SARS-CoV-2's high rate of genetic mutation under immune selective pressure: from oropharyngeal B.1.1.7 to intrapulmonary B.1.533 in a vaccinated patient.
COVID-19
Intra-Host Mutations
Lineages
NGS
Post-vaccine
Journal
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
ISSN: 1878-3511
Titre abrégé: Int J Infect Dis
Pays: Canada
ID NLM: 9610933
Informations de publication
Date de publication:
May 2022
May 2022
Historique:
received:
04
12
2021
revised:
11
02
2022
accepted:
19
02
2022
pubmed:
6
3
2022
medline:
29
4
2022
entrez:
5
3
2022
Statut:
ppublish
Résumé
This is the case report of an 84-year-old man affected by COVID-19 between the 2 doses of vaccination, with negative exitus. We analyzed nasopharyngeal samples of viral RNA collected during the disease and nasopharyngeal and lung samples collected postmortem by reverse transcription LAMP (RT-LAMP) PCR and Next Generation Sequencing (NGS). NGS results were analyzed with different bioinformatic tools to define virus lineages and the related single-nucleotide polymorphisms (SNPs). Both lung and nasopharyngeal samples tested positive for SARS-CoV-2 on RT-LAMP. Through bioinformatic analysis, 2 viral RNAs from the nasal swabs, which belonged to the B.1.1.7 lineage, and 1 viral RNA from the lung sample, which belonged to the B.1.533 lineage, were identified. This genetic observation suggested that SARS-CoV-2 tends to change under selective pressure. The high mutation rate of ORFa1b, containing a replicase gene, was a biological image of a complex viral survival system.
Identifiants
pubmed: 35247550
pii: S1201-9712(22)00123-0
doi: 10.1016/j.ijid.2022.02.044
pmc: PMC8888350
pii:
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Case Reports
Langues
eng
Sous-ensembles de citation
IM
Pagination
169-172Informations de copyright
Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.
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