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released 2020-02-24</a> </span> </div> </div> <div class="content"> <form method="GET" action="/search/q-bio" aria-role="search"> Searching in archive <strong>q-bio</strong>. <a href="/search/?searchtype=author&query=Hozumi%2C+Y">Search in all archives.</a> <div class="field has-addons-tablet"> <div class="control is-expanded"> <label for="query" class="hidden-label">Search term or terms</label> <input class="input is-medium" id="query" name="query" placeholder="Search term..." type="text" value="Hozumi, Y"> </div> <div class="select control is-medium"> <label class="is-hidden" for="searchtype">Field</label> <select class="is-medium" id="searchtype" name="searchtype"><option value="all">All fields</option><option value="title">Title</option><option selected value="author">Author(s)</option><option value="abstract">Abstract</option><option value="comments">Comments</option><option value="journal_ref">Journal reference</option><option value="acm_class">ACM classification</option><option 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value="full_text">Full text</option></select> <input id="query" name="query" type="text" value="Hozumi, Y"> <ul id="abstracts"><li><input checked id="abstracts-0" name="abstracts" type="radio" value="show"> <label for="abstracts-0">Show abstracts</label></li><li><input id="abstracts-1" name="abstracts" type="radio" value="hide"> <label for="abstracts-1">Hide abstracts</label></li></ul> </div> <div class="box field is-grouped is-grouped-multiline level-item"> <div class="control"> <span class="select is-small"> <select id="size" name="size"><option value="25">25</option><option selected value="50">50</option><option value="100">100</option><option value="200">200</option></select> </span> <label for="size">results per page</label>. </div> <div class="control"> <label for="order">Sort results by</label> <span class="select is-small"> <select id="order" name="order"><option selected value="-announced_date_first">Announcement date (newest first)</option><option 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data </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Feng%2C+H">Hongsong Feng</a>, <a href="/search/q-bio?searchtype=author&query=Cottrell%2C+S">Sean Cottrell</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2312.10261v1-abstract-short" style="display: inline;"> Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses challenges attributed to both sparsity and the extensive number of genes implicated. An increasing number of computational tools are devised for analyzing and interpret… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2312.10261v1-abstract-full').style.display = 'inline'; document.getElementById('2312.10261v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2312.10261v1-abstract-full" style="display: none;"> Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses challenges attributed to both sparsity and the extensive number of genes implicated. An increasing number of computational tools are devised for analyzing and interpreting scRNA-seq data. We present a multiscale differential geometry (MDG) strategy to exploit the geometric and biological properties inherent in scRNA-seq data. We assume that those intrinsic properties of cells lies on a family of low-dimensional manifolds embedded in the high-dimensional space of scRNA-seq data. Subsequently, we explore these properties via multiscale cell-cell interactive manifolds. Our multiscale curvature-based representation serves as a powerful approach to effectively encapsulate the complex relationships in the cell-cell network. We showcase the utility of our novel approach by demonstrating its effectiveness in classifying cell types. This innovative application of differential geometry in scRNA-seq analysis opens new avenues for understanding the intricacies of biological networks and holds great potential for network analysis in other fields. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2312.10261v1-abstract-full').style.display = 'none'; document.getElementById('2312.10261v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 15 December, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> December 2023. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2310.14521">arXiv:2310.14521</a> <span> [<a href="https://arxiv.org/pdf/2310.14521">pdf</a>, <a href="https://arxiv.org/format/2310.14521">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Machine Learning">cs.LG</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Algebraic Topology">math.AT</span> </div> </div> <p class="title is-5 mathjax"> K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Cottrell%2C+S">Sean Cottrell</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2310.14521v1-abstract-short" style="display: inline;"> Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a challenge due to sparsity and the large number of genes involved. Therefore, dimensionality reduction and feature selection are important for removing spurious… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2310.14521v1-abstract-full').style.display = 'inline'; document.getElementById('2310.14521v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2310.14521v1-abstract-full" style="display: none;"> Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a challenge due to sparsity and the large number of genes involved. Therefore, dimensionality reduction and feature selection are important for removing spurious signals and enhancing downstream analysis. Traditional PCA, a main workhorse in dimensionality reduction, lacks the ability to capture geometrical structure information embedded in the data, and previous graph Laplacian regularizations are limited by the