Urban Intelligence for Pandemic Response: Viewpoint

UNSTRUCTURED Previous epidemic management research proves the importance of city-level information, but also highlights limited expertise in urban data applications during a pandemic outbreak. In this paper, we provide an overview of city-level information, in combination with analytical and operational capacity, that define urban intelligence for supporting response to disease outbreaks. We present five components (movement, facilities, people, information, and engagement) that have been previously investigated but remain siloed to successfully orchestrate an integrated pandemic response. Reflecting on the coronavirus disease (COVID-19) outbreak that was first identified in Wuhan, China, we discuss the opportunities, technical challenges, and foreseeable controversies for deploying urban intelligence during a pandemic. Finally, we emphasize the urgency of building urban intelligence through cross-disciplinary research and collaborative practice on a global scale.

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‘All In’: A Pragmatic Framework for COVID-19 Testing and Action on a Global Scale

10.31219/osf.io/b2xmp ◽

2020 ◽

Author(s):

Syril D Pettit ◽

Keith Jerome ◽

David Rouquie ◽

Susan Hester ◽

Leah Wehmas ◽

...

Keyword(s):

Public Health ◽

Disease Outbreaks ◽

Global Scale ◽

Material Resource ◽

Public Health Decision ◽

The Public ◽

Health Decision Making ◽

Clinical Community ◽

Health Decision ◽

Broad Consensus

Current demand for SARS-CoV-2 testing is straining material resource and labor capacity around the globe. As a result, the public health and clinical community are hindered in their ability to monitor and contain the spread of COVID-19. Despite broad consensus that more testing is needed, pragmatic guidance towards realizing this objective has been limited. This paper addresses this limitation by proposing a novel and geographically agnostic framework (‘the 4Ps Framework) to guide multidisciplinary, scalable, resource-efficient, and achievable efforts towards enhanced testing capacity. The 4Ps (Prioritize, Propagate, Partition, and Provide) are described in terms of specific opportunities to enhance the volume, diversity, characterization, and implementation of SARS-CoV-2 testing to benefit public health. Coordinated deployment of the strategic and tactical recommendations described in this framework have the potential to rapidly expand available testing capacity, improve public health decision-making in response to the COVID-19 pandemic, and/or to be applied in future emergent disease outbreaks.

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Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2

10.26434/chemrxiv.12622667 ◽

2020 ◽

Author(s):

Parth Chaturvedi ◽

Yanxiao Han ◽

Petr Kral ◽

Lela Vukovic

Keyword(s):

Adaptive Evolution ◽

Disease Outbreaks ◽

Global Scale ◽

Peptide Inhibitors ◽

Free Energies ◽

Angiotensin Converting Enzyme 2 ◽

Binding Domains ◽

Protein Receptor ◽

Dynamics Simulations ◽

Computational Strategy

The SARS-CoV-2 virus is currently causing a worldwide pandemic with dramatic societal consequences for the humankind. In the last decades, disease outbreaks due to such zoonotic pathogens have appeared with an accelerated rate, which calls for an urgent development of adaptive (smart) therapeutics. Here, we develop a computational strategy to adaptively evolve peptides that could selectively inhibit mutating S protein receptor binding domains (RBDs) of different SARS-CoV-2 viral strains from binding to their human host receptor, angiotensin-converting enzyme 2 (ACE2). Starting from suitable peptide templates, based on selected ACE2 segments (natural RBD binder), we gradually modify the templates by random mutations, while retaining those mutations that maximize their RBD-binding free energies. In this adaptive evolution, atomistic molecular dynamics simulations of the template-RBD complexes are iteratively perturbed by the peptide mutations, which are retained under favorable Monte Carlo decisions. The computational search will provide libraries of optimized therapeutics capable of reducing the SARS-CoV-2 infection on a global scale.

