Rxivist logo

Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 128,741 papers from 551,614 authors.

Most downloaded biology preprints, all time

in category molecular biology

3,874 results found. For more information, click each entry to expand.

21: Structural and Evolutionary Analysis Indicate that the SARS-CoV-2 Mpro is an Inconvenient Target for Small-Molecule Inhibitors Design
more details view paper

Posted 02 Mar 2020

Structural and Evolutionary Analysis Indicate that the SARS-CoV-2 Mpro is an Inconvenient Target for Small-Molecule Inhibitors Design
6,473 downloads bioRxiv molecular biology

Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Aleksandra Samol, J. A.Tuszynski, Artur Góra

The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mix-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar SARS Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins show major differences in both shape and size indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding site’s conformational changes during the simulation time indicates its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicates that the virus’ mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design. * Mpro : Main protease CoVs : Coronaviruses ORFs : Open reading frames 3CLpro : Chymotrypsin-like cysteine protease S : Spike surface glycoprotein E : Small envelope protein M : Matrix protein N : Nucleocapsid protein N3 : N-[(5 methylisoxazol-3-yl)carbonyl] alanyl-L-valyl-N~1-((1R,2Z)-4-(benzyloxy)-4-oxo-1--{[(3R)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide cMD : Classical molecular dynamics simulations MixMD : Mixed-solvent molecular dynamics simulations PDB : Protein Data Bank MAV : Maximal accessible volume ACN : Acetonitrile BNZ : Benzene DMSO : Dimethylsulfoxide MEO : Methanol PHN : Phenol URE : Urea CMA : Correlated mutation analysis

22: The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor
more details view paper

Posted 12 Mar 2020

The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor
6,464 downloads bioRxiv molecular biology

Esther S Brielle, Dina Schneidman-Duhovny, Michal Linial

The COVID-19 disease has plagued over 110 countries and has resulted in over 4,000 deaths within 10 weeks. We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. SARS-CoV, SARS-CoV-2, and HCoV-NL63 recognize ACE2 as the natural receptor but present a distinct binding interface to ACE2 and a different network of residue-residue contacts. SARS-CoV and SARS-CoV-2 have comparable binding affinities achieved by balancing energetics and dynamics. The SARS-CoV-2 - ACE2 complex contains a higher number of contacts, a larger interface area, and decreased interface residue fluctuations relative to SARS-CoV. These findings expose an exceptional evolutionary exploration exerted by coronaviruses toward host recognition. We postulate that the versatility of cell receptor binding strategies has immediate implications on therapeutic strategies.

23: Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2
more details view paper

Posted 03 Mar 2020

Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2
6,387 downloads bioRxiv molecular biology

Youngchang Kim, Robert Jedrzejczak, Natalia I. Maltseva, Michael Endres, Adam Godzik, Karolina Michalska, Andrzej Joachimiak

Severe Acute Respiratory Syndrome Coronavirus 2 is rapidly spreading around the world. There is no existing vaccine or proven drug to prevent infections and stop virus proliferation. Although this virus is similar to human and animal SARS- and MERS-CoVs the detailed information about SARS-CoV-2 proteins structures and functions is urgently needed to rapidly develop effective vaccines, antibodies and antivirals. We applied high-throughput protein production and structure determination pipeline at the Center for Structural Genomics of Infectious Diseases to produce SARS-CoV-2 proteins and structures. Here we report the high-resolution crystal structure of endoribonuclease Nsp15/NendoU from SARS-CoV-2 - a virus causing current world-wide epidemics. We compare this structure with previously reported models of Nsp15 from SARS and MERS coronaviruses.

24: One-step RNA extraction for RT-qPCR detection of 2019-nCoV
more details view paper

Posted 05 Apr 2020

One-step RNA extraction for RT-qPCR detection of 2019-nCoV
6,221 downloads bioRxiv molecular biology

Monica Sentmanat, Evguenia Kouranova, Xiaoxia Cui

The global outbreak of coronavirus disease 2019 (COVID-19) has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three month[1]. Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription polymerase chain reaction (RT-PCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from four manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher sensitivity and improved safety. ### Competing Interest Statement The authors have declared no competing interest.

