Patients with uncontrolled HIV infection and severe immunosuppression may be at increased risk for chronic COVID-19 infection, potentially resulting in the emergence of new SARS-CoV-2 variants due to the accumulation of mutations and continued viral shedding. These study findings were published in Clinical Infectious Diseases.
This study involved a 22-year-old woman from South African with uncontrolled HIV infection receiving antiretroviral therapy (ART) with tenofovir plus emtricitabine and efavirenz. The patient was found to be infected with the SARS-COV-2 Beta (B.1.1351) variant for a 9-month period. During this time, the patient received no COVID-19-related treatment as she was asymptomatic throughout the course of infection.
In September 2021, the patient was hospitalized with stridor, reporting a 1-week history of sore throat, malaise, poor appetite, and dysphagia. She was not vaccinated against COVID-19 infection. Results of laboratory studies obtained after admission showed a CD4+ count of 9 cells/µL and a plasma HIV RNA viral load of 4.60 log10 copies/mL, indicating advanced and poorly-controlled HIV infection. The patient reported challenges with ART adherence. At this time, the patient was tested for SARS-CoV-2 infection and was found to be positive for the Delta variant.
One month later, in October 2021, the patient remained hospitalized. After repeat testing was positive for SARS-CoV-2 infection, the patient shared that she had initially tested positive for the infection in January 2021. Whole-genome sequencing of the sample obtained at that time confirmed the patient had been infected with the Delta variant. One month later, the patient tested negative for SARS-CoV-2 infection. Results of laboratory studies showed an HIV viral load of less than 50 copies/mL, suggesting a level of immune reconstitution. The patient was subsequently discharged.
A phylogenetic analysis was performed using all 3 nasopharyngeal swab samples that were obtained from the patient throughout her disease course. The 3 samples were compared against a global reference dataset comprising 7977 genomes. Results suggested that the patient had been infected with COVID-19 infection for the past 9 months. During this period, the virus had acquired at least 10 mutations in the spike glycoprotein and 11 mutations outside the spike glycoprotein, which were beyond the lineage-defining mutations for the Beta variant.
According to the researchers, these findings show “…a potential pathway for the emergence of novel variants but [they do] not prove that any of the variants detected [originated] from such a persistent infection in a severely immunocompromised host.”
Maponga TG, Jeffries M, Tegally H, et al. Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection. Clin Infect Dis. Published online July 6, 2022. doi:10.1093/cid/ciac548