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Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2

10.26434/chemrxiv.12622667.v1 ◽

2020 ◽

Author(s):

Lela Vukovic ◽

Yanxiao Han ◽

Parth Chaturvedi ◽

Petr Kral

Keyword(s):

Adaptive Evolution ◽

Disease Outbreaks ◽

Global Scale ◽

Peptide Inhibitors ◽

Free Energies ◽

Angiotensin Converting Enzyme 2 ◽

Binding Domains ◽

Protein Receptor ◽

Dynamics Simulations ◽

Computational Strategy

The SARS-CoV-2 virus is currently causing a worldwide pandemic with dramatic societal consequences for the humankind. In the last decades, disease outbreaks due to such zoonotic pathogens have appeared with an accelerated rate, which calls for an urgent development of adaptive (smart) therapeutics. Here, we develop a computational strategy to adaptively evolve peptides that could selectively inhibit mutating S protein receptor binding domains (RBDs) of different SARS-CoV-2 viral strains from binding to their human host receptor, angiotensin-converting enzyme 2 (ACE2). Starting from suitable peptide templates, based on selected ACE2 segments (natural RBD binder), we gradually modify the templates by random mutations, while retaining those mutations that maximize their RBD-binding free energies. In this adaptive evolution, atomistic molecular dynamics simulations of the template-RBD complexes are iteratively perturbed by the peptide mutations, which are retained under favorable Monte Carlo decisions. The computational search will provide libraries of optimized therapeutics capable of reducing the SARS-CoV-2 infection on a global scale.

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Molecular Epidemiology of Oyster-Related Human Noroviruses and Their Global Genetic Diversity and Temporal-Geographical Distribution from 1983 to 2014

Applied and Environmental Microbiology ◽

10.1128/aem.01729-15 ◽

2015 ◽

Vol 81 (21) ◽

pp. 7615-7624 ◽

Cited By ~ 32

Author(s):

Yongxin Yu ◽

Hui Cai ◽

Linghao Hu ◽

Rongwei Lei ◽

Yingjie Pan ◽

...

Keyword(s):

Genetic Diversity ◽

Quality Control ◽

Molecular Epidemiology ◽

Geographical Distribution ◽

Acute Gastroenteritis ◽

Phylogenetic Analyses ◽

Disease Outbreaks ◽

Temporal Distribution ◽

Global Scale ◽

Sporadic Cases

ABSTRACTNoroviruses (NoVs) are a leading cause of epidemic and sporadic cases of acute gastroenteritis worldwide. Oysters are well recognized as the main vectors of environmentally transmitted NoVs, and disease outbreaks linked to oyster consumption have been commonly observed. Here, to quantify the genetic diversity, temporal distribution, and circulation of oyster-related NoVs on a global scale, 1,077 oyster-related NoV sequences deposited from 1983 to 2014 were downloaded from both NCBI GenBank and the NoroNet outbreak database and were then screened for quality control. A total of 665 sequences with reliable information were obtained and were subsequently subjected to genotyping and phylogenetic analyses. The results indicated that the majority of oyster-related NoV sequences were obtained from coastal countries and regions and that the numbers of sequences in these regions were unevenly distributed. Moreover, >80% of human NoV genotypes were detected in oyster samples or oyster-related outbreaks. A higher proportion of genogroup I (GI) (34%) was observed for oyster-related sequences than for non-oyster-related outbreaks, where GII strains dominated with an overwhelming majority of >90%, indicating that the prevalences of GI and GII are different in humans and oysters. In addition, a related convergence of the circulation trend was found between oyster-related NoV sequences and human pandemic outbreaks. This suggests that oysters not only act as a vector of NoV through environmental transmission but also serve as an important reservoir of human NoVs. These results highlight the importance of oysters in the persistence and transmission of human NoVs in the environment and have important implications for the surveillance of human NoVs in oyster samples.

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The Laegeren Site: An Augmented Forest Laboratory

Remote Sensing of Plant Biodiversity ◽

10.1007/978-3-030-33157-3_4 ◽

2020 ◽

pp. 83-104

Author(s):

Felix Morsdorf ◽

Fabian D. Schneider ◽

Carla Gullien ◽

Daniel Kükenbrink ◽

Reik Leiterer ◽

...

