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...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-47379-z |
| _version_ | 1797452881008263168 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Praiscillia Kia |
| collection | DOAJ |
| description | 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 reported SARS-CoV-2 from Uganda and the Democratic Republic of Congo (DRC). The main lineages were AY.46 and A.23, which are considered to be Delta SARS-CoV-2 variants. Further, a total of 268 unique single nucleotide variants and 1456 mutations were found, with more than seventy percent mutations in the ORF1ab and S genes. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), which occurred in the S, ORF1ab, ORF7a and N genes, respectively. As well, 28 structural variants—21 insertions and 7 deletions, occurred in 16 samples. Our findings point to the possibility that most SARS-CoV-2 infections in Uganda at the time arose from local spread and were not newly imported. Moreover, the relatedness of variants from Uganda and the DRC reflects high human mobility and interaction between the two countries, which is peculiar to this region of the world. |
| first_indexed | 2024-03-09T15:15:05Z |
| format | Article |
| id | doaj.art-db61a8d437e44d69819bda577891ca8d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:15:05Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-db61a8d437e44d69819bda577891ca8d2023-11-26T13:09:53ZengNature PortfolioScientific Reports2045-23222023-11-011311810.1038/s41598-023-47379-zGenomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencingPraiscillia Kia0Eric Katagirya1Fredrick Elishama Kakembo2Doreen Ato Adera3Moses Luutu Nsubuga4Fahim Yiga5Sharley Melissa Aloyo6Brendah Ronah Aujat7Denis Foe Anguyo8Fred Ashaba Katabazi9Edgar Kigozi10Moses L. Joloba11David Patrick Kateete12Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityThe African Centers of Excellence in Bioinformatics and Date Intensive Sciences, Infectious Disease Institute, College of Health Sciences, Makerere UniversityMultifunctional Research Laboratories, Gulu UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Biology, Muni UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityDepartment of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere UniversityAbstract 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 reported SARS-CoV-2 from Uganda and the Democratic Republic of Congo (DRC). The main lineages were AY.46 and A.23, which are considered to be Delta SARS-CoV-2 variants. Further, a total of 268 unique single nucleotide variants and 1456 mutations were found, with more than seventy percent mutations in the ORF1ab and S genes. The most common mutations were 2042C>G (83.4%), 14143C>T (79.5%), 245T>C (65%), and 1129G>T (51%), which occurred in the S, ORF1ab, ORF7a and N genes, respectively. As well, 28 structural variants—21 insertions and 7 deletions, occurred in 16 samples. Our findings point to the possibility that most SARS-CoV-2 infections in Uganda at the time arose from local spread and were not newly imported. Moreover, the relatedness of variants from Uganda and the DRC reflects high human mobility and interaction between the two countries, which is peculiar to this region of the world.https://doi.org/10.1038/s41598-023-47379-z |
| spellingShingle | 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 Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing Scientific Reports |
| title | Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing |
| title_full | Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing |
| title_fullStr | Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing |
| title_full_unstemmed | Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing |
| title_short | Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing |
| title_sort | genomic characterization of sars cov 2 from uganda using minion nanopore sequencing |
| url | https://doi.org/10.1038/s41598-023-47379-z |
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