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HIV – The Virus Behind One of Human's Biggest Pandemics [Part One]

Editor: This article is the first of a two-part series. Check out Part Two here.

If you have read our article, “Introduction to Virology”, you’ll hopefully know some of the basics about viruses, such as what they are and what they infect (if not, I’d recommend having a read of the article before carrying on with this one).

As a brief reminder, viruses are obligate, intracellular parasites which depend on their host cell to survive and, at their simplest level, are made up of a protein capsid surrounding their nucleic acids (i.e. the genome). They can infect a range of hosts such as animals, plants, bacteria and even other viruses.

In the following two articles, we will be exploring one of the most significant human pathogens – the Human Immunodeficiency Virus (HIV).

Since HIV first infected humans in the early 1900s, the virus has caused approximately 35 million deaths, with around 37 million people currently infected with it. The virus infects vital immune system cells, such as T-helper cells, and if left untreated, can cause the fatal disease known as AIDS (Acquired Immunodeficiency Syndrome).

In the relatively short history of the disease, lots of progress have been made in our understanding of the virus. As a matter of fact, we already know its transmission mechanism and have developed successful therapies to allow patients to live a healthy and almost normal life. However, 1 in 25 people in Africa are still infected with the virus, while in 2019, there were 690,000 HIV-related deaths across the world. So, there is clearly lots more work to be done in order to understand and control the spread of HIV infections.

“Part 1” will look at the HIV’s classification, structure and genome as well as its lifecycle and the stages of infection. On the other hand, “Part 2” will explore the history of the HIV/AIDS pandemic and the search for a cure and vaccine..

Classification of HIV

HIV-1 and HIV-2 are both members of a genus called Lentivirus and the Retroviridae family, as shown in Figure 2.

Under the Baltimore classification system, which categorises viruses based on their genome, retroviruses are in group VI. Group VI viruses are single-stranded RNA (ssRNA) viruses that encode an enzyme known as reverse transcriptase.

Firstly, we will discuss what a retrovirus is. As mentioned before, virion particles (i.e. the complete form of a virus) at their most basic level consist of a capsid and genome. However, retroviruses are much more complex than this. Firstly, retroviruses are enveloped viruses, which means that they have a host-derived lipid membrane surrounding their capsid (basically a protein coat). Secondly, retrovirus virion particles carry a number of proteins, such as reverse transcriptase and protease. The reverse transcriptase enzyme is an RNA-dependent DNA polymerase. This means that it uses the virus’s RNA genome as a template to produce complementary DNA in a process called reverse transcription (See Figure 1). The DNA is then integrated into the host genome.

Figure 1: An illustration of reverse transcription and integration of HIV into the genome of the host cell. Reverse transcriptase produces complementary DNA from the RNA genome of HIV. This DNA is then integrated into the host cell’s genome. Figure created on BioRender.

Figure 2: The classification of retroviruses into genera, with examples of different viruses in each genus. This diagram was adapted from Veterian Key (2016).

HIV groups

In essence, there are two types of HIV which are related (See Figure 1), but their genome differs by around 55%.

The more infectious type, HIV-1, is spread across the world and is responsible for 95% of all HIV cases. HIV-2 is the second type, where it is significantly less common as well as less virulent, and is mainly found in Western Africa.

Figure 3 shows how HIV-1 is divided into distinct groups. Each group is a result of an individual ‘transmission event’ – do remember this term as we will be discussing it later on.

Group O (meaning ‘outlier’) is endemic to a few African countries, meaning it is restricted to these countries and is maintained at a constant level. Meanwhile, Group N (stands for non-M/non-O) and Group P are both very rare, with only a few cases reported in Cameroon. Finally, 90% of HIV-1 cases are caused by Group M (stands for ‘major’), which is the strain that is responsible for the HIV/AIDS pandemic. This group can be further divided into subtypes (Check out Figure 1) or clades (defined as groups of evolutionarily related viruses), with different subtypes being more common in different geographic regions. For example, subtype B is dominant in Western Europe, America, Thailand, Japan and Australia.