25: Inactivating porcine coronavirus before nuclei acid isolation with the temperature higher than 56 °C damages its genome integrity seriously
more details view paper

Posted 22 Feb 2020

Inactivating porcine coronavirus before nuclei acid isolation with the temperature higher than 56 °C damages its genome integrity seriously
6,039 downloads bioRxiv molecular biology

Qingxin Zhang, Qingshun Zhao

2019-Novel Coronavirus (2019-nCoV) is the pathogen of Corona Virus Disease 2019. Nucleic acid detection of 2019-nCoV is one of the key indicators for clinical diagnosis. However, the positive rate is only 30-50%. Currently, fluorescent quantitative RT-PCR technology is mainly used to detect 2019-nCoV. According to "The Laboratory Technical Guidelines for Detection 2019-nCoV (Fourth Edition)" issued by National Health and Commission of China and "The Experts' Consensus on Nucleic Acid Detection of 2019-nCoV" released by Chinese Society of Laboratory Medicine, the human samples must be placed under 56°C or higher to inactivate the viruses in order to keep the inspectors from virus infection before the nucleic acids were isolated as the template of qRT-PCR. In this study, we demonstrated that the virus inactivation treatment disrupts its genome integrity seriously when using porcine epidemic diarrhea virus (vaccine), a kind of coronavirus, as a model. Our results showed that only 50.11% of the detectable viral templates left after the inactivation of 56°C for 30 minutes and only 3.36% left after the inactivation of 92°C for 5 minutes when the samples were preserved by Hank's solution, one of an isotonic salt solutions currently suggested. However, the detectable templates of viral nucleic acids can be unchanged after the samples were incubated at 56°C or higher if the samples were preserved with an optimized solution to protect the RNA from being disrupted. We therefore highly recommend to carry out systematic investigation on the impact of high temperature inactivation on the integrity of 2019-nCoV genome and develop a sample preservation solution to protect the detectable templates of 2019-nCoV nucleic acids from high temperature inactivation damage.

26: Neutralization of UK-variant VUI-202012/01 with COVAXIN vaccinated human serum
more details view paper

Posted 26 Jan 2021

Neutralization of UK-variant VUI-202012/01 with COVAXIN vaccinated human serum
5,831 downloads bioRxiv molecular biology

Gajanan N Sapkal, Pragya Yadav, Raches Ella, Gururaj Deshpande, Rima Sahay, Nivedita Gupta, V Krishna Mohan, Priya Abraham, Samiran Panda, Balram Bhargava

We performed the plaque reduction neutralization test (PRNT50) using sera collected from the 26 recipients of BBV152/COVAXINTM against hCoV-19/India/20203522 (UK-variant) and hCoV27 19/India/2020Q111 (heterologous strain). A comparable neutralization activity of sera of the vaccinated individuals showed against UK-variant and the heterologous strain with similar efficiency, dispel the uncertainty of possible neutralization escape.

27: The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2
more details view paper

Posted 14 Jun 2020

The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2
5,694 downloads bioRxiv molecular biology

Melissa Zimniak, Luisa Kirschner, Helen Hilpert, Jürgen Seibel, Jochen Bodem

To circumvent time-consuming clinical trials, testing whether existing drugs are effective inhibitors of SARS-CoV-2, has led to the discovery of Remdesivir. We decided to follow this path and screened approved medications off-label against SARS-CoV-2. In these screenings, Fluoxetine inhibited SARS-CoV-2 at a concentration of 0.8μg/ml significantly, and the EC50 was determined with 387ng/ml. Fluoxetine is a racemate consisting of both stereoisomers, while the S-form is the dominant serotonin reuptake inhibitor. We found that both isomers show similar activity on the virus. Fluoxetine treatment resulted in a decrease in viral protein expression. Furthermore, Fluoxetine inhibited neither Rabies virus, human respiratory syncytial virus replication nor the Human Herpesvirus 8 or Herpes simplex virus type 1 gene expression, indicating that it acts virus-specific. We see the role of Fluoxetine in the early treatment of SARS-CoV-2 infected patients of risk groups. ### Competing Interest Statement The authors have declared no competing interest.

