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Zika virus (ZIKV) is a mosquito-borne flavivirus. It was first isolated from Uganda in 1947 and has become an emergent event since 2007. However, because of the inconsistency of alignment methods, the evolution of ZIKV remains poorly understood. In this study, we first use the complete protein and an alignment-free method to build a phylogenetic tree of 87 Zika strains in which Asian, East African, and West African lineages are characterized. We also use the NS5 protein to construct the genetic relationship among 44 Zika strains. For the first time, these strains are divided into two clades: African 1 and African 2. This result suggests that ZIKV originates from Africa, then spread to Asia, Pacific islands, and throughout the Americas. We also perform the phylogeny analysis for 53 viruses in genus Flavivirus to which ZIKV belongs using complete proteins. Our conclusion is consistent with the classification by the hosts and transmission vectors.

We study the averaging of fronts moving with positive oscillatory normal velocity, which is periodic in space and stationary ergodic in time. The problem can be formulated as the homogenization of coercive level set Hamilton-Jacobi equations with spatio-temporal oscillations. To overcome the difficulties due to the oscillations in time and the linear growth of the Hamiltonian, we first study the long time averaged behavior of the associated reachable sets using geometric arguments. The results are new for higher than one dimensions even in the space-time periodic setting.

We consider the Stokes conjecture concerning the shape of extreme 2-dimensional water waves. By new geometric methods including a non-linear frequency formula, we prove the Stokes conjecture in the original variables. Our results do not rely on structural assumptions needed in previous results such as isolated singularities, symmetry and monotonicity. Part of our results extends to the mathematical problem in higher dimensions.

We construct a counterexample to the conjugacy of maximal abelian diagonalizable subalgebras in extended affine Lie algebras.