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Most downloaded bioRxiv papers, since beginning of last month

80,059 results found. For more information, click each entry to expand.

41: The structure, function, and evolution of a complete human chromosome 8
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Posted to bioRxiv 08 Sep 2020

The structure, function, and evolution of a complete human chromosome 8
1,766 downloads genomics

Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo G. de Lima, David Porubsky, Andrey V. Bzikadze, Milinn Kremitzki, Tina A Graves-Lindsay, Chirag Jain, Kendra Hoekzema, Shwetha C. Murali, Katherine M. Munson, Carl Baker, Melanie Sorensen, Alexandra M. Lewis, Urvashi Surti, Jennifer L. Gerton, Vladimir Larionov, Mario Ventura, Karen H. Miga, Adam M. Phillippy, Evan E. Eichler

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembly of a human autosome, chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08 Mbp centromeric α-satellite array, a 644 kbp defensin copy number polymorphism important for disease risk, and an 863 kbp variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73 kbp hypomethylated region of diverse higher-order α-satellite enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. Using a dual long-read sequencing approach, we complete the assembly of the orthologous chromosome 8 centromeric regions in chimpanzee, orangutan, and macaque for the first time to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved specifically in the great ape ancestor, and the centromeric region evolved with a layered symmetry, with more ancient higher-order repeats located at the periphery adjacent to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated at least 2.2-fold, and this acceleration extends beyond the higher-order α-satellite into the flanking sequence. ### Competing Interest Statement The authors have declared no competing interest.

42: Human ACE2 peptide mimics block SARS-CoV-2 Pulmonary Cells Infection
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Posted to bioRxiv 24 Aug 2020

Human ACE2 peptide mimics block SARS-CoV-2 Pulmonary Cells Infection
1,756 downloads pharmacology and toxicology

Philippe Karoyan, Vincent Vieillard, Estelle Odile, Alexis Denis, Amélie Guihot, Charles-Edouard Luyt, Luis Gómez-Morales, Pascal Grondin, Olivier Lequin

In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19). ### Competing Interest Statement The authors declare the following competing financial interest(s): The patent application EP20305449.9 included results from this paper. The authors declare that no other competing interests exist.

43: SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness
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Posted to bioRxiv 11 Jun 2020

SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness
1,742 downloads immunology

Kizzmekia S. Corbett, Darin Edwards, Sarah R. Leist, Olubukola M. Abiona, Seyhan Boyoglu-Barnum, Rebecca A Gillespie, Sunny Himansu, Alexandra Schäfer, Cynthia T. Ziwawo, Anthony T. DiPiazza, Kenneth H. Dinnon, Sayda M. Elbashir, Christine A. Shaw, Angela Woods, Ethan J Fritch, David R. Martinez, Kevin W. Bock, Mahnaz Minai, Bianca M. Nagata, Geoffrey B. Hutchinson, Kapil Bahl, Dario Garcia-Dominguez, LingZhi Ma, Isabella Renzi, Wing-Pui Kong, Stephen D. Schmidt, Lingshu Wang, Yi Zhang, Laura J Stevens, Emily Phung, Lauren A. Chang, Rebecca J. Loomis, Nedim Emil Altaras, Elisabeth Narayanan, Mihir Metkar, Vlad Presnyak, Catherine Liu, Mark K. Louder, Wei Shi, Kwanyee Leung, Eun Sung Yang, Ande West, Kendra L Gully, Nianshuang Wang, Daniel Wrapp, Nicole A. Doria-Rose, Guillaume Stewart-Jones, Hamilton Bennett, Martha C. Nason, Tracy J. Ruckwardt, Jason S. McLellan, Mark R. Denison, James D. Chappell, Ian N Moore, Kaitlyn M. Morabito, John R. Mascola, Ralph S. Baric, Andrea Carfi, Barney Graham

