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

Cell Host Microbe. 2022 Feb 9;30(2):154-162.e5. doi: 10.1016/j.chom.2022.01.005. Epub 2022 Jan 14.


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.

Keywords: Beta variant; Delta variant; HIV; SARS-CoV-2; advanced HIV disease; evolution; immune escape; neutralization; variants of concern.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Animals
  • Antibodies, Neutralizing / blood*
  • Antibodies, Neutralizing / immunology
  • Antibodies, Viral / blood
  • Antibodies, Viral / immunology
  • BNT162 Vaccine / immunology*
  • COVID-19 / immunology
  • COVID-19 Vaccines / immunology
  • Cell Line
  • Chlorocebus aethiops
  • Female
  • HIV Infections / pathology*
  • HIV-1 / immunology
  • Humans
  • Immune Evasion / immunology*
  • Immunocompromised Host / immunology
  • Immunogenicity, Vaccine / immunology*
  • Neutralization Tests
  • SARS-CoV-2 / immunology*
  • SARS-CoV-2 / isolation & purification
  • South Africa
  • Vaccination
  • Vaccine Efficacy
  • Vero Cells


  • Antibodies, Neutralizing
  • Antibodies, Viral
  • COVID-19 Vaccines
  • BNT162 Vaccine

Supplementary concepts

  • COVID-19 breakthrough infections
  • SARS-CoV-2 variants