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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.

61: Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
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Posted to bioRxiv 12 Jun 2020

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
1,424 downloads biochemistry

Christiane Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis, Christopher Y. Park, Avinash Boppana, Ethan Fritch, Yixuan J. Hou, Chandra Theesfeld, Olga G. Troyanskaya, Ralph S. Baric, Timothy P. Sheahan, Kevin Weeks, Amy S. Gladfelter

A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5'-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5'-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2. ### Competing Interest Statement K.M.W. is an advisor to and holds equity in Ribometrix, to which mutational profiling (MaP) technologies have been licensed. All other authors declare that they have no competing interests.

62: Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes
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Posted to bioRxiv 05 May 2020

Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes
1,415 downloads genomics

Chandrika Bhattacharyya, Chitrarpita Das, Arnab Ghosh, Animesh K Singh, Souvik Mukherjee, Partha P. Majumder, Analabha Basu, Nidhan K. Biswas

COVID-19 pandemic is a major human tragedy. Worldwide, SARS-CoV-2 has already infected over 3 million and has killed about 230,000 people. SARS-CoV-2 originated in China and, within three months, has evolved to an additional 10 subtypes. One particular subtype with a non-silent (Aspartate to Glycine) mutation at 614th position of the Spike protein (D614G) rapidly outcompeted other pre-existing subtypes, including the ancestral. We assessed that D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. We also identified that a single nucleotide deletion (delC) at a known variant site (rs35074065) in a cis-eQTL of TMPRSS2, is extremely rare in East Asians but is common in Europeans and North Americans. The delC allele facilitates entry of the 614G subtype into host cells, thus accelerating the spread of 614G subtype in Europe and North America where the delC allele is common. The delC allele at the cis-eQTL locus rs35074065 of TMPRSS2 leads to overexpression of both TMPRSS2 and a nearby gene MX1. The cis-eQTL site, rs35074065 overlaps with a transcription factor binding site of an activator (IRF1) and a repressor (IRF2). IRF1 activator can bind to variant delC allele, but IRF2 repressor fails to bind. Thus, in an individual carrying the delC allele, there is only activation, but no repression. On viral entry, IRF1 mediated upregulation of MX1 leads to neutrophil infiltration and processing of 614G mutated Spike protein by neutrophil Elastase. The simultaneous processing of 614G spike protein by TMPRSS2 and Elastase serine proteases facilitates the entry of the 614G subtype into host cells. Thus, SARS-CoV-2, particularly the 614G subtype, has spread more easily and with higher frequency to Europe and North America where the delC allele regulating expression of TMPRSS2 and MX1 host proteins is common, but not to East Asia where this allele is rare. ### Competing Interest Statement The authors have declared no competing interest.

63: Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
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Posted to bioRxiv 15 Jun 2020

Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
1,406 downloads microbiology

Constantin Pape, Roman Remme, Adrian Wolny, Sylvia Olberg, Steffen Wolf, Lorenzo Cerrone, Mirko Cortese, Severina Klaus, Bojana Lucic, Stephanie Ullrich, Maria Anders-Össwein, Stefanie Wolf, Cerikan Berati, Christopher J. Neufeldt, Markus Ganter, Paul Schnitzler, Uta Merle, Marina Lusic, Steeve Boulant, Megan Stanifer, Ralf Bartenschlager, Fred A. Hamprecht, Anna Kreshuk, Christian Tischer, Hans-Georg Kräusslich, Barbara Müller, Vibor Laketa

Emergence of the novel pathogenic coronavirus Sars-CoV-2 and its rapid pandemic spread presents numerous questions and challenges that demand immediate attention. Among these is the urgent need for a better understanding of humoral immune response against the virus and assessment of seroprevalence levels in the population, both of which form the basis for developing public health strategies to control viral spread. For this, sensitive, specific and quantitative serological assays are required. Here we describe the development of a semi-quantitative high-content microscopy-based assay for detection of three major classes (IgG, IgA and IgM) of SARS-CoV-2 specific antibodies in human samples. The possibility to detect antibodies against the entire viral proteome together with a robust semi-automated image analysis workflow resulted in improvement of sensitivity and specificity compared to an approved ELISA-based diagnostic test. Combining both methods resulted in maximum specificity in a negative control cohort, while maintaining high sensitivity. The procedure described here is compatible with high-throughput microscopy approaches and may be applied for serological analysis of other virus infections. ### Competing Interest Statement The authors have declared no competing interest.

