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Life
Special Issues
Ecology, Evolution and Epidemiology of Coronaviruses
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Ecology, Evolution and Epidemiology of Coronaviruses

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Epidemiology".

Deadline for manuscript submissions: closed (20 September 2021) | Viewed by 109332

Special Issue Editors

Dr. Theodoros Rampias

E-Mail Website
Guest Editor
Biomedical Research Foundation of the Academy of Athens (BRFAA), 11741 Athens, Greece
Interests: mechanisms promoting genome integrity; epigenetic regulation; gene expression; translation
Special Issues, Collections and Topics in MDPI journals
Dr. Apostolos Beloukas

E-Mail Website1 Website2
Guest Editor
Department of Biomedical Sciences, University of West Attica, 12243 Egaleo, Greece
Interests: viruses; molecular epidemiology; viral infections; viruses' evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Pavlos Pavlidis

E-Mail Website
Guest Editor
Computational BioMedicine Laboratory (CBML) at the Institute of Computer Science (ICS), FORTH, 70013 Crete, Greece
Interests: genome evolution; evolution of gene regulatory networks; population genetics

Special Issue Information

Dear Colleagues,

Coronaviruses (CoVs) are a class of genetic diverse viruses found in a wide range of host species. CoVs have gained a lot of attention worldwide as in the last two decades, the world has experienced three major outbreaks due to them. Many CoVs infect humans (human Coronoviruses, hCoVs), birds and other mammals, affecting the liver, intestines, as well as the neural and respiratory system. In January 2020, the World Health Organization (WHO) declared the coronavirus disease 2019 (Covid-19) outbreak by a new human coronavirus (named SARS-CoV-2) as a public health emergency of international concern.

The main goal of this special issue is to provide an integrative view of the current state of knowledge about the evolution, the ecology and the epidemiology for this group of RNA viruses. In particular, contributions that provide novel findings in the areas of genomic and transcriptome characterization, sequence variation and evolutionary events, phylogenetic and/or phylogeographic analysis, viral dispersal, cross-species transmission, recombination events, molecular interactions with host cell, immune response, population genetics, outbreaks and ecological adaptations are of great interest. Reviews that highlight the new findings in the above areas will also be welcome.

Dr. Theodoros Rampias
Dr. Apostolos Beloukas
Dr. Pavlos Pavlidis
Guest Editors


Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genomic and transcriptome analysis
  • Sequence variation
  • Phylogenetic and/or phylogeographic analysis
  • Cross species transmission
  • Molecular interactions with host cell
  • Immune response
  • Population genetics
  • Outbreaks
  • Ecological adaptations

Published Papers (18 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 472 KiB  
Editorial
Biological and Clinical Significance of Adaptive Evolution of Coronaviruses
by Apostolos Beloukas and Theodoros Rampias
Life 2021, 11(11), 1129; https://0-doi-org.brum.beds.ac.uk/10.3390/life11111129 - 23 Oct 2021
Cited by 2 | Viewed by 2104
Abstract
RNA viral genomes are generally small genomes that rarely exceed 10 kb in size [...] Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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Research