A number of subtypes called CRFs (stands for ‘circulating recombinant forms’) have also been identified – these are ‘hybrid viruses’, which are produced when 2 different subtypes co-infect (i.e. simultaneously infect) a cell and ‘recombine’ (See Figure 4). Recombination (the exchange of genetic material) in HIV occurs when reverse transcriptase (See Figure 1) switches between two different RNA templates to produce a recombinant DNA.

Figure 3: Diagram showing the two distinct types of HIV (HIV-1 and HIV-2), both of which can be divided into different groups. HIV-1 Group M is responsible for most HIV infections and the global HIV/AIDS pandemic. This group can be further divided into subtypes, whereby different subtypes have different geographic distributions. CRFs (i.e. circulating recombinant forms) are formed when two different HIV-1 subtypes co-infect a host and recombine. Only Group A and Group B have been shown in the diagram for HIV-2 as these cause the majority of HIV-2 infections. On the other hand, Groups C-G are ‘non-epidemic’ as they have only caused single person infections. This figure has been adapted from Avert (2019), HIV strains and subtypes.

Figure 4: Recombination in HIV begins with the co-infection of a single host cell by two different strains of the virus, which can lead to the production of a hybrid virus. When this hybrid virus infects another cell, its reverse transcriptase can switch templates, so a recombinant HIV is produced. Template switching occurs during reverse transcription when reverse transcriptase, which produces viral DNA, falls off the RNA template of one virus and then resumes its job on the other virus’s RNA. This diagram was adapted from Etienne & Holmes (2011)’s Why do viruses recombine?. Figure created on BioRender.

The HIV-1 genome and particle structure

From here onwards, we will look specifically at HIV-1 because it is more significant than HIV-2 as a pathogen in humans (and also therefore more widely understood and studied). Like all retroviruses, HIV-1 has a diploid ssRNA genome, whereby each virion particle carries two copies of its RNA genome (See Figure 4a).

The genome has LTRs (long terminal repeats) at the 5’ and 3’ ends. These are regulatory sequences, meaning that they don’t code for proteins, but are involved in controlling gene expression. The genes gag, pol and env are transcribed and translated into polyproteins, which are later cleaved to give nine single, functional proteins (Take a look at Figure 4b).

What kind of things do these three genes do, you might ask? Env encodes proteins embedded in the lipid envelope, whilst proteins encoded by gag make up the internal structures of the virion particle, such as the capsid. Besides that, Pol is transcribed, translated and cleaved into non-structural proteins like reverse transcriptase (See Figure 4c).

The HIV-1 genome also contains six accessory genes – tat, vif, vpr, vpu, rev and nef. These genes are involved in a variety of processes, including regulating gene expression, virulence and assembly.

Figure 5a: Schematic of the HIV-1 genome. The arrows point to the final protein products, which are cleaved from polyproteins. LTR stands for long terminal repeat; gag = group-specific antigen; pol = polymerases; env = envelope protein; TM = transmembrane protein; SU = surface membrane protein. This diagram was adapted from Nkeze et al. (2015). Figure created on BioRender.

Figure 5b: The structure of the HIV-1 virion particle. Adapted from CUSABIO (2018)

Figure 5c: An overview of the functions of the final protein products – gag, pol and env.

What cells are infected by HIV-1?

A virus is specific to one, or more, receptors on its target host cell. This receptor determines the virus’s tissue tropism (meaning the type of cells or tissues that it can infect).

In particular, HIV targets CD4+ cells (See Figure 6). These are cells that have the CD4 glycoprotein on their cell surface, which includes T-helper cells and macrophages.

T-helper cells are a critical part of the adaptive immune system, as they coordinate a range of responses, such as the release of antibodies from B cells as well as the killing of infected cells by cytotoxic T cells by releasing signalling molecules known as cytokines.

In contrast, macrophages are antigen presenting cells (APCs). In essence, they present antigens (i.e. structural molecules that induce an immune response) from foreign pathogens to B and T cells, and this presentation of antigens helps activate B and T cells. Macrophages also carry out phagocytosis to kill bacteria and other pathogens. Therefore, understanding the vital function of CD4+ cells explains how their decline in number in an HIV-infected leads to an immune suppression.

In addition to the CD4 receptor, HIV also requires the presence of a co-receptor to infect a host cell. This can either be CCR5 co-receptor that is located on macrophages, or the CXCR4 co-receptor which can be found on T-lymphocytes.

