Genomic annotation of Human Coronavirus strains: A Review

UNSTRUCTURED The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. Patients admitted to a pediatric hospital with worsening respiratory symptoms were tested using a multiplex PCR assay from nasopharyngeal swabs. The additive seasonal effects of outdoor temperatures and indoor relative humidity (RH) were evaluated. The 8-year average peak activity of human coronaviruses occurred in the first week of January, when droplet and contact transmission was enabled by the low indoor RH of 20-30%. Previous studies have shown that an increase in RH to 50% has been associated with markedly reduced viability and transmission of influenza virus and animal coronaviruses. As disease incidence was reduced by 50% in early March, to 75% in early April, to greater than 99% at the end of April, a relationship was observed from colder temperatures in January with a low indoor RH to a gradual increase in outdoor temperatures in April with an indoor RH of 45-50%. As a lipid-bound, enveloped virus with similar size characteristics to endemic human coronaviruses, SARS-CoV-2 should be subject to the same dynamics of reduced viability and transmission with increased humidity. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. INTERNATIONAL REGISTERED REPORT RR2-doi.org/10.1101/2020.05.15.20103416

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Virus-Negative Myopericarditis in Human Coronavirus Infection

Circulation Heart Failure ◽

10.1161/circheartfailure.120.007636 ◽

2020 ◽

Vol 13 (11) ◽

Author(s):

Franca del Nonno ◽

Andrea Frustaci ◽

Romina Verardo ◽

Cristina Chimenti ◽

Emanuele Nicastri ◽

...

Keyword(s):

Human Coronavirus ◽

Coronavirus Infection

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Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review

Environmental Chemistry Letters ◽

10.1007/s10311-020-01151-1 ◽

2021 ◽

Vol 19 (2) ◽

pp. 769-785 ◽

Cited By ~ 1

Author(s):

Erwan Sallard ◽

José Halloy ◽

Didier Casane ◽

Etienne Decroly ◽

Jacques van Helden

Keyword(s):

Sequence Analysis ◽

Structure Function ◽

Molecular Mechanisms ◽

Laboratory Strain ◽

Domestic Animals ◽

Scientific Policy ◽

Human Coronavirus ◽

Viral Dissemination ◽

Link Type ◽

Intensive Breeding

AbstractSARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure–function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin—natural or synthetic—of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).

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A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

BMC Biology ◽

10.1186/s12915-020-00940-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Andra Waagmeester ◽

Egon L. Willighagen ◽

Andrew I. Su ◽

Martina Kutmon ◽

Jose Emilio Labra Gayo ◽

...

Keyword(s):

Common Ground ◽

Knowledge Bases ◽

Public Knowledge ◽

Medical Problems ◽

Human Coronavirus ◽

Data Schema ◽

Helping Others ◽

Human Coronaviruses ◽

The Right ◽

Human Coronavirus 229E

Abstract Background Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons.” Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. Results As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Conclusions Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

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Natural and Nature-Derived Products Targeting Human Coronaviruses

Molecules ◽

10.3390/molecules26020448 ◽

2021 ◽

Vol 26 (2) ◽

pp. 448

Author(s):

Konstantina Vougogiannopoulou ◽

Angela Corona ◽

Enzo Tramontano ◽

Michael N. Alexis ◽

Alexios-Leandros Skaltsounis

Keyword(s):

Natural Products ◽

Antiviral Agents ◽

Critical Perspective ◽

Human Coronavirus ◽

State Of Emergency ◽

Pharmacological Agents ◽

Pure Compounds ◽

Total Plant ◽

Human Coronaviruses ◽

The 1960S

The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.

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Examining the persistence of human Coronavirus 229E on fresh produce

Food Microbiology ◽

10.1016/j.fm.2021.103780 ◽

2021 ◽

pp. 103780

Author(s):

Madeleine Blondin-Brosseau ◽

Jennifer Harlow ◽

Tanushka Doctor ◽

Neda Nasheri

Keyword(s):

Fresh Produce ◽

Human Coronavirus ◽

Human Coronavirus 229E

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