SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations
© The Author(s) 2024. Published by Oxford University Press..
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.
Medienart: |
E-Artikel |
---|
Erscheinungsjahr: |
2024 |
---|---|
Erschienen: |
2024 |
Enthalten in: |
Zur Gesamtaufnahme - volume:10 |
---|---|
Enthalten in: |
Virus evolution - 10(2024), 1 vom: 19., Seite vead075 |
Sprache: |
Englisch |
---|
Beteiligte Personen: |
Lustig, Gila [VerfasserIn] |
---|
Links: |
---|
Themen: |
Advanced HIV disease |
---|
Anmerkungen: |
Date Revised 17.02.2024 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
---|
doi: |
10.1093/ve/vead075 |
---|
funding: |
|
---|---|
Förderinstitution / Projekttitel: |
|
PPN (Katalog-ID): |
NLM368519074 |
---|
LEADER | 01000caa a22002652 4500 | ||
---|---|---|---|
001 | NLM368519074 | ||
003 | DE-627 | ||
005 | 20240217232415.0 | ||
007 | cr uuu---uuuuu | ||
008 | 240216s2024 xx |||||o 00| ||eng c | ||
024 | 7 | |a 10.1093/ve/vead075 |2 doi | |
028 | 5 | 2 | |a pubmed24n1297.xml |
035 | |a (DE-627)NLM368519074 | ||
035 | |a (NLM)38361824 | ||
040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
041 | |a eng | ||
100 | 1 | |a Lustig, Gila |e verfasserin |4 aut | |
245 | 1 | 0 | |a SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations |
264 | 1 | |c 2024 | |
336 | |a Text |b txt |2 rdacontent | ||
337 | |a ƒaComputermedien |b c |2 rdamedia | ||
338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
500 | |a Date Revised 17.02.2024 | ||
500 | |a published: Electronic-eCollection | ||
500 | |a Citation Status PubMed-not-MEDLINE | ||
520 | |a © The Author(s) 2024. Published by Oxford University Press. | ||
520 | |a 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 | ||
650 | 4 | |a Journal Article | |
650 | 4 | |a SARS-CoV-2 evolution | |
650 | 4 | |a advanced HIV disease | |
650 | 4 | |a immunosuppression | |
650 | 4 | |a prolonged infection | |
650 | 4 | |a variants of concern | |
700 | 1 | |a Ganga, Yashica |e verfasserin |4 aut | |
700 | 1 | |a Rodel, Hylton E |e verfasserin |4 aut | |
700 | 1 | |a Tegally, Houriiyah |e verfasserin |4 aut | |
700 | 1 | |a Khairallah, Afrah |e verfasserin |4 aut | |
700 | 1 | |a Jackson, Laurelle |e verfasserin |4 aut | |
700 | 1 | |a Cele, Sandile |e verfasserin |4 aut | |
700 | 1 | |a Khan, Khadija |e verfasserin |4 aut | |
700 | 1 | |a Jule, Zesuliwe |e verfasserin |4 aut | |
700 | 1 | |a Reedoy, Kajal |e verfasserin |4 aut | |
700 | 1 | |a Karim, Farina |e verfasserin |4 aut | |
700 | 1 | |a Bernstein, Mallory |e verfasserin |4 aut | |
700 | 1 | |a Ndung'u, Thumbi |e verfasserin |4 aut | |
700 | 1 | |a Moosa, Mahomed-Yunus S |e verfasserin |4 aut | |
700 | 1 | |a Archary, Derseree |e verfasserin |4 aut | |
700 | 1 | |a de Oliveira, Tulio |e verfasserin |4 aut | |
700 | 1 | |a Lessells, Richard |e verfasserin |4 aut | |
700 | 1 | |a Neher, Richard A |e verfasserin |4 aut | |
700 | 1 | |a Abdool Karim, Salim S |e verfasserin |4 aut | |
700 | 1 | |a Sigal, Alex |e verfasserin |4 aut | |
773 | 0 | 8 | |i Enthalten in |t Virus evolution |d 2015 |g 10(2024), 1 vom: 19., Seite vead075 |w (DE-627)NLM256484082 |x 2057-1577 |7 nnns |
773 | 1 | 8 | |g volume:10 |g year:2024 |g number:1 |g day:19 |g pages:vead075 |
856 | 4 | 0 | |u http://dx.doi.org/10.1093/ve/vead075 |3 Volltext |
912 | |a GBV_USEFLAG_A | ||
912 | |a GBV_NLM | ||
951 | |a AR | ||
952 | |d 10 |j 2024 |e 1 |b 19 |h vead075 |