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

F. Karim; M. Y. Moosa; B. Gosnell; C. Sandile; J. Giandhari; S. Pillay; H. Tegally; E. Wilkinson; E. J. San; N. Msomi; K. Mlisana; K. Khan; M. Bernstein; N. Manickchund Nithendra; L. Singh; U. Ramphal; W. Hanekom; R. J. Lessells; A. Sigal; Tulio de Oliveira; Tulio de Oliveira

doi:10.1101/2021.06.03.21258228

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

F. Karim
, M. Y. Moosa
, B. Gosnell
, C. Sandile
, J. Giandhari
, S. Pillay
, H. Tegally
, E. Wilkinson
, E. J. San
, N. Msomi
, K. Mlisana
, K. Khan
, M. Bernstein
, N. Manickchund Nithendra
, L. Singh
, U. Ramphal
, W. Hanekom
, R. J. Lessells
, A. Sigal
, Tulio de Oliveira^*

Tulio de Oliveira^*

^*Corresponding author for this work

Department of Immunology and Cancer Research

Research output: Working paper/preprint › Preprint

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 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.

Original language	English
DOIs	https://doi.org/10.1101/2021.06.03.21258228
State	Published - 2021

Keywords

infectious diseases

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10.1101/2021.06.03.21258228License: CC BY-NC-ND

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Karim, F., Moosa, M. Y., Gosnell, B., Sandile, C., Giandhari, J., Pillay, S., Tegally, H., Wilkinson, E., San, E. J., Msomi, N., Mlisana, K., Khan, K., Bernstein, M., Manickchund Nithendra, N., Singh, L., Ramphal, U., Hanekom, W., Lessells, R. J., Sigal, A., ... de Oliveira, T. (2021). Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection. https://doi.org/10.1101/2021.06.03.21258228

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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 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.",

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Karim, F, Moosa, MY, Gosnell, B, Sandile, C, Giandhari, J, Pillay, S, Tegally, H, Wilkinson, E, San, EJ, Msomi, N, Mlisana, K, Khan, K, Bernstein, M, Manickchund Nithendra, N, Singh, L, Ramphal, U, Hanekom, W, Lessells, RJ, Sigal, A, de Oliveira, T & de Oliveira, T 2021 'Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection'. https://doi.org/10.1101/2021.06.03.21258228

TY - UNPB

T1 - Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection

AU - Karim, F.

AU - Moosa, M. Y.

AU - Gosnell, B.

AU - Sandile, C.

AU - Giandhari, J.

AU - Pillay, S.

AU - Tegally, H.

AU - Wilkinson, E.

AU - San, E. J.

AU - Msomi, N.

AU - Mlisana, K.

AU - Khan, K.

AU - Bernstein, M.

AU - Manickchund Nithendra, N.

AU - Singh, L.

AU - Ramphal, U.

AU - Hanekom, W.

AU - Lessells, R. J.

AU - Sigal, A.

AU - de Oliveira, Tulio

PY - 2021

Y1 - 2021

N2 - 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 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.

AB - 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 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.

KW - infectious diseases

U2 - 10.1101/2021.06.03.21258228

DO - 10.1101/2021.06.03.21258228

M3 - פרסום מוקדם

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

ER -

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

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Keywords

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