Persistence of SARS-CoV-2 infection and viral intra- and inter-host evolution in COVID-19 hospitalized patients.
Humans
COVID-19
/ virology
SARS-CoV-2
/ genetics
Phylogeny
Retrospective Studies
Male
Female
Spike Glycoprotein, Coronavirus
/ genetics
Middle Aged
Longitudinal Studies
Genome, Viral
/ genetics
Aged
Whole Genome Sequencing
Evolution, Molecular
Hospitalization
Nasopharynx
/ virology
Bayes Theorem
Adult
SARS‐CoV‐2 immune escape mutations
SARS‐CoV‐2 persistence
inter‐host viral genetic evolution
intra‐host viral genetic evolution
phylodynamic analysis
phylogenetic analysis
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
Jun 2024
Jun 2024
Historique:
revised:
11
05
2024
received:
10
01
2024
accepted:
14
05
2024
medline:
28
5
2024
pubmed:
28
5
2024
entrez:
28
5
2024
Statut:
ppublish
Résumé
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) persistence in COVID-19 patients could play a key role in the emergence of variants of concern. The rapid intra-host evolution of SARS-CoV-2 may result in an increased transmissibility, immune and therapeutic escape which could be a direct consequence of COVID-19 epidemic currents. In this context, a longitudinal retrospective study on eight consecutive COVID-19 patients with persistent SARS-CoV-2 infection, from January 2022 to March 2023, was conducted. To characterize the intra- and inter-host viral evolution, whole genome sequencing and phylogenetic analysis were performed on nasopharyngeal samples collected at different time points. Phylogenetic reconstruction revealed an accelerated SARS-CoV-2 intra-host evolution and emergence of antigenically divergent variants. The Bayesian inference and principal coordinate analysis analysis showed a host-based genomic structuring among antigenically divergent variants, that might reflect the positive effect of containment practices, within the critical hospital area. All longitudinal antigenically divergent isolates shared a wide range of amino acidic (aa) changes, particularly in the Spike (S) glycoprotein, that increased viral transmissibility (K417N, S477N, N501Y and Q498R), enhanced infectivity (R346T, S373P, R408S, T478K, Q498R, Y505H, D614G, H655Y, N679K and P681H), caused host immune escape (S371L, S375F, T376A, K417N, and K444T/R) and displayed partial or complete resistance to treatments (G339D, R346K/T, S371F/L, S375F, T376A, D405N, N440K, G446S, N460K, E484A, F486V, Q493R, G496S and Q498R). These results suggest that multiple novel variants which emerge in the patient during persistent infection, might spread to another individual and continue to evolve. A pro-active genomic surveillance of persistent SARS-CoV-2 infected patients is recommended to identify genetically divergent lineages before their diffusion.
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e29708Subventions
Organisme : Regione Calabria
ID : COVID19@UMG POR Calabria-FESR/FSE 2014-2020 D.D.R.C. n. 4584 - Azione 10.5.12.
Informations de copyright
© 2024 Wiley Periodicals LLC.
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