The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 (Preprint)

2020 ◽  
Author(s):  
Alan T Evangelista
Keyword(s):  
Hospital Admissions ◽  
Disease Incidence ◽  
Influenza Viruses ◽  
Seasonal Effects ◽  
Human Coronavirus ◽  
Enveloped Virus ◽  
Multiplex Pcr Assay ◽  
Contact Transmission ◽  
Human Coronaviruses

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

scholarly journals The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2

2020 ◽  
Author(s):  
Alan T Evangelista
Keyword(s):  
Hospital Admissions ◽  
Disease Incidence ◽  
Influenza Viruses ◽  
Seasonal Effects ◽  
Human Coronavirus ◽  
Enveloped Virus ◽  
Multiplex Pcr Assay ◽  
Contact Transmission ◽  
Human Coronaviruses

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.

scholarly journals Potential role of cellular miRNAs in coronavirus-host interplay

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9994 ◽  
Author(s):  
Stepan Nersisyan ◽  
Narek Engibaryan ◽  
Aleksandra Gorbonos ◽  
Ksenia Kirdey ◽  
Alexey Makhonin ◽  
...  
Keyword(s):  
Computational Prediction ◽  
Bioinformatic Analysis ◽  
Sequencing Data ◽  
Human Coronavirus ◽  
Cellular Mirnas ◽  
Mirna Sequencing ◽  
Direct Binding ◽  
Human Coronaviruses ◽  
Mouse Lungs

Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV.

scholarly journals The potential role of miR-21-3p in coronavirus-host interplay

2020 ◽  
Author(s):  
Stepan Nersisyan ◽  
Narek Engibaryan ◽  
Aleksandra Gorbonos ◽  
Ksenia Kirdey ◽  
Alexey Makhonin ◽  
...  
Keyword(s):  
Potential Role ◽  
Computational Prediction ◽  
Bioinformatic Analysis ◽  
Sequencing Data ◽  
Human Coronavirus ◽  
Mirna Sequencing ◽  
Direct Binding ◽  
Human Coronaviruses ◽  
Mouse Lungs

ABSTRACTHost miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses by several possible mechanisms including direct binding the viral RNA. Identification of human miRNAs involved in coronavirus-host interplay is becoming important due to the ongoing COVID-19 pandemic. In this work we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. In order to uncover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV. Further bioinformatic analysis of binding sites revealed high conservativity of miR-21-3p binding regions within RNAs of human coronaviruses and their strains.

scholarly journals Pulmonary embolism during the COVID-19 pandemic

2021 ◽  
Vol 28 (Supplement_1) ◽  
Author(s):  
BV Silva ◽  
T Rodrigues ◽  
N Cunha ◽  
J Brito ◽  
P Alves Da Silva ◽  
...  
Keyword(s):  
Physical Activity ◽  
Pulmonary Embolism ◽  
Hospital Admissions ◽  
Reference Group ◽  
Group Versus ◽  
Pulmonary Angiography ◽  
Reference Period ◽  
Funding Sources ◽  
Clinical Probability

Abstract Funding Acknowledgements Type of funding sources: None. Background During the COVID-19 pandemic many countries have imposed lockdown restrictions to movement. Since the 18th of March in Portugal, thousands of people have been confined to their homes. While hospital admissions for COVID-19 patients increased exponentially, admissions for non-COVID-19 patients decreased dramatically. However, it remains unclear whether lockdown-related immobility can contribute to the increased incidence of pulmonary embolism. Purpose To compare the incidence of pulmonary embolism (PE) during the lockdown period (Abril 1 to May 31, 2020) compared to the reference period in 2019. Methods Retrospective study of consecutive outpatients who presented to the emergency department and underwent computed tomography pulmonary angiography (CTPA) due to suspicion of PE. Results Compared to the same period of 2019, the lockdown period was associated with a significant increase in PE diagnosis (29 versus 18 patients). PE patients during lockdown were older (median age 71 years; interquartile range [IQR][60-85] versus 59 years [44-76]; p = 0.046) and have lower prevalence of active cancer (14% versus 33% in the reference period). Women represent 55% (n = 16) of patients in lockdown group (versus 50% in 2019 group). Clinical probability (GENEVA score) was similar in both groups (median score 2.72 in lockdown group and 2.50 in reference group, p = 0.452). None of the patients with PE was diagnosed with COVID-19. Conclusion We have observed a marked increase (62%) in PE diagnosis during lockdown period compared to the reference period, which can be explained by the reduction in physical activity due to teleworking and closure of gyms and sports activities. These data reinforce the importance of promoting physical activity programs at home. The role of pharmacological or mechanical thromboprophylaxis in this scenario remains unclear.

scholarly journals Biosurveillance of Selected Pathogens with Zoonotic Potential in a Zoo

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 428
Author(s):  
Pavel Kvapil ◽  
Joško Račnik ◽  
Marjan Kastelic ◽  
Jiřina Marková ◽  
Jean-Benjamin Murat ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Neospora Caninum ◽  
Field Mouse ◽  
Wild Rodents ◽  
Cygnus Olor ◽  
Multiplex Pcr Assay ◽  
Significant Difference ◽  
Zoo Animals ◽  
Mute Swans

