Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing

Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing

Abstract SARS-CoV-2 undergoes frequent mutations, affecting COVID-19 diagnostics, transmission and vaccine efficacy. Here, we describe the genetic diversity of 49 SARS-CoV-2 samples from Uganda, collected during the COVID-19 waves of 2020/2021. Overall, the samples were similar to previously reporte...

Full description

Bibliographic Details
Main Authors:	Praiscillia Kia, Eric Katagirya, Fredrick Elishama Kakembo, Doreen Ato Adera, Moses Luutu Nsubuga, Fahim Yiga, Sharley Melissa Aloyo, Brendah Ronah Aujat, Denis Foe Anguyo, Fred Ashaba Katabazi, Edgar Kigozi, Moses L. Joloba, David Patrick Kateete
Format:	Article
Language:	English
Published:	Nature Portfolio 2023-11-01
Series:	Scientific Reports
Online Access:	https://doi.org/10.1038/s41598-023-47379-z

Similar Items

Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings [version 1; peer review: 2 approved]
by: Gerald Mboowa, et al.
Published: (2021-07-01)

Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in Mycobacterium tuberculosis isolates from Uganda.
by: Edgar Kigozi, et al.
Published: (2018-01-01)

Prevalence of arps10, fd, pfmdr-2, pfcrt and pfkelch13 gene mutations in Plasmodium falciparum parasite population in Uganda.
by: Moses Ocan, et al.
Published: (2022-01-01)

Rhomboids of Mycobacteria: characterization using an aarA mutant of Providencia stuartii and gene deletion in Mycobacterium smegmatis.
by: David Patrick Kateete, et al.
Published: (2012-01-01)

Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014–2016)
by: David Patrick Kateete, et al.
Published: (2019-07-01)

Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysis
by: Boom Henry W, et al.
Published: (2010-10-01)

Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy
by: David Patrick Kateete, et al.
Published: (2021-12-01)

Determination of circulating <it>Mycobacterium tuberculosis </it>strains and transmission patterns among pulmonary TB patients in Kawempe municipality, Uganda, using MIRU-VNTR
by: Dickman Katherine R, et al.
Published: (2011-08-01)

Genotypic diversity among multidrug resistant Pseudomonas aeruginosa and Acinetobacter species at Mulago Hospital in Kampala, Uganda
by: David P. Kateete, et al.
Published: (2017-07-01)

High prevalence of methicillin resistant <it>Staphylococcus aureus </it>in the surgical units of Mulago hospital in Kampala, Uganda
by: Katabazi Fred A, et al.
Published: (2011-09-01)

Mycobacterium tuberculosis thymidylate kinase antigen assays for designating incipient, high-risk latent M.tb infection
by: Misaki Wayengera, et al.
Published: (2018-03-01)

Immuno-diagnosis of Mycobacterium tuberculosis in sputum, and reduction of timelines for its positive cultures to within 3 h by pathogen-specific thymidylate kinase expression assays
by: Misaki Wayengera, et al.
Published: (2017-08-01)

DNA restriction fragment length polymorphism analysis of <it>Mycobacterium tuberculosis </it>isolates from HIV-seropositive and HIV-seronegative patients in Kampala, Uganda
by: Katabazi Fred A, et al.
Published: (2009-02-01)

Palliative Radiotherapy and Hormonal Deprivation for Prostate Cancer Induced Urinary Obstruction at a Sub-Saharan Tertiary Hospital
by: Sam Kaggwa, et al.
Published: (2016-11-01)

Source-tracking ESBL-producing bacteria at the maternity ward of Mulago hospital, Uganda.
by: Richard Mayanja, et al.
Published: (2023-01-01)

Source-tracking ESBL-producing bacteria at the maternity ward of Mulago hospital, Uganda
by: Richard Mayanja, et al.
Published: (2023-01-01)

Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches
by: George, S, et al.
Published: (2017)

Minionate : The collectible card game
by: Berman, Benjamin S.
Published: (2017)

Incremental yield of serial sputum cultures for diagnosis of tuberculosis among HIV infected smear negative pulmonary TB suspects in Kampala, Uganda.
by: Willy Ssengooba, et al.
Published: (2012-01-01)

Pertussis prevalence and its determinants among children with persistent cough in urban Uganda.
by: Vincent Kayina, et al.
Published: (2015-01-01)

Detection of multiple strains of <it>Mycobacterium tuberculosis </it>using MIRU-VNTR in patients with pulmonary tuberculosis in Kampala, Uganda
by: Mayanja Harriet K, et al.
Published: (2010-12-01)

CA-MRSA and HA-MRSA coexist in community and hospital settings in Uganda
by: David Patrick Kateete, et al.
Published: (2019-06-01)

One-pot removal of pharmaceuticals and toxic heavy metals from water using xerogel-immobilized quartz/banana peels-activated carbon
by: Ibrahim Karume, et al.
Published: (2023-01-01)

Hierarchies of minion tests for PCSPs through tensors
by: Ciardo, L, et al.
Published: (2023)

DNA Barcoding of Nematodes Using the MinION
by: Ineke E. Knot, et al.
Published: (2020-04-01)

MinION nanopore sequencing of an influenza genome
by: Jing eWang, et al.
Published: (2015-08-01)

Oxford Nanopore MinION Sequencing and Genome Assembly
by: Hengyun Lu, et al.
Published: (2016-10-01)

The microprotein Minion controls cell fusion and muscle formation
by: Qiao Zhang, et al.
Published: (2017-06-01)

bla VIM- and bla OXA-mediated carbapenem resistance among Acinetobacter baumannii and Pseudomonas aeruginosa isolates from the Mulago hospital intensive care unit in Kampala, Uganda
by: Dickson Aruhomukama, et al.
Published: (2019-10-01)

Hypovitaminosis D among newly diagnosed pulmonary TB patients and their household contacts in Uganda
by: Ester Lilian Acen, et al.
Published: (2022-03-01)

Microbial characteristics of dental caries in HIV positive individuals
by: Dunstan Kalanzi, et al.
Published: (2022-09-01)

Processing the Raw
by: Ronah Sadan
Published: (2023-11-01)

FOXP3 and GARP (LRRC32): the master and its minion
by: Buer Jan, et al.
Published: (2010-02-01)

Profiling bacterial communities by MinION sequencing of ribosomal operons
by: Lee J. Kerkhof, et al.
Published: (2017-09-01)

First report of whole-genome analysis of an extensively drug-resistant Mycobacterium tuberculosis clinical isolate with bedaquiline, linezolid and clofazimine resistance from Uganda
by: Jupiter Marina Kabahita, et al.
Published: (2022-05-01)

Molecular characterization of Staphylococcus aureus from patients with surgical site infections at Mulago Hospital in Kampala, Uganda.
by: Jeremiah Seni, et al.
Published: (2013-01-01)

Species, antibiotic susceptibility profiles and van gene frequencies among enterococci isolated from patients at Mulago National Referral Hospital in Kampala, Uganda
by: David P. Kateete, et al.
Published: (2019-05-01)

Evaluation of circulating serum cathelicidin levels as a potential biomarker to discriminate between active and latent tuberculosis in Uganda.
by: Ester Lilian Acen, et al.
Published: (2022-01-01)

Impact of vitamin D status and cathelicidin antimicrobial peptide on adults with active pulmonary TB globally: A systematic review and meta-analysis.
by: Ester Lilian Acen, et al.
Published: (2021-01-01)

Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis
by: Edriss Yassine, et al.
Published: (2021-06-01)