SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape

Characterizing SARS-CoV-2 evolution in specific geographies may help predict properties of the variants that come from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from ancestral virus in a person with advanced HIV disease in South Africa; this person was...

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Published in:Cell host & microbe 2022-02, Vol.30 (2), p.154-162.e5
Main Authors: Cele, Sandile, Karim, Farina, Lustig, Gila, San, James Emmanuel, Hermanus, Tandile, Tegally, Houriiyah, Snyman, Jumari, Moyo-Gwete, Thandeka, Wilkinson, Eduan, Bernstein, Mallory, Khan, Khadija, Hwa, Shi-Hsia, Tilles, Sasha W., Singh, Lavanya, Giandhari, Jennifer, Mthabela, Ntombifuthi, Mazibuko, Matilda, Ganga, Yashica, Gosnell, Bernadett I., Karim, Salim S. Abdool, Hanekom, Willem, Van Voorhis, Wesley C., Ndung’u, Thumbi, Lessells, Richard J., Moore, Penny L., Moosa, Mahomed-Yunus S., de Oliveira, Tulio, Sigal, Alex
Format: Article
Language:English
Subjects:
Adult
advanced HIV disease
Animals
Antibodies, Neutralizing - blood
Antibodies, Neutralizing - immunology
Antibodies, Viral - blood
Antibodies, Viral - immunology
Beta variant
BNT162 Vaccine - immunology
Brief Report
Cell Line
Chlorocebus aethiops
COVID-19 - immunology
COVID-19 Vaccines - immunology
Delta variant
evolution
Female
HIV
HIV Infections - pathology
HIV-1 - immunology
Humans
immune escape
Immune Evasion - immunology
Immunocompromised Host - immunology
Immunogenicity, Vaccine - immunology
neutralization
Neutralization Tests
SARS-CoV-2
SARS-CoV-2 - immunology
SARS-CoV-2 - isolation & purification
South Africa
Vaccination
Vaccine Efficacy
variants of concern
Vero Cells
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Summary:Characterizing SARS-CoV-2 evolution in specific geographies may help predict properties of the variants that come from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from ancestral virus in a person with advanced HIV disease in South Africa; this person was infected prior to emergence of the Beta and Delta variants. We longitudinally tracked the evolved virus and tested it against self-plasma and convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, but it evolved a multitude of mutations found in Omicron and other variants. It showed substantial but incomplete Pfizer BNT162b2 escape, weak neutralization by self-plasma, and despite pre-dating Delta, it also showed extensive escape of Delta infection-elicited neutralization. This example is consistent with the notion that SARS-CoV-2 evolving in individual immune-compromised hosts, including those with advanced HIV disease, may gain immune escape of vaccines and enhanced escape of Delta immunity, and this has implications for vaccine breakthrough and reinfections. [Display omitted] •An ancestral SARS-CoV-2 infection that persisted over 6 months evolved neutralization escape•Evolved virus serological relationship is mapped to ancestral virus and key variants•Evolved virus shows greatest escape from Delta-elicited immunity and least from Beta-elicited immunity•Evolved virus substantially but incompletely escapes BNT162b2 vaccine-elicited antibodies Cele et al. examine a SARS-CoV-2 infection persisting over 6 months, starting as ancestral virus but evolving various mutations found in Omicron and other variants. The evolved virus substantially but incompletely escaped BNT162b2-elicited immunity as well as neutralization by self-plasma and showed extensive escape from neutralization elicited by Delta infections.
ISSN:1931-3128
1934-6069
1934-6069
DOI:10.1016/j.chom.2022.01.005