All in all, this would explain why HIV-1 can therefore be classified as M-tropic (meaning that it infects macrophages that have the CD4 and CCR5 receptors), or T-tropic (i.e. infects T-lymphocytes with CD4 and CXCR4 receptors).

Figure 6: HIV-1 uses CD4 as a receptor and also requires a co-receptor to enter its host cell. With that in mind, the M-tropic HIV-1 strain uses CCR5 as a co-receptor to infect macrophages, whilst the T-tropic strain uses CXCR4 to invade T-lymphocytes. Figure created on BioRender.

How is HIV-1 transmitted?

HIV-1 infection occurs when bodily fluids, such as blood, semen and breast milk, from an HIV-positive person are transferred to an uninfected person.

There are three main mechanisms of transmission:

  1. Sexual intercourse: This is the most common route by which HIV spreads

  2. Mother-to-baby: This method, known as vertical transmission, is less common and can occur in utero (which means ‘in the uterus’), during birth or post-natally.

  3. Exposure to infected blood: This is only responsible for a minority of infections and mainly occurs when intravenous drug users share needles. Other than that, needlestick injuries can also facilitate the spread of HIV. And in rare cases, individuals can become infected following blood transfusions or through infected organ/tissue transplants.

1. Acute infection

Two to four weeks after the initial infection by HIV-1, an infected individual will enter the acute infection phase, where they may be asymptomatic or could experience mild flu-like symptoms (known as acute retroviral syndrome).

During this period, which can last between six to twelve weeks, the virus will replicate and disseminate (i.e. spread through the body) from the initial infection site. As you can see in Figure 7a, the increasing viral load (number of HIV particles present in an individual’s bloodstream) during the acute phase is a result of this replication.

Overall, the acute infection is ‘self-limiting’. This means that the free virus will be cleared from circulation by immune system defences, resulting in a rapid decrease in the viral load.

An example of such defences are anti-HIV antibodies – these are proteins produced by the B cells, and they are specific to HIV antigens, so they can help to clear pathogens from our body. In addition to that, cytotoxic (killer) T cells are also capable of killing infected CD4+ cells, and this contributes to the declining CD4 count (measure of the number of CD4 cells present in an individual’s blood) as seen in Figure 7a.

How did they get activated in the first place? Well, the immune system will know if a cell is infected or not, as infected cells would be producing viral proteins (which are basically antigens!).

2. Asymptomatic HIV latency

In the strong immune response described above, B and T cells specific to the invading pathogen will be selected and increase in number. In general, we call B and T cells ‘specific’ because they recognise and target a single antigen. This will include T-helper (CD4+) cells, which are targeted by HIV.

In any normal infection, most antigen-specific B and T cells will die after the infectious agent has been cleared, with the exception of a small number that will become resting memory cells. These memory cells will then remain in the blood for years in case of reinfection by the same pathogen. Therefore, T-helper cells infected by HIV will then become resting memory cells.

The sneaky side of HIV is that – in these cells, HIV will have integrated a copy of its viral genome into the host’s DNA, using reverse transcriptase. As a result, HIV is now known as a provirus, which means that its viral genome has been integrated into host cell.

This provirus will then remain latent (i.e. dormant) for years. In other words, the viral genome will not be expressed, meaning it won’t be transcribed or translated at all, so no viral proteins are present. As a result, the immune system cannot detect and kill the infected cell.

Furthermore, as the host cell replicates its DNA, the provirus is also replicated and persists in daughter cells. The resulting product is a latent HIV reservoir, which is a group of latently infected cells which aren’t producing new HIV particles. This is bad news as our immune system can kill any free virus, but it cannot eliminate this reservoir.

Not to mention, asymptomatic latency (sometimes called incubation period) can last anywhere from nine months to 20 years, with the average being around 12 years.


Throughout asymptomatic latency, the viral load increases and CD4 count decreases at a relatively slow rate.

When the virus can no longer be controlled, the incubation period ends and the final stage of HIV infection, AIDS, takes place.

As illustrated in Figure 7a, AIDS occurs when the number of CD4+ cells drops below 200 cells/mm(^3) of blood. A decrease in these essential immune cells inevitably translates to a decline in immune activity, so the individual becomes increasingly susceptible to a range of opportunistic infections.

