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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 88,669 bioRxiv papers from 380,331 authors.

Most downloaded bioRxiv papers, since beginning of last month

86,465 results found. For more information, click each entry to expand.

81: Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design
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Posted to bioRxiv 29 Apr 2020

Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design
1,204 downloads biochemistry

Wioletta Rut, Zongyang Lv, Mikolaj Zmudzinski, Stephanie Patchett, Digant Nayak, Scott J Snipas, Farid El Oualid, Tony T. Huang, Miklos Bekes, Marcin Drag, Shaun K Olsen

In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning. ### Competing Interest Statement F.E.O. declares competing financial interests as co-founders and shareholder of UbiQ Bio BV. M.B. is an employee and shareholder of Arvinas, Inc. The remaining authors declare no competing interests.

82: LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding
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Posted to bioRxiv 08 Apr 2020

LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding
1,197 downloads molecular biology

Jonathan L. Schmid-Burgk, R.M. Schmithausen, David Li, Ronja Hollstein, Amir Ben-Shmuel, Ofir Israeli, Shay Weiss, Nir Paran, Gero Wilbring, Jana Liebing, David Feldman, Mikołaj Słabicki, Bärbel Lippke, Esther Sib, Jacob Borrajo, Jonathan Strecker, Julia Reinhardt, Per Hoffmann, Brian Cleary, Michael Hölzel, Markus M. Nöthen, Martin Exner, Kerstin U Ludwig, Aviv Regev, Feng Zhang

The ongoing SARS-CoV-2 pandemic has already caused devastating losses. Exponential spread can be slowed by social distancing and population-wide isolation measures, but those place a tremendous burden on society, and, once lifted, exponential spread can re-emerge. Regular population-scale testing, combined with contact tracing and case isolation, should help break the cycle of transmission, but current detection strategies are not capable of such large-scale processing. Here we present a protocol for LAMP-Seq, a barcoded Reverse-Transcription Loop-mediated Isothermal Amplification (RT-LAMP) method that is highly scalable. Individual samples are stabilized, inactivated, and amplified in three isothermal heat steps, generating barcoded amplicons that can be pooled and analyzed en masse by sequencing. Using unique barcode combinations per sample from a compressed barcode space enables extensive pooling, potentially further reducing cost and simplifying logistics. We validated LAMP-Seq on 28 clinical samples, empirically optimized the protocol and barcode design, and performed initial safety evaluation. Relying on world-wide infrastructure for next-generation sequencing, and in the context of population-wide sample collection, LAMP-Seq could be scaled to analyze millions of samples per day. ### Competing Interest Statement J.S.-B., D.L., and F.Z. are inventors on a patent application filed by the Broad Institute related to this work with the specific aim of ensuring this technology can be made freely, widely, and rapidly available for research and deployment. F.Z. is a co-founder of Editas Medicine, Beam Therapeutics, Pairwise Plants, Arbor Biotechnologies, and Sherlock Biosciences. A.R. is a founder of Celsius Therapeutics, equity holder in Immunitas, and an SAB member for ThermoFisher Scientific, Syros Pharmaceuticals, Asimov, and Neogene Therapeutics. P.H. and M.M.N. are SAB members of HMG Systems Bioengineering GmbH. M.M.N. served on SABs for Lundbeck Foundation and Robert-Bosch-Stiftung, was reimbursed travel expenses by Shire GmbH, receives salary from and holds shares in Life & Brain GmbH.

83: An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents
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Posted to bioRxiv 30 May 2020

An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents
1,183 downloads genomics

Daphna Rothschild, Sigal Leviatan, Ariel Hanemann, Yossi Cohen, Omer Weissbrod, Eran Segal

Numerous human conditions are associated with the microbiome, yet studies are inconsistent as to the magnitude of the associations and the bacteria involved, likely reflecting insufficiently employed sample sizes. Here, we collected diverse phenotypes and gut microbiota from 34,057 individuals from Israel and the U.S.. Analyzing these data using a much-expanded microbial genomes set, we derive an atlas of robust and numerous unreported associations between bacteria and numerous human traits, which we show to replicate in cohorts from both continents. Using machine learning models trained on microbiome data, we predict human traits with high accuracy across continents. Subsampling our cohort to smaller cohort sizes yielded highly variable models and thus sensitivity to the selected cohort, underscoring the utility of large cohorts and possibly explaining the source of discrepancies across studies. Finally, many of our prediction models saturate at these numbers of individuals, suggesting that similar analyses on larger cohorts may not further improve these predictions. ### Competing Interest Statement The authors have declared no competing interest.