A SARS-CoV-2 vaccine is needed to control the global COVID-19 public health crisis. Atomic-level structures directed the application of prefusion-stabilizing mutations that improved expression and immunogenicity of betacoronavirus spike proteins. Using this established immunogen design, the release of SARS-CoV-2 sequences triggered immediate rapid manufacturing of an mRNA vaccine expressing the prefusion-stabilized SARS-CoV-2 spike trimer (mRNA-1273). Here, we show that mRNA-1273 induces both potent neutralizing antibody and CD8 T cell responses and protects against SARS-CoV-2 infection in lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a Phase 2 clinical trial with a trajectory towards Phase 3 efficacy evaluation. ### Competing Interest Statement K.S.C., N.W., J.S.M., and B.S.G. are inventors on International Patent Application No. WO/2018/081318 entitled Prefusion Coronavirus Spike Proteins and Their Use. K.S.C., O.M.A., G.B.H., N.W., D.W., J.S.M, and B.S.G. are inventors on US Patent Application No. 62/972,886 entitled 2019-nCoV Vaccine. R.S.B. filed an invention report for the SARS-CoV-2 MA virus (UNC ref. #18752).

44: LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection
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Posted to bioRxiv 01 Oct 2020

LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection
1,731 downloads immunology

Bryan E. Jones, Patricia L. Brown-Augsburger, Kizzmekia S. Corbett, Kathryn Westendorf, Julian Davies, Thomas P. Cujec, Christopher M. Wiethoff, Jamie L. Blackbourne, Beverly A. Heinz, Denisa Foster, Richard E. Higgs, Deepa Balasubramaniam, Lingshu Wang, Roza Bidshahri, Lucas Kraft, Yuri Hwang, Stefanie Žentelis, Kevin R. Jepson, Rodrigo Goya, Maia A. Smith, David W Collins, Samuel J. Hinshaw, Sean A. Tycho, Davide Pellacani, Ping Xiang, Krithika Muthuraman, Solmaz Sobhanifar, Marissa H. Piper, Franz J. Triana, Jorg Hendle, Anna Pustilnik, Andrew C. Adams, Shawn J. Berens, Ralph S. Baric, David R. Martinez, Robert W Cross, Thomas W Geisbert, Viktoriya Borisevich, Olubukola Abiona, Hayley M. Belli, Maren de Vries, Adil Mohamed, Meike Dittmann, Marie Samanovic, Mark J Mulligan, Jory A Goldsmith, Ching-Lin Hsieh, Nicole V Johnson, Daniel Wrapp, Jason S. McLellan, Bryan C. Barnhart, Barney S. Graham, John R. Mascola, Carl L. Hansen, Ester Falconer

SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection. ### Competing Interest Statement M.J.M. has research grant funding from NIH/NIAID, Pfizer, and Sanofi; and personal fees from Meissa Vaccines, Inc. B.E.J., P.LB., J.D., T.P.C., C.M.W., J.L.B., B.A.H., R.E.H., D.B., D.F., M.H.P., F.J.T., J.H., A.P., A.C.A. and S.J.B. are employees and stockholders of Eli Lilly and Company. K.W., R.B., L.K., S.J.H., S.S., B.C.B, and E.F. are employees of AbCellera Biologics Inc. C.L.H., R.G., D.P., P.X., Y.H., R.B., K.R.J. M.A.S., S.Z., D.W.C., and S.A.T. are employees and stockholders of AbCellera Biologics Inc.. K.M. is a former employee and stockholder of AbCellera Biologics Inc. M.D. received a contract from Eli Lilly and Company to support the studies reported herein. Authors from AbCellera Biologics Inc., National Institute of Allergy and Infectious Diseases (K.S.C., B.S.G., and J.R.M.), and Eli Lilly and Company are inventors on patent applications related to the work described here. R.S.B., D.R.M., R.W.C., T.W.G, V.B., O.A., L.W., H.M.B., M.D.V., A.D., M.S., J.A.G., C.L.H., N.V.J., J.S.M., and D.W. declare no competing interests.

45: SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo
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Posted to bioRxiv 29 Sep 2020

SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo
1,729 downloads microbiology

Yixuan J. Hou, Shiho Chiba, Peter Halfmann, Camille Ehre, Makoto Kuroda, Kenneth H. Dinnon, Sarah R. Leist, Alexandra Schäfer, Noriko Nakajima, Kenta Takahashi, Rhianna E. Lee, Teresa M. Mascenik, Caitlin E. Edwards, Longping V Tse, Richard C. Boucher, Scott H Randell, Tadaki Suzuki, Lisa E. Gralinski, Yoshihiro Kawaoka, Ralph S. Baric

The D614G substitution in the S protein is most prevalent SARS-CoV-2 strain circulating globally, but its effects in viral pathogenesis and transmission remain unclear. We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. The D614G variant replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies. Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than the WT virus, early after infection. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission. ### Competing Interest Statement The authors have declared no competing interest.

