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SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution — Europe PMC PPR:PPR206462

Source: Europe PMC
Original: https://europepmc.org/article/PPR/PPR206462
DOI: 10.1101/2020.08.26.267831
License (as archived): CC0-1.0
Archived: 2026-11-07T16:20:29.179Z
SHA-256 of the archived text: c93e887c5d01eef54d6dece1eb5cd352b47a20b5e44eb13f916b6bcf0332e7f1
Stable URL of this page: https://metraipolis.com/documento/dc_fe4f9ddda482

How to cite

SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution — Europe PMC PPR:PPR206462 — Europe PMC, https://europepmc.org/article/PPR/PPR206462 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_fe4f9ddda482 (Metraipolis archive dc_fe4f9ddda482, sha256 c93e887c5d01eef54d6dece1eb5cd352b47a20b5e44eb13f916b6bcf0332e7f1)

BibTeX

@misc{dcfe4f9ddda482,
  title = {SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution — Europe PMC PPR:PPR206462},
  howpublished = {Europe PMC},
  url = {https://europepmc.org/article/PPR/PPR206462},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_fe4f9ddda482; sha256 c93e887c5d01eef54d6dece1eb5cd352b47a20b5e44eb13f916b6bcf0332e7f1},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: Europe PMC, https://europepmc.org/article/PPR/PPR206462. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (HCW; non-cancer controls) by deep sequencing and investigated the within-host viral quasispecies of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2 + swabs from 57 cancer patients and 14 healthcare workers (HCW) from the Brazilian Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants (iSNVs) were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%). Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to HCW (p = 0.009). Intrahost genetic diversity in cancer patients was independent of SARS-CoV-2 Ct values, and was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Such a feature may explain, at least in part, the more adverse outcomes to which cancer/COVID-19 patients experience. Author Summary: Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. In this study, phylogenetic and variation analysis of SARS-CoV-2 genomes from cancer patients and non-cancer healthcare workers at the Brazilian National Cancer Institute were characterized by deep sequencing. Viral genomes showed signatures characteristic of Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. Despite most genomes in patients and healthcare workers belonging to the same lineage, intrahost variability was higher in cancer patients when compared to non-cancer counterparts. The intrahost genomic diversity analysis presented in our study highlights the relaxed evolution of SARS-CoV-2 in a vulnerable population of cancer patients. The high number of minor variations can result in the selection of immune escape variants, resistance to potential drugs, and/or increased pathogenicity. The impact of this higher intrahost variability over time warrants further investigation.

Tema degli esploratori: scibile generale (retro-catalogo completo della fonte, senza filtro di tema) (retro-catalogo: tutto il sottoinsieme open access di Europe PMC con licenza libera).
Pubblicazione: bioRxiv, 2020 (prima pubblicazione 2020-08-26).
Identificativi: DOI 10.1101/2020.08.26.267831.
Pagina: https://europepmc.org/article/PPR/PPR206462 — https://doi.org/10.1101/2020.08.26.267831. Autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza dell'articolo dichiarata da Europe PMC: CC0 (la versione è indicata dall'editore sulla pagina). Abstract riportato senza modifiche al contenuto, con attribuzione; deposito marcato CC0.
Letto il 2026-11-07T16:15:46.015Z tramite l'API REST ufficiale di Europe PMC (EMBL-EBI), nel rispetto del robots.txt e del crawl-delay.