Keyword(s):

Remote Sensing ◽

Laser Scanning ◽

Regional Scale ◽

Imaging Spectroscopy ◽

Remote Sensing Data ◽

Global Scale ◽

Essential Biodiversity Variables ◽

Level Information ◽

Leaf Level ◽

Airborne Imaging

AbstractGiven the increased pressure on forests and their diversity in the context of global change, new ways of monitoring diversity are needed. Remote sensing has the potential to inform essential biodiversity variables on the global scale, but validation of data and products, particularly in remote areas, is difficult. We show how radiative transfer (RT) models, parameterized with a detailed 3-D forest reconstruction based on laser scanning, can be used to upscale leaf-level information to canopy scale. The simulation approach is compared with actual remote sensing data, showing very good agreement in both the spectral and spatial domains. In addition, we compute a set of physiological and morphological traits from airborne imaging spectroscopy and laser scanning data and show how these traits can be used to estimate the functional richness of a forest at regional scale. The presented RT modeling framework has the potential to prototype and validate future spaceborne observation concepts aimed at informing variables of biodiversity, while the trait-based mapping of diversity could augment in situ networks of diversity, providing effective spatiotemporal gap filling for a comprehensive assessment of changes to diversity.

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SARS-CoV2, A Threat to Marine Mammals? A Study From Italian Seawaters

10.21203/rs.3.rs-378165/v1 ◽

2021 ◽

Author(s):

Tania Audino ◽

Carla Grattarola ◽

Cinzia Centelleghe° ◽

Simone Peletto ◽

Federica Giorda ◽

...

Keyword(s):

Marine Mammal ◽

Marine Mammals ◽

Disease Outbreaks ◽

Population Data ◽

Global Scale ◽

Extreme Weather Events ◽

Health Economy ◽

Wastewater Management ◽

Potential Hazard ◽

Cetacean Species

Abstract Zoonotically transmitted coronaviruses were responsible for three disease outbreaks since 2002, with the “Severe Acute Respiratory Syndrome Coronavirus-2” (SARS-CoV-2) causing the dramatic “Coronavirus Disease-2019” (CoViD-19) pandemic, which affected public health, economy, and society on a global scale. The impacts of the SARS-CoV-2 pandemic permeate into our environment and wildlife as well; in particular, concern has been raised about the viral occurrence and persistence in aquatic and marine ecosystems. The discharge of untreated wastewaters carrying infectious SARS-CoV-2 into natural water systems that are home of sea mammals may have dramatic consequences on vulnerable species. The efficient transmission of coronaviruses raises questions regarding the contributions of virus-receptors interactions. The main receptor of SARS-CoV-2 is Angiotensin Converting Enzyme-2 (ACE-2), serving as a functional receptor for the viral spike (S) protein. This study was aimed, through the comparative analysis of the ACE-2 receptor with the human one, at assessing the susceptibility to SARS-CoV-2 of the different species of marine mammals living in Italian waters. We also determined, by means of immunohistochemistry, ACE-2 receptor localization in the lung tissue from different cetacean species, in order to provide a preliminary characterization of ACE-.2 expression in the marine mammals’ respiratory tract. Furthermore, in order to evaluate if and how wastewater management in Italy may lead to susceptible marine mammal populations being exposed to the virus, geo-mapping data of wastewater plants, associated to the identification of specific stretches of coast more exposed to extreme weather events, overlapped to marine mammal population data, were carried out. Results showed the SARS-CoV-2 exposure for marine mammals inhabiting Italian coastal waters. Thus, we highlight the potential hazard of reverse zoonotic transmission of SARS-CoV-2 infection, along with its impact on marine mammals regularly inhabiting the Mediterranean Sea, whilst also stressing the need of appropriate action to prevent further damage to specific vulnerable populations.