46: Multi-study inference of regulatory networks for more accurate models of gene regulation
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Posted to bioRxiv 08 Mar 2018

Multi-study inference of regulatory networks for more accurate models of gene regulation
1,720 downloads systems biology

Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau

Gene regulatory networks are composed of sub-networks that are often shared across biological processes, cell-types, and organisms. Leveraging multiple sources of information, such as publicly available gene expression datasets, could therefore be helpful when learning a network of interest. Integrating data across different studies, however, raises numerous technical concerns. Hence, a common approach in network inference, and broadly in genomics research, is to separately learn models from each dataset and combine the results. Individual models, however, often suffer from under-sampling, poor generalization and limited network recovery. In this study, we explore previous integration strategies, such as batch-correction and model ensembles, and introduce a new multitask learning approach for joint network inference across several datasets. Our method initially estimates the activities of transcription factors, and subsequently, infers the relevant network topology. As regulatory interactions are context-dependent, we estimate model coefficients as a combination of both dataset-specific and conserved components. In addition, adaptive penalties may be used to favor models that include interactions derived from multiple sources of prior knowledge including orthogonal genomics experiments. We evaluate generalization and network recovery using examples from Bacillus subtilis and Saccharomyces cerevisiae, and show that sharing information across models improves network reconstruction. Finally, we demonstrate robustness to both false positives in the prior information and heterogeneity among datasets.

47: Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen
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Posted to bioRxiv 26 Sep 2019

Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen
1,715 downloads physiology

A Wiik, TR Lundberg, E Rullman, DP Andersson, M Holmberg, M Mandić, TB Brismar, O Dahlqvist Leinhard, S Chanpen, J Flanagan, S Arver, T Gustafsson

Objectives: This study explored the effects of gender-affirming treatment, which includes inhibition of endogenous sex hormones and replacement with cross-sex hormones, on muscle function, size and composition in 11 transwomen (TW) and 12 transmen (TM). Methods: Isokinetic knee extensor and flexor muscle strength was assessed at baseline (T00), 4 weeks after gonadal suppression of endogenous hormones but before hormone replacement (T0), and 3 (T3) and 11 (T12) months after hormone replacement. In addition, at T00 and T12, we assessed lower-limb muscle volume using MRI, and cross-sectional area (CSA) and radiological density using CT. Results: Thigh muscle volume increased (15%) in TM, which was paralleled by increased quadriceps CSA (15%) and radiological density (6%). In TW, the corresponding parameters decreased by -5% (muscle volume) and -4% (CSA), while density remained unaltered. The TM increased strength over the assessment period, while the TW generally maintained or slightly increased in strength. Baseline muscle volume correlated highly with strength (R>0.75), yet the relative change in muscle volume and strength correlated only moderately (R=0.65 in TW and R=0.32 in TM). The absolute levels of muscle volume and knee extension strength after the intervention still favored the TW. Conclusion: Cross-sex hormone treatment markedly affects muscle strength, size and composition in transgender individuals. Despite the robust increases in muscle mass and strength in TM, the TW were still stronger and had more muscle mass following 12 months of treatment. These findings add new knowledge that could be relevant when evaluating transwomen's eligibility to compete in the women's category of athletic competitions.

48: Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses
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Posted to bioRxiv 24 Sep 2020

Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses
1,695 downloads microbiology

Ruofan Wang, Camille R. Simoneau, Jessie Kulsuptrakul, Mehdi Bouhaddou, Katherine Travisano, Jennifer M. Hayashi, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Nevan J. Krogan, Melanie Ott, Andreas S. Puschnik

