Defective HIV particles may drive inflammation despite long-term viral suppression

Kateryna Kon/

People with HIV experience ongoing low-level inflammation which may contribute to worsened health outcomes compared to the general population, however it has been challenging to pin it down on an exact cause.  Findings of a collaboration of scientists from the US National Institutes of Health link the persistent inflammation seen in people with HIV to defective HIV particles. Their work also confirms the presence of the virus’ components despite undetectable status as described in the journal AIDS.  

Persistent immune activation and inflammation can lead to the exhaustion of the immune system and damage organs and systems over long stretches of time. A heightened overall inflammatory state is at the root of many chronic health conditions such as heart disease. In people with HIV, there could be many reasons to explain low-level inflammation such as certain HIV drugs, smoking and other lifestyle factors, or co-infections. However, the main suspect has always been the virus itself; despite being suppressed it is thought that the virus somehow keeps triggering the immune system.

The mere fact that defective viruses can keep producing foreign proteins in our body would be enough to keep the immune system alarmed and therefore in a constant inflammatory state. The present study confirms that even after many years of viral suppression the presence of defective HIV sequences and proteins correlates with some inflammatory markers.   

These defective viruses cannot multiply successfully, nor can they infect new cells, but they seem to be actively produced in some infected ‘reservoir’ cells. In this study the researchers measured three types of viral components: viral RNA, DNA, and proteins. The viral RNA is the genetic material of HIV that carries the code for its ‘making’ and it exists either freely inside cells or gets packaged in the virus’ coating when going on to infect other cells. The proteins are the components that serve to make the coating of the virus as well as help it copy itself. Inside cells, the viral RNA gets converted into DNA, which is compatible with our own genetic material so that it can lodge itself in our chromosomes – in a way becoming an inextricable part of our cells.

The study

The researchers looked at the presence of the three viral components in a small cohort of people with HIV most of whom were on antiretroviral therapy (ART) and undetectable. Then they tried to trace the link between the amount of these viral components and levels of inflammatory markers such as C-reactive protein, D-dimer, interleukin 6, CD8 cell count and others.


ribonucleic acid (RNA)

The chemical structure that carries genetic instructions for protein synthesis. Although DNA is the primary genetic material of cells, RNA is the genetic material for some viruses like HIV.


immune system

The body's mechanisms for fighting infections and eradicating dysfunctional cells.


The general term for the body’s response to injury, including injury by an infection. The acute phase (with fever, swollen glands, sore throat, headaches, etc.) is a sign that the immune system has been triggered by a signal announcing the infection. But chronic (or persisting) inflammation, even at low grade, is problematic, as it is associated in the long term to many conditions such as heart disease or cancer. The best treatment of HIV-inflammation is antiretroviral therapy.

detectable viral load

When viral load is detectable, this indicates that HIV is replicating in the body. If the person is taking HIV treatment but their viral load is detectable, the treatment is not working properly. There may still be a risk of HIV transmission to sexual partners.

deoxyribonucleic acid (DNA)

The material in the nucleus of a cell where genetic information is stored.

Twenty-three participants agreed to provide samples for the study. Five participants were sampled before they started ART while they had detectable viral loads, while 15 were sampled when they were on treatment with supressed virus for an average of six years. Three additional participants were sampled periodically every three years for an average of 17 years starting from the time before they were on ART.   

Levels of viral components remained unchanged over time

Despite the lack of active viral replication, in the three participants who were followed up for a long time with periodical sampling, the amount of viral DNA, RNA (the one inside cells) and proteins remained present and unchanged although they had undetectable viral loads. (Even when there is no detectable viral RNA in blood, as measured in a standard viral load test, there may be RNA inside cells).

Samples from the rest of the participants showed similar results. In fact, up to 99.8% of all sequenced samples were of defective viruses. The only explanation for this is the multiplication of the virus through clonal expansion of the infected immune cells and production of defective viral components in them.

Clonal expansion is the ability of some immune cells to quickly make many copies of themselves when triggered by a certain agent. In this way, a small number of cells can grow into millions of identical cells. If they contain an HIV virus in them, they will simultaneously multiply the number of integrated viruses as they clone. 

The presence of viral proteins was measured indirectly by measuring the amount of specific antibodies produced against them. All participants retained HIV-specific antibodies over the years which supports the idea that viral proteins are continually produced even when undetectable and that keeps triggering the immune system.

The level of viral components is linked to inflammatory markers

Despite viral suppression following treatment there was little to no decline in the levels of most inflammatory markers such as C-reactive protein and interleukin 6. Also, there was a strong link between the amount of defective viral RNA and viral proteins which indicates that defective viral sequences can keep producing viral proteins. D-dimer, an inflammatory molecule, also correlated positively to the amount of defective viral RNA and viral proteins. Interestingly, but not unexpectedly, the number of CD8 cells, a subset of immune cells responsible for destroying other infected cells, seemed to increase in response to higher levels of defective viral components.


Coupled with the previous major study that suggested that defective viruses may be responsible for detectable viral load, this study strengthens the importance of these defective viral particles and components as a contributing cause for the heightened inflammation seen in people with HIV. It would be difficult to target these defective viruses with drugs as they are not able to replicate and produce new viruses. In a sense, they are ‘dead’, however they act as a trigger for the immune system and possibly increase inflammatory responses and exhaust the body. Nonetheless, these findings offer us a better understanding of the increased frequency of some health conditions in people with HIV despite effective treatment of the virus. They can also reveal newer avenues for exploration and improvement in HIV treatment that are focused on the immune system rather than the virus itself.


Singh K et al. Long-term persistence of transcriptionally-active “defective” HIV-1 proviruses: Implications for persistent immune activation during antiretroviral therapy. AIDS, online ahead of print, August 8 2023, (open access).

DOI: 10.1097/QAD.0000000000003667