Molecular HIV surveillance: friend or foe?

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As part of routine HIV care in many high-income countries, genetic resistance testing is done prior to starting treatment to ensure that a person’s virus is not resistant to a chosen antiretroviral medication. However, in addition to identifying potential drug resistant mutations, phylogenetic analysis of an individual’s virus is also carried out – when compared to other viruses, this provides information about how different viruses are related.

In countries such as the US and Canada, public health officials store this phylogenetic data and use it for molecular HIV surveillance. This type of laboratory surveillance assists with rapidly identifying risk networks and potential outbreaks by comparing viruses to see if they are genetically related. Thus, public health officials can identify growing viral networks in the population and intervene to offer HIV testing, facilitate linkage to HIV treatment, and provide prevention services to those who remain HIV negative.

However, despite the public health benefits of molecular HIV surveillance, there is concern among networks of people living with HIV and activists regarding the ethics of the practice, and the possible role that molecular data can play in HIV criminalisation cases – this is especially relevant as the US and Canada have some of the highest rates of criminalisation for HIV non-disclosure, exposure and transmission in the world.

How molecular surveillance is used

According to the US Centers for Disease Control and Prevention (CDC), molecular HIV surveillance is conducted on clusters of genetically similar viruses and not on people. They emphasise that phylogenetic data is de-identified and that aggregate data from blood tests are compared to identify viruses that are genetically similar and grouped according to various factors, such as when infection occurred, geography and by stage of infection. This approach forms one of the central pillars to the CDC’s 'Ending the HIV Epidemic' in the US. While molecular surveillance is used in combination with traditional epidemiological approaches (such as partner notification), the CDC argues that traditional methods used in isolation are insufficient to quickly identify and intervene in instances of rapid viral spread within networks.



In HIV, usually refers to legal jurisdictions which prosecute people living with HIV who have – or are believed to have – put others at risk of acquiring HIV (exposure to HIV). Other jurisdictions criminalise people who do not disclose their HIV status to sexual partners as well as actual cases of HIV transmission. 

transmission cluster

By comparing the genetic sequence of the virus in different individuals, scientists can identify viruses that are closely related. A transmission cluster is a group of people who have similar strains of the virus, which suggests (but does not prove) HIV transmission between those individuals.


Social attitudes that suggest that having a particular illness or being in a particular situation is something to be ashamed of. Stigma can be questioned and challenged.


The study of the causes of a disease, its distribution within a population, and measures for control and prevention. Epidemiology focuses on groups rather than individuals.

molecular surveillance

The use of data collected during routine drug resistance testing to compare the genetic sequence of the virus in a population and identify transmission clusters. This may allow public health officials to identify populations where transmission is occurring rapidly, indicating gaps in health services that need be addressed.

Molecular HIV surveillance allows public health officials to identify rapidly growing networks of HIV transmission, often in instances where people are not well connected to care, such as in rural communities, migrant groups or injecting drug users. The CDC is specifically interested in clusters where more than five new transmissions have occurred in the past year, with less than 0.5% genetic variation.

Once these clusters are identified, investigation occurs with the help of regional and local health departments. This investigation will examine other sources of data such as demographic and clinical information along with molecular data in order to identify individuals and networks in which HIV is rapidly spreading. Officials identify individuals viewed as a ‘source’ of potential transmission, conduct interviews and then contact as many partners as possible.

Identifying partners has public health benefits and may also be vital for individuals with undiagnosed HIV, as it could mean the period between infection and starting treatment is significantly shortened. However, often these networks of people represent those who are already marginalised, and possibly also vulnerable to criminalisation, due to behaviours such as injecting drug use and sex work. 

In 2017, the CDC used this approach to identify a cluster of men who have sex with men in San Antonio, Texas. The original cluster contained 24 men with linked viruses. However, a further 87 HIV-positive men were identified as sexual or needle-sharing partners of the original cluster. From this investigation, 25 men who had had a lapse in care were re-engaged in care. Additionally, 28 HIV-negative men who were linked to the cluster, and therefore at high-risk of HIV infection, were re-tested and one new positive case was identified. 

