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in category genomics


1: Introductions and early spread of SARS-CoV-2 in France

Fabiana Gámbaro, Sylvie Behillil et al.

32,211 downloads (posted 24 Apr 2020)

Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections. ### Competing Interest Statement The authors have declared no competing interest.


2: The architecture of SARS-CoV-2 transcriptome

Dongwan Kim, Joo-Yeon Lee et al.

7,606 downloads (posted 14 Mar 2020)

SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in al...


3: Characterizing geographical and temporal dynamics of novel coronavirus SARS-CoV-2 using informative subtype markers

Zhengqiao Zhao, Bahrad A. Sokhansanj et al.

6,927 downloads (posted 09 Apr 2020)

We propose an efficient framework for genetic subtyping of a pandemic virus, with application to the novel coronavirus SARS-CoV-2. Efficient identification of subtypes is particularly important for tracking the geographic distribution and temporal dynamics of infectious spread in real-time. In this paper, we utilize an entropy analysis to identify nucleotide sites within SARS-CoV-2 genome sequences that are highly informative of genetic variation, and thereby define an Informative Subtype Marker (ISM) for each sequence....


4: Profiling the epigenome at home

Steven Henikoff, Jorja G. Henikoff

6,399 downloads (posted 17 Apr 2020)

We recently described CUT&Tag, a general strategy for epigenomic profiing in which antibody-tethered Tn5 transposase integrates DNA sequencing adapters at sites of specific chromatin protein binding or histone modification in intact cells or nuclei. Here we introduce a simplified CUT&Tag method that can be performed at home to help ameliorate the interruption of bench research caused by COVID-19 physical distancing requirements. All steps beginning with frozen nuclei are performed in single PCR tubes through to barcoded...


5: Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world

Jody Phelan, Wouter Deelder et al.

5,285 downloads (posted 29 Apr 2020)

Background: SARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 3 million confirmed cases by the end of April 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansi...


6: Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

Joana Damas, Graham M. Hughes et al.

4,999 downloads (posted 18 Apr 2020)

The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). As for other coronaviruses, there is transmission between animals and humans. The main receptor of SARS-CoV-2, angiotensin I converting enzyme-2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 r...


7: 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

Chandrika Bhattacharyya, Chitrarpita Das et al.

4,887 downloads (posted 05 May 2020)

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 s...


8: Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis

Chuang Guo, Bin Li et al.

4,510 downloads (posted 09 Apr 2020)

Coronavirus disease 2019 (COVID-19) has caused more than 40,000 deaths worldwide. Approximately 14% of patients with COVID-19 experienced severe disease and 5% were critically ill. Studies have shown that dysregulation of the COVID-19 patients' immune system may lead to inflammatory storm and cause severe illness and even death. Tocilizumab treatment targeting interleukin 6 receptor has shown inspiring clinical results of severe COVID-19 patients. However, the immune network with Tocilizumab treatment at single cell res...


9: A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

Brian Glenn St Hilaire, Neva C. Durand et al.

3,827 downloads (posted 25 Apr 2020)

Early detection of infection with SARS-CoV-2 is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosis of SARS-CoV-2 infection, dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), that enhances sensitivity by aiming to amplify the entire SARS-CoV-2 genome rather than targeting particular viral loci, as in typical RT-PCR assays. To achieve this goal, we combine a SARS-CoV-2 ...


10: Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations

Meriem Laamarti, Tarek Alouane et al.

3,281 downloads (posted 03 May 2020)

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mu...


11: A guide to performing Polygenic Risk Score analyses

Shing Wan Choi, Timothy Shin Heng Mak et al.

3,238 downloads (posted 14 Sep 2018)

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 becom...


12: Comprehensive integration of single cell data

Tim Stuart, Andrew Butler et al.

3,092 downloads (posted 02 Nov 2018)

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 devel...


13: Atlas of ACE2 gene expression in mammals reveals novel insights in transmission of SARS-Cov-2

Kun Sun, Liuqi Gu et al.

2,919 downloads (posted 31 Mar 2020)

Background: COVID-19 has become a worldwide pandemic. It is caused by a novel coronavirus named SARS-CoV-2 with elusive origin. SARS-CoV-2 infects mammalian cells by binding to ACE2, a transmembrane protein. Therefore, the conservation of ACE2 and its expression pattern across mammalian species, which are yet to be comprehensively investigated, may provide valuable insights into tracing potential hosts of SARS-CoV-2. Methods: We analyzed gene conservation of ACE2 across mammals and collected more than 140 transcriptome ...


14: Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

Bas B. Oude Munnink, David F. Nieuwenhuijse et al.

2,785 downloads (posted 25 Apr 2020)

SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also, outside the South of the Netherlands. The timely generation of whole genome sequences combined with epidemiological inves...


15: A molecular cell atlas of the human lung from single cell RNA sequencing

Kyle J. Travaglini, Ahmad N. Nabhan et al.

2,588 downloads (posted 27 Aug 2019)

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 cel...


16: The Genomic Formation of South and Central Asia

Vagheesh Narasimhan, Nick Patterson et al.

2,454 downloads (posted 31 Mar 2018)

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, corre...


17: Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Chenyu Li, David N. Debruyne et al.

2,355 downloads (posted 14 Mar 2020)

Many detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations span...


18: CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design

Hayden C. Metsky, Catherine A. Freije et al.

2,302 downloads (posted 02 Mar 2020)

The emergence and outbreak of SARS-CoV-2, the causative agent of COVID-19, has rapidly become a global concern and has highlighted the need for fast, sensitive, and specific tools to surveil circulating viruses. Here we provide assay designs and experimental resources, for use with CRISPR-based nucleic acid detection, that could be valuable for ongoing surveillance. We provide assay designs for detection of 67 viral species and subspecies, including: SARS-CoV-2, phylogenetically-related viruses, and viruses with similar...


19: Cells and gene expression programs in the adult human heart

Monika Litviňuková, Carlos Talavera-Lopez et al.

2,301 downloads (posted 05 Apr 2020)

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human h...


20: Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium

Satria P Sajuthi, Peter DeFord et al.

2,279 downloads (posted 10 Apr 2020)

Coronavirus disease 2019 (COVID-19) outcomes vary from asymptomatic infection to death. This disparity may reflect different airway levels of the SARS-CoV-2 receptor, ACE2, and the spike protein activator, TMPRSS2. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci (eQTL) for both ACE2 and TMPRSS2, that vary in frequency across world populations. ...