The Coronaviridae are a family of viruses that causes disease in humans ranging from mild respiratory infection to potentially lethal acute respiratory distress syndrome. Finding host factors that are common to multiple coronaviruses could facilitate the development of therapies to combat current and future coronavirus pandemics. Here, we conducted parallel genome-wide CRISPR screens in cells infected by SARS-CoV-2 as well as two seasonally circulating common cold coronaviruses, OC43 and 229E. This approach correctly identified the distinct viral entry factors ACE2 (for SARS-CoV-2), aminopeptidase N (for 229E) and glycosaminoglycans (for OC43). Additionally, we discovered phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis as critical host pathways supporting infection by all three coronaviruses. By contrast, the lysosomal protein TMEM106B appeared unique to SARS-CoV-2 infection. Pharmacological inhibition of phosphatidylinositol phosphate biosynthesis and cholesterol homeostasis reduced replication of all three coronaviruses. These findings offer important insights for the understanding of the coronavirus life cycle as well as the potential development of host-directed therapies. ### Competing Interest Statement J.C.S., J.O. and K.H. are employees of Synthego Corporation.

49: Efficient transcription-coupled chromatin accessibility mapping in situ
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Posted to bioRxiv 17 Apr 2020

Efficient transcription-coupled chromatin accessibility mapping in situ
1,690 downloads genomics

Steven Henikoff, Jorja G. Henikoff, Hatice S. Kaya-Okur, Kami Ahmad

Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. In the popular ATAC-seq method, Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here we show that by simply modifying the tagmentation conditions for histone H3K4me2/3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce accessible DNA maps that are indistinguishable from the best ATAC-seq maps. Thus, DNA accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites. ### Competing Interest Statement The authors have declared no competing interest.

50: CRISPR screens in physiologic medium reveal conditionally essential genes in human cells
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Posted to bioRxiv 31 Aug 2020

CRISPR screens in physiologic medium reveal conditionally essential genes in human cells
1,672 downloads cancer biology

Nicholas J. Rossiter, Kimberly S. Huggler, Charles H. Adelmann, Heather R Keys, Ross W. Soens, David M Sabatini, Jason R. Cantor

Forward genetic screens across hundreds of diverse cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly resemble metabolite availability in human blood. To explore how medium composition influences gene essentiality, we performed CRISPR-based screens of human cancer cell lines cultured in traditional versus human plasma-like medium (HPLM). Sets of medium-dependent fitness genes span several cellular processes and can vary with both natural cell-intrinsic diversity and the specific combination of basal and serum components that comprise typical culture media. Notably, we traced the causes for each of three conditional growth phenotypes to the availability of metabolites uniquely defined in HPLM versus traditional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions. ### Competing Interest Statement The authors have declared no competing interest.

51: Accessible and interactive RNA sequencing analysis using serverless computing
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Posted to bioRxiv 13 Mar 2019

Accessible and interactive RNA sequencing analysis using serverless computing
1,664 downloads bioinformatics

Ling-Hong Hung, Xingzhi Niu, Wes Lloyd, Ka Yee Yeung

We present a novel method that yields 1100-fold computational speedup and allows biomedical scientists to interactively adjust alignment parameters in real time to iteratively improve final analytical results. Specifically, the alignment time for a 640 million read human RNA-sequencing dataset is reduced from 19 hours to 1 minute using serverless cloud computing. We provide a graphical interface for the accelerated workflows, thus making our methodology accessible to non-cloud experts. ### Competing Interest Statement Hung - BioDepot LLC: Employment and Ownership. Yeung - BioDepot LLC: Employment and Ownership.

52: A cis-regulatory atlas in maize at single-cell resolution
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Posted to bioRxiv 28 Sep 2020

A cis-regulatory atlas in maize at single-cell resolution
1,649 downloads developmental biology

Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz

Cis -regulatory elements (CREs) encode the genomic blueprints for coordinating spatiotemporal gene expression programs underlying highly specialized cell functions. To identify CREs underlying cell-type specification and developmental transitions, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin in an atlas of Zea mays organs. We describe 92 distinct states of chromatin accessibility across more than 165,913 putative CREs, 56,575 cells, and 52 known cell-types in maize using a novel implementation of regularized quasibinomial logistic regression. Cell states were largely determined by combinatorial accessibility of transcription factors (TFs) and their binding sites. A neural network revealed that cell identity could be accurately predicted (>0.94) solely based on TF binding site accessibility. Co-accessible chromatin recapitulated higher-order chromatin interactions, with distinct sets of TFs coordinating cell type-specific regulatory dynamics. Pseudotime reconstruction and alignment with Arabidopsis thaliana trajectories identified conserved TFs, associated motifs, and cis -regulatory regions specifying sequential developmental progressions. Cell-type specific accessible chromatin regions were enriched with phenotype-associated genetic variants and signatures of selection, revealing the major cell-types and putative CREs targeted by modern maize breeding. Collectively, our analysis affords a comprehensive framework for understanding cellular heterogeneity, evolution, and cis -regulatory grammar of cell-type specification in a major crop species. ### Competing Interest Statement RJS is a co-founder of REquest Genomics, LLC, a company that provides epigenomic services. APM, ZC and AG declare no competing interests.

