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| 1 | Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters显示文摘A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at http://gffzzdbc7b6aaae734bddsu6uvoco6ww5x6cu9.ffgz.tsg.suse.edu.cn/biocode/tools/BT007081. | Qi Liu Shilei Zhao Cheng-Min Shi Shuhui Song Sihui Zhu Yankai Su Wenming Zhao Mingkun Li Yiming Bao Yongbiao Xue Hua Chen | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 1 |
| 2 | Nondestructive N-atom Greenberger-Horne-Zeilinger state analyzer via the cavity input-output process显示文摘 | Zhu Long Wang Hongfu Su Shilei | | 0，，： | 1 |
| 3 | Unidirectional acoustic metamaterials based on nonadiabatic holonomic quantum transformations显示文摘Nonadiabatic holonomic quantum transformations(NHQTs)have attracted wide attention and have been applied in many aspects of quantum computation,whereas related research is usually limited to the field of quantum physics.Here we bring NHQTs into constructing a unidirectional acoustic metamaterial(UDAM)for shaping classical beams.The UDAM is made up of an array of three-waveguide couplers,where the propagation of acoustic waves mimics the evolution of NHQTs.The excellent agreement among analytical predictions,numerical simulations,and experimental measurements confirms the great applicability of NHQTs in acoustic metamaterial engineering.The present work extends research on NHQTs from quantum physics to the field of classical waves for designing metamaterials with simple structures and may pave a new way to design UDAMs that would be of potential applications in acoustic isolation,communication,and stealth. | JinLei Wu Shuai Tang Yan Wang XiaoSai Wang JinXuan Han Cheng Lü Jie Song ShiLei Su Yan Xia YongYuan Jiang | 2022 | Science China(Physics,Mechanics & Astronomy)2022，65，2： | 0 |
| 4 | The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests显示文摘Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes(TCHH and TCHHL1), one nasal morphology gene(PAX3) and a set of genes(such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation. | Xiaoming Zhang Qi Liu Hui Zhang Shilei Zhao Jiahui Huang Tuot Sovannary Long Bunnath Hong Seang Aun Ham Samnom Bing Su Hua Chen | 2022 | National Science Review2022，9，3： | 0 |
| 5 | Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes显示文摘SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively throughout the world since its first outbreak in December,2019.Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving,and driven by adaptation to the new host and environments is still under debate.Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend,and providing guidance for disease control and treatments.Interrogating novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARSCoV-2 genome sequences of 169 countries as of December 30,2021,we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans,1)SARS-CoV-2 genomes are overall conserved under purifying selection,especially for the 14 genes related to viral RNA replication,transcription,and assembly;2)ongoing positive selection is actively driving the evolution of 6 genes(e.g.,S,ORF3a,and N)that play critical roles in molecular processes involving pathogen–host interactions,including viral invasion into and egress from host cells,and viral inhibition and evasion of host immune response,possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution.According to an established haplotype phylogenetic relationship of 138 viral clusters,a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters,of which multiple mutations potentially conferring alterations in viral transmissibility,pathogenicity,and virulence of SARS-CoV-2 are highlighted,warranting attention. | Yali Hou Shilei Zhao Qi Liu Xiaolong Zhang Tong Sha Yankai Su Wenming Zhao Yiming Bao Yongbiao Xue Hua Chen | 2022 | Genomics, Proteomics & Bioinformatics2022，20，6： | 0 |
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