Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection

Author:

Karim Farina,Moosa Mohamed YS,Gosnell Bernadett,Sandile Cele,Giandhari Jennifer,Pillay Sureshnee,Tegally Houriiyah,Wilkinson Eduan,San Emmanuel James,Msomi Nokukhanya,Mlisana Koleka,Khan Khadija,Bernstein Mallory,Manickchund Nithendra Nithendra,Singh Lavanya,Ramphal Upasana,Hanekom Willem,Lessells Richard J,Sigal AlexORCID,de Oliveira TulioORCID

Abstract

While most people effectively clear SARS-CoV-2, there are several reports of prolonged infection in immunosuppressed individuals. Here we present a case of prolonged infection of greater than 6 months with the shedding of high titter SARS-CoV-2 in an individual with advanced HIV and antiretroviral treatment failure. Through whole-genome sequencing at multiple time points, we demonstrate the early emergence of the E484K substitution associated with escape from neutralizing antibodies, followed by other escape mutations and the N501Y substitution found in most variants of concern. This provides support to the hypothesis of intra-host evolution as one mechanism for the emergence of SARS-CoV-2 variants with immune evasion properties.

Publisher

Cold Spring Harbor Laboratory

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