Opportunistic infections are infections that occur more often in immunosuppressed individuals, such as those infected with HIV or receiving chemotherapy. These types of infections can be either viral, bacterial or fungal (Have a look at Figure 7b). For instance, the oncogenic (i.e. tumour-inducing) virus HHV-8 (human herpesvirus-8) is very rare in healthy individuals. However, in immunosuppressed patients, HHV-8 can cause Kaposi’s sarcoma, a type of cancer in the cells lining blood and lymph vessels.

Once an individual has progressed to AIDS, they will die within a few years as a result of such opportunistic infections. Technically speaking, the patient usually dies from these opportunistic infections rather than AIDS itself.

Other symptoms of AIDS include AIDS dementia, which is a consequence of HIV spreading to the brain. The viral load is very high in AIDS patients, so they can typically transmit HIV to uninfected individuals really easily.

Figure 7a: The graph shows how the CD4 count and viral load change as untreated HIV progresses with time. Both CD4 count and viral load are markers that are commonly used to diagnose the stage of HIV infection. In particular, the CD4 count reflects the extent of immunodeficiency, whereas the viral load indicates the amount of HIV particles in the blood by measuring the number of HIV RNA copies present. A healthy individual will have a CD4 count of 500 to 1,600 cells per mm3 of blood. On the other hand, AIDS is diagnosed in individuals with a CD4 count <200 cells/mm(^3). This graph has been adapted from Fauci and Pantaleo, 1996.

Figure 7b: A list of examples of several opportunistic infections that are associated with AIDS.

The life cycle of HIV-1

HIV-1 must undergo several steps to allow it to replicate in humans:

  1. Binding: the gp120 envelope protein of HIV-1 binds to its complementary receptor, CD4, on its host cell before interacting with its co-receptor CCR4/CXCR4 (this would be dependent on the virus’s tropism)

  2. Fusion: gp41 facilitates the fusion of the HIV envelope and host cell membrane, allowing the viral capsid to enter the cell. The outer layers of the virus will remain on the cell surface

  3. Reverse transcription: HIV then uses its reverse transcriptase, which is present in the capsid, to convert its RNA genome to complementary DNA. This is called proviral DNA

  4. Integration: the HIV-1’s integrase, which is also from the capsid, is now used in the host cell nucleus to integrate the proviral DNA into the host genome. The virus is now a provirus. In latently infected cells, the virus remains dormant as a provirus so that it can evade detection by our immune system

  5. Transcription: in an actively infected CD4 cell, HIV proviral DNA will be transcribed – that is, converted to mRNA (messenger RNA) by the host RNA polymerase

  6. Translation: after transcription, the mRNA is translated into viral polyproteins by host ribosomes

  7. Assembly: new HIV proteins and RNA assemble into immature virion particles at the inner surface of the host cell

  8. Budding: the virus is then pushed out of the cell in a process called budding, taking some of the host lipid membrane with it to form its envelope

  9. Maturation: once the virus is released, HIV protease cleaves the polyproteins (product of a single gene, which is cleaved into several, single functional proteins) in the non-infectious immature virion particle to produce the mature virion particle. These mature viruses can now go on to infect more CD4 cells

Do have a look at Figure 8 to guide you through the process!

Figure 8: An illustration of the HIV-1 lifecycle. The steps show the processes that the HIV must go through once it encounters its CD4+ host cell in order to replicate in the host’s body. This diagram was adapted from AIDSinfo (2019), The HIV lifecycle. Figure created on BioRender.

Concluding remarks

Throughout this article, we have looked in some detail at what type of virus HIV is, as well as the structure of HIV-1’s virion particle and genome, and its lifecycle. Furthermore, exploring the nature of HIV-1 as a human pathogen, for example by looking at how it is transmitted and the stages of infection, are essential for understanding therapies for infection and possible cures.

We will discuss HIV treatments in the next article, alongside the origin of HIV and the history of the HIV/AIDS pandemic.

Author: Ambar Khan, BSc Biological Sciences

Disclaimer: All figures created using BioRender are intended solely for educational purposes and not for profit.


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