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Kia P, Katagirya E, Kakembo FE, Adera DA, Nsubuga ML, Yiga F, Aloyo SM, Aujat BR, Anguyo DF, Katabazi FA, Kigozi E, Joloba ML, Kateete DP. Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing. Sci Rep 2023; 13:20507. [PMID: 37993530 PMCID: PMC10665338 DOI: 10.1038/s41598-023-47379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023] Open
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.
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Affiliation(s)
- Praiscillia Kia
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fredrick Elishama Kakembo
- The African Centers of Excellence in Bioinformatics and Date Intensive Sciences, Infectious Disease Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Doreen Ato Adera
- Multifunctional Research Laboratories, Gulu University, Gulu, Uganda
| | - Moses Luutu Nsubuga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fahim Yiga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sharley Melissa Aloyo
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Brendah Ronah Aujat
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
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Nsubuga G, Kateete DP, Aloyo SM, Kigingi LN, Emmanuel N, Dafala K, Ntayi ML, Joloba ML, Rogers K. Biobanking in East and Central Africa: A case of the Integrated Biorepository of H3Africa Uganda. Open Res Afr 2022; 5:33. [PMID: 37224314 PMCID: PMC10175960 DOI: 10.12688/openresafrica.13495.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 05/26/2023]
Abstract
Biorepositories are essential because they guarantee the proper storage and distribution of biospecimens and their associated data for current and future research. In Eastern and Central Africa, the Integrated Biorepository of H3Africa Uganda (IBRH3AU) at Makerere University in Uganda was the first of its kind. It is strategically located at Makerere University College of Health Sciences, which is home to some of Uganda's most relevant and impactful infectious and non-infectious disease research. Since its inception as a pilot project in 2012, the IBRH3AU biorepository has grown into a state-of-the-art facility serving the H3Africa consortium and the rest of the scientific community. IBRH3AU has built a solid infrastructure over the past ten years with cutting-edge methods and technologies for the collection, processing, quality control, handling, management, storage and shipment of biospecimens. H3Africa researchers, local researchers, postgraduate and postdoctoral students, and the greater scientific community in Eastern and Central Africa and beyond have benefited from IBRH3AU's exceptional biobanking services.
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Affiliation(s)
- Gideon Nsubuga
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - David Patrick Kateete
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Sharley Melissa Aloyo
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Lwanga Newton Kigingi
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Nasinghe Emmanuel
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Kezimbira Dafala
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Moses Levi Ntayi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Moses L Joloba
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
| | - Kamulegeya Rogers
- Integrated Biorepository of H3Africa Uganda, Makerere University, Kampala, P.O. BOX 7072, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, P.O. BOX 7072, Uganda
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Bongomin F, Kwizera R, Mande E, Aloyo SM, Achan B, Namusobya M, Sereke SG, Batte C, Kiguli S, Baluku JB, Joloba ML, Kirenga BJ. Aspergillus-specific IgM/IgG antibody serostatus of patients hospitalized with moderate-critical COVID-19 in Uganda. Afr Health Sci 2022; 22:506-511. [PMID: 36910368 PMCID: PMC9993298 DOI: 10.4314/ahs.v22i3.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Invasive pulmonary aspergillosis is known to complicate the coronavirus diseases-2019 (COVID-19), especially those with critical illness. We investigated the baseline anti-Aspergillus antibody serostatus of patients with moderate-critical COVID-19 hospitalized at 3 COVID-19 Treatment Units in Uganda. All 46 tested patients, mean age 30, and 11% with underlying respiratory disease had a negative serum anti-Aspergillus IgM/IgG antibody immunochromatographic test on day 3 (mean) of symptom onset (range 1-26), but follow up specimens to assess seroconversion were not available.
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Affiliation(s)
- Felix Bongomin
- Department of Medical Microbiology and Immunology, Gulu University Medical School, Gulu Uganda
| | - Richard Kwizera
- Translational research laboratory, Department of Research, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418, Kampala, Uganda
| | - Emmanuel Mande
- Translational research laboratory, Department of Research, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418, Kampala, Uganda
| | - Sharley Melissa Aloyo
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Beatrice Achan
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Martha Namusobya
- Department of Internal Medicine, Mulago National Referral Hospital, Kampala, Uganda
| | - Senai Goitom Sereke
- Department of Radiology and Radiotherapy, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Charles Batte
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sarah Kiguli
- Department of Pediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joseph Baruch Baluku
- Department of Internal Medicine, Mulago National Referral Hospital, Kampala, Uganda.,Directorate of Programs, Mildmay Uganda, Wakiso, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bruce J Kirenga
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
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