Omicron, the latest SARS-CoV-2 Variant of Concern (VOC), first appeared in Africa in November 2021. At present, the question of whether a new VOC will out-compete the currently predominant variant is important for governments seeking to determine if current surveillance strategies and responses are appropriate and reasonable. Based on both virus genomes and daily-confirmed cases, we compare the additive differences in growth rates and reproductive numbers (R_0) between VOCs and their predominant variants through a Bayesian framework and phylo-dynamics analysis. Faced with different variants, we evaluate the effects of current policies and vaccinations against VOCs and predominant variants. The model also predicts the date on which a VOC may become dominant based on simulation and real data in the early stage. The results suggest that the overall additive difference in growth rates of B.1.617.2 and predominant variants was 0.44 (95% confidence interval, 95% CI: −0.38, 1.25) in February 2021, and that the VOC had a relatively high R_0. The additive difference in the growth rate of BA.1 in the United Kingdom was 6.82 times the difference between Delta and Alpha, and the model successfully predicted the dominating process of Alpha, Delta and Omicron. Current vaccination strategies remain similarly effective against Delta compared to the previous variants. Our model proposes a reliable Bayesian framework to predict the spread trends of VOCs based on early-stage data, and evaluates the effects of public health policies, which may help us better prepare for the upcoming Omicron variant, which is now spreading at an unprecedented speed.

A comprehensive description of human genomes is essential for understanding human evolution and relationships between modern populations. However, most published literature focuses on local alignment comparison of several genes rather than the complete evolutionary record of individual genomes. Combining with data from the 1,000 Genomes Project, we successfully reconstructed 2,504 individual genomes and propose Divided Natural Vector method to analyze the distribution of nucleotides in the genomes. Comparisons based on autosomes, sex chromosomes and mitochondrial genomes reveal the genetic relationships between populations, and different inheritance pattern leads to different phylogenetic results. Results based on mitochondrial genomes confirm the “out-of-Africa” hypothesis and assert that humans, at least females, most likely originated in eastern Africa. The reconstructed genomes are stored on our server and can be further used for any genome-scale analysis of humans (http://yaulab.math.tsinghua.edu.cn/2022_1000genomesprojectdata/). This project provides the complete genomes of thousands of individuals and lays the groundwork for genome-level analyses of the genetic relationships between populations and the origin of humans.

Every smooth cubic plane curve has 9 flex points and 27 sextatic points. We study the following question asked by Farb: Is it true that the known algebraic structures give all the possible ways to continuously choose n distinct points on every smooth cubic plane curve, for each given positive integer n? We give an affirmative answer to the question when n=9 and 18 (the smallest open cases), and a negative answer for infinitely many n's.

In this paper we survey certain aspects of the classical Weil-Petersson metric and its generalizations. Being a natural L^2 metric on the parameter space of a family of complex manifolds or holomorphic vector bundles which admit some canonical metrics, the Weil-Petersson metric is well defined when the automorphism group of each fiber is discrete and the curvature of the Weil-Petersson metric can be computed via certain integrals over each fiber. We will discuss the case when these fibers have continuous automorphism groups. We also discuss the relation between the Weil-Petersson metric and energy of harmonic maps.

We show that every complete nontrivial gradient Yamabe soliton admits a special global warped product structure with a one-dimensional base. Based on this, we obtain a general classification theorem for complete nontrivial locally conformally flat gradient Yamabe solitons.