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Editorial

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3 pages, 203 KiB

Open AccessEditorial

Coronavirus Disease 2019 (COVID-19)

by Mohamad Goldust

Biology 2022, 11(8), 1250; https://doi.org/10.3390/biology11081250 - 22 Aug 2022

Cited by 2 | Viewed by 1412

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has affected almost all aspects of daily life [...] Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

Research

Jump to: Editorial, Review, Other

15 pages, 11081 KiB

Open AccessArticle

Targeting the RBD of Omicron Variant (B.1.1.529) with Medicinal Phytocompounds to Abrogate the Binding of Spike Glycoprotein with the hACE2 Using Computational Molecular Search and Simulation Approach

by Abdulrahim R. Hakami

Biology 2022, 11(2), 258; https://doi.org/10.3390/biology11020258 - 7 Feb 2022

Cited by 11 | Viewed by 2949

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to inflict chaos globally. The emergence of a novel Omicron variant (B.1.1.529) in South Africa harbors 30 mutations in the spike protein. The variant is distinguished from other variants of concern (VOCs) with [...] Read more.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to inflict chaos globally. The emergence of a novel Omicron variant (B.1.1.529) in South Africa harbors 30 mutations in the spike protein. The variant is distinguished from other variants of concern (VOCs) with an increased (15) number of mutations in the receptor-binding domain (RBD) and suggests higher chances of causing reinfections. Initial reports also claimed that this variant escapes all the neutralizing antibodies, thus demanding a novel strategy against it. Thus, in this study, we performed a computational molecular screening against the RBD of the Omicron (B.1.1.529) variant and assessed the binding affinity of potent drugs against the RBD. The multi-steps screening of the South African Natural Compounds Database (SANCDB) revealed four medicinal compounds as excellent (potential) anti-viral agents against the Omicron variant, namely SANC00944, SANC01032, SANC00992, and SANC00317. The simulation analysis of these compounds in complex with the RBD demonstrated stable dynamics and structural compactness. Moreover, the residual flexibility analysis revealed that the flexibility of three loops required for interaction with hACE2 has been reduced by the binding of these drugs. The post-simulation validation of these compounds such as binding free energy, in silico bioactivity, and dissociation constant prediction validated the anti-viral potency of these compounds. The total binding free energy (TBFE) for the SANC01032–RBD complex was reported to be −46.54 kcal/mol; for the SANC01032–RBD complex, the TBFE was −41.88 kcal/mol; for the SANC00992–RBD complex the TBFE was −29.05 kcal/mol, while for the SANC00317–RBD complex the TBFE was −31.03 kcal/mol. The results showed the inhibition potential of these compounds by targeting the RBD. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging Omicron variant of SARS-CoV-2. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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13 pages, 1440 KiB

Open AccessArticle

Evaluation of Hepatic Biochemical Parameters during Antiviral Treatment in COVID-19 Patients

by Felicia Marc, Corina Moldovan, Anica Hoza, Patricia Restea, Liliana Sachelarie, Laura Ecaterina Romila, Corina Suteu and Dorina Maria Farcas

Biology 2022, 11(1), 13; https://doi.org/10.3390/biology11010013 - 23 Dec 2021

Cited by 6 | Viewed by 2960

Abstract

(1) Background: The antiviral treatment for COVID-19 disease started to be largely used in 2020 and has been found to be efficient, although it is not specific for SARS-CoV-2 virus. There were some concerns that it may produce liver damage or other side [...] Read more.

(1) Background: The antiviral treatment for COVID-19 disease started to be largely used in 2020 and has been found to be efficient, although it is not specific for SARS-CoV-2 virus. There were some concerns that it may produce liver damage or other side effects. (2) Methods: The aim of this study was to observe if antiviral therapy is affecting liver parameters or producing other side-effects in patients hospitalized for COVID-19 disease. The study included a group of patients hospitalized in the internal medicine department of Oradea Municipal Clinical Hospital, Romania, between August 2020–June 2021, diagnosed with SARS-CoV-2 viral infection by RT-PCR method or rapid antigen test. During hospitalization, patients were treated with a Lopinavir/Ritonavir (Kaletra) combination, or with Favipiravir or Remdesivir. In addition to monitoring the evolution of the disease (clinical and biochemical), also hepatic parameters were analyzed at admission, during hospitalization, and at discharge. (3) Results: In the group of studied patients, the mean value of aspartat aminotrensferase did not increase above normal at discharge, alanin aminotransferase increased, but below twice the normal values, and cholestasis registered a statistically insignificant slight increase. (4) Conclusions: In our study, we found that all three antivirals were generally well tolerated and their use did not alter liver function in a significant manner. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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15 pages, 4236 KiB

Open AccessArticle

Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches

by Ziyad Tariq Muhseen, Salim Kadhim, Yahiya Ibrahim Yahiya, Eid A. Alatawi, Faris F. Aba Alkhayl and Ahmad Almatroudi

Biology 2021, 10(12), 1310; https://doi.org/10.3390/biology10121310 - 10 Dec 2021

Cited by 5 | Viewed by 3254

Abstract

Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein’s receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused [...] Read more.

Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein’s receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2–RBD is affected, we used protein–protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be −122.6 +/− 0.7 kcal/mol, while for B.1.620, the docking score was −124.9 +/− 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of −51.14 kcal/mol, while for B.1.628, the total binding energy was −68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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14 pages, 4114 KiB

Open AccessArticle

A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19

by Andrei Lobiuc, Daniel Șterbuleac, Olga Sturdza, Mihai Dimian and Mihai Covasa

Biology 2021, 10(12), 1276; https://doi.org/10.3390/biology10121276 - 5 Dec 2021

Cited by 9 | Viewed by 3299

Abstract

The ongoing COVID-19 pandemic follows an unpredictable evolution, driven by both host-related factors such as mobility, vaccination status, and comorbidities and by pathogen-related ones. The pathogenicity of its causative agent, SARS-CoV-2 virus, relates to the functions of the proteins synthesized intracellularly, as guided [...] Read more.

