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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 88,970 bioRxiv papers from 381,395 authors.

Most downloaded bioRxiv papers, since beginning of last month

86,853 results found. For more information, click each entry to expand.

561: Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines
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Posted to bioRxiv 29 Jan 2020

Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines
386 downloads bioinformatics

Xin Liu, Xiu-Jie Wang

Starting from December 2019, a novel coronavirus, later named 2019-nCoV, was found to cause severe and rapid pandemic in China. Basing on the structural information, we have predicted a list of commercial medicines which may function as inhibitors for 2019-nCoV by targeting its main protease Mpro. These drugs may also be effective for other coronaviruses with similar Mpro binding sites and pocket structures.

562: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2
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Posted to bioRxiv 21 Apr 2020

Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2
386 downloads cell biology

Yuan-Lin Kang, Yi-Ying Chou, Paul W Rothlauf, Zhuoming Liu, Timothy K Soh, David Cureton, James Brett Case, Rita E. Chen, Michael S. Diamond, Sean P. J. Whelan, Tom Kirchhausen

Virus entry is a multistep process. It initiates when the virus attaches to the host cell and ends when the viral contents reach the cytosol. Genetically unrelated viruses can subvert analogous subcellular mechanisms and use similar trafficking pathways for successful entry. Antiviral strategies targeting early steps of infection are therefore appealing, particularly when the probability for successful interference through a common step is highest. We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. We also describe potent inhibition of SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 by Apilimod. These results define new tools for studying the intracellular trafficking of pathogens elicited by inhibition of PIKfyve kinase and suggest the potential for targeting this kinase in developing small-molecule antivirals against SARS-CoV-2. ### Competing Interest Statement M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and on the Scientific Advisory Board of Moderna. The Diamond laboratory at Washington University School of Medicine has received sponsored research agreements from Moderna and Emergent BioSolutions.

563: Potent synthetic nanobodies against SARS-CoV-2 and molecular basis for neutralization
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Posted to bioRxiv 10 Jun 2020

Potent synthetic nanobodies against SARS-CoV-2 and molecular basis for neutralization
385 downloads biochemistry

Tingting Li, Hongmin Cai, Hebang Yao, Bingjie Zhou, Yapei Zhao, Wenming Qin, Cedric A.J. Hutter, Yanling Lai, Juan Bao, Jiaming Lan, Gary Wong, Markus Seeger, Dimitri Lavillette, Dianfan Li

SARS-CoV-2, the Covid-19 causative virus, adheres to human cells through binding of its envelope Spike protein to the receptor ACE2. The Spike receptor-binding domain (S-RBD) mediates this key event and thus is a primary target for therapeutic neutralizing antibodies to mask the ACE2-interacting interface. Here, we generated 99 synthetic nanobodies (sybodies) using ribosome and phage display. The best sybody MR3 binds the RBD with KD of 1.0 nM and neutralizes SARS-CoV-2 pseudovirus with IC50 of 0.40 μg/mL. Crystal structures of two sybody-RBD complexes reveal a common neutralizing mechanism through which the RBD-ACE2 interaction is competitively inhibited by sybodies. The structures allowed the rational design of a mutant with higher affinity and improved neutralization efficiency by ≈24-folds, lowering the IC50 from 12.32 to 0.50 μg/mL. Further, the structures explain the selectivity of sybodies between SARS-CoV strains. Our work presents an alternative approach to generate neutralizers against newly emerged viruses. ### Competing Interest Statement The authors have declared no competing interest.

564: Comparison of SARS-CoV-2 infections among 3 species of non-human primates
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Posted to bioRxiv 12 Apr 2020

Comparison of SARS-CoV-2 infections among 3 species of non-human primates
385 downloads microbiology

Shuaiyao Lu, Yuan Zhao, Wenhai Yu, Yun Yang, Jiahong Gao, Junbin Wang, Dexuan Kuang, Mengli Yang, Jing Yang, Chunxia Ma, Jingwen Xu, Xingli Qian, Haiyan Li, Siwen Zhao, Jingmei Li, Haixuan Wang, Haiting Long, Jingxian Zhou, Fangyu Luo, Kaiyun Ding, Daoju Wu, Yong Zhang, Yinliang Dong, Yuqin Liu, Yingqiu Zheng, Xiaochen Lin, Li Jiao, Huanying Zheng, Qing Dai, Qiangmin Sun, Yunzhang Hu, Changwen Ke, Hongqi Liu, Xiaozhong Peng