64: Scalable, continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities
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Posted to bioRxiv 02 Jun 2020

Scalable, continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities
1,391 downloads synthetic biology

Gordon Rix, Ella J. Watkins-Dulaney, Patrick J. Almhjell, Christina E. Boville, Frances H. Arnold, Chang C. Liu

Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolved the Thermotoga maritima tryptophan synthase β-subunit ( Tm TrpB) through multi-mutation pathways in many independent replicates, selecting only on Tm TrpB's primary activity (synthesizing L-tryptophan from indole and L-serine). We find that the resulting sequence-diverse Tm TrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of new biomolecular functions. ### Competing Interest Statement C.E.B and F.H.A. are co-founders of Aralez Bio, focusing on the enzymatic synthesis of unnatural amino acids.

65: Shared SARS-CoV-2 diversity suggests localised transmission of minority variants
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Posted to bioRxiv 28 May 2020

Shared SARS-CoV-2 diversity suggests localised transmission of minority variants
1,386 downloads genomics

Katrina A. Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett, Amy Trebes, Monique Andersson, Newton Otecko, Emma L Wise, Nathan Moore, Jessica Lynch, Stephen Kidd, Nicholas Cortes, Matilde Mori, Anita Justice, Angie Green, M. Azim Ansari, Lucie Abeler-Dörner, Catrin E Moore, Tim E A Peto, Robert Shaw, Peter Simmonds, David Buck, John A. Todd, on behalf of OVSG Analysis Group, David Bonsall, Christophe Fraser, Tanya Golubchik

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 causing a global pandemic, with the United Kingdom (UK) one of the hardest hit countries. Rapid sequencing and publication of consensus genomes have enabled phylogenetic analysis of the virus, demonstrating SARS-CoV-2 evolves relatively slowly, but with multiple sites in the genome that appear inconsistent with the overall consensus phylogeny. To understand these discrepancies, we used veSEQ, a targeted RNA-seq approach, to quantify minor allele frequencies in 413 clinical samples from two UK locations. We show that SARS-CoV-2 infections are characterised by extensive within-host diversity, which is frequently shared among infected individuals with patterns consistent with geographical structure. These results were reproducible in data from other sequencing locations around the UK, where we find evidence of mixed infection by major circulating lineages with patterns that cannot readily be explained by artefacts in the data. We conclude that SARS-CoV-2 diversity is transmissible, and propose that geographic patterns are generated by co-circulation of distinct viral populations. Co-transmission of mixed populations fundamentally changes our understanding of transmission of SARS-CoV-2 and could prove significant for treatment and vaccine design, as well as opening opportunities for resolving clusters of transmission and understanding pathogenesis. ### Competing Interest Statement The authors have declared no competing interest.

66: Hijacking SARS-Cov-2/ACE2 receptor interaction by natural and semi-synthetic steroidal agents acting on functional pockets on receptor binding region
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Posted to bioRxiv 11 Jun 2020

Hijacking SARS-Cov-2/ACE2 receptor interaction by natural and semi-synthetic steroidal agents acting on functional pockets on receptor binding region
1,381 downloads pharmacology and toxicology

Adriana Carino, Federica Moraca, Bianca Fiorillo, Silvia Marchianò, Valentina Sepe, Michele Biagioli, Claudia Finamore, Silvia Bozza, Daniela Francisci, Eleonora Distrutti, Bruno Catalanotti, Angela Zampella, Stefano Fiorucci

The coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by the severe acute respiratory syndrome coronavirus (SARS)-CoV-2. In the light of the urgent need to identify novel approaches to be used in the emergency phase, a largely explored strategy has been the repurpose of clinically available drugs as new antivirals, by targeting different viral proteins. In this paper, we describe a drug repurposing strategy based on a virtual screening of druggable pockets located in the central β-sheet core of the SARS-CoV-2 Spike protein RBD supported by in vitro tests identifying several steroidal derivatives as SARS-CoV-2 entry inhibitors. Our results demonstrate that several potential binding sites exist in the SARS CoV-2 S protein, and that the occupancy of these pockets reduces the ability of the S protein RBD to bind to the ACE2 consensus in vitro. In particular, natural occurring and clinically available steroids as glycyrrhetinic and oleanolic acids, as well as the bile acids derivatives glyco-UDCA and obeticholic acid have been shown to be effective in preventing virus entry in the case of low viral load. All together, these results might help to define novel approaches to reduce the viral load by using SARS-CoV-2 entry inhibitors. ### Competing Interest Statement This paper was supported by a research grant by BAR Pharmaceuticals S.r.L. to the Department of Pharmacy of the University of Napoli Federico II and to the Department of Surgical and Biomedical Sciences, University of Perugia. The authors declare the following competing financial interest(s): S.F., A.Z. and B.C. have filed an Italian patent application no.102020000011092 in the name of BAR Pharmaceuticals S.r.L. on the compounds described in this paper.