The ongoing COVID-19 pandemic follows an unpredictable evolution, driven by both host-related factors such as mobility, vaccination status, and comorbidities and by pathogen-related ones. The pathogenicity of its causative agent, SARS-CoV-2 virus, relates to the functions of the proteins synthesized intracellularly, as guided by viral RNA. These functions are constantly altered through mutations resulting in increased virulence, infectivity, and antibody-evasion abilities. Well-characterized mutations in the spike protein, such as D614G, N439K, Δ69–70, E484K, or N501Y, are currently defining specific variants; however, some less studied mutations outside the spike region, such as p. 3691 in NSP6, p. 9659 in ORF-10, 8782C > T in ORF-1ab, or 28144T > C in ORF-8, have been proposed for altering SARS-CoV-2 virulence and pathogenicity. Therefore, in this study, we focused on A105V mutation of SARS-CoV-2 ORF7a accessory protein, which has been associated with severe COVID-19 clinical manifestation. Molecular dynamics and computational structural analyses revealed that this mutation differentially alters ORF7a dynamics, suggesting a gain-of-function role that may explain its role in the severe form of COVID-19 disease. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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14 pages, 1910 KiB

Open AccessArticle

Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics

by Hendrick Gao-Min Lim, Shih-Hsin Hsiao and Yuan-Chii Gladys Lee

Biology 2021, 10(10), 1023; https://doi.org/10.3390/biology10101023 - 11 Oct 2021

Cited by 4 | Viewed by 2792

Abstract

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently become a novel pandemic event following the swine flu that occurred in 2009, which was caused by the influenza A virus (H1N1 subtype). The accurate identification of the [...] Read more.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently become a novel pandemic event following the swine flu that occurred in 2009, which was caused by the influenza A virus (H1N1 subtype). The accurate identification of the huge number of samples during a pandemic still remains a challenge. In this study, we integrate two technologies, next-generation sequencing and cloud computing, into an optimized workflow version that uses a specific identification algorithm on the designated cloud platform. We use 182 samples (92 for COVID-19 and 90 for swine flu) with short-read sequencing data from two open-access datasets to represent each pandemic and evaluate our workflow performance based on an index specifically created for SARS-CoV-2 or H1N1. Results show that our workflow could differentiate cases between the two pandemics with a higher accuracy depending on the index used, especially when the index that exclusively represented each dataset was used. Our workflow substantially outperforms the original complete identification workflow available on the same platform in terms of time and cost by preserving essential tools internally. Our workflow can serve as a powerful tool for the robust identification of cases and, thus, aid in controlling the current and future pandemics. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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13 pages, 1312 KiB

Open AccessArticle

Effect of Different Types of Face Masks on the Ventilatory and Cardiovascular Response to Maximal-Intensity Exercise

by Miguel A. Rojo-Tirado, José A. Benítez-Muñoz, María Alcocer-Ayuga, Víctor M. Alfaro-Magallanes, Nuria Romero-Parra, Ana B. Peinado, Beatriz Rael, Eliane A. Castro and Pedro J. Benito

Biology 2021, 10(10), 969; https://doi.org/10.3390/biology10100969 - 27 Sep 2021

Cited by 7 | Viewed by 2868

Abstract

The development of new models of face masks makes it necessary to compare their impact on exercise. Therefore, the aim of this work was to compare the cardiopulmonary response to a maximal incremental test, perceived ventilation, exertion, and comfort using FFP2 or Emotion [...] Read more.

The development of new models of face masks makes it necessary to compare their impact on exercise. Therefore, the aim of this work was to compare the cardiopulmonary response to a maximal incremental test, perceived ventilation, exertion, and comfort using FFP2 or Emotion masks in young female athletes. Thirteen healthy sportswomen (22.08 ± 1.75 years) performed a spirometry, and a graded exercise test on a treadmill, with a JAEGER^® Vyntus CPX gas analyzer using an ergospirometry mask (ErgoMask) or wearing the FFP2 or the Emotion mask below the ErgoMask, randomized on 3 consecutive days. Also, menstrual cycle status was monitored to avoid possible intrasubject alterations. The results showed lower values for the ErgoMask+FFP2, compared to ErgoMask or ErgoMask+Emotion, in forced vital capacity (3.8 ± 0.2, 4.5 ± 0.2 and 4.1 ± 0.1 l, respectively); forced expiratory volume in 1 s (3.3 ± 0.2, 3.7 ± 0.2 and 3.5 ± 0.1 l); ventilation (40.9 ± 1.5, 50.6 ± 1.5 and 46.9 ± 1.2 l/min); breathing frequency (32.7 ± 1.1, 37.4 ± 1.1 and 35.3 ± 1.4 bpm); VE/VO₂ (30.5 ± 0.7, 34.6 ± 0.9 and 33.6 ± 0.7); VE/VCO₂ (32.2 ± 0.6, 36.2 ± 0.9 and 34.4 ± 0.7) and time to exhaustion (492.4 ± 9.7, 521.7 ± 8.6 and 520.1 ± 9.5 s) and higher values in inspiratory time (0.99 ± 0.04, 0.82 ± 0.03 and 0.88 ± 0.03 s). In conclusion, in young healthy female athletes, the Emotion showed better preservation of cardiopulmonary responses than the FFP2. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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20 pages, 13530 KiB

Open AccessArticle

Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation

by Ismail Celik, Rohitash Yadav, Zekeriya Duzgun, Sarah Albogami, Ahmed M. El-Shehawi, Fatimawali, Rinaldi Idroes, Trina Ekawati Tallei and Talha Bin Emran

Biology 2021, 10(9), 880; https://doi.org/10.3390/biology10090880 - 7 Sep 2021

Cited by 38 | Viewed by 5765

Abstract

Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). [...] Read more.

Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug–S protein binding and its potential therapeutic effect. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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19 pages, 3582 KiB

Open AccessArticle

Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations

by Mycal Dutta, Abu Montakim Tareq, Ahmed Rakib, Shafi Mahmud, Saad Ahmed Sami, Jewel Mallick, Mohammad Nazmul Islam, Mohuya Majumder, Md. Zia Uddin, Abdullah Alsubaie, Abdulraheem S. A. Almalki, Mayeen Uddin Khandaker, D.A. Bradley, Md. Sohel Rana and Talha Bin Emran

Biology 2021, 10(8), 789; https://doi.org/10.3390/biology10080789 - 17 Aug 2021

Cited by 36 | Viewed by 5279

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (M^pro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography–mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 M^pro. In addition, prime molecular mechanics–generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 M^pro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (−5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (−5.39 kcal/mol), and lorazepam, 2TMS derivative (−5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary M^pro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand–M^pro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar M^pro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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21 pages, 1373 KiB

Open AccessArticle

Side Effects of mRNA-Based and Viral Vector-Based COVID-19 Vaccines among German Healthcare Workers

by Miloslav Klugar, Abanoub Riad, Mohamed Mekhemar, Jonas Conrad, Mayte Buchbender, Hans-Peter Howaldt and Sameh Attia

Biology 2021, 10(8), 752; https://doi.org/10.3390/biology10080752 - 5 Aug 2021

Cited by 165 | Viewed by 16632

Abstract

Background: the increasing number of COVID-19 vaccines available to the public may trigger hesitancy or selectivity towards vaccination. This study aimed to evaluate the post-vaccination side effects of the different vaccines approved in Germany; Methods: a cross-sectional survey-based study was carried out using [...] Read more.

Background: the increasing number of COVID-19 vaccines available to the public may trigger hesitancy or selectivity towards vaccination. This study aimed to evaluate the post-vaccination side effects of the different vaccines approved in Germany; Methods: a cross-sectional survey-based study was carried out using an online questionnaire validated and tested for a priori reliability. The questionnaire inquired about demographic data, medical and COVID-19-related anamneses, and local, systemic, oral, and skin-related side effects following COVID-19 vaccination; Results: out of the 599 participating healthcare workers, 72.3% were females, and 79.1% received mRNA-based vaccines, while 20.9% received a viral vector-based vaccine. 88.1% of the participants reported at least one side effect. Injection site pain (75.6%) was the most common local side effect, and headache/fatigue (53.6%), muscle pain (33.2%), malaise (25%), chills (23%), and joint pain (21.2%) were the most common systemic side effects. The vast majority (84.9%) of side effects resolved within 1–3 days post-vaccination; Conclusions: the mRNA-based vaccines were associated with a higher prevalence of local side effects (78.3% vs. 70.4%; Sig. = 0.064), while the viral vector-based vaccine was associated with a higher prevalence of systemic side effects (87.2% vs. 61%; Sig. < 0.001). Females and the younger age group were associated with an increased risk of side effects either after mRNA-based or viral vector-based vaccines. The gender- and age-based differences warrant further rigorous investigation and standardized methodology. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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19 pages, 2865 KiB

Open AccessArticle

Protection Strategy against an Epidemic Disease on Edge-Weighted Graphs Applied to a COVID-19 Case

by Ronald Manríquez, Camilo Guerrero-Nancuante and Carla Taramasco

Biology 2021, 10(7), 667; https://doi.org/10.3390/biology10070667 - 15 Jul 2021

Cited by 4 | Viewed by 2956

Abstract

Among the diverse and important applications that networks currently have is the modeling of infectious diseases. Immunization, or the process of protecting nodes in the network, plays a key role in stopping diseases from spreading. Hence the importance of having tools or strategies [...] Read more.

Among the diverse and important applications that networks currently have is the modeling of infectious diseases. Immunization, or the process of protecting nodes in the network, plays a key role in stopping diseases from spreading. Hence the importance of having tools or strategies that allow the solving of this challenge. In this paper, we evaluate the effectiveness of the DIL-W

^{α}

ranking in immunizing nodes in an edge-weighted network with 3866 nodes and 6,841,470 edges. The network is obtained from a real database and the spread of COVID-19 was modeled with the classic SIR model. We apply the protection to the network, according to the importance ranking list produced by DIL-W

^{α}

, considering different protection budgets. Furthermore, we consider three different values for

α

; in this way, we compare how the protection performs according to the value of

α

. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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16 pages, 311 KiB

Open AccessArticle

Dental Students in Germany throughout the COVID-19 Pandemic: A Psychological Assessment and Cross-Sectional Survey

by Mohamed Mekhemar, Sameh Attia, Christof Dörfer and Jonas Conrad

Biology 2021, 10(7), 611; https://doi.org/10.3390/biology10070611 - 1 Jul 2021

Cited by 26 | Viewed by 3628

Abstract

Multiple investigations have reported high psychological distress among students since the coronavirus (COVID-19) outbreak started. This survey examined the associations between psychological features, and several demographic and social factors among dental students in German universities. Dental students registered in German universities nationwide were [...] Read more.

Multiple investigations have reported high psychological distress among students since the coronavirus (COVID-19) outbreak started. This survey examined the associations between psychological features, and several demographic and social factors among dental students in German universities. Dental students registered in German universities nationwide were asked to join this survey via a self-directed online questionnaire, from July 2020 to January 2021. This study assembled data on demographic statistics, the depression anxiety stress scales (DASS-21), and the impact of events scale—revised (IES-R) instrument. The relationships between demographic-related variables and mental consequences of depression, anxiety, stress, intrusion, avoidance, and hyperarousal were inspected. Two hundred and eleven students contributed to the questionnaire and conveyed overall normal or mild outcomes of depression, anxiety, stress, intrusion, avoidance, and hyperarousal. In addition, female gender, cardiovascular diseases, smoking habits, and seeing the COVID-19 outbreak as a financial risk were stated as significant related factors (p < 0.05), with increased IES-R and DASS-21 scores. These results highlight the features that should be considered to better protect dental students’ mental health in German universities during the crisis. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

18 pages, 5115 KiB

Open AccessArticle

Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors

by Shafi Mahmud, Suvro Biswas, Gobindo Kumar Paul, Mohasana Akter Mita, Maria Meha Promi, Shamima Afrose, Md. Robiul Hasan, Shahriar Zaman, Md. Salah Uddin, Kuldeep Dhama, Talha Bin Emran, Md. Abu Saleh and Jesus Simal-Gandara

Biology 2021, 10(7), 589; https://doi.org/10.3390/biology10070589 - 26 Jun 2021

Cited by 48 | Viewed by 5472

Abstract

Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted [...] Read more.

Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted in a high mortality rate, bringing the world economy to its knees. Thus, mechanistic investigations of drugs capable of counteracting this disease are in high demand. The main protease (M^pro) expressed by SARS-CoV-2 has been targeted for the development of potential drug candidates due to the crucial role played by M^pro in viral replication and transcription. We generated a phytochemical library containing 1672 phytochemicals derived from 56 plants, which have been reported as having antiviral, antibacterial, and antifungal activity. A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate, which had respective binding affinities of −8.4, −8.5, and −8.8 kcal/mol. Several active sites in the targeted protein, including Cys145, His41, Met49, Glu66, and Met165, were found to interact with the top three candidate compounds. The multiple simulation profile, root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and solvent-accessible surface area values supported the inflexible nature of the docked protein–compound complexes. The toxicity and carcinogenicity profiles were assessed, which showed that epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate had favorable pharmacological properties with no adverse effects. These findings suggest that these compounds could be developed as part of an effective drug development pathway to treat COVID-19. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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11 pages, 864 KiB

Open AccessArticle

Associations between the Severity of the Post-Acute COVID-19 Syndrome and Echocardiographic Abnormalities in Previously Healthy Outpatients Following Infection with SARS-CoV-2

by Cristina Tudoran, Mariana Tudoran, Gheorghe Nicusor Pop, Catalina Giurgi-Oncu, Talida Georgiana Cut, Voichita Elena Lazureanu, Cristian Oancea, Florina Parv, Tudor Ciocarlie and Felix Bende

Biology 2021, 10(6), 469; https://doi.org/10.3390/biology10060469 - 26 May 2021

Cited by 29 | Viewed by 4068

Abstract

The COVID-19 pandemic affected over 130 million individuals during more than one year. Due to the overload of health-care services, a great number of people were treated as outpatients, many of them subsequently developing post-acute COVID-19 syndrome. Our study was conducted on 150 [...] Read more.

The COVID-19 pandemic affected over 130 million individuals during more than one year. Due to the overload of health-care services, a great number of people were treated as outpatients, many of them subsequently developing post-acute COVID-19 syndrome. Our study was conducted on 150 subjects without a history of cardiovascular diseases, treated as outpatients for a mild/moderate form of COVID-19 4 to 12 weeks prior to study inclusion, and who were diagnosed with post-acute COVID-19 and attended a cardiology evaluation with transthoracic echocardiography (TTE) for persisting symptoms. We detected various cardiac abnormalities in 38 subjects (25.33%), including pulmonary hypertension (9.33%), impaired left ventricular performance (8.66%), diastolic dysfunction (14%) and/or evidence of pericarditis (10%). We highlighted statistically significant correlations between the intensity of symptoms and quality of life scores with the severity of initial pulmonary injury, the number of weeks since COVID-19 and with TTE parameters characterizing the systolic and diastolic performance and pulmonary hypertension (p < 0.001). (Post-acute COVID-19 is a complex syndrome characterized by various symptoms, the intensity of which seem to be related to the severity and the time elapsed since the acute infection, and with persisting cardiac abnormalities. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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35 pages, 7249 KiB

Open AccessArticle

Molecular Docking and Dynamics Simulation Study of Hyrtios erectus Isolated Scalarane Sesterterpenes as Potential SARS-CoV-2 Dual Target Inhibitors

by Sameh S. Elhady, Reda F. A. Abdelhameed, Rania T. Malatani, Abdulrahman M. Alahdal, Hanin A. Bogari, Ahmad J. Almalki, Khadijah A. Mohammad, Safwat A. Ahmed, Amgad I. M. Khedr and Khaled M. Darwish

Biology 2021, 10(5), 389; https://doi.org/10.3390/biology10050389 - 1 May 2021

Cited by 49 | Viewed by 5019

Abstract

Presently, the world is under the toll of pandemic coronavirus disease-2019 (COVID-19) outbreak caused by SARS-CoV-2. Lack of effective and safe therapeutics has stressed the scientific community for developing novel therapeutics capable of alleviating and stopping this pandemic. Within the presented study, molecular [...] Read more.

Presently, the world is under the toll of pandemic coronavirus disease-2019 (COVID-19) outbreak caused by SARS-CoV-2. Lack of effective and safe therapeutics has stressed the scientific community for developing novel therapeutics capable of alleviating and stopping this pandemic. Within the presented study, molecular docking, ADME properties and all-atom molecular dynamic (MD) simulation, along with two standard antiviral agents (lopinavir and benzopurpurin-4B), were applied to investigate 15 scalaranes sesterterpenes natural compounds, purified from the Red Sea marine sponge Hyrtios erectus, as potential COVID-19 dual-target inhibitors. Following multi-step docking within COVID-19 main protease and Nsp15 endoribonuclease cavities, nine promising drug-like compounds exhibited higher docking scores as well as better interactions with the target’s crucial residues than those of reference ligands. Compounds 2, 6, 11, and 15, were predicted to simultaneously subdue the activity of the two COVID-19 targets. Dynamics behavior of the best-docked molecules, compounds 15 and 6, within COVID-19 target pockets showed substantial stability of ligand-protein complexes as presented via several MD simulation parameters. Furthermore, calculated free-binding energies from MD simulation illustrated significant ligand’s binding affinity towards respective target pockets. All provided findings supported the utility of scalarane-based sesterterpenes, particularly compounds 15 and 6, as promising lead candidates guiding the development of effective therapeutics against SARS-CoV-2. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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10 pages, 3312 KiB

Open AccessArticle

Coronavirus Disease 2019 (COVID-19) in Italy: Double Reading of Chest CT Examination

by Alfonso Reginelli, Roberta Grassi, Beatrice Feragalli, Maria Paola Belfiore, Alessandro Montanelli, Gianluigi Patelli, Michelearcangelo La Porta, Fabrizio Urraro, Roberta Fusco, Vincenza Granata, Antonella Petrillo, Giuliana Giacobbe, Gaetano Maria Russo, Palmino Sacco, Roberto Grassi and Salvatore Cappabianca

Biology 2021, 10(2), 89; https://doi.org/10.3390/biology10020089 - 25 Jan 2021

Cited by 23 | Viewed by 2951

Abstract

To assess the performance of the second reading of chest compute tomography (CT) examinations by expert radiologists in patients with discordance between the reverse transcription real-time fluorescence polymerase chain reaction (RT-PCR) test for COVID-19 viral pneumonia and the CT report. Three hundred and [...] Read more.