Jump to: Editorial, Review, Other

19 pages, 32478 KiB  
Article
COVID-19 and Antimicrobial Resistance: Data from the Greek Electronic System for the Surveillance of Antimicrobial Resistance—WHONET-Greece (January 2018–March 2021)
by Michalis Polemis, Georgia Mandilara, Olga Pappa, Athina Argyropoulou, Efstathia Perivolioti, Nikolaos Koudoumnakis, Spyros Pournaras, Alexandra Vasilakopoulou, Sophia Vourli, Helen Katsifa, Theodoros Karampatakis, Anastasia Papavasiliou, Efthymia Petinaki, Stylianos Xitsas, Lemonia Skoura, Efthymia Protonotariou, Paraskevi Mantzana, Konstantina Gartzonika, Efthalia Priavali, Amalia Kallinteri, Panagiota Giannopoulou, Nikoletta Charalampaki, Meletis Memezas, Zervaki Calina Oana, Marina Papadogianni, Maria Panopoulou, Athanasia Koutsidou, Alkiviadis Vatopoulos and Kyriaki Tryfinopoulouadd Show full author list remove Hide full author list
Life 2021, 11(10), 996; https://0-doi-org.brum.beds.ac.uk/10.3390/life11100996 - 22 Sep 2021
Cited by 31 | Viewed by 4236
Abstract
Changes in hospitals’ daily practice due to COVID-19 pandemic may have an impact on antimicrobial resistance (AMR). We aimed to assess this possible impact as captured by the Greek Electronic System for the Surveillance of Antimicrobial Resistance (WHONET-Greece). Routine susceptibility data of 17,837 [...] Read more.
Changes in hospitals’ daily practice due to COVID-19 pandemic may have an impact on antimicrobial resistance (AMR). We aimed to assess this possible impact as captured by the Greek Electronic System for the Surveillance of Antimicrobial Resistance (WHONET-Greece). Routine susceptibility data of 17,837 Gram-negative and Gram-positive bacterial isolates from blood and respiratory specimens of hospitalized patients in nine COVID-19 tertiary hospitals were used in order to identify potential differences in AMR trends in the last three years, divided into two periods, January 2018–March 2020 and April 2020–March 2021. Interrupted time-series analysis was used to evaluate differences in the trends of non-susceptibility before and after the changes due to COVID-19. We found significant differences in the slope of non-susceptibility trends of Acinetobacter baumannii blood and respiratory isolates to amikacin, tigecycline and colistin; of Klebsiella pneumoniae blood and respiratory isolates to meropenem and tigecycline; and of Pseudomonas aeruginosa respiratory isolates to imipenem, meropenem and levofloxacin. Additionally, we found significant differences in the slope of non-susceptibility trends of Staphylococcus aureus isolates to oxacillin and of Enterococcus faecium isolates to glycopeptides. Assessing in this early stage, through surveillance of routine laboratory data, the way a new global threat like COVID-19 could affect an already ongoing pandemic like AMR provides useful information for prompt action. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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11 pages, 2674 KiB  
Article
Update on the Phylodynamics of SADS-CoV
by Fabio Scarpa, Daria Sanna, Ilenia Azzena, Piero Cossu, Marta Giovanetti, Domenico Benvenuto, Elisabetta Coradduzza, Ivailo Alexiev, Marco Casu, Pier Luigi Fiori and Massimo Ciccozzi
Life 2021, 11(8), 820; https://0-doi-org.brum.beds.ac.uk/10.3390/life11080820 - 11 Aug 2021
Cited by 14 | Viewed by 2819
Abstract
Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, [...] Read more.