67: A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
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Posted to bioRxiv 31 May 2020

A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
1,367 downloads genomics

Sofia Banu, Bani Jolly, Payel Mukherjee, Priya Singh, Shagufta Khan, Lamuk Zaveri, Sakshi Shambhavi, Namami Gaur, Rakesh Mishra, Vinod Scaria, Divya Tej Sowpati

From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants - C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 x 10-3 variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India. ### Competing Interest Statement The authors have declared no competing interest.

68: Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
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Posted to bioRxiv 05 Jun 2020

Frequent loss-of-heterozygosity in CRISPR-Cas9-edited early human embryos
1,336 downloads developmental biology

Gregorio Alanis-Lobato, Jasmin Zohren, Afshan McCarthy, Norah M.E. Fogarty, Nada Kubikova, Emily Hardman, Maria Greco, Dagan Wells, James MA Turner, Kathy K. Niakan

CRISPR-Cas9 genome editing is a promising technique for clinical applications, such as the correction of disease-associated alleles in somatic cells. The use of this approach has also been discussed in the context of heritable editing of the human germline. However, studies assessing gene correction in early human embryos report low efficiency of mutation repair, high rates of mosaicism and the possibility of unintended editing outcomes that may have pathologic consequences. We developed computational pipelines to assess single-cell genomics and transcriptomics datasets from OCT4 (POU5F1) CRISPR-Cas9-targeted and Cas9-only control human preimplantation embryos. This allowed us to evaluate on-target mutations that would be missed by more conventional genotyping techniques. We observed loss-of-heterozygosity in edited cells that spanned regions beyond the POU5F1 on-target locus, as well as segmental loss and gain of chromosome 6, on which the POU5F1 gene is located. Unintended genome editing outcomes were present in approximately 22% of the human embryo cells analysed and spanned 4 to 20kb. Our observations are consistent with recent findings indicating complexity at on-target sites following CRISPR-Cas9 genome editing. Our work underscores the importance of further basic research to assess the safety of genome editing techniques in human embryos, which will inform debates about the potential clinical use of this technology. ### Competing Interest Statement The authors have declared no competing interest.

69: Comprehensive integration of single cell data
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Posted to bioRxiv 02 Nov 2018

Comprehensive integration of single cell data
1,308 downloads genomics

Tim Stuart, Andrew Butler, Paul J. Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M. Mauck, Marlon Stoeckius, Peter Smibert, Rahul Satija

Single cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate cell types and states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, and spatial positioning, a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function. Here, we develop a computational strategy to "anchor" diverse datasets together, enabling us to integrate and compare single cell measurements not only across scRNA-seq technologies, but different modalities as well. After demonstrating substantial improvement over existing methods for data integration, we anchor scRNA-seq experiments with scATAC-seq datasets to explore chromatin differences in closely related interneuron subsets, and project single cell protein measurements onto a human bone marrow atlas to annotate and characterize lymphocyte populations. Lastly, we demonstrate how anchoring can harmonize in-situ gene expression and scRNA-seq datasets, allowing for the transcriptome-wide imputation of spatial gene expression patterns, and the identification of spatial relationships between mapped cell types in the visual cortex. Our work presents a strategy for comprehensive integration of single cell data, including the assembly of harmonized references, and the transfer of information across datasets. Availability: Installation instructions, documentation, and tutorials are available at: https://www.satijalab.org/seurat

70: Genomic analysis of early SARS-CoV-2 strains introduced in Mexico
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Posted to bioRxiv 30 May 2020

Genomic analysis of early SARS-CoV-2 strains introduced in Mexico
1,308 downloads genomics

Blanca Taboada, Joel Armando Vazquez-Perez, José Esteban Muñoz Medina, Pilar Ramos Cervantes, Marina Escalera-Zamudio, Celia Boukadida, Alejandro Sanchez-Flores, Pavel Isa, Edgar Mendieta Condado, José Arturo Martínez-Orozco, Eduardo Becerril-Vargas, Jorge Salas-Hernández, Ricardo Grande, Carolina González-Torres, Francisco Javier Gaytán-Cervantes, Gloria Vazquez, Francisco Pulido, Adnan Araiza Rodríguez, Fabiola Garcés Ayala, Cesar Raúl González Bonilla, Concepción Grajales Muñiz, Víctor Hugo Borja Aburto, Gisela Barrera Badillo, Susana López, Lucía Hernández Rivas, Rogelio Perez-Padilla, Irma López Martínez, Santiago Ávila-Ríos, Guillermo Ruiz-Palacios, José Ernesto Ramírez-González, Carlos Federico Arias

The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described in the country. Within this Mexican cluster, we also identified an H49Y amino acid change in the spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.

