Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic
Background: Genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Tanzania remain scarce in GISAID, thus hindering our understanding of how the pandemic evolved in the country. Methods: We performed whole genome sequencing on SARS-CoV-2 samples collected between Marc...
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| Language: | English |
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Elsevier
2025-06-01
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| Series: | Journal of Clinical Virology Plus |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667038025000110 |
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| author | Nicholaus P. Mnyambwa Jinxin Gao Alex Magesa Edina Mgimba Swaminathan Mahesh Pawan Angra Juma Kisuse Clara Lubinza Lawrence Mapunda Aman Wilfred Godfather Kimaro George P. Judicate Ambele Eliah Augustino Msanga Senkoro Mbazi Esther Ngadaya Mukurasi Kokuhabwa Jackson P. Mushumbusi Medard Beyanga Wangeci Gatei Sayoki Mfinanga |
| author_facet | Nicholaus P. Mnyambwa Jinxin Gao Alex Magesa Edina Mgimba Swaminathan Mahesh Pawan Angra Juma Kisuse Clara Lubinza Lawrence Mapunda Aman Wilfred Godfather Kimaro George P. Judicate Ambele Eliah Augustino Msanga Senkoro Mbazi Esther Ngadaya Mukurasi Kokuhabwa Jackson P. Mushumbusi Medard Beyanga Wangeci Gatei Sayoki Mfinanga |
| author_sort | Nicholaus P. Mnyambwa |
| collection | DOAJ |
| description | Background: Genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Tanzania remain scarce in GISAID, thus hindering our understanding of how the pandemic evolved in the country. Methods: We performed whole genome sequencing on SARS-CoV-2 samples collected between March 2021 and December 2022 to characterize the virus in Tanzania. Nasal and oropharyngeal swabs were collected from patients seeking health care, incoming travelers as well as from outgoing travelers undergoing pre-travel COVID-19 testing (required for flight boarding). Sample collection, and testing were coordinated by the National Public Health Laboratory. Results: Among 515 samples, 260 (50.49 %) were from outgoing travelers, 227 (44.08 %) Covid-19 suspects seeking care, and 28 (5.44 %) incoming travelers identified at the airport. The majority of the samples came from Dar es Salaam (n = 380, 73.7 %), the country's largest city and the main port of entry. We identified 74 Pango lineages from all the samples, with Omicron 430 (83.50 %) and Delta 79 (15 %) variants being predominant. From the 380 Dar es Salaam samples, 67 Pango lineages were identified, showing both overlapping and unique lineages in each sample type. Conclusion: Our findings reveal a dynamic circulation of SARS-CoV-2 variants over time, with Delta predominantly observed in 2021 and Omicron in 2022 in Tanzania. The temporal prevalence of the identified lineages was consistent with the global epidemiology of the virus. Sustained and expanded genomic surveillance is recommended to track and respond effectively to emerging variants. |
| format | Article |
| id | doaj-art-7aad076fea4444a9837918bfdcccb9cf |
| institution | Kabale University |
| issn | 2667-0380 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Clinical Virology Plus |
| spelling | doaj-art-7aad076fea4444a9837918bfdcccb9cf2025-08-20T03:46:38ZengElsevierJournal of Clinical Virology Plus2667-03802025-06-015210021210.1016/j.jcvp.2025.100212Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemicNicholaus P. Mnyambwa0Jinxin Gao1Alex Magesa2Edina Mgimba3Swaminathan Mahesh4Pawan Angra5Juma Kisuse6Clara Lubinza7Lawrence Mapunda8Aman Wilfred9Godfather Kimaro10George P. Judicate11Ambele Eliah12Augustino Msanga13Senkoro Mbazi14Esther Ngadaya15Mukurasi Kokuhabwa16Jackson P. Mushumbusi17Medard Beyanga18Wangeci Gatei19Sayoki Mfinanga20National Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, Tanzania; Kampla International University in Tanzania, Faculty of Medicine and Pharmaceutical Sciences, Dar es Salaam, Tanzania; Alliance for Africa Health and Research (A4A), Dar es Salaam, Tanzania; Corresponding author at: National Institute for Medical Research, Muhimbili Research Centre, P.O. Box 3436, Dar es Salaam, Tanzania.Centers for Disease Control and Prevention, Dar es Salaam, TanzaniaMinistry of Health, Dodoma, TanzaniaNational Public Health Laboratory, Dar es Salaam, TanzaniaCenters for Disease Control and Prevention, Dar es Salaam, TanzaniaCenters for Disease Control and Prevention, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Public Health Laboratory, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Public Health Laboratory, Dar es Salaam, TanzaniaCenters for Disease Control and Prevention, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaCenters for Disease Control and Prevention, Dar es Salaam, TanzaniaMinistry of Health, Dodoma, TanzaniaNational Public Health Laboratory, Dar es Salaam, TanzaniaCenters for Disease Control and Prevention, Dar es Salaam, TanzaniaNational Institute for Medical Research, Muhimbili Research Centre, Dar es Salaam, TanzaniaBackground: Genomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from Tanzania remain scarce in GISAID, thus hindering our understanding of how the pandemic evolved in the country. Methods: We performed whole genome sequencing on SARS-CoV-2 samples collected between March 2021 and December 2022 to characterize the virus in Tanzania. Nasal and oropharyngeal swabs were collected from patients seeking health care, incoming travelers as well as from outgoing travelers undergoing pre-travel COVID-19 testing (required for flight boarding). Sample collection, and testing were coordinated by the National Public Health Laboratory. Results: Among 515 samples, 260 (50.49 %) were from outgoing travelers, 227 (44.08 %) Covid-19 suspects seeking care, and 28 (5.44 %) incoming travelers identified at the airport. The majority of the samples came from Dar es Salaam (n = 380, 73.7 %), the country's largest city and the main port of entry. We identified 74 Pango lineages from all the samples, with Omicron 430 (83.50 %) and Delta 79 (15 %) variants being predominant. From the 380 Dar es Salaam samples, 67 Pango lineages were identified, showing both overlapping and unique lineages in each sample type. Conclusion: Our findings reveal a dynamic circulation of SARS-CoV-2 variants over time, with Delta predominantly observed in 2021 and Omicron in 2022 in Tanzania. The temporal prevalence of the identified lineages was consistent with the global epidemiology of the virus. Sustained and expanded genomic surveillance is recommended to track and respond effectively to emerging variants.http://www.sciencedirect.com/science/article/pii/S2667038025000110SARS-CoV-2 variantsCOVID-19genomic surveillancesequencing |
| spellingShingle | Nicholaus P. Mnyambwa Jinxin Gao Alex Magesa Edina Mgimba Swaminathan Mahesh Pawan Angra Juma Kisuse Clara Lubinza Lawrence Mapunda Aman Wilfred Godfather Kimaro George P. Judicate Ambele Eliah Augustino Msanga Senkoro Mbazi Esther Ngadaya Mukurasi Kokuhabwa Jackson P. Mushumbusi Medard Beyanga Wangeci Gatei Sayoki Mfinanga Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic Journal of Clinical Virology Plus SARS-CoV-2 variants COVID-19 genomic surveillance sequencing |
| title | Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic |
| title_full | Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic |
| title_fullStr | Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic |
| title_full_unstemmed | Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic |
| title_short | Genomic analysis of SARS-CoV-2 sequences obtained in Tanzania during the pandemic |
| title_sort | genomic analysis of sars cov 2 sequences obtained in tanzania during the pandemic |
| topic | SARS-CoV-2 variants COVID-19 genomic surveillance sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2667038025000110 |
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