28: A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2
more details view paper

Posted 27 Feb 2020

A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2
5,680 downloads bioRxiv molecular biology

Zhen Zhao, Haodong Cui, Wenxing Song, Xiaoling Ru, Wenhua Zhou, Xuefeng Yu

The ongoing outbreak of the novel coronavirus disease 2019 (COVID-19) originating from Wuhan, China, draws worldwide concerns due to its long incubation period and strong infectivity. Although RT-PCR-based molecular diagnosis techniques are being widely applied for clinical diagnosis currently, timely and accurate diagnosis are still limited due to labour intensive and time-consuming operations of these techniques. To address the issue, herein we report the synthesis of poly (amino ester) with carboxyl groups (PC)-coated magnetic nanoparticles (pcMNPs), and the development of pcMNPs-based viral RNA extraction method for the sensitive detection of COVID-19 causing virus, the SARS-CoV-2. This method combines the lysis and binding steps into one step, and the pcMNPs-RNA complexes can be directly introduced into subsequent RT-PCR reactions. The simplified process can purify viral RNA from multiple samples within 20 min using a simple manual method or an automated high-throughput approach. By identifying two different regions (ORFlab and N gene) of viral RNA, a 10-copy sensitivity and a strong linear correlation between 10 and 100,000 copies of SARS-CoV-2 pseudovirus particles are achieved. Benefitting from the simplicity and excellent performances, this new extraction method can dramatically reduce the turn-around time and operational requirements in current molecular diagnosis of COVID-19, in particular for the early clinical diagnosis.

29: In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations
more details view paper

Posted 27 Feb 2018

In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations
5,462 downloads bioRxiv molecular biology

Pinar Akcakaya, Maggie L. Bobbin, Jimmy A. Guo, Jose M Lopez, M. Kendell Clement, Sara P. Garcia, Mick D. Fellows, Michelle J. Porritt, Mike A. Firth, Alba Carreras, Tania Baccega, Frank Seeliger, Mikael Bjursell, Shengdar Q. Tsai, Nhu T. Nguyen, Roberto Nitsch, Lorenz M Mayr, Luca Pinello, Mohammad Bohlooly-Y, Martin J Aryee, Marcello Maresca, J. Keith Joung

CRISPR-Cas genome-editing nucleases hold substantial promise for human therapeutics but identifying unwanted off-target mutations remains an important requirement for clinical translation. For ex vivo therapeutic applications, previously published cell-based genome-wide methods provide potentially useful strategies to identify and quantify these off-target mutation sites. However, a well-validated method that can reliably identify off-targets in vivo has not been described to date, leaving the question of whether and how frequently these types of mutations occur. Here we describe Verification of In Vivo Off-targets (VIVO), a highly sensitive, unbiased, and generalizable strategy that we show can robustly identify genome-wide CRISPR-Cas nuclease off-target effects in vivo. To our knowledge, these studies provide the first demonstration that CRISPR-Cas nucleases can induce substantial off-target mutations in vivo, a result we obtained using a deliberately promiscuous guide RNA (gRNA). More importantly, we used VIVO to show that appropriately designed gRNAs can direct efficient in vivo editing without inducing detectable off-target mutations. Our findings provide strong support for and should encourage further development of in vivo genome editing therapeutic strategies.