71: Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD
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Posted to bioRxiv 20 Mar 2020

Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD
1,289 downloads bioengineering

G. Zhang, S. Pomplun, A. R. Loftis, X. Tan, A. Loas, B. L. Pentelute

Coronavirus disease 19 (COVID-19) is an emerging global health crisis. With over 7 million confirmed cases to date, this pandemic continues to expand, spurring research to discover vaccines and therapies. SARS-CoV-2 is the novel coronavirus responsible for this disease. It initiates entry into human cells by binding to angiotensin-converting enzyme 2 (ACE2) via the receptor binding domain (RBD) of its spike protein (S). Disrupting the SARS-CoV-2-RBD binding to ACE2 with designer drugs has the potential to inhibit the virus from entering human cells, presenting a new modality for therapeutic intervention. Peptide-based binders are an attractive solution to inhibit the RBD-ACE2 interaction by adequately covering the extended protein contact interface. Using molecular dynamics simulations based on the recently solved cryo-EM structure of ACE2 in complex with SARS-CoV-2-RBD, we observed that the ACE2 peptidase domain (PD) α1 helix is important for binding SARS-CoV-2-RBD. Using automated fast-flow peptide synthesis, we chemically synthesized a 23-mer peptide fragment of the ACE2 PD α1 helix (SBP1) composed entirely of proteinogenic amino acids. Chemical synthesis of SBP1 was complete in 1.5 hours, and after work up and isolation >20 milligrams of pure material was obtained. Bio-layer interferometry (BLI) revealed that SBP1 associates with micromolar affinity to insect-derived SARS-CoV-2-RBD protein obtained from Sino Biological. Association of SBP1 was not observed to an appreciable extent to HEK cell-expressed SARS-CoV-2-RBD proteins and insect-derived variants acquired from other vendors. Moreover, competitive BLI assays showed SBP1 does not outcompete ACE2 binding to Sino Biological insect-derived SARS-CoV-2-RBD. Further investigations are ongoing to gain insight into the molecular and structural determinants of the variable binding behavior to different SARS-CoV-2-RBD protein variants. ### Competing Interest Statement Bradley L. Pentelute is a co-founder of Resolute Bio and Amide Technologies.

72: Divergent SARS-CoV-2-specific T and B cell responses in severe but not mild COVID-19
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Posted to bioRxiv 18 Jun 2020

Divergent SARS-CoV-2-specific T and B cell responses in severe but not mild COVID-19
1,273 downloads immunology

Anna E. Oja, Anno Saris, Cherien A. Ghandour, Natasja A.M. Kragten, Boris M. Hogema, Esther J Nossent, Leo M.A. Heunks, Susan Cuvalay, Ed Slot, Francis H. Swaneveld, Hans Vrielink, Theo Rispens, Ellen van der Schoot, René A.W. van Lier, Anja Ten Brinke, Pleun Hombrink

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. Understanding both the immunological processes providing specific immunity and potential immunopathology underlying the pathogenesis of this disease may provide valuable insights for potential therapeutic interventions. Here, we quantified SARS-CoV-2 specific immune responses in patients with different clinical courses. Compared to individuals with a mild clinical presentation, CD4+ T cell responses were qualitatively impaired in critically ill patients. Strikingly, however, in these patients the specific IgG antibody response was remarkably strong. The observed disparate T and B cell responses could be indicative of a deregulated immune response in critically ill COVID-19 patients. ### Competing Interest Statement The authors have declared no competing interest.

73: The impact of super-spreaders in COVID-19: mapping genome variation worldwide
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Posted to bioRxiv 19 May 2020

The impact of super-spreaders in COVID-19: mapping genome variation worldwide
1,259 downloads genomics

Alberto Gómez-Carballa, Xabier Bello, Jacobo Pardo-Seco, Federico Martinón-Torres, Antonio Salas

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effects, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent. ### Competing Interest Statement The authors have declared no competing interest.

