Zhang Tianran, Shi Yaqi, Zhang Leyi, Wang Jian, Yu Chengchao, Lv Binbin, Wu Sisi, Huang Yiru, Liu Xuewei, Dai Hupiao, Zhou Mingshi, Liao Yanjuan, Wang Wei, Lin Guankai
Wenzhou Municipal Center for Disease Control and Prevention, Wenzhou Municipal Institute of Health Supervision, Wenzhou, China.
Yunnan Animal Health Supervision Institute, Kunming, China.
Front Microbiol. 2025 Aug 8;16:1607085. doi: 10.3389/fmicb.2025.1607085. eCollection 2025.
The evolutionary dynamics of dengue virus type 1 (DENV-1) in non-endemic settings such as southeastern coastal China where outbreaks predominantly stem from imported cases, remains insufficiently defined, particularly in relation to lineage displacement dynamics.
Ninety-three DENV-1 isolates (56 from 2019, 37 from 2024) collected in southeastern coastal China underwent whole-genome sequencing. Phylogenetic relationships were inferred using maximum likelihood methods under the GTR + G + I model. Selection pressures were assessed through FEL, MEME, SLAC, and FUBAR. Recombination was analyzed using seven detection algorithms implemented in RDP4. Hamming distances were used to profile amino acid substitutions. Epitope mapping was performed by comparative alignment against CYD-TDV and TAK-003 vaccine reference strains.
Phylogenetic inference placed all isolates within genotype I, yet 2019 and 2024 sequences segregated into distinct clades: 1I_E.1 and 1I_K.2, respectively. Codon-level analyses consistently indicated purifying selection. Eighteen recombination events were identified, predominantly involving strains of Vietnamese and Cambodian origin. A total of 40 non-synonymous substitutions were conserved across both periods, while 24 mutations were exclusive to 2024 isolates, with marked enrichment in NS3 and NS5 proteins. Epitope analyses revealed 9 and 17 antigenic variants within neutralizing domains of CYD-TDV and TAK-003, respectively.
Complete genotype turnover of DENV-1 occurred in southeastern coastal China between 2019 and 2024, driven by displacement of lineage 1I_E.1 by 1I_K.2, with implications for local transmission patterns. Observed antigenic divergence between temporal isolates emphasizes the importance of sustained genomic monitoring and targeted intervention strategies tailored to circulating strains in this region.
在非流行地区，如中国东南沿海地区，登革热1型病毒（DENV-1）的进化动态仍未得到充分界定，该地区的疫情主要源于输入病例，尤其是在谱系替代动态方面。
对在中国东南沿海地区收集的93株DENV-1分离株（2019年的56株，2024年的37株）进行全基因组测序。使用GTR+G+I模型下的最大似然法推断系统发育关系。通过FEL、MEME、SLAC和FUBAR评估选择压力。使用RDP4中实现的七种检测算法分析重组情况。汉明距离用于分析氨基酸替换情况。通过与CYD-TDV和TAK-003疫苗参考株进行比较比对来进行表位作图。
系统发育推断将所有分离株归入基因型I，但2019年和2024年的序列分别分为不同的进化枝：1I_E.1和1I_K.2。密码子水平分析一致表明存在纯化选择。共鉴定出18个重组事件，主要涉及越南和柬埔寨来源的毒株。两个时期共有40个非同义替换保守存在，而24个突变是2024年分离株特有的，在NS3和NS5蛋白中显著富集。表位分析分别在CYD-TDV和TAK-003的中和域内揭示了9个和17个抗原变体。
2019年至2024年间，中国东南沿海地区发生了DENV-1基因型的完全更替，由1I_K.2取代1I_E.1谱系所致，这对当地传播模式产生了影响。不同时期分离株之间观察到的抗原差异强调了持续进行基因组监测以及针对该地区流行毒株制定针对性干预策略的重要性。