30: Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR
more details view paper

Posted 23 Apr 2020

Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR
5,439 downloads bioRxiv molecular biology

Sanjay Srivatsan, Peter D. Han, Katrina van Raay, Caitlin R Wolf, Denise J McCulloch, Ashley E Kim, Elisabeth Brandstetter, Beth Martin, Jase Gehring, Wei Chen, Seattle Flu Study Investigators, Sriram Kosuri, Eric Q. Konnick, Christina M. Lockwood, Mark J. Rieder, Deborah A. Nickerson, Helen Y. Chu, Jay Shendure, Lea M Starita

The urgent need for massively scaled clinical or surveillance testing for SARS-CoV-2 has necessitated a reconsideration of the methods by which respiratory samples are collected, transported, processed and tested. Conventional testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab, storage of the swab during transport in universal transport medium (UTM), extraction of RNA, and quantitative reverse transcription PCR (RT-qPCR). As testing has scaled across the world, supply chain challenges have emerged across this entire workflow. Here we sought to evaluate how eliminating the UTM storage and RNA extraction steps would impact the results of molecular testing. Using paired mid-turbinate swabs self-collected by 11 individuals with previously established SARS-CoV-2 positivity, we performed a comparison of conventional (swab → UTM → RNA extraction → RT-qPCR) vs. simplified (direct elution from dry swab → RT-qPCR) protocols. Our results suggest that dry swabs eluted directly into a simple buffered solution (TE) can support molecular detection of SARS-CoV-2 via endpoint RT-qPCR without substantially compromising sensitivity. Although further confirmation with a larger sample size and variation of other parameters is necessary, these results are encouraging for the possibility of a simplified workflow that could support massively scaled testing for COVID-19 control. ### Competing Interest Statement The authors have declared no competing interest.

31: Reagent contamination can critically impact sequence-based microbiome analyses
more details view paper

Posted 16 Jul 2014

Reagent contamination can critically impact sequence-based microbiome analyses
5,354 downloads bioRxiv molecular biology

Susannah J Salter, Michael J Cox, Elena M Turek, Szymon Calus, William O Cookson, Miriam F. Moffatt, Paul Turner, Julian Parkhill, Nick Loman, Alan W Walker

The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.

32: Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs
more details view paper

Posted 10 Apr 2015

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs
5,289 downloads bioRxiv molecular biology

Gali Housman, Igor Ulitsky

Long noncoding RNAs (lncRNAs) are a diverse class of RNAs with increasingly appreciated functions in vertebrates, yet much of their biology remains poorly understood. In particular, it is unclear to what extent the current catalog of over 10,000 distinct annotated lncRNAs is indeed devoid of genes coding for proteins. Here we review the available computational and experimental schemes for distinguishing between recent genome-wide applications. We conclude that the model most consistent with available data is that a large number of mammalian lncRNAs undergo translation, but only a very small minority of such translation events result in stable and functional peptides. The outcome of the majority of the translation events and their potential biological purposes remain an intriguing topic for future investigation.

33: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2
more details view paper

Posted 18 May 2020

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2
5,265 downloads bioRxiv molecular biology

Matthias Thoms, Robert Buschauer, Michael Ameismeier, Lennart Koepke, Timo Denk, Maximilian Hirschenberger, Hanna Kratzat, Manuel Hayn, Timur Mackens-Kiani, Jingdong Cheng, Christina M. Stürzel, Thomas Fröhlich, Otto Berninghausen, Thomas Becker, Frank Kirchhoff, Konstantin M.J. Sparrer, Roland Beckmann

SARS-CoV-2 is the causative agent of the current COVID-19 pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1) which suppresses host gene expression by ribosome association via an unknown mechanism. Here, we show that Nsp1 from SARS-CoV-2 binds to 40S and 80S ribosomes, resulting in shutdown of capped mRNA translation both in vitro and in cells. Structural analysis by cryo-electron microscopy (cryo-EM) of in vitro reconstituted Nsp1-40S and of native human Nsp1-ribosome complexes revealed that the Nsp1 C-terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks RIG-Idependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2. ### Competing Interest Statement The authors have declared no competing interest.