53: Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection
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Posted to bioRxiv 06 Sep 2020

Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection
1,643 downloads immunology

Anne C. Moore, Emery G. Dora, Nadine Peinovich, Kiersten P. Tucker, Karen Lin, Mario Cortese, Sean N. Tucker

There is an urgent need to develop efficacious vaccines against SARS-CoV-2 that also address the issues of deployment, equitable access, and vaccine acceptance. Ideally, the vaccine would prevent virus infection and transmission as well as preventing COVID-19 disease. We previously developed an oral adenovirus-based vaccine technology that induces both mucosal and systemic immunity in humans. Here we investigate the immunogenicity of a range of candidate adenovirusbased vaccines, expressing full or partial sequences of the spike and nucleocapsid proteins, in mice. We demonstrate that, compared to expression of the S1 domain or a stabilized spike antigen, the full length, wild-type spike antigen induces significantly higher neutralizing antibodies in the periphery and in the lungs, when the vaccine is administered mucosally. Antigen-specific CD4+ and CD8+ T cells were induced by this leading vaccine candidate at low and high doses. This fulllength spike antigen plus nucleocapsid adenovirus construct has been prioritized for further clinical development. ### Competing Interest Statement EGD, ND, KPT, KLM MC and SNT are current employees and/or own stock options in Vaxart, the sponsor of the studies. EGD and SNT are named as inventors covering a SARS-CoV-2 (nCoV-19) vaccine. SNT is named as an inventor on patents covering the vaccine platform. ACM declares no competing interest.

54: Detection dogs as a help in the detection of COVID-19: Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples? Proof-of-concept study
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Posted to bioRxiv 05 Jun 2020

Detection dogs as a help in the detection of COVID-19: Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples? Proof-of-concept study
1,619 downloads animal behavior and cognition

Dominique Grandjean, Riad Sarkis, Jean-Pierre Tourtier, Clothilde Julien-Lecocq, Aymeric Benard, Vinciane Roger, Eric Levesque, Eric Bernes-Luciani, Bruno Maestracci, Pascal Morvan, Eric Gully, David Berceau-Falancourt, Jean-Luc Pesce, Bernard Lecomte, Pierre Haufstater, Gregory Herin, Joaquin Cabrera, Quentin Muzzin, Capucine Gallet, Hélène Bacqué, Jean-Marie Broc, Leo Thomas, Anthony Lichaa, Georges Moujaes, Michele Saliba, Aurore Kuhn, Mathilde Galey, Benoit Berthail, Lucien Lapeyre, Olivier Méreau, Marie-Nicolas Matteï, Audrey Foata, Louisa Bey, Anne-Sophie Philippe, Paul Abassi, Ferri Pisani, Marlène Delarbre, Jean-Marc Orsini, Anthoni Capelli, Steevens Renault, Karim Bachir, Anthony Kovinger, Eric Comas, Aymeric Stainmesse, Erwan Etienne, Sébastien Voeltzel, Sofiane Mansouri, Marlène Berceau-Falancourt, Brice Leva, Frederic Faure, Aimé Dami, Marc Antoine Costa, Jean-Jacques Tafanelli, Jean-Benoit Luciani, Jean-Jacques Casalot, Lary Charlet, Eric Ruau, Mario Issa, Carine Grenet, Christophe Billy, Loic Desquilbet

The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time. The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone. We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus. ### Competing Interest Statement The authors have declared no competing interest.

