Publication date: Sep 05, 2025
Ongoing viral evolution in immunocompromised individuals with persistent infection may facilitate the evolution of SARS-CoV-2 and emergence of variants of concern (VOC). This study was conducted in the Western Cape Province of South Africa where the HIV prevalence is around 8%, with limited information on the frequency of persistent SARS-CoV-2 infection, the pattern of evolution in these individuals, and if these variants contribute to the diversity of circulating viruses. This study investigated 75 individuals with two or more SARS-CoV-2 diagnoses at least one month apart. Of the 75, 13 were people living with Human Immunodeficiency Virus (PLWH) of which three were immunocompromised, 23 were HIV-negative, and the status of the remaining 39 was unknown. SARS-CoV-2 full-length genome sequence analysis identified 72 as reinfections with a distinct variant and 3 as persistent infections with B. 1.1 (20B), B. 1.1. 459 (20B), and B. 1.351 (20H) for 7, 4, and 3 months, respectively. All persistent infections were in severely immunocompromised PLWH with CD4+ T cell count below 30 cells/uL. We identified the emergence of uncommon mutations (global prevalence
| Concepts | Keywords |
|---|---|
| 20h | COVID-19 |
| Africa | evolution |
| Genome | immunocompromised |
| Hiv | intra-host |
| Host | SARS-CoV-2 |
Semantics
| Type | Source | Name |
|---|---|---|
| disease | IDO | host |
| disease | MESH | persistent infection |
| disease | MESH | SARS-CoV-2 infection |
| pathway | REACTOME | SARS-CoV-2 Infection |
| disease | IDO | immunodeficiency |
| disease | MESH | reinfections |
| disease | IDO | cell |