Coronaviruses are known to be harmful and heterogeneous viruses, able to infect a large number of hosts. Among them, SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alphacoronavirus), or SeA-CoV (Swine Enteric Alphacoronavirus), is the most recent Alphacoronavirus discovered, and caused several outbreaks reported in Chinese swine herds between late 2016 and 2019. We performed an upgraded phylodinamic reconstruction of SADS-CoV based on all whole genomes available on 21 June 2021. Results showed a very close relationship between SADS-CoV and HKU2-like CoV, which may represent the evolutionary intermediate step towards the present SADS-CoV. The direct progenitor of SADS-CoV is so far unknown and, although it is well known that horseshoe bats are reservoirs for Rhinolophus bat coronavirus HKU2-like (HKU2-like CoVs), the transmission path from bats to pigs is still unclear. The discrepancies in the phylogenetic position of rodent CoV, when different molecular markers were considered, corroborate the recombination hypothesis, suggesting that wild rats, which are frequent in farms, may have played a key role. The failure of the attempt at molecular dating, due to the lack of a clock signal, also corroborates the occurrence of a recombination event hypothesis. Zoonotic infections originating in wildlife can easily become a significant threat for human health. In such a context, due to the high recombination and cross-species capabilities of Coronavirus, SADS-CoV represents a possible high-risk pathogen for humans which needs a constant molecular monitoring. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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9 pages, 1673 KiB  
Article
Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation
by Evangelia Georgia Kostaki, Ioulia Tseti, Sotirios Tsiodras, George N. Pavlakis, Petros P. Sfikakis and Dimitrios Paraskevis
Life 2021, 11(5), 375; https://0-doi-org.brum.beds.ac.uk/10.3390/life11050375 - 22 Apr 2021
Cited by 10 | Viewed by 2369
Abstract
Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and [...] Read more.
Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and vaccination sera. To test this hypothesis, we examined the proportion of VOC over time across different geographic areas where the two VOC, B.1.1.7 and B.1.351, co-circulate. Our comparative analysis was based on the number of SARS-CoV-2 sequences on GISAID database. We report that B.1.1.7 dominates over B.1.351 in geographic areas where both variants co-circulate and the B.1.1.7 was the first variant introduced in the population. The only areas where B.1.351 was detected at higher proportion were South Africa and Mayotte in Africa, where this strain was associated with increased community transmission before the detection of B.1.1.7. The dominance of B.1.1.7 over B.1.351 could be important since B.1.351 was more resistant to certain mAbs, as well as heterologous convalescent and vaccination sera, thus suggesting that it may be transmitted more effectively in people with pre-existing immunity to other VOC. This scenario would lessen the effectiveness of vaccine and urge the need to update them with new strains. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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16 pages, 2510 KiB  
Article
SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave
by Maria Bousali, Aristea Dimadi, Evangelia-Georgia Kostaki, Sotirios Tsiodras, Georgios K. Nikolopoulos, Dionyssios N. Sgouras, Gkikas Magiorkinis, George Papatheodoridis, Vasiliki Pogka, Giota Lourida, Aikaterini Argyraki, Emmanouil Angelakis, George Sourvinos, Apostolos Beloukas, Dimitrios Paraskevis and Timokratis Karamitros
Life 2021, 11(3), 219; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030219 - 09 Mar 2021
Cited by 7 | Viewed by 2948
Abstract
Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight [...] Read more.
Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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19 pages, 1969 KiB  
Article
Population Genomics Insights into the First Wave of COVID-19
by Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas and Pavlos Pavlidis
Life 2021, 11(2), 129; https://0-doi-org.brum.beds.ac.uk/10.3390/life11020129 - 07 Feb 2021
Cited by 14 | Viewed by 3176
Abstract