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Social media: A new tool for outbreak surveillance

Antimicrobial Stewardship & Healthcare Epidemiology ◽

10.1017/ash.2021.225 ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Averi E. Wilson ◽

Christoph U. Lehmann ◽

Sameh N. Saleh ◽

John Hanna ◽

Richard J. Medford

Keyword(s):

Social Media ◽

Disease Surveillance ◽

Disease Incidence ◽

Disease Outbreaks ◽

Global Scale ◽

Social Media Platforms ◽

Monitoring And Forecasting ◽

Use Of Social Media ◽

Scale Data ◽

Data Processing Methods

Abstract Social media platforms allow users to share news, ideas, thoughts, and opinions on a global scale. Data processing methods allow researchers to automate the collection and interpretation of social media posts for efficient and valuable disease surveillance. Data derived from social media and internet search trends have been used successfully for monitoring and forecasting disease outbreaks such as Zika, Dengue, MERS, and Ebola viruses. More recently, data derived from social media have been used to monitor and model disease incidence during the coronavirus disease 2019 (COVID-19) pandemic. We discuss the use of social media for disease surveillance.

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The Effects of Blame and Politicization on Responses to Pandemics

Journal of Student Research ◽

10.47611/jsrhs.v10i1.1320 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Jason Ding ◽

Claude Kananack

Keyword(s):

Public Perception ◽

Scientific Evidence ◽

State Legislatures ◽

Global Scale ◽

Hate Crimes ◽

The Other ◽

Direct Response ◽

Historical Trends ◽

Health Response ◽

Pandemic Response

COVID-19 has caused widespread discrimination and blame; however, analyzing history, it becomes apparent that racially motivated blame is common during pandemics. Placed for religious, ethnic, or socioeconomic reasons, blame has caused discrimination and stigma for the “other”. Blaming a specific race without scientific evidence causes discrimination and hate crimes, creating more problems that require attention and resources to resolve and diverting them from the pandemic response. A quick and direct response is vital for minimizing the impacts of pandemics, while blame only distracts and leads to politicizing the disease. This paper finds that unfounded blame throughout history results in delays in the health response, inefficient resource allocation, and the undermining of cooperation. This blame is part of politicizing pandemics, which exacerbates the impacts of the disease by diverting attention away from the health response and disease’s containment. Racist accusations during pandemics against Asians in America since the turn of the 20th century also led to hate crimes and increased discrimination, resulting in discriminatory public perception reflected even through government actions. COVID-19 is reflecting these historical trends. The latest disease to be politicized, the coronavirus has widened the scope of scapegoating beyond blaming Asians. Its politicization is creating further divisions in society and leading to tension on both a global scale with the WHO and domestically with the CDC and state legislatures. Consistent with former diseases, unfounded blame during the coronavirus is a practice that ultimately causes more deaths and needs to end immediately.

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Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2

10.26434/chemrxiv.12622667.v2 ◽

2020 ◽

Author(s):

Parth Chaturvedi ◽

Yanxiao Han ◽

Petr Kral ◽

Lela Vukovic

Keyword(s):

Adaptive Evolution ◽

Disease Outbreaks ◽

Global Scale ◽

Peptide Inhibitors ◽

Free Energies ◽

Angiotensin Converting Enzyme 2 ◽

Binding Domains ◽

Protein Receptor ◽

Dynamics Simulations ◽

Computational Strategy

The SARS-CoV-2 virus is currently causing a worldwide pandemic with dramatic societal consequences for the humankind. In the last decades, disease outbreaks due to such zoonotic pathogens have appeared with an accelerated rate, which calls for an urgent development of adaptive (smart) therapeutics. Here, we develop a computational strategy to adaptively evolve peptides that could selectively inhibit mutating S protein receptor binding domains (RBDs) of different SARS-CoV-2 viral strains from binding to their human host receptor, angiotensin-converting enzyme 2 (ACE2). Starting from suitable peptide templates, based on selected ACE2 segments (natural RBD binder), we gradually modify the templates by random mutations, while retaining those mutations that maximize their RBD-binding free energies. In this adaptive evolution, atomistic molecular dynamics simulations of the template-RBD complexes are iteratively perturbed by the peptide mutations, which are retained under favorable Monte Carlo decisions. The computational search will provide libraries of optimized therapeutics capable of reducing the SARS-CoV-2 infection on a global scale.

Download Full-text