84: DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP
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Posted to bioRxiv 21 Mar 2020

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP
1,178 downloads microbiology

Emily A. Bruce, Meei-Li Huang, Garrett A. Perchetti, Scott Tighe, Pheobe Laaguiby, Jessica J Hoffman, Diana L Gerrard, Arun K. Nalla, Yulun Wei, Alexander L. Greninger, Sean A. Diehl, David J. Shirley, Debra G. B. Leonard, Christopher D. Huston, Beth D. Kirkpatrick, Julie A. Dragon, Jessica W. Crothers, Keith R. Jerome, Jason W. Botten

The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.

85: Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy
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Posted to bioRxiv 25 Mar 2020

Glycoengineering of NK cells with glycan ligands of CD22 and selectins for B-cell lymphoma therapy
1,173 downloads bioengineering

Senlian Hong, Chenhua Yu, Peng Wang, Yujie Shi, Bo Cheng, Mingkuan Chen, Digantkumar G. Chapla, Natalie Reigh, Yoshiki Narimatsu, Xing Chen, Henrik Clausen, Kelly W. Moremen, Matthew Scott Macauley, James C. Paulson, Peng Wu

CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 (RituxanTM) on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced killer (CIK) cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The cells containing the ligands of both CD22 and selectins resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that NK cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.

86: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols
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Posted to bioRxiv 17 Mar 2020

Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols
1,172 downloads microbiology

Annika Kratzel, Daniel Todt, Philip V’kovski, Silvio Steiner, Mitra L Gultom, Tran Thi Nhu Thao, Nadine Ebert, Melle Holwerda, Jörg Steinmann, Daniela Niemeyer, Ronald Dijkman, Günter Kampf, Christian Drosten, Eike Steinmann, Volker Thiel, Stephanie Pfaender

The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 is a major burden for health care systems worldwide. It is important to address if the current infection control instructions based on active ingredients are sufficient. We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. Efficient SARS-CoV-2 inactivation was demonstrated for all tested alcohol-based disinfectants. These findings show the successful inactivation of SARS-CoV-2 for the first time and provide confidence in its use for the control of COVID-19.

87: A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals
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Posted to bioRxiv 17 Apr 2020

A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals
1,171 downloads microbiology

Laura Riva, Shuofeng Yuan, Xin Yin, Laura Martin-Sancho, Naoko Matsunaga, Sebastian Burgstaller-Muehlbacher, Lars Pache, Paul P. De Jesus, Mitchell V. Hull, Max Chang, Jasper Fuk-Woo Chan, Jianli Cao, Vincent Kwok-Man Poon, Kristina Herbert, Tu-Trinh Nguyen, Yuan Pu, Courtney Nguyen, Andrey Rubanov, Luis Martinez-Sobrido, Wen-Chun Liu, Lisa Miorin, Kris M. White, Jeffrey R. Johnson, Christopher Benner, Ren Sun, Peter G. Schultz, Andrew Su, Adolfo Garcia-Sastre, Arnab K. Chatterjee, Kwok-Yung Yuen, Sumit K. Chanda

The emergence of novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, more than 2.1 million confirmed cases and 139,500 deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. As the development of a vaccine could require at least 12-18 months, and the typical timeline from hit finding to drug registration of an antiviral is >10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDAapproved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment. ### Competing Interest Statement The authors have declared no competing interest.

