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Currently indexing 93,394 bioRxiv papers from 398,421 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 1 through 20 out of 91517

 

1: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

Takuya Sekine, Andre Perez-Potti et al.

53,328 downloads (posted 29 Jun 2020) immunology

SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19. We systematically mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in a large cohort of unexposed individuals as well as exposed family members and individuals with acute or convalescent COVID-19. Acute phase SARS-CoV-2-specific T cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent phase SARS-CoV-2-specific T cells were polyfunctional and displayed a stem-like memory phenotype. Importantly, SARS-CoV-2-specific T cells were detectable in antibody-seronegative family members and individuals with a history of asymptomatic or mild COVID-19. Our collective dataset shows that SARS-CoV-2 elicits robust memory T cell responses akin to those observed in the context of successful vaccines, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19 also in seronegative individuals. ### Competing Interest Statement The authors have declared no competing interest.

https://rxivist.org/papers/89288
https://doi.org/10.1101/2020.06.29.174888

2: The major genetic risk factor for severe COVID-19 is inherited from Neandertals

Hugo Zeberg, Svante Pääbo

26,196 downloads (posted 03 Jul 2020) genomics

A recent genetic association study (Ellinghaus et al. 2020) identified a gene cluster on chromosome 3 as a risk locus for respiratory failure in SARS-CoV-2. Recent data comprising 3,199 hospitalized COVID-19 patients and controls reproduce this and find that it is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% ...

https://rxivist.org/papers/89844
https://doi.org/10.1101/2020.07.03.186296

3: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

Prashant Pradhan, Ashutosh Kumar Pandey et al.

11,627 downloads (posted 31 Jan 2020) evolutionary biology

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.

https://rxivist.org/papers/72514
https://doi.org/10.1101/2020.01.30.927871

4: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

B Korber, WM Fischer et al.

10,799 downloads (posted 30 Apr 2020) evolutionary biology

We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages i...

https://rxivist.org/papers/81793
https://doi.org/10.1101/2020.04.29.069054

5: The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity

Lizhou Zhang, Cody B Jackson et al.

9,575 downloads (posted 12 Jun 2020) microbiology

SARS coronavirus 2 (SARS-CoV-2) isolates encoding a D614G mutation in the viral spike (S) protein predominate over time in locales where it is found, implying that this change enhances viral transmission. We therefore compared the functional properties of the S proteins with aspartic acid (SD614) and glycine (SG614) at residue 614. We observed that retroviruses pseudotyped with SG614 infected ACE2-expressing cells markedly more efficiently than those with SD614. This greater infectivity was correlated with less S1 shedd...

https://rxivist.org/papers/87211
https://doi.org/10.1101/2020.06.12.148726

6: ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques

Neeltje van Doremalen, Teresa Lambe et al.

9,570 downloads (posted 13 May 2020) microbiology

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in December 20191,2 and is responsible for the COVID-19 pandemic3. Vaccines are an essential countermeasure urgently needed to control the pandemic4. Here, we show that the adenovirus-vectored vaccine ChAdOx1 nCoV-19, encoding the spike protein of SARS-CoV-2, is immunogenic in mice, eliciting a robust humoral and cell-mediated response. This response was not Th2 dominated, as demonstrated by IgG subclass and cytokine expression profiling. A single vacc...

https://rxivist.org/papers/83296
https://doi.org/10.1101/2020.05.13.093195

7: An integrated brain-machine interface platform with thousands of channels

Elon Musk, Neuralink

9,465 downloads (posted 17 Jul 2019) neuroscience

Brain-machine interfaces (BMIs) hold promise for the restoration of sensory and motor function and the treatment of neurological disorders, but clinical BMIs have not yet been widely adopted, in part because modest channel counts have limited their potential. In this white paper, we describe Neuralink’s first steps toward a scalable high-bandwidth BMI system. We have built arrays of small and flexible electrode “threads”, with as many as 3,072 electrodes per array distributed across 96 threads. We have also built a neur...

https://rxivist.org/papers/55953
https://doi.org/10.1101/703801

8: A Targeted Vaccine against COVID-19: S1-Fc Vaccine Targeting the Antigen-Presenting Cell Compartment Elicits Protection against SARS-CoV-2 Infection

Andreas Herrmann, Junki Maruyama et al.

6,469 downloads (posted 30 Jun 2020) microbiology

Vaccination efficacy is enhanced by targeting the antigen-presenting cell compartment. Here, we show that S1-Fc antigen delivery targeting the FcgammaR+ antigen-presenting cell compartment elicits anti-SARS-CoV-2 S1-antigen specific IgG production in vivo exerting biologically functional and protective activity against live virus infection, assessed in a stringent experimental virus challenge assay in vitro. The S1-domain of the SARS-CoV-2 spike protein was genetically fused to a human immunoglobulin Fc moiety, which co...

https://rxivist.org/papers/89431
https://doi.org/10.1101/2020.06.29.178616

9: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants

Yiska Weisblum, Fabian Schmidt et al.