analysis of only a single scale. We propose a topological Principal Components Analysis (tPCA) method by the combination of persistent Laplacian (PL) technique and L$_{2,1}$ norm regularization to address multiscale and multiclass heterogeneity issues in data. We further introduce a k-Nearest-Neighbor (kNN) persistent Laplacian technique to improve the robustness of our persistent Laplacian method. The proposed kNN-PL is a new algebraic topology technique which addresses the many limitations of the traditional persistent homology. Rather than inducing filtration via the varying of a distance threshold, we introduced kNN-tPCA, where filtrations are achieved by varying the number of neighbors in a kNN network at each step, and find that this framework has significant implications for hyper-parameter tuning. We validate the efficacy of our proposed tPCA and kNN-tPCA methods on 11 diverse benchmark scRNA-seq datasets, and showcase that our methods outperform other unsupervised PCA enhancements from the literature, as well as popular Uniform Manifold Approximation (UMAP), t-Distributed Stochastic Neighbor Embedding (tSNE), and Projection Non-Negative Matrix Factorization (NMF) by significant margins. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2310.14521v1-abstract-full').style.display = 'none'; document.getElementById('2310.14521v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 22 October, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> October 2023. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">28 pages, 11 figures</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2210.09485">arXiv:2210.09485</a> <span> [<a href="https://arxiv.org/pdf/2210.09485">pdf</a>, <a href="https://arxiv.org/format/2210.09485">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> </div> </div> <p class="title is-5 mathjax"> Emerging dominant SARS-CoV-2 variants </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Chen%2C+J">Jiahui Chen</a>, <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Liu%2C+G">Gengzhuo Liu</a>, <a href="/search/q-bio?searchtype=author&query=Qiu%2C+Y">Yuchi Qiu</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+X">Xiaoqi Wei</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2210.09485v1-abstract-short" style="display: inline;"> Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of SARS-CoV-2 infections caused by dominant variants Omicron (BA.1), BA.2, and BA.4/BA.5 were accurately foretold by our artificial intelligence (AI) models built wit… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2210.09485v1-abstract-full').style.display = 'inline'; document.getElementById('2210.09485v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2210.09485v1-abstract-full" style="display: none;"> Accurate and reliable forecasting of emerging dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants enables policymakers and vaccine makers to get prepared for future waves of infections. The last three waves of SARS-CoV-2 infections caused by dominant variants Omicron (BA.1), BA.2, and BA.4/BA.5 were accurately foretold by our artificial intelligence (AI) models built with biophysics, genotyping of viral genomes, experimental data, algebraic topology, and deep learning. Based on newly available experimental data, we analyzed the impacts of all possible viral spike (S) protein receptor-binding domain (RBD) mutations on the SARS-CoV-2 infectivity. Our analysis sheds light on viral evolutionary mechanisms, i.e., natural selection through infectivity strengthening and antibody resistance. We forecast that BA.2.10.4, BA.2.75, BQ.1.1, and particularly, BA.2.75+R346T, have high potential to become new dominant variants to drive the next surge. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2210.09485v1-abstract-full').style.display = 'none'; document.getElementById('2210.09485v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 17 October, 2022; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> October 2022. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2109.04509">arXiv:2109.04509</a> <span> [<a href="https://arxiv.org/pdf/2109.04509">pdf</a>, <a href="https://arxiv.org/format/2109.04509">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Emerging vaccine-breakthrough SARS-CoV-2 variants </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Chen%2C+J">Jiahui Chen</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2109.04509v1-abstract-short" style="display: inline;"> The recent global surge in COVID-19 infections has been fueled by new SARS-CoV-2 variants, namely Alpha, Beta, Gamma, Delta, etc. The molecular mechanism underlying such surge is elusive due to 4,653 non-degenerate mutations on the spike protein, which is the target of most COVID-19 vaccines. The understanding of the molecular mechanism of transmission and evolution is a prerequisite to foresee th… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2109.04509v1-abstract-full').style.display = 'inline'; document.getElementById('2109.04509v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2109.04509v1-abstract-full" style="display: none;"> The recent global surge in COVID-19 infections has been fueled by new SARS-CoV-2 variants, namely Alpha, Beta, Gamma, Delta, etc. The molecular mechanism underlying such surge is elusive due to 4,653 non-degenerate mutations on the spike protein, which is the target of most COVID-19 vaccines. The understanding of the molecular mechanism of transmission and evolution is a prerequisite to foresee the trend of emerging vaccine-breakthrough variants and the design of mutation-proof vaccines and monoclonal antibodies. We integrate the genotyping of 1,489,884 SARS-CoV-2 genomes isolates, 130 human antibodies, tens of thousands of mutational data