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'abstract': '<jats:title>Abstract</jats:title><jats:sec>\n'
' <jats:title>Background</jats:title>\n'
' <jats:p>SARS-CoV-2 remains rapidly evolving, and many biologically important '
'genomic substitutions/indels have characterised novel SARS-CoV-2 lineages, which have emerged '
'during successive global waves of the pandemic. Worldwide genomic sequencing has been able to '
'monitor these waves, track transmission clusters, and examine viral evolution in real time to '
'help inform healthcare policy. One school of thought is that an apparent greater than average '
'divergence in an emerging lineage from contemporary variants may require persistent '
'infection, for example in an immunocompromised host. Due to the nature of the COVID-19 '
'pandemic and sampling, there were few studies that examined the evolutionary trajectory of '
'SARS-CoV-2 in healthy individuals.</jats:p>\n'
' </jats:sec><jats:sec>\n'
' <jats:title>Methods</jats:title>\n'
' <jats:p>We investigated viral evolutionary trends and participant '
'symptomatology within a cluster of 16 SARS-CoV-2 infected, immunocompetent individuals with '
'no co-morbidities in a closed transmission chain. Longitudinal nasopharyngeal swab sampling '
'allowed characterisation of SARS-CoV-2 intra-host variation over time at both the dominant '
'and minor genomic variant levels through Nimagen-Illumina sequencing.</jats:p>\n'
' </jats:sec><jats:sec>\n'
' <jats:title>Results</jats:title>\n'
' <jats:p>A change in viral lineage assignment was observed in individual '
'infections; however, there was only one indel and no evidence of recombination over the '
'period of an acute infection. Minor and dominant genomic modifications varied between '
'participants, with some minor genomic modifications increasing in abundance to become the '
'dominant viral sequence during infection.</jats:p>\n'
' </jats:sec><jats:sec>\n'
' <jats:title>Conclusions</jats:title>\n'
' <jats:p>Data from this cohort of SARS-CoV-2-infected participants '
'demonstrated that long-term persistent infection in an immunocompromised host was not '
'necessarily a prerequisite for generating a greater than average frequency of amino acid '
'substitutions. Amino acid substitutions at both the dominant and minor genomic sequence level '
'were observed in immunocompetent individuals during infection showing that viral lineage '
'changes can occur generating viral diversity.</jats:p>\n'
' </jats:sec>',
'DOI': '10.1186/s13073-024-01360-1',
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'title': 'SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain '
'shows genomic diversity over the course of infection',
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're-infection from pre-existing minor variant reactivation. Infect Genet '
'Evol. 2021;90:104772.',
'journal-title': 'Infect Genet Evol'},
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'unstructured': 'Lin MJ, Rachleff VM, Xie H, Shrestha L, Lieberman NAP, Peddu V, Addetia '
'A, Casto AM, Breit N, Mathias PC, et al. Host-pathogen dynamics in '
'longitudinal clinical specimens from patients with COVID-19. Sci Rep. '
'2022;12:5856.',
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'unstructured': 'Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Gunther S, '
'Kerber R, Ng LFP, Elmore MJ, Magassouba N, et al. Variation around the '
'dominant viral genome sequence contributes to viral load and outcome in '
'patients with Ebola virus disease. Genome Biol. 2020;21:238.',
'journal-title': 'Genome Biol'},
{ 'key': '1360_CR85',
'unstructured': 'Goldswain H, Penrice-Randal R, Donovan-Banfield I, Duffy CW, Dong X, '
'Randle N, Ryan Y, Rzeszutek AM, Pilgrim J, Keyser E, et al. Longitudinal '
'sequencing of SARS-CoV-2 in immunocompetent individuals raw sequence '
'reads. Sequence Read Archive. 2024. '
'https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1012698.'}],
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'language': 'en',
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'references-count': 85,
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{'order': 1, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Declarations'}},
{ 'value': 'During the early phase of the COVID-19 pandemic emergency public health and '
'workforce protection measures were in place, so health surveillance was '
'undertaken to prevent and manage transmission risk and morbidity. As part of '
'these health surveillance measures, subjects consented to routine '
'nasopharyngeal swab COVID-19 analysis and regular self-report of symptoms and '
'signs such that disease outbreak could be prevented or controlled. In the UK, '
'such public health surveillance measures do not require Research Ethics '
'Committee review (UK Health Research Agency Guidance\xa0'
'(hra-decisiontools.org.uk)). The Senior Medical Advisor is the sample database '
'owner; all samples and clinical data were fully anonymised to the research '
'team. All samples and data were GDPR compliant and the study conformed to the '
'principles defined in the Declaration of Helsinki as adopted at the 64th WMA '
'General Assembly at Fortaleza, Brazil in October 2013.',
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{ 'value': 'Not applicable.',
'order': 3,
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{ 'value': 'The authors declare that they have no competing interests.',
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