First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador.
COVID19
NGS
SARS-CoV-2
co-infection
genome sequencing
Journal
New microbes and new infections
ISSN: 2052-2975
Titre abrégé: New Microbes New Infect
Pays: England
ID NLM: 101624750
Informations de publication
Date de publication:
Jul 2022
Jul 2022
Historique:
received:
29
01
2022
accepted:
24
06
2022
pubmed:
13
7
2022
medline:
13
7
2022
entrez:
12
7
2022
Statut:
ppublish
Résumé
COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.
Sections du résumé
Background
UNASSIGNED
COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported.
Methodology
UNASSIGNED
A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained.
Results
UNASSIGNED
The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample.
Conclusions
UNASSIGNED
We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.
Identifiants
pubmed: 35818397
doi: 10.1016/j.nmni.2022.101001
pii: S2052-2975(22)00053-1
pmc: PMC9259011
doi:
Types de publication
Journal Article
Langues
eng
Pagination
101001Subventions
Organisme : NIAID NIH HHS
ID : U01 AI151788
Pays : United States
Informations de copyright
© 2022 The Author(s).
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