To assess the performance of the second reading of chest compute tomography (CT) examinations by expert radiologists in patients with discordance between the reverse transcription real-time fluorescence polymerase chain reaction (RT-PCR) test for COVID-19 viral pneumonia and the CT report. Three hundred and seventy-eight patients were included in this retrospective study (121 women and 257 men; 71 years median age, with a range of 29–93 years) and subjected to RT-PCR tests for suspicious COVID-19 infection. All patients were subjected to CT examination in order to evaluate the pulmonary disease involvement by COVID-19. CT images were reviewed first by two radiologists who identified COVID-19 typical CT patterns and then reanalyzed by another two radiologists using a CT structured report for COVID-19 diagnosis. Weighted k values were used to evaluate the inter-reader agreement. The median temporal window between RT-PCRs execution and CT scan was zero days with a range of (−9, 11) days. The RT-PCR test was positive in 328/378 (86.8%). Discordance between RT-PCR and CT findings for viral pneumonia was revealed in 60 cases. The second reading changed the CT diagnosis in 16/60 (26.7%) cases contributing to an increase the concordance with the RT-PCR. Among these 60 cases, eight were false negative with positive RT-PCR, and 36 were false positive with negative RT-PCR. Sensitivity, specificity, positive predictive value and negative predictive value of CT were respectively of 97.3%, 53.8%, 89.0%, and 88.4%. Double reading of CT scans and expert second readers could increase the diagnostic confidence of radiological interpretation in COVID-19 patients. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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12 pages, 1224 KiB

Open AccessArticle

Cutaneous Manifestations in COVID-19: Report on 31 Cases from Five Countries

by Carmen Rodriguez-Cerdeira, Brianda I. Uribe-Camacho, Lianet Silverio-Carrasco, Wennia Méndez, Ashwini R. Mahesh, Anakaren Tejada, Angelica Beirana, Erick Martinez-Herrera, Alfonso Alba, Roberto Arenas and Jacek C. Szepietowski

Biology 2021, 10(1), 54; https://doi.org/10.3390/biology10010054 - 13 Jan 2021

Cited by 11 | Viewed by 6352

Abstract

The increasingly frequent cutaneous manifestations of coronavirus disease (COVID-19) remain to pose a problem to clinicians. Herein, we aimed to describe the clinical and pathological findings of skin lesions in patients with COVID-19. The case series, which was based on the International Dermatological [...] Read more.

The increasingly frequent cutaneous manifestations of coronavirus disease (COVID-19) remain to pose a problem to clinicians. Herein, we aimed to describe the clinical and pathological findings of skin lesions in patients with COVID-19. The case series, which was based on the International Dermatological Registry circulated to dermatologists worldwide, was conducted across organizations and societies belonging to five different countries. We documented 31 patients with dermatologic manifestations associated with COVID-19, including maculopapular rashes (16.10%), urticarial lesions (26.80%), pseudochilblains (22.60%), petechiae/purpura (6.50%), distal ischaemia and necrosis (6.50%), livedo racemosa (12.90%), and others (9.70%). Twenty-six cases (83.90%) were qRT-PCR-confirmed COVID-19 cases, two (6.50%) were serologically confirmed, while two others (9.7%) were suspected cases owing to previous contact with COVID-19-positive patients. Therefore, our findings indicate that a febrile rash or even a rash in an afebrile state in the early stages of the disease may be the only clinical manifestation of COVID-19. In the future, we recommend close monitoring of all patients with skin lesions not attributable to other causal factors; in the diagnostic perspective, clinicians should aim to confirm if the skin lesions are associated with COVID-19. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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14 pages, 3702 KiB

Open AccessArticle

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

by Kamrul Hasan Chowdhury, Md. Riad Chowdhury, Shafi Mahmud, Abu Montakim Tareq, Nujhat Binte Hanif, Naureen Banu, A. S. M. Ali Reza, Talha Bin Emran and Jesus Simal-Gandara

Biology 2021, 10(1), 2; https://doi.org/10.3390/biology10010002 - 23 Dec 2020

Cited by 69 | Viewed by 6865

Abstract

Novel coronavirus disease (COVID-19) was identified from China in December 2019 and spread rapidly through human-to-human transmission, affecting so many people worldwide. Until now, there has been no specific treatment against the disease and repurposing of the drug. Our investigation aimed to screen [...] Read more.

Novel coronavirus disease (COVID-19) was identified from China in December 2019 and spread rapidly through human-to-human transmission, affecting so many people worldwide. Until now, there has been no specific treatment against the disease and repurposing of the drug. Our investigation aimed to screen potential inhibitors against coronavirus for the repurposing of drugs. Our study analyzed sequence comparison among SARS-CoV, SARS-CoV-2, and MERS-CoV to determine the identity matrix using discovery studio. SARS-CoV-2 M^pro was targeted to generate an E-pharmacophore hypothesis to screen drugs from the DrugBank database having similar features. Promising drugs were used for docking-based virtual screening at several precisions. Best hits from virtual screening were subjected to MM/GBSA analysis to evaluate binding free energy, followed by the analysis of binding interactions. Furthermore, the molecular dynamics simulation approaches were carried out to assess the docked complex’s conformational stability. A total of 33 drug classes were found from virtual screening based on their docking scores. Among them, seven potential drugs with several anticancer, antibiotic, and immunometabolic categories were screened and showed promising MM/GBSA scores. During interaction analysis, these drugs exhibited different types of hydrogen and hydrophobic interactions with amino acid residue. Besides, 17 experimental drugs selected from virtual screening might be crucial for drug discovery against COVID-19. The RMSD, RMSF, SASA, Rg, and MM/PBSA descriptors from molecular dynamics simulation confirmed the complex’s firm nature. Seven promising drugs for repurposing against SARS-CoV-2 main protease (M^pro), namely sapanisertib, ornidazole, napabucasin, lenalidomide, daniquidone, indoximod, and salicylamide, could be vital for the treatment of COVID-19. However, extensive in vivo and in vitro studies are required to evaluate the mentioned drug’s activity. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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10 pages, 250 KiB