34: Validation of a Lysis Buffer Containing 4 M Guanidinium Thiocyanate (GITC)/ Triton X-100 for Extraction of SARS-CoV-2 RNA for COVID-19 Testing: Comparison of Formulated Lysis Buffers Containing 4 to 6 M GITC, Roche External Lysis Buffer and Qiagen RTL Lysis Buffer
more details view paper

Posted 08 Apr 2020

Validation of a Lysis Buffer Containing 4 M Guanidinium Thiocyanate (GITC)/ Triton X-100 for Extraction of SARS-CoV-2 RNA for COVID-19 Testing: Comparison of Formulated Lysis Buffers Containing 4 to 6 M GITC, Roche External Lysis Buffer and Qiagen RTL Lysis Buffer
5,143 downloads bioRxiv molecular biology

Martina F Scallan, Catherine Dempsey, John MacSharry, Isabelle O’Callaghan, Paula M. O’Connor, Conor P. Horgan, Edel Durack, Paul D Cotter, Sarah Hudson, Humphrey A. Moynihan, Brigid Lucey

The COVID-19 pandemic has resulted in increased need for diagnostic testing using reverse transcriptase real-time PCR (RT-PCR). An exponential increase in demand has resulted in a shortage of numerous reagents in particular those associated with the lysis buffer required to extract the viral RNA. Herein, we describe a rapid collective effort by hospital laboratory scientists, academic researchers and the biopharma industry to generate a validated lysis buffer. We have formulated a 4M Guanidinium thiocyanate (GITC)/ Triton X-100 Lysis buffer which provides comparable results with the recommended reagents. This buffer will ease the burden on hospital labs in their heroic efforts to diagnose a large population of patients. ### Competing Interest Statement The authors have declared no competing interest.

35: A Simple Enhancement for Gibson Isothermal Assembly
more details view paper

Posted 15 Jun 2020

A Simple Enhancement for Gibson Isothermal Assembly
5,054 downloads bioRxiv molecular biology

Brian A Rabe, Constance L Cepko

Gibson Isothermal Assembly has become a widespread cloning method, with a multitude of advantages over traditional cut-and-paste cloning. It allows for scarless assembly of multiple fragments simultaneously and has become widely used for molecular cloning. We have found that a simple change to the formulation of the reaction mix, the addition of a single-stranded DNA binding protein, can substantially improve both the accuracy and efficiency of assembly, especially as the number of fragments being assembled increases. In addition, when creating this Enhanced Gibson Isothermal Assembly reaction mix in-house with homemade DNA ligase, the cost of the reaction can be reduced to less than $10 per milliliter. ### Competing Interest Statement The authors have declared no competing interest.

36: Glycyrrhizin effectively neutralizes SARS-CoV-2 in vitro by inhibiting the viral main protease
more details view paper

Posted 20 Dec 2020

Glycyrrhizin effectively neutralizes SARS-CoV-2 in vitro by inhibiting the viral main protease
5,040 downloads bioRxiv molecular biology

L. van de Sand, M. Bormann, M. Alt, L. Schipper, C.S. Heilingloh, D. Todt, U. Dittmer, C. Elsner, O. Witzke, A. Krawczyk

The newly emerged coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 disease. High effective and well-tolerated medication for hospitalized and non-hospitalized patients is urgently needed. Traditional herbal medicine substances were discussed as promising candidates for the complementary treatment of viral diseases and recently suggested for the treatment of COVID-19. In the present study, we investigated aqueous licorice root extract for its neutralizing activity against SARS-CoV-2 in vitro, identified the active compound glycyrrhizin and uncovered the respective mechanism of viral neutralization. We demonstrated that glycyrrhizin, the primary active ingredient of the licorice root, potently neutralizes SARS-CoV-2 by inhibiting the viral main protease. Our experiments highlight glycyrrhizin as a potential antiviral compound that should be further investigated for the treatment of COVID-19.

37: Ferrets not infected by SARS-CoV-2 in a high-exposure domestic setting
more details view paper

Posted 22 Aug 2020

Ferrets not infected by SARS-CoV-2 in a high-exposure domestic setting
4,917 downloads bioRxiv molecular biology

Kaitlin Sawatzki, Nichola Hill, Wendy Puryear, Alexa Foss, Jonathon Stone, Jonathan Runstadler