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the [...] Read more.
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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32 pages, 4814 KiB  
Article
Outcomes Evaluated in Controlled Clinical Trials on the Management of COVID-19: A Methodological Systematic Review
by Alexander G. Mathioudakis, Markus Fally, Rola Hashad, Ahmed Kouta, Ali Sina Hadi, Sean Blandin Knight, Nawar Diar Bakerly, Dave Singh, Paula R. Williamson, Tim Felton and Jørgen Vestbo
Life 2020, 10(12), 350; https://0-doi-org.brum.beds.ac.uk/10.3390/life10120350 - 15 Dec 2020
Cited by 12 | Viewed by 3926
Abstract
It is crucial that randomized controlled trials (RCTs) on the management of coronavirus disease 2019 (COVID-19) evaluate the outcomes that are critical to patients and clinicians, to facilitate relevance, interpretability, and comparability. This methodological systematic review describes the outcomes evaluated in 415 RCTs [...] Read more.
It is crucial that randomized controlled trials (RCTs) on the management of coronavirus disease 2019 (COVID-19) evaluate the outcomes that are critical to patients and clinicians, to facilitate relevance, interpretability, and comparability. This methodological systematic review describes the outcomes evaluated in 415 RCTs on the management of COVID-19, that were registered with ClinicalTrials.gov, by 5 May 2020, and the instruments used to measure these outcomes. Significant heterogeneity was observed in the selection of outcomes and instruments. Mortality, adverse events and treatment success or failure are only evaluated in 64.4%, 48.4% and 43% of the included studies, respectively, while other outcomes are selected less often. Studies focusing on more severe presentations (hospitalized patients or requiring intensive care) most frequently evaluate mortality (72.5%) and adverse events (55.6%), while hospital admission (50.8%) and viral detection/load (55.6%) are most frequently assessed in the community setting. Outcome measurement instruments are poorly reported and heterogeneous. Follow-up does not exceed one month in 64.3% of these earlier trials, and long-term COVID-19 burden is rarely assessed. The methodological issues identified could delay the introduction of potentially life-saving treatments in clinical practice. Our findings demonstrate the need for greater consistency, to enable decision makers to compare and contrast studies. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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8 pages, 224 KiB  
Communication
Seroprevalence of Antibodies against SARS-CoV-2 among the Personnel and Students of the National and Kapodistrian University of Athens, Greece: A Preliminary Report
by Ourania E. Tsitsilonis, Dimitrios Paraskevis, Evi Lianidou, Vassilios Pierros, Athanasios Akalestos, Efstathios Kastritis, Paraskevi Moutsatsou, Andreas Scorilas, Thomas Sphicopoulos, Evangelos Terpos, Nikolaos Thomaidis, Athanassios Tsakris, Nikolaos Voulgaris, Christina C. Daskalaki, Zoi Evangelakou, Christina Fouki, Despoina D. Gianniou, Sentiljana Gumeni, Evangelia-Georgia Kostaki, Ioannis V. Kostopoulos, Maria S. Manola, Nikolaos Orologas-Stavrou, Chrysanthi Panteli, Eleni-Dimitra Papanagnou, Pantelis Rousakis, Aimilia D. Sklirou, Stavroula Smilkou, Dimitra Stergiopoulou, Ioannis P. Trougakos, Soritios Tsiodras, Petros P. Sfikakis and Meletios-Athanasios Dimopoulosadd Show full author list remove Hide full author list
Life 2020, 10(9), 214; https://0-doi-org.brum.beds.ac.uk/10.3390/life10090214 - 21 Sep 2020
Cited by 25 | Viewed by 4672
Abstract
Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. The National and Kapodistrian University of Athens (ΝΚUA), especially its health-care/medical personnel, has been actively involved in the first line of [...] Read more.
