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Currently indexing 83,779 bioRxiv papers from 360,790 authors.

Most downloaded bioRxiv papers, since beginning of last month

Results 1 through 20 out of 81854

 

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

Bette T. Korber, WM Fischer et al.

184,499 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 in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; after beginning to spread in Europe in early February, when introduced to new regions it repeatedly and rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions. ### Competing Interest Statement The authors have declared no competing interest.

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

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

Prashant Pradhan, Ashutosh Kumar Pandey et al.

118,910 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This paper has been withdrawn by its authors.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

3: Reversing age: dual species measurement of epigenetic age with a single clock

Steve Horvath, Kavita Singh et al.

89,768 downloads (posted 08 May 2020) developmental biology

Young blood plasma is known to confer beneficial effects on various organs in mice. However, it was not known whether young plasma rejuvenates cells and tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly-accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=593 tissue samples. As indicated by their respective names, the rat pan-tissue clock ...

https://rxivist.org/papers/82741
https://doi.org/10.1101/2020.05.07.082917

4: Susceptibility of ferrets, cats, dogs, and different domestic animals to SARS-coronavirus-2

Jianzhong Shi, Zhiyuan Wen et al.

88,144 downloads (posted 31 Mar 2020) microbiology

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the infectious disease COVID-19, which was first reported in Wuhan, China in December, 2019. Despite the tremendous efforts to control the disease, COVID-19 has now spread to over 100 countries and caused a global pandemic. SARS-CoV-2 is thought to have originated in bats; however, the intermediate animal sources of the virus are completely unknown. Here, we investigated the susceptibility of ferrets and animals in close contact with humans to SARS-CoV-...

https://rxivist.org/papers/78358
https://doi.org/10.1101/2020.03.30.015347

5: Rapid development of an inactivated vaccine for SARS-CoV-2

Qiang Gao, Linlin Bao et al.

74,587 downloads (posted 19 Apr 2020) microbiology

The COVID-19 caused by SARS-CoV-2 has brought about an unprecedented crisis, taking a heavy toll on human health, lives as well as the global economy. There are no SARS-CoV-2-specific treatments or vaccines available due to the novelty of this virus. Hence, rapid development of effective vaccines against SARS-CoV-2 is urgently needed. Here we developed a pilot-scale production of a purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc), which induced SARS-CoV-2-specific neutralizing antibodies in mice, rats ...

https://rxivist.org/papers/80174
https://doi.org/10.1101/2020.04.17.046375

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

David E Gordon, Gwendolyn M. Jang et al.

60,255 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

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

Fabiana Gámbaro, Sylvie Behillil et al.

32,211 downloads (posted 24 Apr 2020) genomics

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 introducti...

https://rxivist.org/papers/81032
https://doi.org/10.1101/2020.04.24.059576

8: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity

Yong Jia, Gangxu Shen et al.

29,776 downloads (posted 11 Apr 2020) evolutionary biology

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...

https://rxivist.org/papers/79548
https://doi.org/10.1101/2020.04.09.034942

9: Lack of Reinfection in Rhesus Macaques Infected with SARS-CoV-2

Linlin Bao, Wei Deng et al.

27,249 downloads (posted 14 Mar 2020) microbiology

A global pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is ongoing spread. It remains unclear whether the convalescing patients have a risk of reinfection. Rhesus macaques were rechallenged with SARS-CoV-2 during an early recovery phase from initial infection characterized by weight loss, interstitial pneumonia and systemic viral dissemination mainly in respiratory and gastrointestinal tracts. The monkeys rechallenged with the identical SARS-CoV-2 strain h...

https://rxivist.org/papers/76736
https://doi.org/10.1101/2020.03.13.990226

10: Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2

Brandi N. Williamson, Friederike Feldmann et al.

21,080 downloads (posted 15 Apr 2020) microbiology

Background: Effective therapeutics to treat COVID-19 are urgently needed. Remdesivir is a nucleotide prodrug with in vitro and in vivo efficacy against coronaviruses. Here, we tested the efficacy of remdesivir treatment in a rhesus macaque model of SARS-CoV-2 infection. Methods: To evaluate the effect of remdesivir treatment on SARS-CoV-2 disease outcome, we used the recently established rhesus macaque model of SARS-CoV-2 infection that results in transient lower respiratory tract disease. Two groups of six rhesus macaq...

https://rxivist.org/papers/80014
https://doi.org/10.1101/2020.04.15.043166

11: 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.

20,137 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

12: 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.

