviation. HIV is the only animal virus with a cone-shaped capsid. Moreover, some accessory proteins like Vpr are enclosed within the nucleocapsid. HIV's genomic RNA is 9 kb in length, slightly longer than that of basic retroviruses.


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# The Lifecycle of HIV

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Entry: Unlike simple retroviruses that enter cells by receptor-mediated endocytosis, HIV enters cells mostly through direct fusion.

Nuclear entry: HIV can infect both nondividing and dividing cells, which distinguishes it from simple retroviruses. The viral capsids of simplex retroviruses reach the nucleus by nuclear membrane breakdown that occurs during the M phase of proliferating cells. In nondividing cells, the HIV capsid can reach the nucleus through a nuclear pore.

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HIV genotypes are divided into two: HIV-1 and HIV-2.

HIV-1 is mainly responsible for the global HIV epidemic, whereas HIV-2 is the cause of AIDS in West African countries.

The genome structure of HIV-2 is remarkably similar to that of HIV-1, with the exception that Vpu is not present in HIV-2; instead, Vpx is present. We're concentrating on HIV-1 in here.

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Source: [Nuclear landscape of HIV-1 infection and integration, 2017](https://www.nature.com/articles/nrmicro.2016.162)

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The use of bioengineering techniques has the potential to lead to the discovery and development of an effective HIV vaccine. The overall goal is to engineer immunity using a combination of virology and bioengineering to generate innovative vaccine design, and development of delivery systems.
Source: [Engineering immunity for next generation HIV vaccines, 2020](sciencedirect.com/science/article/pii/S0264410X19314094)

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HIV is one of the most difficult infections to target with a vaccine, affecting more than 38 million people worldwide. Here is a video about latest vaccine approach (Feb, 2021):

{%youtube BrmXpMmvHWw%}

These fascinating findings are the result of incredibly innovative and ingenious science.

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