Due to early implementation of public health measures, Greece had low number of SARS-CoV-2 infections and COVID-19 severe incidents in hospitalized patients. The National and Kapodistrian University of Athens (ΝΚUA), especially its health-care/medical personnel, has been actively involved in the first line of state responses to COVID-19. To estimate the prevalence of antibodies (Igs) against SARS-CoV-2 among NKUA members, we designed a five consecutive monthly serosurvey among randomly selected NKUA consenting volunteers. Here, we present the results from the first 2500 plasma samples collected during June–July 2020. Twenty-five donors were tested positive for anti-SARS-CoV-2 Igs; thus, the overall seroprevalence was 1.00%. The weighted overall seroprevalence was 0.93% (95% CI: 0.27, 2.09) and varied between males [1.05% (95% CI: 0.18, 2.92)] and females [0.84% (95% CI: 0.13, 2.49)], age-groups and different categories (higher in participants from the School of Health Sciences and in scientific affiliates/faculty members/laboratory assistants), but no statistical differences were detected. Although focused on the specific population of NKUA members, our study shows that the prevalence of anti-SARS-CoV-2 Igs for the period June–July 2020 remained low and provides knowledge of public health importance for the NKUA members. Given that approximately one in three infections was asymptomatic, continuous monitoring of the progression of the pandemic by assessing Ig seroprevalence is needed. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
13 pages, 2102 KiB  
Article
Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic
by Marius Surleac, Leontina Banica, Corina Casangiu, Marius Cotic, Dragos Florea, Oana Sandulescu, Petre Milu, Anca Streinu-Cercel, Ovidiu Vlaicu, Dimitrios Paraskevis, Simona Paraschiv and Dan Otelea
Life 2020, 10(8), 152; https://0-doi-org.brum.beds.ac.uk/10.3390/life10080152 - 14 Aug 2020
Cited by 9 | Viewed by 5549
Abstract
BACKGROUND: The spread of SARS-CoV-2 generated an unprecedented global public health crisis. Soon after Asia, Europe was seriously affected. Many countries, including Romania, adopted lockdown measures to limit the outbreak. AIM: We performed a molecular epidemiology analysis of SARS-CoV-2 viral strains circulating in [...] Read more.
BACKGROUND: The spread of SARS-CoV-2 generated an unprecedented global public health crisis. Soon after Asia, Europe was seriously affected. Many countries, including Romania, adopted lockdown measures to limit the outbreak. AIM: We performed a molecular epidemiology analysis of SARS-CoV-2 viral strains circulating in Romania during the first two months of the epidemic in order to detect mutation profiles and phylogenetic relatedness. METHODS: Respiratory samples were directly used for shotgun sequencing. RESULTS: All Romanian sequences belonged to lineage B, with a different subtype distribution between northern and southern regions (subtype B.1.5 and B.1.1). Phylogenetic analysis suggested that the Romanian epidemic started with multiple introduction events from other European countries followed by local transmission. Phylogenetic links between northern Romania and Spain, Austria, Scotland and Russia were observed, as well as between southern Romania and Switzerland, Italy, France and Turkey. One viral strain presented a previously unreported mutation in the Nsp2 gene, namely K489E. Epidemiologically-defined clusters displayed specific mutations, suggesting molecular signatures for strains coming from areas that were isolated during the lockdown. CONCLUSIONS: Romanian epidemic was initiated by multiple introductions from European countries followed by local transmissions. Different subtype distribution between northern and southern Romania was observed after two months of the pandemic. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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Review