88: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
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Posted to bioRxiv 20 Apr 2020

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
1,165 downloads bioinformatics

Christoph Muus, Malte D Luecken, Gokcen Eraslan, Avinash Waghray, Graham Heimberg, Lisa Sikkema, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smilie, Karthik Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L. Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, J. Samuel, Allon Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Marie Deprez, David S. Fischer, Astrid Gillich, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Alok Jaiswal, Peiyong Jiang, Theodoros Kapellos, Christin S Kuo, Ludvig Larsson, Michael A. Leney-Greene, Kyungtae Lim, Monika Litviňuková, Ji Lu, Leif S Ludwig, Wendy Luo, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Charles-Hugo Marquette, Ian Mbano, Alexi Marie McAdams, Ross J Metzger, Ahmad N. Nabhan, Sarah K. Nyquist, Lolita Penland, Olivier Poirion, Sergio Poli, CanCan Qi, Rachel Queen, Daniel Reichart, Ivan Rosas, Jonas Schupp, Rahul Sinha, Rene V Sit, Dorothee Diogo, Michal Slyper, Neal Smith, Alex Sountoulidis, Maximilian Strunz, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J. Travaglini, Nathan R. Tucker, Katherine Vernon, Marc H Wadsworth, Julia Waldman, Xiuting Wang, Wenjun Yan, William Zhao, Carly G. K. Ziegler, The NHLBI LungMAP Consortium, The Human Cell Atlas Lung Biological Network

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis. ### Competing Interest Statement N.K. was a consultant to Biogen Idec, Boehringer Ingelheim, Third Rock, Pliant, Samumed, NuMedii, Indaloo, Theravance, LifeMax, Three Lake Partners, Optikira and received non-financial support from MiRagen. All of these outside the work reported. J.L. is a scientific consultant for 10X Genomics Inc A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas, and an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Asimov, and Neogene Therapeutics O.R.R., is a co-inventor on patent applications filed by the Broad Institute to inventions relating to single cell genomics applications, such as in PCT/US2018/060860 and US Provisional Application No. 62/745,259. A.K.S. compensation for consulting and SAB membership from Honeycomb Biotechnologies, Cellarity, Cogen Therapeutics, Orche Bio, and Dahlia Biosciences. S.A.T. was a consultant at Genentech, Biogen and Roche in the last three years. F.J.T. reports receiving consulting fees from Roche Diagnostics GmbH, and ownership interest in Cellarity Inc. L.V. is funder of Definigen and Bilitech two biotech companies using hPSCs and organoid for disease modelling and cell based therapy.

89: An association between sexes of successive siblings in the data from Demographic and Health Survey program
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Posted to bioRxiv 12 Nov 2015

An association between sexes of successive siblings in the data from Demographic and Health Survey program
1,150 downloads physiology

Mikhail Monakhov

The prediction of future child's sex is a question of keen public interest. The probability of having a child of either sex is close to 50%, although multiple factors may slightly change this value. Some demographic studies suggested that sex determination can be influenced by previous pregnancies, although this hypothesis was not commonly accepted. This paper explores the correlations between siblings' sexes using data from the Demographic and Health Survey program. In the sample of about 2,214,601 women (7,985,855 children), the frequencies of sibships with multiple siblings of the same sex were significantly higher than can be expected by chance. A formal modelling demonstrated that sexes of the children were dependent on three kinds of sex ratio variation: a variation between families (Lexian), a variation within a family (Poisson) and a variation contingent upon the sex of preceding sibling (Markovian). There was a positive correlation between the sexes of successive siblings (coefficient = 0.067, p < 0.001), i.e. a child was more likely to be of the same sex as its preceding sibling. This correlation could be caused by secondary sex ratio adjustment in utero since the effect was decreasing with the length of birth-to-birth interval, and the birth-to-birth interval was longer for siblings with unlike sex.

