Dieng Idrissa, Balde Diamilatou, Talla Cheikh, Camara Diogop, Barry Mamadou Aliou, Sagne Samba Niang, Gueye Khadim, Dia Cheikh Abdou Khadre Mbacké, Sambe Babacar Souleymane, Fall Gamou, Sall Amadou Alpha, Faye Ousmane, Loucoubar Cheikh, Faye Oumar
Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal.
Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal.
Vaccines (Basel). 2023 Sep 28;11(10):1537. doi: 10.3390/vaccines11101537.
Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV-2 in south-eastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV-3. Following the notification by Senegal, many other West African countries reported DENV-3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV-3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV-3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV-3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV-3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.
登革热是全球最普遍的虫媒病毒病。其病原体登革病毒（DENV）自1970年以来就在塞内加尔传播，不过在很长一段时间内，病毒流行病学仅限于塞内加尔东南部（凯杜古地区）的丛林型DENV-2的传播。2009年出现了重大转变，首次城市疫情发生在达喀尔地区，由DENV-3引起。在塞内加尔通报疫情后，许多其他西非国家也报告了DENV-3疫情。尽管有这些通报，但关于西非DENV-3的遗传多样性和分子进化的研究和数据却很少。我们利用纳米孔测序、系统发育和系统地理学方法，对历史毒株和36个新测序的毒株进行研究，分析了2009年至2022年期间塞内加尔DENV-3的分子进化情况。然后，我们通过将氨基酸变化与疫苗毒株进行比对，评估了观察到的遗传多样性对预防措施和疫苗接种效果的影响。结果表明，在塞内加尔传播的DENV-3毒株属于基因型III，与其他西非国家的毒株相似，但属于不同的进化枝。基于近乎完整基因组的系统地理学分析揭示了来自亚洲和布基纳法索的三次独立引入事件。将塞内加尔毒株基因组的CprM-E区域的氨基酸与疫苗毒株进行比较，与CYD-3相比，发现有22个替换（7个在PrM内，15个在E基因内），而与TV003相比，观察到23个变化（6个在PrM内，17个在E基因内）。在E基因内，与疫苗毒株相比，大多数变化位于ED-III结构域，已知该结构域在中和抗体产生中至关重要。总之，这些数据为塞内加尔DENV-3基因组进化提供了最新见解，未来的疫苗接种策略需要考虑这些因素。此外，它们突出了非洲新兴病原体基因组流行病学的重要性，并呼吁建立一个泛非登革病毒基因组监测网络。