COVID-19, caused by SARS-CoV-2 infection, has recently been announced as a pandemic all over the world. Plenty of diagnostic, preventive and therapeutic knowledges have been enriched from clinical studies since December 2019. However, animal models, particularly non-human primate models, are urgently needed for critical questions that could not be answered in clinical patients, evaluations of anti-viral drugs and vaccines. In this study, two families of non-human primates, old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and new world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Clinical signs were recorded. Samples were collected for analysis of viral shedding, viremia and histopathological examination. Increased body temperature was observed in 100% (12/12) M. mulatta, 33.3% (2/6) M. fascicularis and none (0/6) of C. jacchus post inoculation of SARS-CoV-2. All of M. mulatta and M. fascicularis showed chest radiographic abnormality. Viral genomes were detected in nasal swabs, throat swabs, anal swabs and blood from all 3 species of monkeys. Viral shedding from upper respiratory reached the peak between day 6 and day 8 post inoculation. From necropsied M. mulatta and M. fascicularis, tissues showing virus positive were mainly lung, weasand, bronchus and spleen. No viral genome was seen in any of tissues from 2 necropsied C. jacchus. Severe gross lesions and histopathological changes were observed in lung, heart and stomach of SARS-CoV-2 infected animals. In summary, we have established a NHP model for COVID-19, which could be used to evaluate drugs and vaccines, and investigate viral pathogenesis. M. mulatta is the most susceptible to SARS-CoV2 infection, followed by M. fascicularis and C. jacchus. ### Competing Interest Statement

565: Tools for Visualizing and Analyzing Fourier Space Sampling in Cryo-EM
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Posted to bioRxiv 09 Jun 2020

Tools for Visualizing and Analyzing Fourier Space Sampling in Cryo-EM
384 downloads biophysics

Philip R. Baldwin, Dmitry Lyumkis

A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced the sampling compensation factor (SCF), which incorporates how the collection geometry might change the spectral signal-to-noise ratio (SSNR), irrespective of the other experimental aspects. We show here that knowledge of the sampling restricted to spherical surfaces of sufficiently large radii in Fourier space is equivalent to knowledge of the set of projection views. Moreover, the SCF geometrical factor may be calculated from one such surface. To aid cryo-EM researchers, we developed a graphical user interface (GUI) tool that evaluates experimental orientation distributions. The GUI returns plots of projection directions, sampling constrained to the surface of a sphere, the SCF value, the fraction of the empty region of Fourier space, and a histogram of the sampling values over the points on a sphere. Finally, a fixed tilt angle may be incorporated to determine how tilting the grid during collection may improve the distribution of views and Fourier space sampling. We advocate this simple conception of sampling and the use of such tools as a complement to the distribution of views to capture the different aspects of the effect of projection directions on cryo-EM reconstructions. ### Competing Interest Statement The authors have declared no competing interest.

566: Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival
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Posted to bioRxiv 11 Jun 2020

Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival
383 downloads cell biology

Paolo Armando Gagliardi, Maciej Dobrzyński, Marc-Antoine Jacques, Coralie Dessauges, Robert M. Hughes, Olivier Pertz

Cell death events continuously challenge epithelial barrier function, yet are crucial to eliminate old or critically damaged cells. How such apoptotic events are spatio-temporally organized to maintain epithelial homeostasis remains unclear. We observe waves of Extracellular Signal-Regulated Kinase (ERK) and AKT serine/threonine kinase (Akt) activity pulses that originate from apoptotic cells and propagate radially to healthy surrounding cells. Such a propagation requires Epidermal Growth Factor Receptor (EGFR) and matrix metalloproteinase (MMP) signaling. At the single-cell level, ERK/Akt waves act as spatial survival signals that locally protect cells in the vicinity of the epithelial injury from apoptosis for a period of 3-4 hours. At the cell population level, ERK/Akt waves maintain epithelial homeostasis (EH) in response to mild or intense insults. Disruption of this spatial signaling system results in the inability of a model epithelial tissue to ensure barrier function in response to cellular stress. ### Competing Interest Statement The authors have declared no competing interest.

