Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation
Abstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection, and immune escape. Therefore, this study aimed to determine the SARS-CoV-2 lineages and better characterize the dynamics of the pandem...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-024-10411-2 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559805345398784 |
|---|---|
| author | Aminata Mbaye Haby Diallo Thibaut Armel Cherif Gnimadi Kadio Jean Jacques Olivier Kadio Abdoul Karim Soumah Joel Balle Koivogui Jean Louis Monemou Moriba Kowa Povogui Djiba Kaba Castro Hounmenou Laetitia Serrano Christelle Butel Nicolas Fernandez Nuñez Nicole Vidal Emilande Guichet Eric Delaporte Ahidjo Ayouba Martine Peeters Abdoulaye Toure Alpha Kabinet Keita AFROSCREEN Team |
| author_facet | Aminata Mbaye Haby Diallo Thibaut Armel Cherif Gnimadi Kadio Jean Jacques Olivier Kadio Abdoul Karim Soumah Joel Balle Koivogui Jean Louis Monemou Moriba Kowa Povogui Djiba Kaba Castro Hounmenou Laetitia Serrano Christelle Butel Nicolas Fernandez Nuñez Nicole Vidal Emilande Guichet Eric Delaporte Ahidjo Ayouba Martine Peeters Abdoulaye Toure Alpha Kabinet Keita AFROSCREEN Team |
| author_sort | Aminata Mbaye |
| collection | DOAJ |
| description | Abstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection, and immune escape. Therefore, this study aimed to determine the SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the different waves in Guinea. Methods Whole genome sequencing of 363 samples with PCR cycle threshold (Ct) values under thirty was undertaken between May 2020 and May 2023. The Illumina iSeq 100 technology was used. The sequences were then analyzed using the GeVarli pipeline to generate consensus sequences and variant calling. All sequences isolated in Guinea and available on GISAID were included in the analysis for phylogenetic tree and phylodynamic determination. Nextstain tools were used for these analyses. Statistical analysis was done using GraphPad Prism version 10. Results The circulation of SARS-CoV-2 in Guinea can be distributed in three different periods. The first, lasting from May to June 2020, was characterized by lineages B1 and B.1.1. The second period, from January 2021 to July 2021, was characterized by the lineages B.1.1.7 (Alpha), AY.122, B.1.1.318, R1, B.1.525 and B.1.629. The third period, between December 2021 and May 2023, was characterized by the Omicron variant, with nine subvariant majorities found. In addition, detecting variants in the period out of their circulation was documented. The importation and exportation investigation showed the strong movement viral association between Guinea and Senegal on the one hand and Guinea and Nigeria on the other. Conclusion In summary, this study contributes to understanding the epidemic dynamics of the disease by describing the significant variants that circulated in Guinee and the distribution of this variant in the population. It also shows the importation and exportation of the virus during the pandemic. Sub-sampling and degradation of samples for sequences were observed. Organization and collaboration between laboratories are needed for a good sample-collecting and storage system for future direction. |
| format | Article |
| id | doaj-art-556b8341762e437696b0d5ddebb4c1d3 |
| institution | Kabale University |
| issn | 1471-2334 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj-art-556b8341762e437696b0d5ddebb4c1d32025-01-05T12:09:42ZengBMCBMC Infectious Diseases1471-23342025-01-0125111310.1186/s12879-024-10411-2Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementationAminata Mbaye0Haby Diallo1Thibaut Armel Cherif Gnimadi2Kadio Jean Jacques Olivier Kadio3Abdoul Karim Soumah4Joel Balle Koivogui5Jean Louis Monemou6Moriba Kowa Povogui7Djiba Kaba8Castro Hounmenou9Laetitia Serrano10Christelle Butel11Nicolas Fernandez Nuñez12Nicole Vidal13Emilande Guichet14Eric Delaporte15Ahidjo Ayouba16Martine Peeters17Abdoulaye Toure18Alpha Kabinet Keita19AFROSCREEN TeamCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMTransVIHMI, University of Montpellier, Institut de Recherche pour le Développement (IRD), INSERMCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryCentre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de ConakryAbstract Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection, and immune escape. Therefore, this study aimed to determine the SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the different waves in Guinea. Methods Whole genome sequencing of 363 samples with PCR cycle threshold (Ct) values under thirty was undertaken between May 2020 and May 2023. The Illumina iSeq 100 technology was used. The sequences were then analyzed using the GeVarli pipeline to generate consensus sequences and variant calling. All sequences isolated in Guinea and available on GISAID were included in the analysis for phylogenetic tree and phylodynamic determination. Nextstain tools were used for these analyses. Statistical analysis was done using GraphPad Prism version 10. Results The circulation of SARS-CoV-2 in Guinea can be distributed in three different periods. The first, lasting from May to June 2020, was characterized by lineages B1 and B.1.1. The second period, from January 2021 to July 2021, was characterized by the lineages B.1.1.7 (Alpha), AY.122, B.1.1.318, R1, B.1.525 and B.1.629. The third period, between December 2021 and May 2023, was characterized by the Omicron variant, with nine subvariant majorities found. In addition, detecting variants in the period out of their circulation was documented. The importation and exportation investigation showed the strong movement viral association between Guinea and Senegal on the one hand and Guinea and Nigeria on the other. Conclusion In summary, this study contributes to understanding the epidemic dynamics of the disease by describing the significant variants that circulated in Guinee and the distribution of this variant in the population. It also shows the importation and exportation of the virus during the pandemic. Sub-sampling and degradation of samples for sequences were observed. Organization and collaboration between laboratories are needed for a good sample-collecting and storage system for future direction.https://doi.org/10.1186/s12879-024-10411-2GenomicEpidemiologySARS-CoV-2Guinea |
| spellingShingle | Aminata Mbaye Haby Diallo Thibaut Armel Cherif Gnimadi Kadio Jean Jacques Olivier Kadio Abdoul Karim Soumah Joel Balle Koivogui Jean Louis Monemou Moriba Kowa Povogui Djiba Kaba Castro Hounmenou Laetitia Serrano Christelle Butel Nicolas Fernandez Nuñez Nicole Vidal Emilande Guichet Eric Delaporte Ahidjo Ayouba Martine Peeters Abdoulaye Toure Alpha Kabinet Keita AFROSCREEN Team Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation BMC Infectious Diseases Genomic Epidemiology SARS-CoV-2 Guinea |
| title | Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation |
| title_full | Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation |
| title_fullStr | Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation |
| title_full_unstemmed | Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation |
| title_short | Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation |
| title_sort | genomic and epidemiological analysis of sars cov 2 variants isolated in guinea a routine sequencing implementation |
| topic | Genomic Epidemiology SARS-CoV-2 Guinea |
| url | https://doi.org/10.1186/s12879-024-10411-2 |
| work_keys_str_mv | AT aminatambaye genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT habydiallo genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT thibautarmelcherifgnimadi genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT kadiojeanjacquesolivierkadio genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT abdoulkarimsoumah genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT joelballekoivogui genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT jeanlouismonemou genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT moribakowapovogui genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT djibakaba genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT castrohounmenou genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT laetitiaserrano genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT christellebutel genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT nicolasfernandeznunez genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT nicolevidal genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT emilandeguichet genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT ericdelaporte genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT ahidjoayouba genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT martinepeeters genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT abdoulayetoure genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT alphakabinetkeita genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation AT afroscreenteam genomicandepidemiologicalanalysisofsarscov2variantsisolatedinguineaaroutinesequencingimplementation |