Monitoring of infectious diseases is one of the most important pillars of preventive medicine in zoos. Screening for parasitic and bacterial infections is important to keep animals and equipment safe from pathogens that may pose a risk to animal and human health. Zoos usually contain many different animal species living in proximity with people and wild animals. As an epidemiological probe, 188 animals (122 mammals, 65 birds, and one reptile) from a zoo in Slovenia were examined for selected pathogens. Antibodies to Toxoplasma gondii and Neospora caninum were detected by ELISA in 38% (46/122) and 3% (4/122) of mammals, and in 0% (0/64) and 2% (1/57) of birds, respectively; the reptile (0/1) was negative. A statistically significant difference in T. gondii prevalence was found in Carnivora compared to Cetartiodactyla and primate antibodies to Encephalitozoon cuniculi were detected by IFAT in 44% (52/118) of mammals and 20% (11/56) of birds, respectively; the reptile (0/1) was negative. Herbivores had a higher chance of being infected with E. cuniculi compared to omnivores. Antibodies to Chlamydia abortus and Coxiella burnetii were not detected in any of the 74 tested zoo animals. The sera of 39 wild rodents found in the zoo were also examined; they were negative for all three parasites. The parasite T. gondii was detected by PCR in the tissue of two mute swans (Cygnus olor), three eastern house mice (Mus musculus), one yellow-necked field mouse (Apodemus flavicollis), and one striped field mouse (A. agrarius). Positive samples were genotyped by a single multiplex PCR assay using 15 microsatellite markers; one sample from a mute swan was characterized as type II. This micro-epidemiological study offers a better understanding of pathogens in zoo animals and an understanding of the role of zoos in biosurveillance.

scholarly journals Sialic Acids as Receptors for Pathogens

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 831
Author(s):  
Patrycja Burzyńska ◽  
Łukasz F. Sobala ◽  
Krzysztof Mikołajczyk ◽  
Marlena Jodłowska ◽  
Ewa Jaśkiewicz
Keyword(s):  
Malaria Parasite ◽  
Sialic Acids ◽  
Influenza Viruses ◽  
Disease Vectors ◽  
Animal Disease ◽  
Parasite Plasmodium ◽  
Parasite Plasmodium Falciparum ◽  
Infection Biology ◽  
Species Specific

Carbohydrates have long been known to mediate intracellular interactions, whether within one organism or between different organisms. Sialic acids (Sias) are carbohydrates that usually occupy the terminal positions in longer carbohydrate chains, which makes them common recognition targets mediating these interactions. In this review, we summarize the knowledge about animal disease-causing agents such as viruses, bacteria and protozoa (including the malaria parasite Plasmodium falciparum) in which Sias play a role in infection biology. While Sias may promote binding of, e.g., influenza viruses and SV40, they act as decoys for betacoronaviruses. The presence of two common forms of Sias, Neu5Ac and Neu5Gc, is species-specific, and in humans, the enzyme converting Neu5Ac to Neu5Gc (CMAH, CMP-Neu5Ac hydroxylase) is lost, most likely due to adaptation to pathogen regimes; we discuss the research about the influence of malaria on this trait. In addition, we present data suggesting the CMAH gene was probably present in the ancestor of animals, shedding light on its glycobiology. We predict that a better understanding of the role of Sias in disease vectors would lead to more effective clinical interventions.

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

BMC Biology ◽  
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).

scholarly journals COVID-19 Shuts Doors to Flu but Keeps Them Open to Rhinoviruses

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 733
Author(s):  
Irina Kiseleva ◽  
Andrey Ksenafontov
Keyword(s):  
Influenza Pandemic ◽  
Age Groups ◽  
Influenza Viruses ◽  
Interferon Response ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Mild Disease ◽  
Viral Interference ◽  
The Common

It is well known that rhinoviruses are distributed across the globe and are the most common cause of the common cold in all age groups. Rhinoviruses are widely considered to be harmless because they are generally perceived as respiratory viruses only capable of causing mild disease. However, they may also infect the lower respiratory tract, inducing chronic obstructive pulmonary disease and exacerbations of asthma, bronchiolitis, etc. The role of rhinoviruses in pathogenesis and the epidemiological process is underestimated, and they need to be intensively studied. In the light of recent data, it is now known that rhinoviruses could be one of the key epidemiological barriers that may influence the spread of influenza and novel coronaviruses. It has been reported that endemic human rhinoviruses delayed the development of the H1N1pdm09 influenza pandemic through viral interference. Moreover, human rhinoviruses have been suggested to block SARS-CoV-2 replication in the airways by triggering an interferon response. In this review, we summarized the main biological characteristics of genetically distinct viruses such as rhinoviruses, influenza viruses, and SARS-CoV-2 in an attempt to illuminate their main discrepancies and similarities. We hope that this comparative analysis will help us to better understand in which direction research in this area should move.

scholarly journals Natural and Nature-Derived Products Targeting Human Coronaviruses

Molecules ◽  
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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