55: Towards Reproducible Brain-Wide Association Studies
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Posted to bioRxiv 22 Aug 2020

Towards Reproducible Brain-Wide Association Studies
1,595 downloads neuroscience

Scott Marek, Brenden Tervo-Clemmens, Finnegan J. Calabro, David F. Montez, Benjamin P. Kay, Alexander S. Hatoum, Meghan Rose Donohue, William Foran, Ryland L. Miller, Eric Feczko, Oscar Miranda Dominguez, Alice Graham, Eric A. Earl, Anders Perrone, Michaela Cordova, Olivia Doyle, Lucille A. Moore, Greg Conan, Johnny Uriarte, Kathy Snider, Angela Tam, Jianzhong Chen, Dillan J. Newbold, Annie Zheng, Nicole A. Seider, Andrew N. Van, Timothy O. Laumann, Wesley K. Thompson, Deanna J. Greene, Steven E. Petersen, Thomas Nichols, B.T. Thomas Yeo, Deanna Barch, Hugh Garavan, Beatriz Luna, Damien A. Fair, Nico UF Dosenbach

Magnetic resonance imaging (MRI) continues to drive many important neuroscientific advances. However, progress in uncovering reproducible associations between individual differences in brain structure/function and behavioral phenotypes (e.g., cognition, mental health) may have been undermined by typical neuroimaging sample sizes (median N=25)1,2. Leveraging the Adolescent Brain Cognitive Development (ABCD) Study3 (N=11,878), we estimated the effect sizes and reproducibility of these brain wide associations studies (BWAS) as a function of sample size. The very largest, replicable brain wide associations for univariate and multivariate methods were r=0.14 and r=0.34, respectively. In smaller samples, typical for brain wide association studies, irreproducible, inflated effect sizes were ubiquitous, no matter the method (univariate, multivariate). Until sample sizes started to approach consortium levels, BWAS were underpowered and statistical errors assured. Multiple factors contribute to replication failures4,5,6; here, we show that the pairing of small brain behavioral phenotype effect sizes with sampling variability is a key element in widespread BWAS replication failure. Brain behavioral phenotype associations stabilize and become more reproducible with sample sizes of N>2,000. While investigator initiated brain behavior research continues to generate hypotheses and propel innovation, large consortia are needed to usher in a new era of reproducible human brain wide association studies. ### Competing Interest Statement Nico Dosenbach and Damien Fair are co-founders of Nous Imaging

56: A molecular cell atlas of the human lung from single cell RNA sequencing
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Posted to bioRxiv 27 Aug 2019

A molecular cell atlas of the human lung from single cell RNA sequencing
1,590 downloads genomics

Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V Sit, Stephen Chang, Stephanie D Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B Shrager, Ross J Metzger, Christin S Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake, Mark A Krasnow

Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ∼75,000 human lung and blood cells, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. This comprehensive molecular atlas elucidates the biochemical functions of lung cell types and the cell-selective transcription factors and optimal markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signaling interactions including sources and targets of chemokines in immune cell trafficking and expression changes on lung homing; and identifies the cell types directly affected by lung disease genes and respiratory viruses. Comparison to mouse identified 17 molecular types that appear to have been gained or lost during lung evolution and others whose expression profiles have been substantially altered, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.

57: A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing
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Posted to bioRxiv 23 Jun 2020

A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing
1,585 downloads molecular biology

Max J. Kellner, James J Ross, Jakob Schnabl, Marcus P.S. Dekens, Robert Heinen, Irina Grishkovskaya, Benedikt Bauer, Johannes Stadlmann, Luis Menéndez-Arias, Robert Fritsche-Polanz, Marianna Traugott, Tamara Seitz, Alexander Zoufaly, Manuela Födinger, Christoph Wenisch, Johannes Zuber, Vienna Covid-19 Diagnostics Initiative (VCDI), Andrea Pauli, Julius Brennecke

Global efforts to combat the Covid-19 pandemic caused by the beta coronavirus SARS-CoV-2 are currently based on RT-qPCR-based diagnostic tests. However, their high cost, moderate throughput and reliance on sophisticated equipment limit widespread implementation. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative detection method that has the potential to overcome these limitations. Here we present a rapid, robust, highly sensitive and versatile RT-LAMP based SARS-CoV-2 detection assay. Our forty-minute procedure bypasses a dedicated RNA isolation step, is insensitive to carry-over contamination, and uses a hydroxynaphthol blue (HNB)-based colorimetric readout, which allows robust SARS-CoV-2 detection from various sample types. Based on this assay we have substantially increased sensitivity and scalability by a simple nucleic acid enrichment step (bead-LAMP), established a pipette-free version for home testing (HomeDip-LAMP), and developed a version with open source enzymes that could be produced in any molecular biology setting. Our advanced, universally applicable RT-LAMP assay is a major step towards population-scale SARS-CoV-2 testing. ### Competing Interest Statement The authors have declared no competing interest.