567: Characterization and validation of 15 α-synuclein conformation-specific antibodies using well-characterized preparations of α-synuclein monomers, fibrils and oligomers with distinct structures and morphology: How specific are the conformation-specific α-synuclein antibodies?
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Posted to bioRxiv 15 Jun 2020

Characterization and validation of 15 α-synuclein conformation-specific antibodies using well-characterized preparations of α-synuclein monomers, fibrils and oligomers with distinct structures and morphology: How specific are the conformation-specific α-synuclein antibodies?
383 downloads neuroscience

Senthil T. Kumar, Somanath Jagannath, Cindy Francois, Hugo Vanderstichele, Erik Stoops, Hilal A. Lashuel

Increasing evidence suggests that alpha-synuclein (α-syn) oligomers are obligate intermediates in the pathway involved in α-syn fibrillization and Lewy body (LB) formation, and may also accumulate within LBs in Parkinson's disease (PD) and other synucleinopathies. Therefore, the development of tools and methods to detect and quantify α-syn oligomers has become increasingly crucial for mechanistic studies to understand the role of these oligomers in PD, and to develop new diagnostic methods and therapies for PD and other synucleinopathies. The majority of these tools and methods rely primarily on the use of aggregation state-specific or conformation-specific antibodies. Given the impact of the data and knowledge generated using these antibodies on shaping the foundation and directions of α-syn and PD research, it is crucial that these antibodies are thoroughly characterized, and their specificity or ability to capture diverse α-syn species is tested and validated. Herein, we describe an antibody characterization and validation pipeline that allows a systematic investigation of the specificity of α-syn antibodies using well-defined and well-characterized preparations of various α-syn species, including monomers, fibrils, and different oligomer preparations that are characterized by distinct morphological, chemical and secondary structure properties. This pipeline was used to characterize 17 α-syn antibodies, 15 of which have been reported as conformation- or oligomer-specific antibodies, using an array of techniques, including immunoblot analysis (slot blot and Western blot), a digital ELISA assay using single molecule array technology and surface plasmon resonance. Our results show that i) none of the antibodies tested are specific for one particular type of α-syn species, including monomers, oligomers or fibrils; ii) all antibodies that were reported to be oligomer-specific also recognized fibrillar α-syn; and iii) a few antibodies showed high specificity for oligomers and fibrils but did not bind to monomers. These findings suggest that the majority of α-syn aggregate-specific antibodies do not differentiate between oligomers and fibrils, thus highlighting the importance of exercising caution when interpreting results obtained using these antibodies. Our results also underscore the critical importance of the characterization and validation of antibodies before their use in mechanistic studies and as diagnostic and therapeutic agents. This will not only improve the quality of research and reduce costs but will also reduce the number of therapeutic antibody failures in the clinic. ### Competing Interest Statement Prof. Hilal A. Lashuel is the founder and chief scientific officer of ND BioSciences, Epalinges, Switzerland.

568: Ramping activity in midbrain dopamine neurons signifies the use of a cognitive map
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Posted to bioRxiv 22 May 2020

Ramping activity in midbrain dopamine neurons signifies the use of a cognitive map
383 downloads neuroscience

Akash Guru, Changwoo Seo, Ryan J. Post, Durga S Kullakanda, Julia A Schaffer, Melissa R. Warden

Journeys to novel and familiar destinations employ different navigational strategies. The first drive to a new restaurant relies on map-based planning, but after repeated trips the drive is automatic and guided by local environmental cues. Ventral striatal dopamine rises during navigation toward goals and reflects the spatial proximity and value of goals, but the impact of experience, the neural mechanisms, and the functional significance of dopamine ramps are unknown. Here, we used fiber photometry to record the evolution of activity in midbrain dopamine neurons as mice learned a variety of reward-seeking tasks, starting recordings before training had commenced and continuing daily for weeks. When mice navigated through space toward a goal, robust ramping activity in dopamine neurons appeared immediately - after the first rewarded trial on the first training day in completely naive animals. In this task spatial cues were available to guide behavior, and although ramps were strong at first, they gradually faded away as training progressed. If instead mice learned to run a fixed distance on a stationary wheel for reward, a task that required an internal model of progress toward the goal, strong dopamine ramps persisted indefinitely. In a passive task in which a visible cue and reward moved together toward the mouse, ramps appeared and then faded over several days, but in an otherwise identical task with a stationary cue and reward ramps never appeared. Our findings provide strong evidence that ramping activity in midbrain dopamine neurons reflects the use of a cognitive map - an internal model of the distance already covered and the remaining distance until the goal is reached. We hypothesize that dopamine ramps may be used to reinforce locations on the way to newly-discovered rewards in order to build a graded ventral striatal value landscape for guiding routine spatial behavior. ### Competing Interest Statement The authors have declared no competing interest.

