ArticleVirus evolution2024
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations.
Article in Virus evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 12 citations in OpenAlex.
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- Improved DNA Extraction for Dairy and Blood Products: A Comparative Evaluation of Yield, Purity, and PCR Compatibility.Foods (Basel, Switzerland) · 2026Article
- Cross- Wellcome Africa Asian Programmes (AAPs) Acceleration of Genomics for Escalating infectious Diseases, (CAGED) Consortium.Wellcome open research · 2026Article
- Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant.Virus evolution · 2026Article
- Intrahost population dynamics of chikungunya virus in humans and naturally infectedVirus evolution · 2026Article
- A public health perspective of SARS-CoV-2 evolution and surveillance strategies in Germany from 2020 to 2023.Communications medicine · 2025Review
- Intra-host SARS-CoV-2 diversity in immunocompromised people living with HIV provides insight into the evolutionary trajectory of SARS-CoV-2.Journal of virology · 2025Article
- Mutation profiling, evolution analysis, molecular dynamics simulation, and functional characterization of Omicron sub-strains.Virus research · 2025Article
- The consequences of SARS-CoV-2 within-host persistence.Nature reviews. Microbiology · 2025Review
- Characterisation of the antibody-mediated selective pressure driving intra-host evolution of SARS-CoV-2 in prolonged infection.PLoS pathogens · 2024Article
- A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.Cell reports. Medicine · 2024Article
- SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs.Cell chemical biology · 2024Review
- Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation.Nature communications · 2024Article
Corrections and comments
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Authors and funding
20 authors at 8 institutions in 4 countries.
Funding
Abstract
One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.