points, topological data analysis, and deep learning to reveal SARS-CoV-2 evolution mechanism and forecast emerging vaccine-escape variants. We show that infectivity-strengthening and antibody-disruptive co-mutations on the S protein RBD can quantitatively explain the infectivity and virulence of all prevailing variants. We demonstrate that Lambda is as infectious as Delta but is more vaccine-resistant. We analyze emerging vaccine-breakthrough co-mutations in 20 countries, including the United Kingdom, the United States, Denmark, Brazil, and Germany, etc. We envision that natural selection through infectivity will continue to be the main mechanism for viral evolution among unvaccinated populations, while antibody disruptive co-mutations will fuel the future growth of vaccine-breakthrough variants among fully vaccinated populations. Finally, we have identified the co-mutations that have the great likelihood of becoming dominant: [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y]. We predict they, particularly the last four, will break through existing vaccines. We foresee an urgent need to develop new vaccines that target these co-mutations. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2109.04509v1-abstract-full').style.display = 'none'; document.getElementById('2109.04509v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 9 September, 2021; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> September 2021. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">15 pages, 5 figures</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2012.15268">arXiv:2012.15268</a> <span> [<a href="https://arxiv.org/pdf/2012.15268">pdf</a>, <a href="https://arxiv.org/format/2012.15268">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> </div> </div> <p class="title is-5 mathjax"> UMAP-assisted $K$-means clustering of large-scale SARS-CoV-2 mutation datasets </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2012.15268v1-abstract-short" style="display: inline;"> Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide devastating effect. The understanding of evolution and transmission of SARS-CoV-2 is of paramount importance for the COVID-19 control, combating, and prevention. Due to the rapid growth of both the number of SARS-CoV-2 genome sequences and the number of unique mutations, the p… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2012.15268v1-abstract-full').style.display = 'inline'; document.getElementById('2012.15268v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2012.15268v1-abstract-full" style="display: none;"> Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide devastating effect. The understanding of evolution and transmission of SARS-CoV-2 is of paramount importance for the COVID-19 control, combating, and prevention. Due to the rapid growth of both the number of SARS-CoV-2 genome sequences and the number of unique mutations, the phylogenetic analysis of SARS-CoV-2 genome isolates faces an emergent large-data challenge. We introduce a dimension-reduced $k$-means clustering strategy to tackle this challenge. We examine the performance and effectiveness of three dimension-reduction algorithms: principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP). By using four benchmark datasets, we found that UMAP is the best-suited technique due to its stable, reliable, and efficient performance, its ability to improve clustering accuracy, especially for large Jaccard distanced-based datasets, and its superior clustering visualization. The UMAP-assisted $k$-means clustering enables us to shed light on increasingly large datasets from SARS-CoV-2 genome isolates. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2012.15268v1-abstract-full').style.display = 'none'; document.getElementById('2012.15268v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 30 December, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> December 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">30 pages, 10 figures</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2008.07488">arXiv:2008.07488</a> <span> [<a href="https://arxiv.org/pdf/2008.07488">pdf</a>, <a href="https://arxiv.org/format/2008.07488">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Host immune response driving SARS-CoV-2 evolution </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Zheng%2C+Y">Yong-Hui Zheng</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2008.07488v2-abstract-short" style="display: inline;"> The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance to the controlling and combating of coronavirus disease 2019 (COVID-19) pandemic. Currently, near 15,000 SARS-CoV-2 single mutations have been recorded, having a great ramification to the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is k… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2008.07488v2-abstract-full').style.display = 'inline'; document.getElementById('2008.07488v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2008.07488v2-abstract-full" style="display: none;"> The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance to the controlling and combating of coronavirus disease 2019 (COVID-19) pandemic. Currently, near 15,000 SARS-CoV-2 single mutations have been recorded, having a great ramification to the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is known about SARS-CoV-2 evolutionary characteristics and general trend. In this work, we present a comprehensive genotyping analysis of existing SARS-CoV-2 mutations. We reveal that host immune response via APOBEC and ADAR gene editing gives rise to near 65\% of recorded mutations. Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 because of their overreacting to the viral infection. Moreover, we uncover that populations of Oceania and Africa react significantly more intensively to SARS-CoV-2 infection than those of Europe and Asia, which may explain why African Americans were shown to be at increased risk of dying from COVID-19, in addition to their high risk of getting sick from COVID-19 caused by systemic health and social inequities. Finally, our study indicates that for two viral genome sequences of the same origin, their evolution order may be determined from the ratio of mutation type C$>$T over T$>$C. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2008.07488v2-abstract-full').style.display = 'none'; document.getElementById('2008.07488v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 20 August, 2020; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 17 August, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> August 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">22 pages, 15 figures</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2007.12692">arXiv:2007.12692</a> <span> [<a href="https://arxiv.org/pdf/2007.12692">pdf</a>, <a href="https://arxiv.org/format/2007.12692">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Characterizing SARS-CoV-2 mutations in the United States </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Chen%2C+J">Jiahui Chen</a>, <a href="/search/q-bio?searchtype=author&query=Gao%2C+K">Kaifu Gao</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2007.12692v1-abstract-short" style="display: inline;"> The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been mutating since it was first sequenced in early January 2020. The genetic variants have developed into a few distinct clusters with different properties. Since the United States (US) has the highest number of viral infected patients globally, it is essential to understand the US SARS-CoV-2. Using genotyping, sequence-alignmen… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2007.12692v1-abstract-full').style.display = 'inline'; document.getElementById('2007.12692v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2007.12692v1-abstract-full" style="display: none;"> The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been mutating since it was first sequenced in early January 2020. The genetic variants have developed into a few distinct clusters with different properties. Since the United States (US) has the highest number of viral infected patients globally, it is essential to understand the US SARS-CoV-2. Using genotyping, sequence-alignment, time-evolution, $k$-means clustering, protein-folding stability, algebraic topology, and network theory, we reveal that the US SARS-CoV-2 has four substrains and five top US SARS-CoV-2 mutations were first detected in China (2 cases), Singapore (2 cases), and the United Kingdom (1 case). The next three top US SARS-CoV-2 mutations were first detected in the US. These eight top mutations belong to two disconnected groups. The first group consisting of 5 concurrent mutations is prevailing, while the other group with three concurrent mutations gradually fades out. Our analysis suggests that female immune systems are more active than those of males in responding to SARS-CoV-2 infections. We identify that one of the top mutations, 27964C$>$T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we further uncover that three of four US SASR-CoV-2 substrains become more infectious. Our study calls for effective viral control and containing strategies in the US. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2007.12692v1-abstract-full').style.display = 'none'; document.getElementById('2007.12692v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 24 July, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> July 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">31 pages, 20 figures, and 4 tables</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2007.01344">arXiv:2007.01344</a> <span> [<a href="https://arxiv.org/pdf/2007.01344">pdf</a>, <a href="https://arxiv.org/format/2007.01344">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> </div> </div> <p class="title is-5 mathjax"> Decoding asymptomatic COVID-19 infection and transmission </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2007.01344v1-abstract-short" style="display: inline;"> Coronavirus disease 2019 (COVID-19) is a continuously devastating public health and the world economy. One of the major challenges in controlling the COVID-19 outbreak is its asymptomatic infection and transmission, which are elusive and defenseless in most situations. The pathogenicity and virulence of asymptomatic COVID-19 remain mysterious. Based on the genotyping of 20656 Severe Acute Respirat… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2007.01344v1-abstract-full').style.display = 'inline'; document.getElementById('2007.01344v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2007.01344v1-abstract-full" style="display: none;"> Coronavirus disease 2019 (COVID-19) is a continuously devastating public health and the world economy. One of the major challenges in controlling the COVID-19 outbreak is its asymptomatic infection and transmission, which are elusive and defenseless in most situations. The pathogenicity and virulence of asymptomatic COVID-19 remain mysterious. Based on the genotyping of 20656 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome isolates, we reveal that asymptomatic infection is linked to SARS-CoV-2 11083G>T mutation, i.e., leucine (L) to phenylalanine (F) substitution at the residue 37 (L37F) of nonstructure protein 6 (NSP6). By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2. Moreover, we show a global decaying tendency of the 11083G>T mutation ratio indicating that 11083G>T hinders SARS-CoV-2 transmission capacity. Sequence alignment found both NSP6 and residue 37 neighborhoods are relatively conservative over a few coronaviral species, indicating their importance in regulating host cell autophagy to undermine innate cellular defense against viral infection. Using machine learning and topological data analysis, we demonstrate that mutation L37F has made NSP6 energetically less stable. The rigidity and flexibility index and several network models suggest that mutation L37F may have compromised the NSP6 function, leading to a relatively weak SARS-CoV subtype. This assessment is a good agreement with our genotyping of SARS-CoV-2 evolution and transmission across various countries and regions over the past few months. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2007.01344v1-abstract-full').style.display = 'none'; document.getElementById('2007.01344v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 2 July, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> July 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">18 pages, 5 figures</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2005.02188">arXiv:2005.02188</a> <span> [<a href="https://arxiv.org/pdf/2005.02188">pdf</a>, <a href="https://arxiv.org/ps/2005.02188">ps</a>, <a href="https://arxiv.org/format/2005.02188">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> </div> </div> <p class="title is-5 mathjax"> Mutations on COVID-19 diagnostic targets </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2005.02188v1-abstract-short" style="display: inline;"> Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It would be an absolute tragedy if currently used diagnostic reagents are undermined in any manner. Based on th… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2005.02188v1-abstract-full').style.display = 'inline'; document.getElementById('2005.02188v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2005.02188v1-abstract-full" style="display: none;"> Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It would be an absolute tragedy if currently used diagnostic reagents are undermined in any manner. Based on the genotyping of 7818 SARS-CoV-2 genome samples collected up to May 1, 2020, we reveal that essentially all of the current COVID-19 diagnostic targets have had mutations. We further show that SARS-CoV-2 has the most devastating mutations on the targets of various nucleocapsid (N) gene primers and probes, which have been unfortunately used by countries around the world to diagnose COVID-19. Our findings explain what has seriously gone wrong with a specific diagnostic reagent made in China. To understand whether SARS-CoV-2 genes have mutated unevenly, we have computed the mutation ratio and mutation $h$-index of all SARS-CoV genes, indicating that the N gene is the most non-conservative gene in the SARS-CoV-2 genome. Our findings enable researchers to target the most conservative SARS-CoV-2 genes and proteins for the design and development of COVID-19 diagnostic reagents, preventive vaccines, and therapeutic medicines. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2005.02188v1-abstract-full').style.display = 'none'; document.getElementById('2005.02188v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 5 May, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> May 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">3 tables and 6 pages, and 48 tables in the Supporting Material</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2004.14114">arXiv:2004.14114</a> <span> [<a href="https://arxiv.org/pdf/2004.14114">pdf</a>, <a href="https://arxiv.org/format/2004.14114">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Populations and Evolution">q-bio.PE</span> </div> </div> <p class="title is-5 mathjax"> Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Wang%2C+R">Rui Wang</a>, <a href="/search/q-bio?searchtype=author&query=Hozumi%2C+Y">Yuta Hozumi</a>, <a href="/search/q-bio?searchtype=author&query=Yin%2C+C">Changchuan Yin</a>, <a href="/search/q-bio?searchtype=author&query=Wei%2C+G">Guo-Wei Wei</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2004.14114v1-abstract-short" style="display: inline;"> Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 6156 genome samples collected up to April 24, 2… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.14114v1-abstract-full').style.display = 'inline'; document.getElementById('2004.14114v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2004.14114v1-abstract-full" style="display: none;"> Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of this development has been based on the reference genome collected on January 5, 2020. Based on the genotyping of 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five subtypes. We introduce mutation ratio and mutation $h$-index to characterize the protein conservativeness and unveil that SARS-CoV-2 envelope protein, main protease, and endoribonuclease protein are relatively conservative, while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like protease are relatively non-conservative. In particular, the nucleocapsid protein has more than half its genes changed in the past few months, signaling devastating impacts on the ongoing development of COVID-19 diagnosis, vaccines, and drugs. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.14114v1-abstract-full').style.display = 'none'; document.getElementById('2004.14114v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 29 April, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> April 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">23 pages, 13 figures and 13 tables</span> </p> </li> </ol> <div class="is-hidden-tablet"> <!-- feedback for mobile only --> <span class="help" style="display: inline-block;"><a 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