569: Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
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Posted to bioRxiv 01 Apr 2020

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
383 downloads neuroscience

Trygve Bakken, Nikolas L. Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian Kalmbach, Megan Crow, Rebecca Hodge, Fenna M. Krienen, Staci Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D. Aevermann, Andrew I. Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G. Castanon, Kirsten Crichton, Tanya L. Daigle, Rachel Dalley, Nick Dee, Nikolai Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T. Graybuck, Brian R. Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S. Liu, Hanqing Liu, Jacinta Lucero, Anup Mahurkar, Delissa McMillen, Jeremy Miller, Marmar Moussa, Joseph R. Nery, Philip R Nicovich, Joshua Orvis, Julia K. Osteen, Scott Owen, Carter R. Palmer, Trangthanh Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M. Reed, Christine Rimorin, Angeline Rivkin, William J. Romanow, Adriana E. Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M. Margarita Behrens, Héctor Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R. Hof, Thomas Höllt, Gregory D. Horwitz, C.Dirk Keene, Peter V. Kharchenko, Andrew L. Ko, Boudewijn P.F. Lelieveldt, Chongyuan Luo, Eran A. Mukamel, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly Smith, William J. Spain, Owen R. White, Christof Koch, Michael J. Hawrylycz, Bosiljka Tasic, Evan Z. Macosko, Steven A. McCarroll, Jonathan Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph Ecker, Sten Linnarsson, Ed Lein

The primary motor cortex (M1) is essential for voluntary fine motor control and is functionally conserved across mammals. Using high-throughput transcriptomic and epigenomic profiling of over 450,000 single nuclei in human, marmoset monkey, and mouse, we demonstrate a broadly conserved cellular makeup of this region, whose similarity mirrors evolutionary distance and is consistent between the transcriptome and epigenome. The core conserved molecular identity of neuronal and non-neuronal types allowed the generation of a cross-species consensus cell type classification and inference of conserved cell type properties across species. Despite overall conservation, many species specializations were apparent, including differences in cell type proportions, gene expression, DNA methylation, and chromatin state. Few cell type marker genes were conserved across species, providing a short list of candidate genes and regulatory mechanisms responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allowed the Patch-seq identification of layer 5 (L5) corticospinal Betz cells in non-human primate and human and characterization of their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell type diversity in M1 across mammals and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

570: Increasing Host Cellular Receptor—Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection
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Posted to bioRxiv 27 Feb 2020

Increasing Host Cellular Receptor—Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection
382 downloads microbiology

Pei-Hui Wang, Yun Cheng

The ongoing outbreak of a new coronavirus (2019-nCoV) causes an epidemic of acute respiratory syndrome in humans. 2019-nCoV rapidly spread to national regions and multiple other countries, thus, pose a serious threat to public health. Recent studies show that spike (S) proteins of 2019-nCoV and SARS-CoV may use the same host cell receptor called angiotensin-converting enzyme 2 (ACE2) for entering into host cells. The affinity between ACE2 and 2019-nCoV S is much higher than ACE2 binding to SARS-CoV S protein, explaining that why 2019-nCoV seems to be more readily transmitted from the human to human. Here, we reported that ACE2 can be significantly upregulated after infection of various viruses including SARS-CoV and MERS-CoV. Basing on findings here, we propose that coronavirus infection can positively induce its cellular entry receptor to accelerate their replication and spread, thus drugs targeting ACE2 expression may be prepared for the future emerging infectious diseases caused by this cluster of viruses.

