A new study shows how Covid-19 infection persisted at high levels for over six months in a woman living with advanced HIV disease, and led to potentially dangerous Covid-19 mutations developing. The research reveals a possible route for how new variants of concern may emerge, and underlines the importance of appropriate antiretroviral therapy for people living with HIV.

The work, which is deposited as a pre-print on medRxiv, was led by Farina Karim and Professor Alex Sigal from Africa Health Research Institute (AHRI) and Professor Tulio de Oliveira from the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP). It adds to a growing body of evidence that shows mutations can arise in people with severely compromised immune systems and prolonged infection with Covid-19.

In this study, the researchers describe the case of a 36-year-old, HIV positive woman who is a participant in AHRI’s Covid-19 research cohort in Durban, South Africa. AHRI established the cohort, which currently tracks over 500 people, in 2020 to investigate the effect of HIV on Covid-19 infection over time. South Africa has an estimated 7.5 million people living with HIV, and the world’s largest HIV treatment programme with an estimated 5.2-million people on ART. Despite this, there remains a large burden of advanced HIV disease, which the WHO defines as a CD4 count of under 200. While previous research from the cohort has shown that people with well-controlled HIV do not necessarily have worse outcomes from Covid-19 infection, little is known about the effects of Covid-19 on those with advanced HIV disease.

The research participant had been on ART since 2006 but developed drug resistance to therapy. She was admitted to hospital in September 2020 with Covid-19. She stayed in hospital for nine days but continued to test positive for Covid-19 for 216 days. A dedicated team of clinicians associated with the study started intensive monitoring of the participant and changed her ART regimen to include dolutegravir. Her HIV was successfully suppressed with this regimen and, shortly after, she tested negative for Covid-19. The researchers analysed the stored virus from the participant and found evolution of SARS-CoV-2, the virus which causes Covid-19, with many mutations – or changes in the virus’ genetic code. Some of the changes were similar to those common to variants of concern.

Above: HIV-1 viral load in log scale (blue, left y-axis) and mean SARS-CoV-2 RT-PCR cycle threshold (Ct) value (orange, right y-axis) at each sampling time point. 

“This research underlines the importance of prioritising getting people on effective ART, especially those living with advanced HIV. This will help prevent the spread of Covid-19, as well as associated mutations and variants,” said Prof Sigal. “Our next steps are to explore whether the mutated viruses which we identified in this research can escape neutralisation from antibodies generated from previous infection. This will help us to understand if the mutations which we identified are in fact steps to a new variant.”

Access the full paper here.