Explore the vast range of titles available.

Background Identifying polymorphism clades on phylogenetic trees could help detect punctual mutations that are associated with viral functions. With visualization tools coloring the tree, it is easy to visually find clades where most sequences have the same polymorphism state. However, with the fast accumulation of viral sequences, a computational tool to automate this process is urgently needed. Results Here, by implementing a branch-and-bound-like search method, we developed an R package named sitePath to identify polymorphism clades automatically. Based on the identified polymorphism clades, fixed and parallel mutations could be inferred. Furthermore, sitePath also integrated visualization tools to generate figures of the calculated results. In an example with the influenza A virus H3N2 dataset, the detected fixed mutations coincide with antigenic shift mutations. The highly specificity and sensitivity of sitePath in finding fixed mutations were achieved for a range of parameters and different phylogenetic tree inference software. Conclusions The result suggests that sitePath can identify polymorphism clades per site. The clustering of sequences on a phylogenetic tree can be used to infer fixed and parallel mutations. High-quality figures of the calculated results could also be generated by sitePath.

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.

The Omicron variant of SARS-CoV-2 has become dominant in most countries and has raised significant global health concerns. As a global commerce center, New York, New York, USA, constantly faces the risk for multiple variant introductions of SARS-CoV-2. To elucidate the introduction and transmission of the Omicron variant in the city of New York, we created a comprehensive genomic and epidemiologic analysis of 392 Omicron virus specimens collected during November 25-December 11, 2021. We found evidence of 4 independent introductions of Omicron subclades, including the Omicron subclade BA.1.1 with defining substitution of R346K in the spike protein. The continuous genetic divergence within each Omicron subclade revealed their local community transmission and co-circulation in New York, including both household and workplace transmissions supported by epidemiologic evidence. Our study highlights the urgent need for enhanced genomic surveillance and effective response planning for better prevention and management of emerging SARS-CoV-2 variants.

Abstract Phylogenetic analysis has been widely used to describe, display, and infer the evolutionary patterns of viruses. The unprecedented accumulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes has provided valuable materials for the real-time study of SARS-CoV-2 evolution. However, the large number of SARS-CoV-2 genome sequences also poses great challenges for data analysis. Several methods for subsampling these large data sets have been introduced. However, current methods mainly focus on the spatiotemporal distribution of genomes without considering their genetic diversity, which might lead to post-subsampling bias. In this study, a subsampling method named covSampler was developed for the subsampling of SARS-CoV-2 genomes with consideration of both their spatiotemporal distribution and their genetic diversity. First, covSampler clusters all genomes according to their spatiotemporal distribution and genetic variation into groups that we call divergent pathways. Then, based on these divergent pathways, two kinds of subsampling strategies, representative subsampling and comprehensive subsampling, were provided with adjustable parameters to meet different users’ requirements. Our performance and validation tests indicate that covSampler is efficient and stable, with an abundance of options for user customization. Overall, our work has developed an easy-to-use tool and a webserver (https://www.covsampler.net) for the subsampling of SARS-CoV-2 genome sequences.

Based on the processing and analysis of the fixed-point horizontal deformation data across the fault in the middle and southern part of the Tan-Lu fault zone in recent 20 years, this paper preliminarily analyzes the vertical deformation characteristics of the middle and southern section of the Tan-Lu fault. The research shows that the overall activity level of the middle and southern part of the Tan-Lu fault zone is not high, and the average combining rate is 0.19 mm/a. However, it has obvious characteristics of time-sharing activities: from 2000 to 2010, the activity in Huaibai-Suqian section was large, while the activity in Xinyi-Linyi section was relatively small. There was a relatively closed section between Suqian and Xinyi; The overall activity rate has decreased from 2011 to 2019, but the activity rate of Anqiu station has increased significantly compared with that of 2000 to 2011. There is a certain correspondence between the activitycharacteristics of the fault zone and the seismicity of the region i