571: ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis
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Posted to bioRxiv 29 Apr 2020

ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis
382 downloads genomics

Jeffrey M. Granja, M. Ryan Corces, Sarah E Pierce, S. Tansu Bagdatli, Hani Choudhry, Howard Y. Chang, William J. Greenleaf

The advent of large-scale single-cell chromatin accessibility profiling has accelerated our ability to map gene regulatory landscapes, but has outpaced the development of robust, scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; www.ArchRProject.com) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses including doublet removal, single-cell clustering and cell type identification, robust peak set generation, cellular trajectory identification, DNA element to gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility, and multi-omic integration with scRNA-seq. Enabling the analysis of over 1.2 million single cells within 8 hours on a standard Unix laptop, ArchR is a comprehensive analytical suite for end-to-end analysis of single-cell chromatin accessibility data that will accelerate the understanding of gene regulation at the resolution of individual cells. ### Competing Interest Statement W.J.G. and H.Y.C. are consultants for 10x Genomics who has licensed IP associated with ATAC-seq. W.J.G. has additional affiliations with Guardant Health (consultant) and Protillion Biosciences (co-founder and consultant). H.Y.C. is a co-founder of Accent Therapeutics, Boundless Bio, and a consultant for Arsenal Biosciences and Spring Discovery.

572: Natural image reconstruction from brain waves: a novel visual BCI system with native feedback
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Posted to bioRxiv 01 Oct 2019

Natural image reconstruction from brain waves: a novel visual BCI system with native feedback
381 downloads neuroscience

Grigory Rashkov, Anatoly Bobe, Dmitry Fastovets, Maria Komarova

Here we hypothesize that observing the visual stimuli of different categories trigger distinct brain states that can be decoded from noninvasive EEG recordings. We introduce an effective closed-loop BCI system that reconstructs the observed or imagined stimuli images from the co-occurring brain wave parameters. The reconstructed images are presented to the subject as a visual feedback. The developed system is applicable to training BCI-naïve subjects because of the user-friendly and intuitive way the visual patterns are employed to modify the brain states.

573: Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
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Posted to bioRxiv 18 Feb 2020

Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
377 downloads evolutionary biology

Juan Ángel Patiño-Galindo, Ioan Filip, Mohammed AlQuraishi, Raul Rabadan

The recent outbreak of a new coronavirus (SARS-CoV-2) in Wuhan, China, underscores the need for understanding the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. Here, we show that recombination in betacoronaviruses, including human-infecting viruses like SARS-CoV and MERS-CoV, frequently encompasses the Receptor Binding Domain (RBD) in the Spike gene. We find that this common process likely led to a recombination event at least 11 years ago in an ancestor of the SARS-CoV-2 involving the RBD. As a result of this recombination event, SARS-CoV and SARS-CoV-2 share a similar genotype in RBD, including two insertions (positions 432-436 and 460-472), and alleles 427N and 436Y. Both 427N and 436Y belong to a helix that interacts with the human ACE2 receptor. Ancestral state analyses revealed that SARS-CoV-2 differentiated from its most recent common ancestor with RaTG13 by accumulating a significant number of amino acid changes in the RBD. In sum, we propose a two-hit scenario in the emergence of the SARS-CoV-2 virus whereby the SARS-CoV-2 ancestors in bats first acquired genetic characteristics of SARS-CoV by incorporation of a SARS-like RBD through recombination before 2009, and subsequently, the lineage that led to SARS-CoV-2 accumulated further, unique changes specifically in the RBD.

574: Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers
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Posted to bioRxiv 09 Apr 2020

Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers
376 downloads genomics

Zhengqiao Zhao, Bahrad A. Sokhansanj, Gail Rosen

We propose an efficient framework for genetic subtyping of a pandemic virus, with application to the novel coronavirus SARS-CoV-2. Efficient identification of subtypes is particularly important for tracking the geographic distribution and temporal dynamics of infectious spread in real-time. In this paper, we utilize an entropy analysis to identify nucleotide sites within SARS-CoV-2 genome sequences that are highly informative of genetic variation, and thereby define an Informative Subtype Marker (ISM) for each sequence. We further apply an error correction technique to the ISMs, for more robust subtype definition given ambiguity and noise in sequence data. We show that, by analyzing the ISMs of global SARS-CoV-2 sequence data, we can distinguish interregional differences in viral subtype distribution, and track the emergence of subtypes in different regions over time. Based on publicly available data up to April 5, 2020, we show, for example: (1) distinct genetic subtypes of infections in Europe, with earlier transmission linked to subtypes prevalent in Italy with later development of subtypes specific to other countries over time; (2) within the United States, the emergence of an endogenous U.S. subtype that is distinct from the outbreak in New York, which is linked instead to subtypes found in Europe; and (3) dynamic emergence of SARS-CoV-2 from localization in China to a pattern of distinct regional subtypes in different countries around the world over time. Our results demonstrate that utilizing ISMs for genetic subtyping can be an important complement to conventional phylogenetic tree-based analyses of the COVID-19 pandemic. Particularly, because ISMs are efficient and compact subtype identifiers, they will be useful for modeling, data-mining, and machine learning tools to help enhance containment, therapeutic, and vaccine targeting strategies for fighting the COVID-19 pandemic. We have made the subtype identification pipeline described in this paper publicly available at https://github.com/EESI/ISM. ### Competing Interest Statement The authors have declared no competing interest.

