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original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2025―Oct―31 |
SARS-CoV-2 Evolution in Humans Enables its Transmission to Nonhuman Primates |
Yu-Ting Chiu, Yu-Sung Huang, Max Yu-Chen Pan, Chih-Yao Chang, Chih-Chien Chiu, Vinh Nguyen, Ting-Hui Lee, Yuh-Ju Sun, Wen-Hsiung Li, Lily Hui-Ching Wang, Crystal Hepp |
| 2 |
[GO] |
2025―Oct―27 |
Convergent evolution and host-limiting impacts of SARS-CoV-2 revealed by cellular experiments |
Ting Zhang, Ren-Rong Tian, Fengyi Li, Xiaolu Tang, Wenbin He, Zhen-Ping Hao, Lin Zhuo, Jian Lu, Xuemei Lu, Yong-Tang Zheng, Adi Stern |
| 3 |
[GO] |
2025―Oct―23 |
Highly recurrent multi-nucleotide mutations in SARS-CoV-2 |
Nicola De Maio, Olivier Anoufa, Kyle Smith, Yatish Turakhia, Nick Goldman, Koichiro Tamura |
| 4 |
[GO] |
2025―Oct―15 |
Importance of De Novo Gene Evolution to Emerging Viral Threats: The ORF10 Strain-Restricted Orphan Gene of SARS-CoV-2 Promotes Pathogenesis |
Jeffrey A Haltom, Nidia S Trovao, Joseph W Guarnieri, Vincent Pan, Urminder Singh, Sergey Tsoy, Collin A O’Leary, Yaron Bram, Gabrielle A Widjaja, Zimu Cen, Robert Meller, Stephen B Baylin, Walter N Moss, Basil J Nikolau, Francisco J Enguita, Douglas C Wallace, Afshin Beheshti, Robert E Schwartz, Eve Syrkin Wurtele, Anne-Ruxandra Carvunis |
| 5 |
[GO] |
2025―Jun―09 |
A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data |
Florence Débarre, Zach Hensel, Brandon Gaut |
| 6 |
[GO] |
2025―Jun―09 |
The Data are Insufficient to Confidently Root the SARS-CoV-2 Phylogenetic Tree |
Jesse D Bloom, Brandon Gaut |
| 7 |
[GO] |
2025―Mar―18 |
A phylogenetic method identifies candidate drivers of the evolution of the SARS-CoV-2 mutation spectrum |
Russ Corbett-Detig, Kelley Harris |
| 8 |
[GO] |
2024―Jun―27 |
CMAPLE: efficient phylogenetic inference in the pandemic era |
Nhan Ly-Trong, Chris Bielow, Nicola De Maio, Bui Quang Minh, Andrey Rzhetsky |
| 9 |
[GO] |
2023―Sep―29 |
Correction to: Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic |
|
| 10 |
[GO] |
2023―Sep―19 |
A proofreading mutation with an allosteric effect allows a cluster SARS-CoV-2 viruses to rapidly evolve |
Andrew H Mack, Georgina Menzies, Alex Southgate, D Dafydd Jones, Thomas R Connor, Thomas Leitner |
| 11 |
[GO] |
2023―Sep―12 |
Intra- vs. inter-host evolution of SARS-CoV-2 driven by uncorrelated selection -The evolution thwarted |
Mei Hou, Jingrong Shi, Zanke Gong, Haijun Wen, Yun Lan, Xizi Deng, Qinghong Fan, Jiaojiao Li, Mengling Jiang, Xiaoping Tang, Chung-I Wu, Feng Li, Yongsen Ruan, Weiwei Zhai |
| 12 |
[GO] |
2023―Apr―13 |
Adaptive evolution of the Spike protein in coronaviruses |
Xiaolu Tang, Zhaohui Qian, Xuemei Lu, Jian Lu, Daniel Falush |
| 13 |
[GO] |
2023―Apr―11 |
Evolution of the SARS-CoV-2 mutational spectrum |
Jesse D Bloom, Annabel C Beichman, Richard A Neher, Kelley Harris, Crystal Hepp |
| 14 |
[GO] |
2023―Mar―02 |
Global dynamics of porcine enteric coronavirus PEDV epidemiology, evolution and transmission |
Hao Zhang, Chuangchao Zou, Ouyang Peng, Usama Ashraf, Qiuping Xu, Lang Gong, Baochao Fan, Yun Zhang, Zhichao Xu, Chunyi Xue, Xiaona Wei, Qingfeng Zhou, Xiaoyan Tian, Hanqin Shen, Bin Li, Xiangbin Zhang, Yongchang Cao |