74: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity
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Posted to bioRxiv 11 Apr 2020

Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity
1,237 downloads evolutionary biology

Yong Jia, Gangxu Shen, Yujuan Zhang, Keng-Shiang Huang, Hsing-Ying Ho, Wei-Shio Hor, Chih-Hui Yang, Chengdao Li, Wei-Lung Wang

Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a mutation that leads to weaker receptor binding capability, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and raises the alarm that the ongoing vaccine development may become futile in future epidemic if more mutations were identified. ### Competing Interest Statement The authors have declared no competing interest.

75: Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife
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Posted to bioRxiv 14 Jun 2020

Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife
1,235 downloads cell biology

Dongsheng Chen, Jian Sun, Jiacheng Zhu, Xiangning Ding, Tianming Lan, Linnan Zhu, Rong Xiang, Peiwen Ding, Haoyu Wang, Xiaoling Wang, Weiying Wu, Jiaying Qiu, Shiyou Wang, Haimeng Li, Fuyu An, Heng Bao, Le Zhang, Lei Han, Yixin Zhu, Xiran Wang, Feiyue Wang, Yuting Yuan, Wendi Wu, Chengcheng Sun, Haorong Lu, Jihong Wu, Xinghuai Sun, Shenghai Zhang, Sunil Kumar Sahu, Haixia Chen, Dongming Fang, Lihua Luo, Yuying Zeng, Yiquan Wu, ZeHua Cui, Qian He, Sanjie Jiang, Xiaoyan Ma, Weimin Feng, Yan Xu, Fang Li, Zhongmin Liu, Lei Chen, Fang Chen, Xin Jin, Wei Qiu, Huanming Yang, Jian Wang, Yan Hua, Yahong Liu, Huan Liu, Xun Xu

A few animals have been suspected to be intermediate hosts of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, a large-scale single-cell screening of SARS-CoV-2 target cells on a wide variety of animals is missing. Here, we constructed the single-cell atlas for 11 representative species in pets, livestock, poultry, and wildlife. Notably, the proportion of SARS-CoV-2 target cells in cat was found considerably higher than other species we investigated and SARS-CoV-2 target cells were detected in multiple cell types of domestic pig, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic and keep pigs under surveillance for the possibility of becoming intermediate hosts in future coronavirus outbreak. Furthermore, we screened the expression patterns of receptors for 144 viruses, resulting in a comprehensive atlas of virus target cells. Taken together, our work provides a novel and fundamental strategy to screen virus target cells and susceptible species, based on single-cell transcriptomes we generated for domesticated animals and wildlife, which could function as a valuable resource for controlling current pandemics and serve as an early warning system for coping with future infectious disease threats. ### Competing Interest Statement The authors have declared no competing interest.

76: Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures
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Posted to bioRxiv 15 Jun 2020

Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures
1,227 downloads genetics

Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K. Wirecki, Tycho Marinus, Natacha S. Ogando, Eric J. Snijder, Martijn J. van Hemert, Janusz M. Bujnicki, Danny Incarnato

SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of ~30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date. Here, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5′ UTR, ribosomal frameshifting element, and 3′ UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, ~8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections. ### Competing Interest Statement The authors have declared no competing interest.

77: The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I
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Posted to bioRxiv 24 May 2020

The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I
1,224 downloads microbiology

Yiwen Zhang, Junsong Zhang, Yingshi Chen, Baohong Luo, Yaochang Yuan, Feng Huang, Tao Yang, Fei Yu, Jun Liu, Bingfen Liu, Zheng Song, Jingliang Chen, Ting Pan, Xu Zhang, Yuzhuang Li, Rong Li, Wenjing Huang, Fei Xiao, Hui Zhang

SARS-CoV-2 infection have caused global pandemic and claimed over 5,000,000 tolls. Although the genetic sequences of their etiologic viruses are of high homology, the clinical and pathological characteristics of COVID-19 significantly differ from SARS. Especially, it seems that SARS-CoV-2 undergoes vast replication in vivo without being effectively monitored by anti-viral immunity. Here, we show that the viral protein encoded from open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all the viral proteins, can directly interact with MHC-I molecules and significantly down-regulates their surface expression on various cell types. In contrast, ORF8a and ORF8b of SARS-CoV do not exert this function. In the ORF8-expressing cells, MHC-I molecules are selectively target for lysosomal degradation by an autophagy-dependent mechanism. As a result, CTLs inefficiently eliminate the ORF8-expressing cells. Our results demonstrate that ORF8 protein disrupts antigen presentation and reduces the recognition and the elimination of virus-infected cells by CTLs. Therefore, we suggest that the inhibition of ORF8 function could be a strategy to improve the special immune surveillance and accelerate the eradication of SARS-CoV-2 in vivo. ### Competing Interest Statement The authors have declared no competing interest.