575: In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03
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Posted to bioRxiv 14 Jun 2020

In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03
375 downloads bioinformatics

Muniba Faiza, Tariq Abdullah, Jose Franklin Calderon-Tantalean, Manish Ravindranath Upadhyay, Abdelrahman H. Abdelmoneim, Fareeha Akram, Bhupender Singh Thakur, Ibrahim Abdulaziz, Chimaobi James Ononamadu, Dina Abdelazim Ghoraba, Saba Munawar, MD Fakhrul Islam Faruque, Collins Kigen, Abhishek Sharma, Ashwani Kumar, Aqsa Khalid, Ali Gharip, Ankit Gupta, Manne Manikumar, Uma Chaudhary

The recent outbreak of severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) causing coronavirus disease (covid19) has posed a great threat to human health. Previous outbreaks of SARS-CoV and Middle East respiratory Syndrome CoV (MERS-CoV) from the same CoV family had posed similar threat to human health and economic growth. To date, not even a single drug specific to any of these CoVs has been developed nor any anti-viral vaccine is available for the treatment of diseases caused by CoVs. Subunits present in spike glycoproteins of SARS-CoV and SARS-CoV-2 are involved in binding to human ACE2 Receptor which is the primary method of viral invasion. As it has been observed in the previous studies that there are very minor differences in the spike glycoproteins of SARS-CoV and SARS-CoV-2. SARS-CoV-2 has an additional furin cleavage site that makes it different from SARS-CoV (Walls et al., 2020). In this study, we have analyzed spike glycoproteins of SARS-CoV-2 and SARS-CoV phylogenetically and subjected them to selection pressure analysis. Selection pressure analysis has revealed some important sites in SARS-CoV-2 and SARS-CoV spike glycoproteins that might be involved in their pathogenicity. Further, we have developed a potential multi-epitope vaccine candidate against SARS-CoV-2 by analyzing its interactions with HLA-B*15:03 subtype. This vaccine consists of multiple T-helper (TH) cells, B-cells, and Cytotoxic T-cells (CTL) epitopes joined by linkers and an adjuvant to increase its immunogenicity. Conservation of selected epitopes in SARS, MERS, and human hosts, suggests that the designed vaccine could provide cross-protection. The vaccine is designed in silico by following a reverse vaccinology method acknowledging its antigenicity, immunogenicity, toxicity, and allergenicity. The vaccine candidate that we have designed as a result of this work shows promising result indicating its potential capability of simulating an immune response. ### Competing Interest Statement The authors have declared no competing interest.

576: Spatiotemporal Dynamics of Sound Representations Reveal a Hierarchical Progression of Category Selectivity
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Posted to bioRxiv 13 Jun 2020

Spatiotemporal Dynamics of Sound Representations Reveal a Hierarchical Progression of Category Selectivity
375 downloads neuroscience

Matthew X Lowe, Yalda Mohsenzadeh, Benjamin Lahner, Ian Charest, Aude Oliva, Santani Teng

As the human brain transforms incoming sounds, it remains unclear whether semantic meaning is assigned via distributed, domain-general architectures or specialized hierarchical streams. Here we show that the spatiotemporal progression from acoustic to semantically dominated representations is consistent with a hierarchical processing scheme. Combining magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) patterns, we found superior temporal responses beginning ~80 ms post-stimulus onset, spreading to extratemporal cortices by ~130 ms. Early acoustically-dominated representations trended systematically toward semantic category dominance over time (after ~200 ms) and space (beyond primary cortex). Semantic category representation was spatially specific: vocalizations were preferentially distinguished in temporal and frontal voice-selective regions and the fusiform face area; scene and object sounds were distinguished in parahippocampal and medial place areas. Our results are consistent with an extended auditory processing hierarchy in which acoustic representations give rise to multiple streams specialized by category, including areas typically considered visual cortex. ### Competing Interest Statement The authors have declared no competing interest.