58: Evaluation of heating and chemical protocols for inactivating SARS-CoV-2
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Posted to bioRxiv 11 Apr 2020

Evaluation of heating and chemical protocols for inactivating SARS-CoV-2
1,568 downloads microbiology

Boris Pastorino, Franck Touret, Magali Gilles, Xavier de Lamballerie, Remi N Charrel

Clinical samples collected in COVID-19 patients are commonly manipulated in BSL-2 laboratories for diagnostic purpose. We used the French norm NF-EN-14476+A2 derived from the European standard EN-14885. To avoid the risk of exposure of laboratory workers, we showed that Triton-X100 must be added to guanidinium thiocyanate-lysis buffers to obtain a 6-log reduction of infectious virus. Although heating protocol consisting of 92C-15min was more effective rather than 56C-30min and 60C-60min to achieve 6-log reduction, it is not amenable for molecular detection on respiratory specimens because of important decrease of detectable RNA copies in the treated sample vs untreated sample. The 56C-30min and 60C-60min should be used for inactivation of serum / plasma samples for serology because of the 5log10 reduction of infectivity and low viral loads in blood specimens. ### Competing Interest Statement The authors have declared no competing interest.

59: Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans
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Posted to bioRxiv 15 May 2020

Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans
1,551 downloads immunology

Kevin W Ng, Nikhil Faulkner, Georgina H. Cornish, Annachiara Rosa, Ruth Harvey, Saira Hussain, Rachel Ulferts, Christopher Earl, Antoni Wrobel, Donald Benton, Chloe Roustan, William Bolland, Rachael Thompson, Ana Agua-Doce, Philip Hobson, Judith Heaney, Hannah Rickman, Stavroula Paraskevopoulou, Catherine F Houlihan, Kirsty Thomson, Emilie Sanchez, David Brealey, Gee Yen Shin, Moira J Spyer, Dhira Joshi, Nicola O’Reilly, Philip A Walker, Svend Kjaer, Andrew Riddell, Catherine Moore, Bethany R Jebson, Meredyth G.Ll. Wilkinson, Lucy R Marshall, Elizabeth C Rosser, Anna Radziszewska, Hannah Peckham, Coziana Ciurtin, Lucy R Wedderburn, Rupert Beale, Charles Swanton, Sonia Gandhi, Brigitta Stockinger, John McCauley, Steve Gamblin, Laura E McCoy, Peter Cherepanov, Eleni Nastouli, George Kassiotis

Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections[1][1]. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic proportions[2][2],[3][3]. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 spike (S) glycoprotein, we demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. These were predominantly of the IgG class and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, as well as concomitant IgM and IgA antibodies, lasting throughout the observation period of 6 weeks since symptoms onset. SARS-CoV-2-uninfected donor sera also variably reacted with SARS-CoV-2 S and nucleoprotein (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralising activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3

60: A guide to performing Polygenic Risk Score analyses
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Posted to bioRxiv 14 Sep 2018

A guide to performing Polygenic Risk Score analyses
1,527 downloads genomics

Shing Wan Choi, Timothy Shin Heng Mak, Paul O’Reilly

The application of polygenic risk scores (PRS) has become routine in genetic epidemiological studies. Among a range of applications, PRS are commonly used to assess shared aetiology among different phenotypes and to evaluate the predictive power of genetic data, while they are also now being exploited as part of study design, in which experiments are performed on individuals, or their biological samples (eg. tissues, cells), at the tails of the PRS distribution and contrasted. As GWAS sample sizes increase and PRS become more powerful, they are also set to play a key role in personalised medicine. Despite their growing application and importance, there are limited guidelines for performing PRS analyses, which can lead to inconsistency between studies and misinterpretation of results. Here we provide detailed guidelines for performing polygenic risk score analyses relevant to different methods for their calculation, outlining standard quality control steps and offering recommendations for best-practice. We also discuss different methods for the calculation of PRS, common misconceptions regarding the interpretation of results and future challenges.

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