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2030-12-31
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13 Ação contra a mudança global do clima
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AN EMERGING CLADE OF CHIKUNGUNYA WEST AFRICAN GENOTYPE DISCOVERED IN REAL-TIME DURING 2023 OUTBREAK IN SENEGAL
Padane, Abdou et al. | Date Issued: 2023
Author
Padane, Abdou
Tegally, Houriiyah
Ramphal, Yajna
Seyni, Ndiaye
Sarr, Mariéma
Diop, Mame Matar
Diedhiou, Cyrille Kouligueul
Mboup, Aminata
Diouf, Ndèye Dieyna
Souaré, Abdoulaye
Diagne, Ndéye Diabou
Aza-Gnandji, Marilyne
Dabo, Ndèye Astou
Dia, Yacine Amet
Diaw, Ndeye Aminata
Leye, Nafissatou
Diaw, Papa Alassane
Ahouidi, Ambroise
Cissé, Badara
Diallo, Abdoulaye Samba
Diop, Ousmane
Diallo, Abdou Aziz
Ndoye, Souadou
Sanko, Tomasz J.
Baxter, Cheryl
Wilkinson, Eduan
San, James E.
Tshabuila, Derek
Naidoo, Yeshnee
Pillay, Sureshnee
Lessells, Richard
Cissé, Khady
Leye, Abdoulaye
Mbaye, Khalifa Ababacar
Kania, Dramane
Tinto, Bachirou
Traoré, Isidore
Kagone, Sampawendé Thérèse
Ouedraogo, Abdoul Salam
Gifford, Robert J.
Lourenço, José
Giovanetti, Marta
Giandhari, Jennifer
Oliveira, Tulio de
Mboup, Souleymane
Affilliation
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal/Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa
KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa.
District of Kédougou. Kédougou, Senegal.
District of Kédougou. Kédougou, Senegal.
District of Kédougou. Kédougou, Senegal.
Centre MURAZ. Bobo-Dioulasso, Burkina Faso.
Centre MURAZ. Bobo-Dioulasso, Burkina Faso.
Centre MURAZ. Bobo-Dioulasso, Burkina Faso.
Centre MURAZ. Bobo-Dioulasso, Burkina Faso.
Centre MURAZ. Bobo-Dioulasso, Burkina Faso.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa.
Universidade Católica Portuguesa. Faculty of Medicine, Biomedical Research Centre. Lisbon, Portugal
Fundação Oswaldo Cruz. Instituto Rene Rachou. Belo Horizonte, MG, Brazil
KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa.
Centre for Epidemic Response and Innovation. School of Data Science and Computational Thinking. Stellenbosch University. Stellenbosch, South Africa/KwaZulu-Natal Research Innovation and Sequencing Platform. Nelson R Mandela School of Medicine. University of KwaZulu-Natal. Durban, South Africa.
Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation. Dakar, Senegal.
Abstract
Chikungunya (CHIKV) is a re-emerging endemic arbovirus in West Africa. Since July 2023, Senegal and Burkina Faso have been experiencing an ongoing outbreak, with over 300 confirmed cases detected so far in the regions of Kédougou and Tambacounda in Senegal, the largest recorded outbreak yet. CHIKV is typically maintained in a sylvatic cycle in Senegal but its evolution and factors contributing to re-emergence are so far unknown in West Africa, leaving a gap in understanding and responding to recurrent epidemics. We produced, in real-time, the first locally-generated and publicly available CHIKV whole genomes in West Africa, to characterize the genetic diversity of circulating strains, along with phylodynamic analysis to estimate time of emergence and population growth dynamics. A novel strain of the West African genotype, phylogenetically distinct from strains circulating in previous outbreaks, was identified. This suggests a likely new spillover from sylvatic cycles in rural Senegal and potential of seeding larger epidemics in urban settings in Senegal and elsewhere.
Keywords
Chikungunya virus
West African genotype
Genomic monitoring
Senegal
West Africa
Climate change
 
Publisher
Cold Spring Harbor Laboratory
Citation
PADANE, Abdou et al. An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal. medRxiv. Preprint. 2023. doi: 10.1101/2023.11.14.23298527