78: Unsupervised Neural Network Models of the Ventral Visual Stream
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Posted to bioRxiv 18 Jun 2020

Unsupervised Neural Network Models of the Ventral Visual Stream
1,220 downloads neuroscience

Chengxu Zhuang, Siming Yan, Aran Nayebi, Martin Schrimpf, Michael C. Frank, James J. DiCarlo, Daniel L. K. Yamins

Deep neural networks currently provide the best quantitative models of the response patterns of neurons throughout the primate ventral visual stream. However, such networks have remained implausible as a model of the development of the ventral stream, in part because they are trained with supervised methods requiring many more labels than are accessible to infants during development. Here, we report that recent rapid progress in unsupervised learning has largely closed this gap. We find that neural network models learned with deep unsupervised contrastive embedding methods achieve neural prediction accuracy in multiple ventral visual cortical areas that equals or exceeds that of models derived using today's best supervised methods, and that the mapping of these neural network models' hidden layers is neuroanatomically consistent across the ventral stream. Moreover, we find that these methods produce brain-like representations even when trained on noisy and limited data measured from real children's developmental experience. We also find that semi-supervised deep contrastive embeddings can leverage small numbers of labelled examples to produce representations with substantially improved error-pattern consistency to human behavior. Taken together, these results suggest that deep contrastive embedding objectives may be a biologically-plausible computational theory of primate visual development. ### Competing Interest Statement The authors have declared no competing interest.

79: The Genomic Formation of South and Central Asia
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Posted to bioRxiv 31 Mar 2018

The Genomic Formation of South and Central Asia
1,217 downloads genomics

Vagheesh M. Narasimhan, Nick Patterson, Priya Moorjani, Iosif Lazaridis, Mark Lipson, Swapan Mallick, Nadin Rohland, Rebecca Bernardos, Alexander M Kim, Nathan Nakatsuka, Iñigo Olalde, Alfredo Coppa, James Mallory, Vyacheslav Moiseyev, Janet Monge, Luca M Olivieri, Nicole Adamski, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel M. Fernandes, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Éadaoin Harney, Thomas K Harper, Denise Keating, Ann Marie Lawson, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Bauryzhan Baitanayev, Gian Luca Bonora, Tatiana Chikisheva, Anatoly Derevianko, Enshin Dmitry, Katerina Douka, Nadezhda Dubova, Andrey Epimakhov, Suzanne Freilich, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Egor Kitov, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhod Maksudov, Christopher Meiklejohn, Deborah Merrett, Roberto Micheli, Oleg Mochalov, Zahir Muhammed, Samariddin Mustafokulov, Ayushi Nayak, Rykun M Petrovna, Davide Pettener, Richard Potts, Dmitry Razhev, Stefania Sarno, Kulyan Sikhymbaeva, Sergey M Slepchenko, Nadezhda Stepanova, Svetlana Svyatko, Sergey Vasilyev, Massimo Vidale, Dmitriy Voyakin, Antonina Yermolayeva, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasamy Thangaraj, Douglas J. Kennett, Michael Frachetti, Ron Pinhasi, David Reich

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

80: HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
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Posted to bioRxiv 02 Jun 2020

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
1,208 downloads genomics

Jamie L. Marshall, Benjamin R. Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G. Rodriques, Kaite Zhang, Philine Guckelberger, Charles P Fulco, Joseph Nasser, Elizabeth J. Grinkevich, Teia Noel, Sarah Mangiameli, Anna Greka, Eric S Lander, Fei Chen, Jesse M. Engreitz

Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells. ### Competing Interest Statement F.C., J.M.E., J.L.M., V.S., and S.R. are inventors on patent applications filed by the Broad Institute related to this work (62/676,069 and 62/780,889). E.S.L. serves on the Board of Directors for Codiak BioSciences and Neon Therapeutics, and serves on the Scientific Advisory Board of F-Prime Capital Partners and Third Rock Ventures; he is also affiliated with several non-profit organizations including serving on the Board of Directors of the Innocence Project, Count Me In, and Biden Cancer Initiative, and the Board of Trustees for the Parker Institute for Cancer Immunotherapy. He has served and continues to serve on various federal advisory committees.

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