19,760 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

13: Evaluation of heating and chemical protocols for inactivating SARS-CoV-2

Boris Pastorino, Franck Touret et al.

19,391 downloads (posted 11 Apr 2020) microbiology

Clinical samples collected in COVID-19 patients are commonly manipulated in BSL-2 laboratories for diagnostic purpose. We used the French norm NF-EN-14476+A2 derived from the European standard EN-14885. To avoid the risk of exposure of laboratory workers, we showed that Triton-X100 must be added to guanidinium thiocyanate-lysis buffers to obtain a 6-log reduction of infectious virus. Although heating protocol consisting of 92C-15min was more effective rather than 56C-30min and 60C-60min to achieve 6-log reduction, it is...

https://rxivist.org/papers/79629
https://doi.org/10.1101/2020.04.11.036855

14: SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation

Qiang Zhang, Huajun Zhang et al.

17,347 downloads (posted 03 Apr 2020) microbiology

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, and rapidly spread worldwide. Previous studies suggested cat could be a potential susceptible animal of SARS-CoV-2. Here, we investigated the infection of SARS-CoV-2 in cats by detecting specific serum antibodies. A cohort of serum samples were collected from cats in Wuhan, including 102 sampled after COVID-19 outbreak, and 39 prior to the outbreak. 15 of 102 (14.7%) cat sera col...

https://rxivist.org/papers/78641
https://doi.org/10.1101/2020.04.01.021196

15: Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak

Yuan Liu, Zhi Ning et al.

17,012 downloads (posted 10 Mar 2020) microbiology

Background: The ongoing outbreak of COVID-19 has spread rapidly and sparked global concern. While the transmission of SARS-CoV-2 through human respiratory droplets and contact with infected persons is clear, the aerosol transmission of SARS-CoV-2 has been little studied. Methods: Thirty-five aerosol samples of three different types (total suspended particle, size segregated and deposition aerosol) were collected in Patient Areas (PAA) and Medical Staff Areas (MSA) of Renmin Hospital of Wuhan University (Renmin) and Wuch...

https://rxivist.org/papers/76328
https://doi.org/10.1101/2020.03.08.982637

16: SARS-CoV-2 invades host cells via a novel route: CD147-spike protein

Ke Wang, Wei Chen et al.

16,140 downloads (posted 14 Mar 2020) microbiology

Currently, COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world; nevertheless, so far there exist no specific antiviral drugs for treatment of the disease, which poses great challenge to control and contain the virus. Here, we reported a research finding that SARS-CoV-2 invaded host cells via a novel route of CD147-spike protein (SP). SP bound to CD147, a receptor on the host cells, thereby mediating the viral invasion. Our further research confirmed thi...

https://rxivist.org/papers/76744
https://doi.org/10.1101/2020.03.14.988345

17: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

David Brann, Tatsuya Tsukahara et al.

14,964 downloads (posted 27 Mar 2020) neuroscience

Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing revealed that mouse, non-human primate and human olfactory...

https://rxivist.org/papers/77996
https://doi.org/10.1101/2020.03.25.009084

18: A human monoclonal 1 antibody blocking SARS-CoV-2 infection

Chunyan Wang, Wentao Li et al.

14,273 downloads (posted 12 Mar 2020) microbiology

The emergence of the novel human coronavirus SARS-CoV-2 in Wuhan, China has caused a worldwide epidemic of respiratory disease (COVID-19). Vaccines and targeted therapeutics for treatment of this disease are currently lacking. Here we report a human monoclonal antibody that neutralizes SARS-CoV-2 (and SARS-CoV). This cross-neutralizing antibody targets a communal epitope on these viruses and offers potential for prevention and treatment of COVID-19.

https://rxivist.org/papers/76533
https://doi.org/10.1101/2020.03.11.987958

19: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Christoph Muus, Malte D. Luecken et al.

14,124 downloads (posted 20 Apr 2020) bioinformatics

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 10...

https://rxivist.org/papers/80570
https://doi.org/10.1101/2020.04.19.049254

20: Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals

Davide F. Robbiani, Christian Gaebler et al.

13,364 downloads (posted 15 May 2020) immunology

During the COVID-19 pandemic, SARS-CoV-2 infected millions of people and claimed hundreds of thousands of lives. Virus entry into cells depends on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S). Although there is no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-2. Here we report on 149 COVID-19 convalescent individuals. Plasmas collected an average of 39 days after the onset of symptoms had variable ha...

https://rxivist.org/papers/83646
https://doi.org/10.1101/2020.05.13.092619