90: SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins
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Posted to bioRxiv 10 Jun 2020

SARS-CoV-2 nucleocapsid protein undergoes liquid-liquid phase separation stimulated by RNA and partitions into phases of human ribonucleoproteins
1,150 downloads biochemistry

Theodora Myrto Perdikari, Anastasia C. Murthy, Veronica H. Ryan, Scott Watters, Mandar T. Naik, Nicolas L. Fawzi

Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and may assemble within viral factories, dynamic compartments formed within the host cells. Here, we examine the possibility that the multivalent RNA-binding nucleocapsid protein (N) from the severe acute respiratory syndrome coronavirus (SARS-CoV-2) compacts RNA via protein-RNA liquid-liquid phase separation (LLPS) and that N interactions with host RNA-binding proteins are mediated by phase separation. To this end, we created a construct expressing recombinant N fused to a N-terminal maltose binding protein tag which helps keep the oligomeric N soluble for purification. Using in vitro phase separation assays, we find that N is assembly-prone and phase separates avidly. Phase separation is modulated by addition of RNA and changes in pH and is disfavored at high concentrations of salt. Furthermore, N enters into in vitro phase separated condensates of full-length human hnRNPs (TDP-43, FUS, and hnRNPA2) and their low complexity domains (LCs). However, N partitioning into the LC of FUS, but not TDP-43 or hnRNPA2, requires cleavage of the solubilizing MBP fusion. Hence, LLPS may be an essential mechanism used for SARS-CoV-2 and other RNA viral genome packing and host protein co-opting, functions necessary for viral replication and hence infectivity. ### Competing Interest Statement N.L.F. is a member of the Scientific Advisory Board of Dewpoint Therapeutics.

91: Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
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Posted to bioRxiv 25 Mar 2020

Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray
1,136 downloads immunology

Saahir Khan, Rie Nakajima, Aarti Jain, Rafael Ramiro de Assis, Al Jasinskas, Joshua M. Obiero, Oluwasanmi Adenaiye, Sheldon Tai, Filbert Hong, Donald K. Milton, Huw Davies, Philip L. Felgner, Prometheus Study Group

The current practice for diagnosis of SARS-CoV-2 infection relies on PCR testing of nasopharyngeal or respiratory specimens in a symptomatic patient at high epidemiologic risk. This testing strategy likely underestimates the true prevalence of infection, creating the need for serologic methods to detect infections missed by the limited testing to date. Here, we describe the development of a coronavirus antigen microarray containing immunologically significant antigens from SARS-CoV-2, in addition to SARS-CoV, MERS-CoV, common human coronavirus strains, and other common respiratory viruses. A preliminary study of human sera collected prior to the SARS-CoV-2 pandemic demonstrates overall high IgG reactivity to common human coronaviruses and low IgG reactivity to epidemic coronaviruses including SARS-CoV-2, with some cross-reactivity of conserved antigenic domains including S2 domain of spike protein and nucleocapsid protein. This array can be used to answer outstanding questions regarding SARS-CoV-2 infection, including whether baseline serology for other coronaviruses impacts disease course, how the antibody response to infection develops over time, and what antigens would be optimal for vaccine development.

92: Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak
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Posted to bioRxiv 10 Mar 2020

Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak
1,134 downloads microbiology

Yuan Liu, Zhi Ning, Yu Chen, Ming Guo, Yingle Liu, Nirmal Kumar Gali, Li Sun, Yusen Duan, Jing Cai, Dane Westerdahl, Xinjin Liu, Kin-fai Ho, Haidong Kan, Qingyan Fu, Ke Lan

Background: The ongoing outbreak of COVID-19 has spread rapidly and sparked global concern. While the transmission of SARS-CoV-2 through human respiratory droplets and contact with infected persons is clear, the aerosol transmission of SARS-CoV-2 has been little studied. Methods: Thirty-five aerosol samples of three different types (total suspended particle, size segregated and deposition aerosol) were collected in Patient Areas (PAA) and Medical Staff Areas (MSA) of Renmin Hospital of Wuhan University (Renmin) and Wuchang Fangcang Field Hospital (Fangcang), and Public Areas (PUA) in Wuhan, China during COVID-19 outbreak. A robust droplet digital polymerase chain reaction (ddPCR) method was employed to quantitate the viral SARS-CoV-2 RNA genome and determine aerosol RNA concentration. Results: The ICU, CCU and general patient rooms inside Renmin, patient hall inside Fangcang had undetectable or low airborne SARS-CoV-2 concentration but deposition samples inside ICU and air sample in Fangcang patient toilet tested positive. The airborne SARS-CoV-2 in Fangcang MSA had bimodal distribution with higher concentration than those in Renmin during the outbreak but turned negative after patients number reduced and rigorous sanitization implemented. PUA had undetectable airborne SARS-CoV-2 concentration but obviously increased with accumulating crowd flow. Conclusions: Room ventilation, open space, proper use and disinfection of toilet can effectively limit aerosol transmission of SARS-CoV-2. Gathering of crowds with asymptomatic carriers is a potential source of airborne SARS-CoV-2. The virus aerosol deposition on protective apparel or floor surface and their subsequent resuspension is a potential transmission pathway and effective sanitization is critical in minimizing aerosol transmission of SARS-CoV-2.