577: Adipose Tissue is a Critical Regulator of Osteoarthritis
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Posted to bioRxiv 05 Jun 2020

Adipose Tissue is a Critical Regulator of Osteoarthritis
375 downloads physiology

Kelsey H. Collins, Kristin L. Lenz, Eleanor N. Pollitt, Daniel Ferguson, Irina Hutson, Luke E. Springer, Arin K. Oestreich, Ruhang Tang, Yun-Rak Choi, Gretchen A. Meyer, Steven L. Teitelbaum, Christine T.N. Pham, Charles A. Harris, Farshid Guilak

Osteoarthritis (OA), the leading cause of pain and disability worldwide, disproportionally affects obese individuals. The mechanisms by which adipose tissue leads to the onset and progression of OA are unclear due to the complex interactions between the metabolic, biomechanical, and inflammatory factors that accompany obesity. We used a murine model of lipodystrophy (LD) to examine the direct contribution of adipose tissue to OA. Knee joints of LD mice were protected from spontaneous or post-traumatic OA, on either a chow and high fat diet, despite similar body weight and the presence of systemic inflammation. These findings indicate that adipose tissue itself plays a critical role in the pathophysiology of OA. Susceptibility to post-traumatic OA was reintroduced into LD mice using implantation of adipose tissue derived from wildtype animals or mouse embryonic fibroblasts that undergo spontaneous adipogenesis, implicating paracrine signaling from fat, rather than body weight, as a critical mediator of joint degeneration. ### Competing Interest Statement The authors have declared no competing interest.

578: An enhanced isothermal amplification assay for viral detection
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Posted to bioRxiv 29 May 2020

An enhanced isothermal amplification assay for viral detection
375 downloads molecular biology

Jason Qian, Sarah A. Boswell, Christopher Chidley, Zhi-xiang Lu, Mary E. Pettit, Benjamin L. Gaudio, Jesse M Fajnzylber, Ryan T Ingram, Rebecca H Ward, Jonathan Z Li, Michael Springer

Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available. ### Competing Interest Statement 3 patents have been filed U.S. Provisional Patent Application 63/993,521, 63/003,555, and 63/006,372. A company, Qtection LLC, has been launched to commercialize FIND and provide effective testing options to the public. MS is a founder of the company.

579: Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure
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Posted to bioRxiv 05 Jun 2020

Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure
374 downloads evolutionary biology

Leandro R. Jones, Julieta M. Manrique

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid spread on the virus evolution are under investigation. In this work, we analyzed ca. 9,000 SARS-CoV-2 genomes from Africa, America, Asia, Europe, and Oceania. We show that the virus is a complex of slightly different genetic variants that are unevenly distributed on Earth. Furthermore, we demonstrate that SARS-CoV-2 phylogeny is spatially structured. We hypothesize this could be the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersal. In light of our results, we discuss how dispersal may constitute an opportunity for the virus to fix otherwise rare, and/or develop new, mutations. Based on previous studies, the possibility that this could significantly affect the virus phenotype is not remote. ### Competing Interest Statement The authors have declared no competing interest.

580: Phylogenetic analysis of migration, differentiation, and class switching in B cells
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Posted to bioRxiv 31 May 2020

Phylogenetic analysis of migration, differentiation, and class switching in B cells
374 downloads immunology

Kenneth B Hoehn, Oliver G Pybus, Steven H. Kleinstein

B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subsets, and switching between functional isotypes. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. To address this, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We use simulations to demonstrate the effectiveness of this approach. We then use this framework to infer patterns of cellular differentiation and isotype switching from high throughput BCR sequence datasets obtained from patients in a study of HIV infection and a study of food allergy. These methods are implemented in the R package dowser, available at https://bitbucket.org/kleinstein/dowser. ### Competing Interest Statement S.H.K. receives consulting fees from Northrop Grumman.

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