Open AccessArticle

Increased Prevalence of Face Mask—Induced Itch in Health Care Workers

by Piotr K. Krajewski, Łukasz Matusiak, Marta Szepietowska, Rafał Białynicki-Birula and Jacek C. Szepietowski

Biology 2020, 9(12), 451; https://doi.org/10.3390/biology9120451 - 7 Dec 2020

Cited by 25 | Viewed by 3968

Abstract

Background: Face mask use has increased significantly due to the COVID-19 pandemic. Health care workers (HCW) wear masks for prolonged periods and are prone to adverse effects. Very little is known about face-mask-associated itch. Methods: This Internet survey study investigated the prevalence, intensity [...] Read more.

Background: Face mask use has increased significantly due to the COVID-19 pandemic. Health care workers (HCW) wear masks for prolonged periods and are prone to adverse effects. Very little is known about face-mask-associated itch. Methods: This Internet survey study investigated the prevalence, intensity and clinical characteristics of itch related to the use of face masks by HCW during the COVID-19 pandemic. The results were subsequently compared to the students’ group. Results: A total of 1156 HCW completed the survey. Among them, 31.6% (365) reported suffering from itch associated with face mask use. Itch was more frequent among females. Moreover, subjects who reported sensitive skin, atopic predispositions and facial dermatoses tended to report itch more frequently. The worst case of itch in the seven days prior to the study, assessed with the numeric rating scale (NRS), was 4.6 ± 2.0 points. Itch prevalence increased along with the duration of face mask use, being 34.6% among those who wore masks for more than 4 h. HCW reported itch significantly more frequently than students. Conclusions: Face-mask-associated itch is a frequent problem among HCW in the COVID-19 pandemic. Itch sensation may cause scratching, which may decrease necessary protection during the pandemic. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

12 pages, 698 KiB

Open AccessEditor’s ChoiceArticle

National Publication Productivity during the COVID-19 Pandemic—A Preliminary Exploratory Analysis of the 30 Countries Most Affected

by Simon M. Müller, Georg F. Mueller, Alexander A. Navarini and Oliver Brandt

Biology 2020, 9(9), 271; https://doi.org/10.3390/biology9090271 - 5 Sep 2020

Cited by 20 | Viewed by 4850

Abstract

Background: The COVID 19 pandemic increased publication productivity enormously with numerous new COVID-19-related articles appearing daily, despite the fact that many health care workers in the partially overburdened national health care systems were faced with major challenges. Methods: In a cross-sectional, observational, retrospective [...] Read more.

Background: The COVID 19 pandemic increased publication productivity enormously with numerous new COVID-19-related articles appearing daily, despite the fact that many health care workers in the partially overburdened national health care systems were faced with major challenges. Methods: In a cross-sectional, observational, retrospective study we compared and correlated 17 epidemiologic, health care system-related and health-economic factors from medical databases and intergovernmental organisations potentially influencing the COVID-19 and non-COVID-19 publication productivity between 1 January and 30 April 2020 amongst the 30 countries most severely affected by the pandemic. These factors were additionally correlated with the national pre-COVID-19 publication rate for the same pre-year period to identify potential changes in the general publication behaviour. Findings: COVID-19 and non-COVID-19 publication rates correlated strongest with access to and quality of health care (ρ = 0.80 and 0.87, p < 0.0001), COVID-19 cases per capita (ρ = 0.78 and 0.72, p < 0.0001), GDP per capita (ρ = 0.69 and 0.76, p < 0.0001), health spending per capita (ρ = 0.61 and 0.73, p < 0.0001) and the pre-COVID-19 Hirsch-Index (ρ = 0.61 and 0.62, p = 0.002 and <0.0001). Ratios of publication rates for “Cancer”, “Diabetes” and “Stroke” in 2020 versus the pre-year period were 0.88 ± 0.06, 1.02 ± 0.18 and 0.9 ± 0.20, resulting in a pooled ratio of 0.93 ± 0.06 for non-COVID-19 publications. Interpretation: There are marked geographic and national differences in publication productivity during the COVID-19 pandemic. Both COVID-19- and non-COVID-19 publication productivity correlates with epidemiologic, health care system-related and healtheconomic factors, and pre-COVID publication expertise. Countries with a stable scientific infrastructure appear to maintain non-COVID-19 publication productivity nearly at the pre-year level and at the same time use their resilience to produce COVID-19 publications at high rates. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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13 pages, 1419 KiB

Open AccessEditor’s ChoiceArticle

CoVid-19 Pandemic Trend Modeling and Analysis to Support Resilience Decision-Making

by Romney B. Duffey and Enrico Zio

Biology 2020, 9(7), 156; https://doi.org/10.3390/biology9070156 - 7 Jul 2020

Cited by 10 | Viewed by 4131

Abstract

Policy decision-making for system resilience to a hazard requires the estimation and prediction of the trends of growth and decline of the impacts of the hazard. With focus on the recent worldwide spread of CoVid-19, we take the infection rate as the relevant [...] Read more.

Policy decision-making for system resilience to a hazard requires the estimation and prediction of the trends of growth and decline of the impacts of the hazard. With focus on the recent worldwide spread of CoVid-19, we take the infection rate as the relevant metric whose trend of evolution to follow for verifying the effectiveness of the countermeasures applied. By comparison with the theories of growth and recovery in coupled socio-medical systems, we find that the data for many countries show infection rate trends that are exponential in form. In particular, the recovery trajectory is universal in trend and consistent with the learning theory, which allows for predictions useful in the assistance of decision-making of emergency recovery actions. The findings are validated by extensive data and comparison to medical pandemic models. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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Review

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23 pages, 3339 KiB

Open AccessReview

Viral and Host Genetic and Epigenetic Biomarkers Related to SARS-CoV-2 Cell Entry, Infection Rate, and Disease Severity

by Jernej Gaspersic and Vita Dolzan

Biology 2022, 11(2), 178; https://doi.org/10.3390/biology11020178 - 23 Jan 2022

Cited by 6 | Viewed by 4387

Abstract

The rapid spread of COVID-19 outbreak lead to a global pandemic declared in March 2020. The common features of corona virus family helped to resolve structural characteristics and entry mechanism of SARS-CoV-2. However, rapid mutagenesis leads to the emergence of new strains that [...] Read more.