93: pyrpipe: a python package for RNA-Seq workflows
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Posted to bioRxiv 08 Mar 2020

pyrpipe: a python package for RNA-Seq workflows
1,129 downloads bioinformatics

Urminder Singh, Jing Li, Arun S. Seetharam, Eve Syrkin Wurtele

Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of workflows. Scripting is often used, but it has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides high level APIs to popular RNA-Seq tools. Pipelines can be customized by integrating new python code, third-party programs, or python libraries. Researchers can create checkpoints in the pipeline or integrate pyrpipe into a workflow management system, thus allowing execution on multiple computing environments. pyrpipe produces detailed analysis, and benchmark reports which can be shared or included in publications. pyrpipe is implemented in python and is compatible with python versions 3.6 and higher. All source code is available at <https://github.com/urmi-21/pyrpipe>; the package can be installed from the source or from PyPi (<https://pypi.org/project/pyrpipe>). Documentation is available on Read the Docs (<http://pyrpipe.rtfd.io>).

94: Benchmarking atlas-level data integration in single-cell genomics
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Posted to bioRxiv 23 May 2020

Benchmarking atlas-level data integration in single-cell genomics
1,125 downloads bioinformatics

Malte D Luecken, M Büttner, Kridsadakorn Chaichoompu, A Danese, M Interlandi, MF Mueller, DC Strobl, Luke Zappia, M Dugas, Maria Colomé-Tatché, Fabian J. Theis

Cell atlases often include samples that span locations, labs, and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. Choosing a data integration method is a challenge due to the difficulty of defining integration success. Here, we benchmark 38 method and preprocessing combinations on 77 batches of gene expression, chromatin accessibility, and simulation data from 23 publications, altogether representing >1.2 million cells distributed in nine atlas-level integration tasks. Our integration tasks span several common sources of variation such as individuals, species, and experimental labs. We evaluate methods according to scalability, usability, and their ability to remove batch effects while retaining biological variation. Using 14 evaluation metrics, we find that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, BBKNN, Scanorama, and scVI perform well, particularly on complex integration tasks; Seurat v3 performs well on simpler tasks with distinct biological signals; and methods that prioritize batch removal perform best for ATAC-seq data integration. Our freely available reproducible python module can be used to identify optimal data integration methods for new data, benchmark new methods, and improve method development. ### Competing Interest Statement F.J.T. reports receiving consulting fees from Roche Diagnostics GmbH and Cellarity Inc., and ownership interest in Cellarity, Inc. and Dermagnostix

95: Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids
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Posted to bioRxiv 17 Jun 2020

Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids
1,124 downloads bioengineering

Nicholas C. Flytzanis, Nick Goeden, David Goertsen, Alexander Cummins, James Pickel, Viviana Gradinaru

Genetic intervention is increasingly explored as a therapeutic option for debilitating disorders of the central nervous system. The safety and efficacy of gene therapies relies upon expressing a transgene in affected cells while minimizing off-target expression. To achieve organ/cell-type specific targeting after intravenous delivery, we employed a Cre-transgenic-based screening platform for fast and efficient capsid selection, paired with sequential engineering of multiple surface exposed loops. We identified capsid variants that are enriched in the brain and detargeted from the liver in mice. The improved enrichment in the brain extends to non-human primates, enabling robust, non-invasive gene delivery to the marmoset brain following IV administration. Importantly, the capsids identified display non-overlapping cell-type tropisms within the brain, with one exhibiting high specificity to neurons. The ability to cross the blood-brain barrier with cell-type specificity in rodents and non-human primates enables new avenues for basic research and therapeutic possibilities unattainable with naturally occurring serotypes. ### Competing Interest Statement The California Institute of Technology has filed and licensed patent applications for the work described in this manuscript with N.C.F., N.G., and V.G. listed as inventors.