Ferrets ( Mustela putorius furo ) are mustelids of special relevance to laboratory studies of respiratory viruses and have been shown to be susceptible to SARS-CoV-2 infection and onward transmission. Here, we report the results of a natural experiment where 29 ferrets in one home had prolonged, direct contact and constant environmental exposure to two humans with symptomatic COVID-19. We observed no evidence of SARS-CoV-2 transmission from humans to ferrets based on RT-PCR and ELISA. To better understand this discrepancy in experimental and natural infection in ferrets, we compared SARS-CoV-2 sequences from natural and experimental mustelid infections and identified two surface glycoprotein (Spike) mutations associated with mustelids. While we found evidence that ACE2 provides a weak host barrier, one mutation only seen in ferrets is located in the novel S1/S2 cleavage site and is computationally predicted to decrease furin activity. These data support that host factors interacting with the novel S1/S2 cleavage site may be a barrier in ferret SARS-CoV-2 susceptibility and that domestic ferrets are at low risk of natural infection from currently circulating SARS-CoV-2. This may be overcome in laboratory settings using concentrated viral inoculum, but the effects of ferret host-adaptations require additional investigation. ### Competing Interest Statement The authors have declared no competing interest.

38: C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
more details view paper

Posted 21 May 2016

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
4,737 downloads bioRxiv molecular biology

Omar O Abudayyeh, Jonathan S Gootenberg, Silvana Konermann, Julia Joung, Ian M Slaymaker, David B.T. Cox, Sergey Shmakov, Kira S Makarova, Ekaterina Semenova, Leonid Minakhin, Konstantin Severinov, Aviv Regev, Eric S Lander, Eugene V. Koonin, Feng Zhang

The CRISPR-Cas adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the Class 2 type VI-A CRISPR-Cas effector C2c2 and demonstrate its RNA-guided RNase function. C2c2 from the bacterium Leptotrichia shahii provides interference against RNA phage. In vitro biochemical analysis show that C2c2 is guided by a single crRNA and can be programmed to cleave ssRNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved HEPN domains, mutations in which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.

39: Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic
more details view paper

Posted 08 Apr 2020

Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic
4,722 downloads bioRxiv molecular biology

Paul R. Grant, Melanie A Turner, Gee Yen Shin, Eleni Nastouli, Lisa J Levett

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus disease 2019 (COVID-19), a respiratory tract infection. The standard molecular diagnostic test is a multistep process involving viral RNA extraction and real-time quantitative reverse transcriptase PCR (qRT-PCR). Laboratories across the globe face constraints on equipment and reagents during the COVID-19 pandemic. We have developed a simplified qRT-PCR assay that removes the need for an RNA extraction process and can be run on a real-time thermal cycler. The assay uses custom primers and probes, and maintains diagnostic sensitivity within 98.0% compared to the assay run on a high-throughput, random-access automated platform, the Panther Fusion (Hologic). This assay can be used to increase capacity for COVID-19 testing for national programmes worldwide. ### Competing Interest Statement The authors have declared no competing interest.

40: Rapid, field-deployable nucleobase detection and identification using FnCas9
more details view paper

Posted 09 Apr 2020

Rapid, field-deployable nucleobase detection and identification using FnCas9
4,717 downloads bioRxiv molecular biology

Mohd. Azhar, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Namrata Sharma, Manoj Kumar, Meghali Aich, Saumya Sharma, Riya Rauthan, Khushboo Singhal, Harsha Lad, Pradeep Kumar Patra, Govind Makharia, Giriraj Ratan Chandak, Debojyoti Chakraborty, Souvik Maiti

Detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for rapid clinical prognosis. In recent times, CRISPR based detection of nucleic acids have provided an economical and quicker alternative to sequencing-based platforms which are often difficult to implement in the field. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a highly accurate enzymatic readout for detecting nucleotide sequences, identifying nucleobase identity and inferring zygosity with precision. We demonstrate that FELUDA output can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications including rapid diagnosis during infectious disease outbreaks like COVID-19. ### Competing Interest Statement D.C., S.M., M.A., R.P., A.S.A, D.S., N.S. and S.S. are authors in provisional patent applications that have been filed in relation to this work.

Previous page 1 2 3 4 5 6 . . . 194 Next page

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News