The rapid spread of COVID-19 outbreak lead to a global pandemic declared in March 2020. The common features of corona virus family helped to resolve structural characteristics and entry mechanism of SARS-CoV-2. However, rapid mutagenesis leads to the emergence of new strains that may have different reproduction rates or infectivity and may impact the course and severity of the disease. Host related factors may also play a role in the susceptibility for infection as well as the severity and outcomes of the COVID-19. We have performed a literature and database search to summarize potential viral and host-related genomic and epigenomic biomarkers, such as genetic variability, miRNA, and DNA methylation in the molecular pathway of SARS-CoV-2 entry into the host cell, that may be related to COVID-19 susceptibility and severity. Bioinformatics tools may help to predict the effect of mutations in the spike protein on the binding to the ACE2 receptor and the infectivity of the strain. SARS-CoV-2 may also target several transcription factors and tumour suppressor genes, thus influencing the expression of different host genes and affecting cell signalling. In addition, the virus may interfere with RNA expression in host cells by exploiting endogenous miRNA and its viral RNA. Our analysis showed that numerous human miRNA may form duplexes with different coding and non-coding regions of viral RNA. Polymorphisms in human genes responsible for viral entry and replication, as well as in molecular damage response and inflammatory pathways may also contribute to disease prognosis and outcome. Gene ontology analysis shows that proteins encoded by such polymorphic genes are highly interconnected in regulation of defense response. Thus, virus and host related genetic and epigenetic biomarkers may help to predict the course of the disease and the response to treatment. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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15 pages, 3799 KiB

Open AccessReview

The Role of Acidosis in the Pathogenesis of Severe Forms of COVID-19

by Yury D. Nechipurenko, Denis A. Semyonov, Igor A. Lavrinenko, Denis A. Lagutkin, Evgenii A. Generalov, Anna Y. Zaitceva, Olga V. Matveeva and Yegor E. Yegorov

Biology 2021, 10(9), 852; https://doi.org/10.3390/biology10090852 - 31 Aug 2021

Cited by 46 | Viewed by 16370

Abstract

COVID-19 has specific characteristics that distinguish this disease from many other infections. We suggest that the pathogenesis of severe forms of COVID-19 can be associated with acidosis. This review article discusses several mechanisms potentially linking the damaging effects of COVID-19 with acidosis and [...] Read more.

COVID-19 has specific characteristics that distinguish this disease from many other infections. We suggest that the pathogenesis of severe forms of COVID-19 can be associated with acidosis. This review article discusses several mechanisms potentially linking the damaging effects of COVID-19 with acidosis and shows the existence of a vicious cycle between the development of hypoxia and acidosis in COVID-19 patients. At the early stages of the disease, inflammation, difficulty in gas exchange in the lungs and thrombosis collectively contribute to the onset of acidosis. In accordance with the Verigo-Bohr effect, a decrease in blood pH leads to a decrease in oxygen saturation, which contributes to the exacerbation of acidosis and results in a deterioration of the patient’s condition. A decrease in pH can also cause conformational changes in the S-protein of the virus and thus lead to a decrease in the affinity and avidity of protective antibodies. Hypoxia and acidosis lead to dysregulation of the immune system and multidirectional pro- and anti-inflammatory reactions, resulting in the development of a “cytokine storm”. In this review, we highlight the potential importance of supporting normal blood pH as an approach to COVID-19 therapy. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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22 pages, 993 KiB

Open AccessReview

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

by Irina Kiseleva and Andrey Ksenafontov

Biology 2021, 10(8), 733; https://doi.org/10.3390/biology10080733 - 31 Jul 2021

Cited by 19 | Viewed by 10117

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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28 pages, 569 KiB

Open AccessEditor’s ChoiceReview

Cutaneous Manifestations in Confirmed COVID-19 Patients: A Systematic Review

by Claudio Conforti, Caterina Dianzani, Marina Agozzino, Roberta Giuffrida, Giovanni Francesco Marangi, Nicola di Meo, Silviu-Horia Morariu, Paolo Persichetti, Francesco Segreto, Iris Zalaudek and Nicoleta Neagu

Biology 2020, 9(12), 449; https://doi.org/10.3390/biology9120449 - 5 Dec 2020

Cited by 43 | Viewed by 7689

Abstract

There have been increasing reports of skin manifestations in COVID-19 patients. We conducted a systematic review and included manuscripts describing patients with positive RT-PCR coronavirus testing from nasopharyngeal swabs who also developed cutaneous manifestations. A total of 655 patients were selected, with different [...] Read more.

There have been increasing reports of skin manifestations in COVID-19 patients. We conducted a systematic review and included manuscripts describing patients with positive RT-PCR coronavirus testing from nasopharyngeal swabs who also developed cutaneous manifestations. A total of 655 patients were selected, with different types of skin rashes: Erythematous maculopapular (n = 250), vascular (n = 146), vesicular (n = 99), urticarial (n = 98), erythema multiforme/generalized pustular figurate erythema/Stevens-Johnson syndrome (n = 22), ocular/periocular (n = 14), polymorphic pattern (n = 9), generalized pruritus (n = 8), Kawasaki disease (n = 5), atypical erythema nodosum (n = 3), and atypical Sweet syndrome (n = 1). Chilblain-like lesions were more frequent in the younger population and were linked to a milder disease course, while fixed livedo racemosa and retiform purpura appeared in older patients and seemed to predict a more severe prognosis. For vesicular rashes, PCR determined the presence of herpesviruses in the vesicle fluid, which raised the possibility of herpesvirus co-infections. The erythema-multiforme-like pattern, generalized pustular figurate erythema and Stevens-Johnson syndrome were most frequently linked to hydroxychloroquine intake. A positive PCR determination of SARS-COV-2 from conjunctival swabs suggest that eye discharge can also be contagious. These cutaneous manifestations may aid in identifying otherwise asymptomatic COVID-19 carriers in some cases or predict a more severe evolution in others. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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14 pages, 2420 KiB