| 15 |
[GO] |
2022―Aug―08 |
Contrasting patterns in the early stage of SARS-CoV-2 evolution between humans and minks |
Jui Hung Tai, Hsiao Yu Sun, Yi Cheng Tseng, Guanghao Li, Sui Yuan Chang, Shiou Hwei Yeh, Pei Jer Chen, Shu Miaw Chaw, Hurng Yi Wang, Meredith Yeager |
| 16 |
[GO] |
2022―Jul―11 |
Variational phylodynamic inference using pandemic-scale data |
Caleb Ki, Jonathan Terhorst, Rebekah Rogers |
| 17 |
[GO] |
2022―Jun―14 |
Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses |
Chuanyi Zhang, Palash Sashittal, Michael Xiang, Yichi Zhang, Ayesha Kazi, Mohammed El-Kebir, Thomas Leitner |
| 18 |
[GO] |
2022―Mar―01 |
The runaway evolution of SARS-CoV-2 leading to the highly evolved Delta strain |
Yongsen Ruan, Mei Hou, Xiaolu Tang, Xionglei He, Xuemei Lu, Jian Lu, Chung-I Wu, Haijun Wen |
| 19 |
[GO] |
2022―Jan―13 |
The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the substitution rate |
John H Tay, Ashleigh F Porter, Wytamma Wirth, Sebastian Duchene, Thomas Leitner |
| 20 |
[GO] |
2021―Sep―14 |
Corrigendum to: Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design |
Alan M Rice, Atahualpa Castillo Morales, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D Hurst |
| 21 |
[GO] |
2021―Sep―08 |
Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses |
Han Mei, Sergei Kosakovsky Pond, Anton Nekrutenko, Aya Takahashi |
| 22 |
[GO] |
2021―Sep―01 |
A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees |
Jakob McBroome, Bryan Thornlow, Angie S Hinrichs, Alexander Kramer, Nicola De Maio, Nick Goldman, David Haussler, Russell Corbett-Detig, Yatish Turakhia, Jian Lu |
| 23 |
[GO] |
2021―Aug―14 |
Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic |
Jesse D Bloom, Rasmus Nielsen |
| 24 |
[GO] |
2021―Feb―18 |
Comparative genomics reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2 |
Matteo Chiara, David S Horner, Carmela Gissi, Graziano Pesole, Li Liu |
| 25 |
[GO] |
2020―Dec―30 |
Population dynamics and structural effects at short and long range support the hypothesis of the selective advantage of the G614 SARS-Cov2 spike variant |
Emiliano Trucchi, Paolo Gratton, Fabrizio Mafessoni, Stefano Motta, Francesco Cicconardi, Filippo Mancia, Giorgio Bertorelle, Ilda D’Annessa, Daniele Di Marino, Jian Lu |
| 26 |
[GO] |
2020―Dec―07 |
Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny |
Lenore Pipes, Hongru Wang, John P Huelsenbeck, Rasmus Nielsen, Harmit Malik |
| 27 |
[GO] |
2020―Nov―02 |
Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination |
Yiyan Yang, Wei Yan, A Brantley Hall, Xiaofang Jiang, Rasmus Nielsen |
| 28 |
[GO] |
2020―Sep―15 |
Potential pathogenicity determinants identified from structural proteomics of SARS-CoV and SARS-CoV-2 |
Erica T Prates, Michael R Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Omar Demerdash, B Kirtley Amos, Armin Geiger, Daniel Jacobson, Harmit Malik |
| 29 |
[GO] |
2020―Apr―07 |
Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense |
Xuhua Xia, Sudhir Kumar |
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