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21 pages, 401 KiB  
Review
What Happens to the Immune System after Vaccination or Recovery from COVID-19?
by Bruna T. Tiyo, Gabriela J. H. Schmitz, Marina M. Ortega, Laís T. da Silva, Alexandre de Almeida, Telma M. Oshiro and Alberto J. da S. Duarte
Life 2021, 11(11), 1152; https://0-doi-org.brum.beds.ac.uk/10.3390/life11111152 - 29 Oct 2021
Cited by 9 | Viewed by 5062
Abstract
Due to its leading role in fighting infections, the human immune system has been the focus of many studies in the context of Coronavirus disease 2019 (COVID-19). In a worldwide effort, the scientific community has transitioned from reporting about the effects of the [...] Read more.
Due to its leading role in fighting infections, the human immune system has been the focus of many studies in the context of Coronavirus disease 2019 (COVID-19). In a worldwide effort, the scientific community has transitioned from reporting about the effects of the novel coronavirus on the human body in the early days of the pandemic to exploring the body’s many immunopathological and immunoprotecting properties that have improved disease treatment and enabled the development of vaccines. The aim of this review is to explain what happens to the immune system after recovery from COVID-19 and/or vaccination against SARS-CoV-2, the virus that causes the disease. We detail the way in which the immune system responds to a SARS-CoV-2 infection, including innate and adaptive measures. Then, we describe the role of vaccination, the main types of COVID-19 vaccines and how they protect us. Further, we explain the reason why immunity after COVID-19 infection plus a vaccination appears to induce a stronger response compared with virus exposure alone. Additionally, this review reports some correlates of protection from SARS-CoV-2 infection. In conclusion, we reinforce that vaccination is safe and important in achieving herd immunity. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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17 pages, 1875 KiB  
Review
The Role of Coronavirus RNA-Processing Enzymes in Innate Immune Evasion
by Georgia Mandilara, Marianna A. Koutsi, Marios Agelopoulos, Georgios Sourvinos, Apostolos Beloukas and Theodoros Rampias
Life 2021, 11(6), 571; https://0-doi-org.brum.beds.ac.uk/10.3390/life11060571 - 17 Jun 2021
Cited by 10 | Viewed by 3260
Abstract
Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic [...] Read more.
Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic RNA and sub-genomic RNAs. These include Nsp15 and Nsp16, whose respective roles in RNA capping and dsRNA degradation play a crucial role in coronavirus escape from immune surveillance. Evolutionary studies on coronaviruses demonstrate that genome expansion in Nidoviruses was promoted by the emergence of Nsp14-ExoN activity and led to the acquisition of Nsp15- and Nsp16-RNA-processing activities. In this review, we discuss the main RNA-sensing mechanisms in humans as well as recent structural, functional, and evolutionary insights into coronavirus Nsp15 and Nsp16 with a view to potential antiviral strategies. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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14 pages, 290 KiB  
Review
Screening, Diagnostic and Prognostic Tests for COVID-19: A Comprehensive Review
by Mariana Ulinici, Serghei Covantev, James Wingfield-Digby, Apostolos Beloukas, Alexander G. Mathioudakis and Alexandru Corlateanu
Life 2021, 11(6), 561; https://0-doi-org.brum.beds.ac.uk/10.3390/life11060561 - 14 Jun 2021
Cited by 17 | Viewed by 6828
Abstract
While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of-care antigen testing, despite being less sensitive compared to molecular assays, [...] Read more.
While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of-care antigen testing, despite being less sensitive compared to molecular assays, might be preferable for wider screening initiatives. Simple laboratory, imaging and clinical parameters could facilitate prognostication and triage. This comprehensive review summarises current evidence on the diagnostic, screening and prognostic tests for COVID-19. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
21 pages, 1097 KiB  
Review
Animal Coronaviruses Induced Apoptosis
by Katerina Gioti, Christine Kottaridi, Chrysa Voyiatzaki, Dimitrios Chaniotis, Theodoros Rampias and Apostolos Beloukas
Life 2021, 11(3), 185; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030185 - 26 Feb 2021
Cited by 9 | Viewed by 3084
Abstract
Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the adaptive immune response. [...] Read more.