To address problems that the incident highlighted, the CDC sent out alerts to their healthcare providers focused on HIV testing and signs of acute infection. They also sent out alerts focused on pre-exposure prophylaxis (PrEP), as it was discovered that very few men who were at-risk for HIV infection were on PrEP at the time. In addition to funds being redirected to assist with scaling up of PrEP, this intervention also led to a coalition with people living with HIV, providers and public health officials aimed at reducing stigma, improving care and eliminating new HIV cases in the city.

In 2018, the North Carolina Department of Public Health identified a large increase in new HIV diagnoses among people who inject drugs between 2016 and 2017. This prompted an investigation, resulting in the identification of a group of seven people with HIV who were linked with each other as sexual or needle-sharing partners. In order to further investigate, public health officials used molecular HIV surveillance combined with traditional epidemiological methods to identify additional contacts. This resulted in 96 contacts being identified, with HIV infection identified in seven individuals, including two new cases of HIV. Additionally, hepatitis C was also newly diagnosed in 20 people. All those who tested positive were referred to treatment. Information about harm reduction services and kits containing materials for hygiene and wound care were provided.

Informed consent?

An issue frequently raised by HIV activists is an ethical one: as phylogenetic analysis is conducted as a secondary use of routinely collected information, people living with HIV have not provided informed consent for their health data to be used for the purposes of public health surveillance. While data may be de-identified and aggregated, the examples above show that, when molecular surveillance is combined with traditional forms of epidemiological investigation, the technique rapidly identifies marginalised and stigmatised individuals and groups.

Role in HIV criminalisation cases

In countries such as the US and Canada, molecular HIV surveillance is viewed critically against a backdrop of widespread HIV criminalisation, including for non-disclosure, possible exposure or alleged transmission. While these laws have not been shown to reduce the number of new HIV cases, and instead contribute towards HIV-related stigma, they have been incredibly resistant to change or efforts at modernisation.

"Often these networks are of groups who are already marginalised, and possibly also vulnerable to criminalisation."

Molecular HIV surveillance cannot indicate with certainty the direction of HIV transmission. Various possibilities could exist, even in the case of linked viruses, that make it challenging to say for sure that one person infected another – for instance, both people could have been infected by a third person whose viral genetic information is not in the system.

However, phylogenetic information has frequently been used in HIV criminalisation cases. Despite courts not being able to prove the direction of transmission with certainty, genetic data has been used to identify a relationship between viral samples in numerous cases. When combined with other pieces of information, molecular HIV data has the potential to be used by courts to infer the direction of transmission. (Similarly, if no phylogenetic link exists, this can be used as a defence.) Critics argue that any tool which leads to increased policing, criminalisation and prosecution of those living with HIV should be handled with caution.

While molecular HIV surveillance may hold some promise for more effective and rapid public health responses, it raises crucial questions regarding consent, of both individuals living with HIV and the broader community of those affected by HIV, as well as the possibility of public health data serving the detrimental ends of further marginalisation and criminalisation of people living with HIV.


Bernard EJ et al. "We Are People, Not Clusters!The American Journal of Bioethics 20.10,  2020 (open access).

McClelland A et al. The rise of molecular HIV surveillance: implications on consent and criminalization. Critical Public Health 30: 487-493, 2020.

Monterosso AC et al. Identifying and investigating a rapidly growing HIV transmission cluster in Texas. Conference on Retroviruses and Opportunistic Infections, Seattle, poster 845LB, 2017.

Oster MA. Hugging phylogenetic trees: use of molecular analysis for public health intervention. Conference on Retroviruses and Opportunistic Infections, Seattle, presentation 68, 2019.

Samoff E et al. HIV Outbreak Control With Effective Access to Care and Harm Reduction in North Carolina, 2017–2018. American Journal of Public Health 110: 394-400, 2020.