Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo
Objectives: Using whole genome sequencing of SARS-CoV-2 to identify variants circulating in DRC and obtaining molecular information useful for diagnosis, improving treatment and general pandemic control strategies. Methods: Seventy-four SARS-CoV-2 isolates were sequenced using Oxford Nanopore pla...
| Autores principales: | , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2022
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| Acceso en línea: | https://hdl.handle.net/10568/119630 |
| _version_ | 1855516680101298176 |
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| author | Ntagereka, P.B. Oyola, Samuel O. Baenyi, S.P. Rono, Gilbert K. Birindwa, A.B. Shukuru, D.W. Baharanyi, T.C. Kashosi, T.M. Buhendwa, J.C. Bisimwa, P.B. Kusinza, A.B. Basengere, R.A. Mukwege, D. |
| author_browse | Baenyi, S.P. Baharanyi, T.C. Basengere, R.A. Birindwa, A.B. Bisimwa, P.B. Buhendwa, J.C. Kashosi, T.M. Kusinza, A.B. Mukwege, D. Ntagereka, P.B. Oyola, Samuel O. Rono, Gilbert K. Shukuru, D.W. |
| author_facet | Ntagereka, P.B. Oyola, Samuel O. Baenyi, S.P. Rono, Gilbert K. Birindwa, A.B. Shukuru, D.W. Baharanyi, T.C. Kashosi, T.M. Buhendwa, J.C. Bisimwa, P.B. Kusinza, A.B. Basengere, R.A. Mukwege, D. |
| author_sort | Ntagereka, P.B. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Objectives: Using whole genome sequencing of SARS-CoV-2 to identify variants circulating in DRC and obtaining molecular information useful for diagnosis, improving treatment and general pandemic control strategies.
Methods: Seventy-four SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with over 80% genome coverage were used for variant calling, phylogenetic analysis and classification using pangolin lineage annotation nomenclature.
Results: Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16 and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on Wuhan reference genome a total of 289 distinct mutations were detected including 141 missenses, 123 synonymous and 25 insertions/deletions when our isolates were mapped to Wuhan reference strain. The majority of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes Spike, ORF1ab, ORF3, and nucleocapsid protein (N) genes. The most common mutation was D614G (1841A>G) observed in 61 sequences followed by L4715L (14143C>T) found in 60 sequences.
Conclusion: Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control. |
| format | Journal Article |
| id | CGSpace119630 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1196302025-01-27T15:00:52Z Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo Ntagereka, P.B. Oyola, Samuel O. Baenyi, S.P. Rono, Gilbert K. Birindwa, A.B. Shukuru, D.W. Baharanyi, T.C. Kashosi, T.M. Buhendwa, J.C. Bisimwa, P.B. Kusinza, A.B. Basengere, R.A. Mukwege, D. covid-19 genomics health infectious diseases Objectives: Using whole genome sequencing of SARS-CoV-2 to identify variants circulating in DRC and obtaining molecular information useful for diagnosis, improving treatment and general pandemic control strategies. Methods: Seventy-four SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with over 80% genome coverage were used for variant calling, phylogenetic analysis and classification using pangolin lineage annotation nomenclature. Results: Phylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16 and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on Wuhan reference genome a total of 289 distinct mutations were detected including 141 missenses, 123 synonymous and 25 insertions/deletions when our isolates were mapped to Wuhan reference strain. The majority of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes Spike, ORF1ab, ORF3, and nucleocapsid protein (N) genes. The most common mutation was D614G (1841A>G) observed in 61 sequences followed by L4715L (14143C>T) found in 60 sequences. Conclusion: Our findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control. 2022-09 2022-05-23T10:21:45Z 2022-05-23T10:21:45Z Journal Article https://hdl.handle.net/10568/119630 en Open Access Elsevier Ntagereka, P.B., Oyola, S.O., Baenyi, S.P., Rono, G.K., Birindwa, A.B., Shukuru, D.W., Baharanyi, T.C., Kashosi, T.M., Buhendwa, J.C., Bisimwa, P.B., Kusinza, A.B., Basengere, R.A. and Mukwege, D. 2022. Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo. International Journal of Infectious Diseases 122: 136–143. |
| spellingShingle | covid-19 genomics health infectious diseases Ntagereka, P.B. Oyola, Samuel O. Baenyi, S.P. Rono, Gilbert K. Birindwa, A.B. Shukuru, D.W. Baharanyi, T.C. Kashosi, T.M. Buhendwa, J.C. Bisimwa, P.B. Kusinza, A.B. Basengere, R.A. Mukwege, D. Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title | Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title_full | Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title_fullStr | Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title_full_unstemmed | Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title_short | Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second and third waves of COVID-19 in South Kivu, east of the Democratic Republic of Congo |
| title_sort | whole genome sequencing of sars cov 2 reveals diverse mutations in circulating alpha and delta variants during the first second and third waves of covid 19 in south kivu east of the democratic republic of congo |
| topic | covid-19 genomics health infectious diseases |
| url | https://hdl.handle.net/10568/119630 |
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