Apoptosis is a form of programmed death that has also been observed in cells infected by several viruses. It is considered one of the most critical innate immune mechanisms that limits pathogen proliferation and propagation before the initiation of the adaptive immune response. Recent studies investigating the cellular responses to SARS-CoV and SARS-CoV-2 infection have revealed that coronaviruses can alter cellular homeostasis and promote cell death, providing evidence that the modulation of apoptotic pathways is important for viral replication and propagation. Despite the genetic diversity among different coronavirus clades and the infection of different cell types and several hosts, research studies in animal coronaviruses indicate that apoptosis in host cells is induced by common molecular mechanisms and apoptotic pathways. We summarize and critically review current knowledge on the molecular aspects of cell-death regulation during animal coronaviruses infection and the viral–host interactions to this process. Future research is expected to lead to a better understanding of the regulation of cell death during coronavirus infection. Moreover, investigating the role of viral proteins in this process will help us to identify novel antiviral targets related to apoptotic signaling pathways. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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27 pages, 1856 KiB  
Review
How Do Inflammatory Mediators, Immune Response and Air Pollution Contribute to COVID-19 Disease Severity? A Lesson to Learn
by Cinzia Signorini, Patrizia Pignatti and Teresa Coccini
Life 2021, 11(3), 182; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030182 - 25 Feb 2021
Cited by 13 | Viewed by 3500
Abstract
Inflammatory and immune processes are defensive mechanisms that aim to remove harmful agents. As a response to infections, inflammation and immune response contribute to the pathophysiological mechanisms of diseases. Coronavirus disease 2019 (COVID-19), whose underlying mechanisms remain not fully elucidated, has posed new [...] Read more.
Inflammatory and immune processes are defensive mechanisms that aim to remove harmful agents. As a response to infections, inflammation and immune response contribute to the pathophysiological mechanisms of diseases. Coronavirus disease 2019 (COVID-19), whose underlying mechanisms remain not fully elucidated, has posed new challenges for the knowledge of pathophysiology. Chiefly, the inflammatory process and immune response appear to be unique features of COVID-19 that result in developing a hyper-inflammatory syndrome, and air pollution, the world’s largest health risk factor, may partly explain the behaviour and fate of COVID-19. Understanding the mechanisms involved in the progression of COVID-19 is of fundamental importance in order to avoid the late stage of the disease, associated with a poor prognosis. Here, the role of the inflammatory and immune mediators in COVID-19 pathophysiology is discussed. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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16 pages, 1354 KiB  
Review
Post-Infectious Guillain–Barré Syndrome Related to SARS-CoV-2 Infection: A Systematic Review
by Pasquale Sansone, Luca Gregorio Giaccari, Caterina Aurilio, Francesco Coppolino, Valentina Esposito, Marco Fiore, Antonella Paladini, Maria Beatrice Passavanti, Vincenzo Pota and Maria Caterina Pace
Life 2021, 11(2), 167; https://0-doi-org.brum.beds.ac.uk/10.3390/life11020167 - 21 Feb 2021
Cited by 27 | Viewed by 3641
Abstract
Background. Guillain-Barré syndrome (GBS) is the most common cause of flaccid paralysis, with about 100,000 people developing the disorder every year worldwide. Recently, the incidence of GBS has increased during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemics. We reviewed the literature to [...] Read more.
Background. Guillain-Barré syndrome (GBS) is the most common cause of flaccid paralysis, with about 100,000 people developing the disorder every year worldwide. Recently, the incidence of GBS has increased during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemics. We reviewed the literature to give a comprehensive overview of the demographic characteristics, clinical features, diagnostic investigations, and outcome of SARS-CoV-2-related GBS patients. Methods. Embase, MEDLINE, Google Scholar, and Cochrane Central Trials Register were systematically searched on 24 September 2020 for studies reporting on GBS secondary to COVID-19. Results. We identified 63 articles; we included 32 studies in our review. A total of 41 GBS cases with a confirmed or probable COVID-19 infection were reported: 26 of them were single case reports and 6 case series. Published studies on SARS-CoV-2-related GBS typically report a classic sensorimotor type of GBS often with a demyelinating electrophysiological subtype. Miller Fisher syndrome was reported in a quarter of the cases. In 78.1% of the cases, the response to immunomodulating therapy is favourable. The disease course is frequently severe and about one-third of the patients with SARS-CoV-2-associated GBS requires mechanical ventilation and Intensive Care Unit (ICU) admission. Rarely the outcome is poor or even fatal (10.8% of the cases). Conclusion. Clinical presentation, course, response to treatment, and outcome are similar in SARS-CoV-2-associated GBS and GBS due to other triggers. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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17 pages, 641 KiB  
Review
Animal Coronaviruses and SARS-COV-2 in Animals, What Do We Actually Know?
by Paolo Bonilauri and Gianluca Rugna
Life 2021, 11(2), 123; https://0-doi-org.brum.beds.ac.uk/10.3390/life11020123 - 05 Feb 2021
Cited by 25 | Viewed by 4905
Abstract
Coronaviruses (CoVs) are a well-known group of viruses in veterinary medicine. We currently know four genera of Coronavirus, alfa, beta, gamma, and delta. Wild, farmed, and pet animals are infected with CoVs belonging to all four genera. Seven human respiratory coronaviruses have still [...] Read more.