96: Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies
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Posted to bioRxiv 29 May 2020

Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies
1,119 downloads immunology

Christopher O. Barnes, Anthony P. West, Kathryn E. Huey-Tubman, Magnus A.G. Hoffmann, Naima G. Sharaf, Pauline R. Hoffman, Nicholas Koranda, Harry B. Gristick, Christian Gaebler, Frauke Muecksch, Julio C Cetrulo Lorenzi, Shlomo Finkin, Thomas Hagglof, Arlene Hurley, Katrina G Millard, Yiska Weisblum, Fabian Schmidt, Theodora Hatziioannou, Paul D. Bieniasz, Marina Caskey, Davide F. Robbiani, Michel C. Nussenzweig, Pamela J. Bjorkman

Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1A and RBD epitopes. In addition, a 3.4 Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on up RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies. ### Competing Interest Statement The authors have declared no competing interest.

97: Phase separation induced by cohesin SMC protein complexes
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Posted to bioRxiv 14 Jun 2020

Phase separation induced by cohesin SMC protein complexes
1,106 downloads biophysics

Je-Kyung Ryu, Celine Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph de Groot, Allard J. Katan, Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Frank Uhlmann, Cees Dekker

Cohesin is a key protein complex that organizes the spatial structure of chromosomes during interphase. Here, we show that yeast cohesin shows pronounced clustering on DNA in an ATP-independent manner, exhibiting all the hallmarks of phase separation. In vitro visualization of cohesin on DNA shows DNA-cohesin clusters that exhibit liquid-like behavior. This includes mutual fusion and reversible dissociation upon depleting the cohesin concentration, increasing the ionic strength, or adding 1,6-hexanediol, conditions that disrupt weak interactions. We discuss how bridging-induced phase separation can explain the DNA-cohesin clustering through DNA-cohesin-DNA bridges. We confirm that, in vivo, a fraction of cohesin associates with chromatin in yeast cells in a manner consistent with phase separation. Our findings establish that SMC proteins can exhibit phase separation, which has potential to clarify previously unexplained aspects of in vivo SMC behavior and constitute an additional principle by which SMC complexes impact genome organization. ### Competing Interest Statement The authors have declared no competing interest.

98: SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems
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Posted to bioRxiv 24 Mar 2020

SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems
1,103 downloads microbiology

Daniel Blanco-Melo, Benjamin E. Nilsson-Payant, Wen-Chun Liu, Rasmus Møller, Maryline Panis, David Sachs, Randy A. Albrecht, Benjamin R. tenOever

One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.

99: A thermostable, closed, SARS-CoV-2 spike protein trimer.
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Posted to bioRxiv 17 Jun 2020

A thermostable, closed, SARS-CoV-2 spike protein trimer.
1,064 downloads biochemistry

Xiaoli Xiong, Kun Qu, Katarzyna A Ciazynska, Myra Hosmillo, Andrew P. Carter, Soraya Ebrahimi, Zunlong Ke, Sjors H.W. Scheres, Laura Bergamaschi, Guinevere L. Grice, Ying Zhang, The CITIID-NIHR COVID-19 BioResource Collaboration, James A Nathan, Stephen Baker, Leo C. James, Helen E. Baxendale, Ian Goodfellow, Rainer Doffinger, John A.G. Briggs

The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen. ### Competing Interest Statement The authors have declared no competing interest.

100: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction
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Posted to bioRxiv 18 Jun 2020

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction
1,050 downloads microbiology

Diana Rose E. Ranoa, Robin L. Holland, Fadi G Alnaji, Kelsie J. Green, Leyi Wang, Christopher B Brooke, Martin D. Burke, Timothy M. Fan, Paul J. Hergenrother

Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. ### Competing Interest Statement The authors have declared no competing interest.

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