Infectious Diseases

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F1000Research facilitates the rapid and transparent sharing of research by providing fast, open publication alongside access to any underlying data, software code and resources. All research articles are reviewed post publication, with expert peer review reports freely available.

F1000Research is particularly suited to fast-paced areas of research such as infectious diseases research and epidemiology, where immediate access to robust and rigorous science is essential for informing clinical and public health responses in real time.

Research on any aspect of epidemiology or infectious disease outbreaks is welcome including but not limited to:

  • Epidemiological modelling
  • Disease transmission
  • Pathogen genetics and genomics
  • Antimicrobial resistance
  • Immune defense mechanisms
  • Guidelines on protective equipment
  • Clinical case reports
  • In silico, in vitro and in vivo candidate therapeutics studies

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Introducing the Emerging Diseases and Outbreaks Gateway

 The Emerging Diseases and Outbreaks Gateway brings together all content published on F1000Research related to global disease outbreaks, making the information about localised outbreaks, epidemics or pandemics rapidly and openly accessible for others to consult and use.

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Featured articles

Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China

Robert L. Kruse

A novel coronavirus (2019-nCoV) originating in Wuhan, China presents a potential respiratory viral pandemic to the world population. Current efforts are focused on containment and quarantine of infected individuals. Ultimately, the outbreak could be controlled with a protective vaccine to prevent 2019-nCoV infection. While vaccine research should be pursued intensely, there exists today no therapy to treat 2019-nCoV upon infection, despite an urgent need to find options to help these patients and preclude potential death. Herein, I review the potential options to treat 2019-nCoV in patients, with an emphasis on the necessity for speed and timeliness in developing new and effective therapies in this outbreak. I consider the options of drug repurposing, developing neutralizing monoclonal antibody therapy, and an oligonucleotide strategy targeting the viral RNA genome, emphasizing the promise and pitfalls of these approaches. Finally, I advocate for the fastest strategy to develop a treatment now, which could be resistant to any mutations the virus may have in the future. The proposal is a biologic that blocks 2019-nCoV entry using a soluble version of the viral receptor, angiotensin-converting enzyme 2 (ACE2), fused to an immunoglobulin Fc domain (ACE2-Fc), providing a neutralizing antibody with maximal breath to avoid any viral escape, while also helping to recruit the immune system to build lasting immunity. The ACE2-Fc therapy would also supplement decreased ACE2 levels in the lungs during infection, thereby directly treating acute respiratory distress pathophysiology as a third mechanism of action. The sequence of the ACE2-Fc protein is provided to investigators, allowing its possible use in recombinant protein expression systems to start producing drug today to treat patients under compassionate use, while formal clinical trials are later undertaken. Such a treatment could help infected patients before a protective vaccine is developed and widely available in the coming months to year(s).

A review of open source ventilators for COVID-19 and future pandemics

Joshua M. Pearce

Coronavirus Disease 2019 (COVID-19) threatens to overwhelm our medical infrastructure at the regional level causing spikes in mortality rates because of shortages of critical equipment, like ventilators. Fortunately, with the recent development and widespread deployment of small-scale manufacturing technologies like RepRap-class 3-D printers and open source microcontrollers, mass distributed manufacturing of ventilators has the potential to overcome medical supply shortages. In this study, after providing a background on ventilators, the academic literature is reviewed to find the existing and already openly-published, vetted designs for ventilators systems



Epidemic curves made easy using the R package incidence

Zhian N. Kamvar, Jun Cai, Juliet R.C. Pulliam, Jakob Schumacher, Thibaut Jombart

The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling.

Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CLpro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates

Yu Wai Chen, Chin-Pang Bennu Yiu, Kwok-Yin Wong

We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CLpro) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CLpro molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.


Ending the neglect: Introducing the Neglected Tropical Disease Collection

The Neglected Tropical Diseases Collection brings together all content published on F1000Research related to neglected tropical diseases. We welcome all outputs from basic microbiological research, to clinical studies, public health policy and research into the impact of these diseases on the populations affected.
F1000Research’s open transparent publishing model along with our open data policy will ensure the Collection presents open, transparently reported and reusable findings and data that can contribute towards the WHO goal of a 90% reduction in individuals requiring interventions for NTDs by 2030.

Browse the Collection Read the blog article about this topic

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