Coronaviruses (CoVs) are a well-known group of viruses in veterinary medicine. We currently know four genera of Coronavirus, alfa, beta, gamma, and delta. Wild, farmed, and pet animals are infected with CoVs belonging to all four genera. Seven human respiratory coronaviruses have still been identified, four of which cause upper-respiratory-tract diseases, specifically, the common cold, and the last three that have emerged cause severe acute respiratory syndromes, SARS-CoV-1, MERS-CoV, and SARS-CoV-2. In this review we briefly describe animal coronaviruses and what we actually know about SARS-CoV-2 infection in farm and domestic animals. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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17 pages, 609 KiB  
Review
A Focus on the Nowadays Potential Antiviral Strategies in Early Phase of Coronavirus Disease 2019 (Covid-19): A Narrative Review
by Caterina Monari, Valeria Gentile, Clarissa Camaioni, Giulia Marino, Nicola Coppola and Vanvitelli COVID-19 group
Life 2020, 10(8), 146; https://0-doi-org.brum.beds.ac.uk/10.3390/life10080146 - 09 Aug 2020
Cited by 6 | Viewed by 3159
Abstract
Background: The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the related disease (COVID-19) has rapidly spread to a pandemic proportion, increasing the demands on health systems for the containment and management of COVID-19. Nowadays, one of the [...] Read more.
Background: The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the related disease (COVID-19) has rapidly spread to a pandemic proportion, increasing the demands on health systems for the containment and management of COVID-19. Nowadays, one of the critical issues still to be pointed out regards COVID-19 treatment regimens and timing: which drug, in which phase, for how long? Methods: Our narrative review, developed using MEDLINE and EMBASE, summarizes the main evidences in favor or against the current proposed treatment regimens for COVID-19, with a particular focus on antiviral agents. Results: Although many agents have been proposed as possible treatment, to date, any of the potential drugs against SARS-CoV-2 has shown to be safe and effective for treating COVID-19. Despite the lack of definitive evidence, remdesivir remains the only antiviral with encouraging effects in hospitalized patients with COVID-19. Conclusions: In such a complex moment of global health emergency, it is hard to demand scientific evidence. Nevertheless, randomized clinical trials aiming to identify effective and safe drugs against SARS-CoV-2 infection are urgently needed in order to confirm or reject the currently available evidence. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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13 pages, 1735 KiB  
Brief Report
Self-Reported Real-World Safety and Reactogenicity of COVID-19 Vaccines: A Vaccine Recipient Survey
by Alexander G. Mathioudakis, Murad Ghrew, Andrew Ustianowski, Shazaad Ahmad, Ray Borrow, Lida Pieretta Papavasileiou, Dimitrios Petrakis and Nawar Diar Bakerly
Life 2021, 11(3), 249; https://0-doi-org.brum.beds.ac.uk/10.3390/life11030249 - 17 Mar 2021
Cited by 82 | Viewed by 41147
Abstract
An online survey was conducted to compare the safety, tolerability and reactogenicity of available COVID-19 vaccines in different recipient groups. This survey was launched in February 2021 and ran for 11 days. Recipients of a first COVID-19 vaccine dose ≥7 days prior to [...] Read more.
An online survey was conducted to compare the safety, tolerability and reactogenicity of available COVID-19 vaccines in different recipient groups. This survey was launched in February 2021 and ran for 11 days. Recipients of a first COVID-19 vaccine dose ≥7 days prior to survey completion were eligible. The incidence and severity of vaccination side effects were assessed. The survey was completed by 2002 respondents of whom 26.6% had a prior COVID-19 infection. A prior COVID-19 infection was associated with an increased risk of any side effect (risk ratio 1.08, 95% confidence intervals (1.05–1.11)), fever (2.24 (1.86–2.70)), breathlessness (2.05 (1.28–3.29)), flu-like illness (1.78 (1.51–2.10)), fatigue (1.34 (1.20–1.49)) and local reactions (1.10 (1.06–1.15)). It was also associated with an increased risk of severe side effects leading to hospital care (1.56 (1.14–2.12)). While mRNA vaccines were associated with a higher incidence of any side effect (1.06 (1.01–1.11)) compared with viral vector-based vaccines, these were generally milder (p < 0.001), mostly local reactions. Importantly, mRNA vaccine recipients reported a considerably lower incidence of systemic reactions (RR < 0.6) including anaphylaxis, swelling, flu-like illness, breathlessness and fatigue and of side effects requiring hospital care (0.42 (0.31–0.58)). Our study confirms the findings of recent randomised controlled trials (RCTs) demonstrating that COVID-19 vaccines are generally safe with limited severe side effects. For the first time, our study links prior COVID-19 illness with an increased incidence of vaccination side effects and demonstrates that mRNA vaccines cause milder, less frequent systemic side effects but more local reactions. Full article
(This article belongs to the Special Issue Ecology, Evolution and Epidemiology of Coronaviruses)
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