6,445 downloads (posted 22 Jul 2020) microbiology

Neutralizing antibodies elicited by prior infection or vaccination are likely to be key for future protection of individuals and populations against SARS-CoV-2. Moreover, passively administered antibodies are among the most promising therapeutic and prophylactic anti-SARS-CoV-2 agents. However, the degree to which SARS-CoV-2 will adapt to evade neutralizing antibodies is unclear. Using a recombinant chimeric VSV/SARS-CoV-2 reporter virus, we show that functional SARS-CoV-2 S protein variants with mutations in the recept...

https://rxivist.org/papers/91976
https://doi.org/10.1101/2020.07.21.214759

10: Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans

Kevin W Ng, Nikhil Faulkner et al.

5,867 downloads (posted 15 May 2020) immunology

Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections. 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. 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 SAR...

https://rxivist.org/papers/83614
https://doi.org/10.1101/2020.05.14.095414

11: Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses

Willianne Hoepel, Hung-Jen Chen et al.

5,415 downloads (posted 13 Jul 2020) immunology

For yet unknown reasons, severely ill COVID-19 patients often become critically ill around the time of activation of adaptive immunity. Here, we show that anti-Spike IgG from serum of severely ill COVID-19 patients induces a hyper-inflammatory response by human macrophages, which subsequently breaks pulmonary endothelial barrier integrity and induces microvascular thrombosis. The excessive inflammatory capacity of this anti-Spike IgG is related to glycosylation changes in the IgG Fc tail. Moreover, the hyper-inflammator...

https://rxivist.org/papers/90909
https://doi.org/10.1101/2020.07.13.190140

12: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice

Jing-Hui Tian, Nita Patel et al.

4,758 downloads (posted 30 Jun 2020) microbiology

The COVID-19 pandemic continues to spread throughout the world with an urgent need for a safe and protective vaccine to effectuate herd immunity to control the spread of SARS-CoV-2. Here, we report the development of a SARS-CoV-2 subunit vaccine (NVX-CoV2373) produced from the full-length spike (S) protein, stabilized in the prefusion conformation. Purified NVX-CoV2373 S form 27.2nm nanoparticles that are thermostable and bind with high affinity to the human angiotensin-converting enzyme 2 (hACE2) receptor. In mice and ...

https://rxivist.org/papers/89426
https://doi.org/10.1101/2020.06.29.178509

13: Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Atreyee Basu, Tatyana Zinger et al.

4,426 downloads (posted 12 May 2020) microbiology

The recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xper...

https://rxivist.org/papers/83167
https://doi.org/10.1101/2020.05.11.089896

14: Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals

Nina Le Bert, Anthony T Tan et al.

4,170 downloads (posted 27 May 2020) immunology

Memory T cells induced by previous infections can influence the course of new viral infections. Little is known about the pattern of SARS-CoV-2 specific pre-existing memory T cells in human. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of ORF1) regions of SARS-CoV-2 in convalescent from COVID-19 (n=24). In all of them we demonstrated the presence of CD4 and CD8 T cells recognizing multiple regions of the NP protein. We then show that SARS-recovered ...

https://rxivist.org/papers/85055
https://doi.org/10.1101/2020.05.26.115832

15: A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

David E Gordon, Gwendolyn M. Jang et al.

4,060 downloads (posted 22 Mar 2020) systems biology

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption[1][1],[2][2]. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 vi...

https://rxivist.org/papers/77469
https://doi.org/10.1101/2020.03.22.002386

16: Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

Peng Zhou, Xing-Lou Yang et al.

3,976 downloads (posted 23 Jan 2020) microbiology

Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laborat...

https://rxivist.org/papers/71702
https://doi.org/10.1101/2020.01.22.914952

17: SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness

Kizzmekia S. Corbett, Darin Edwards et al.

3,699 downloads (posted 11 Jun 2020) immunology

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 antibod...

https://rxivist.org/papers/86991
https://doi.org/10.1101/2020.06.11.145920

18: Origin and cross-species transmission of bat coronaviruses in China

Alice Latinne, Ben Hu et al.

3,316 downloads (posted 31 May 2020) evolutionary biology

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and ...

https://rxivist.org/papers/85678
https://doi.org/10.1101/2020.05.31.116061

19: Severe acute respiratory syndrome-related coronavirus – The species and its viruses, a statement of the Coronavirus Study Group

Alexander E. Gorbalenya, Susan C. Baker et al.

3,119 downloads (posted 11 Feb 2020) microbiology

The present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylog...

https://rxivist.org/papers/73529
https://doi.org/10.1101/2020.02.07.937862

20: Molecular architecture of the SARS-CoV-2 virus

Hangping Yao, Yutong Song et al.

3,012 downloads (posted 09 Jul 2020) microbiology

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins and the complexes of the spike (S) proteins with the cellular receptor ACE2 or neutralizing antibodies, detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). Native str...

https://rxivist.org/papers/90460
https://doi.org/10.1101/2020.07.08.192104