Open AccessEditor’s ChoiceReview

Recommendations, Practices and Infrastructural Model for the Dental Radiology Set-up in Clinical and Academic Institutions in the COVID-19 Era

by Anu Sushanth. A, Kumar Chandan Srivastava, Deepti Shrivastava, Hala A. Hosni, Zafar Ali Khan, Khalid Al-Johani, Ibrahim A Alzoubi, Sasirekha B, Mohammed Ghazi Sghaireen and Mohammad Khursheed Alam

Biology 2020, 9(10), 334; https://doi.org/10.3390/biology9100334 - 13 Oct 2020

Cited by 12 | Viewed by 5220

Abstract

The pandemic of Coronavirus disease (COVID-19) has emerged as a global catastrophe that is plaguing mankind. In the past eight months since the world discovered about COVID-19, we learned a lot about server acute respiratory syndrome coronavirus 2 (SARS CoV-2) and perhaps there [...] Read more.

The pandemic of Coronavirus disease (COVID-19) has emerged as a global catastrophe that is plaguing mankind. In the past eight months since the world discovered about COVID-19, we learned a lot about server acute respiratory syndrome coronavirus 2 (SARS CoV-2) and perhaps there is much more to discover and understand about the virus. With the current understanding of the disease, we assume it will remain in an active state of transmission and progression among the community for a long time. Thus, it is advisable to adopt the disease’s prevention protocol in our daily and work routine. During this pandemic patient requiring dental treatment cannot be neglected and the role of dental imaging is crucial in delivering treatment. Hence, this article attempts to provide an evidence-based compilation about the mode of transmission and clinical features of COVID-19. It also throws light on the potential source of disease transmission in the dental radiology setting. In addition, it suggests preventive measures to curb the infection and infrastructural model of the clinical setting that will assist in achieving control over the disease transmission. This article intends to project a strategy about protocols, infrastructure, and daily activities in a dental radiology office that institutions can adopt with modifications according to their local scenario. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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24 pages, 1726 KiB

Open AccessReview

Factors Associated with Increased Morbidity and Mortality of Obese and Overweight COVID-19 Patients

by Amany Magdy Beshbishy, Helal F. Hetta, Diaa E. Hussein, Abdullah A. Saati, Christian C. Uba, Nallely Rivero-Perez, Adrian Zaragoza-Bastida, Muhammad Ajmal Shah, Tapan Behl and Gaber El-Saber Batiha

Biology 2020, 9(9), 280; https://doi.org/10.3390/biology9090280 - 9 Sep 2020

Cited by 29 | Viewed by 8053

Abstract

Overweight and obesity are defined as an unnecessary accumulation of fat, which poses a risk to health. It is a well-identified risk factor for increased mortality due to heightened rates of heart disease, certain cancers, musculoskeletal disorders, and bacterial, protozoan and viral infections. [...] Read more.

Overweight and obesity are defined as an unnecessary accumulation of fat, which poses a risk to health. It is a well-identified risk factor for increased mortality due to heightened rates of heart disease, certain cancers, musculoskeletal disorders, and bacterial, protozoan and viral infections. The increasing prevalence of obesity is of concern, as conventional pathogenesis may indeed be increased in obese hosts rather than healthy hosts, especially during this COVID-19 pandemic. COVID-19 is a new disease and we do not have the luxury of cumulative data. Obesity activates the development of gene induced hypoxia and adipogenesis in obese animals. Several factors can influence obesity, for example, stress can increase the body weight by allowing people to consume high amounts of food with a higher propensity to consume palatable food. Obesity is a risk factor for the development of immune-mediated and some inflammatory-mediated diseases, including atherosclerosis and psoriasis, leading to a dampened immune response to infectious agents, leading to weaker post-infection impacts. Moreover, the obese host creates a special microenvironment for disease pathogenesis, marked by persistent low-grade inflammation. Therefore, it is advisable to sustain healthy eating habits by increasing the consumption of various plant-based and low-fat foods to protect our bodies and decrease the risk of infectious diseases, especially COVID-19. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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24 pages, 808 KiB

Open AccessReview

Immune Dysfunction and Multiple Treatment Modalities for the SARS-CoV-2 Pandemic: Races of Uncontrolled Running Sweat?

by Ashish Kothari, Vanya Singh, Uttam Kumar Nath, Sandeep Kumar, Vineeta Rai, Karanvir Kaushal, Balram Ji Omar, Atul Pandey and Neeraj Jain

Biology 2020, 9(9), 243; https://doi.org/10.3390/biology9090243 - 24 Aug 2020

Cited by 7 | Viewed by 6109

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic threat with more than 11.8 million confirmed cases and more than 0.5 million deaths as of 3 July 2020. Given the lack of definitive pharmaceutical interventions against SARS-CoV-2, multiple therapeutic strategies and [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic threat with more than 11.8 million confirmed cases and more than 0.5 million deaths as of 3 July 2020. Given the lack of definitive pharmaceutical interventions against SARS-CoV-2, multiple therapeutic strategies and personal protective applications are being used to reduce the risk of high mortality and community spread of this infection. Currently, more than a hundred vaccines and/or alternative therapeutic regimens are in clinical trials, and some of them have shown promising results in improving the immune cell environment and controlling the infection. In this review, we discussed high-performance multi-directory strategies describing the uncontrolled deregulation of the host immune landscape associated with coronavirus disease (COVID-19) and treatment strategies using an anti-neoplastic regimen. We also followed selected current treatment plans and the most important on-going clinical trials and their respective outcomes for blocking SARS-CoV-2 pathogenesis through regenerative medicine, such as stem cell therapy, chimeric antigen receptors, natural killer (NK) cells, extracellular vesicular-based therapy, and others including immunomodulatory regimens, anti-neoplastic therapy, and current clinical vaccine therapy. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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12 pages, 778 KiB

Open AccessReview

The Antiviral Properties of Cyclosporine. Focus on Coronavirus, Hepatitis C Virus, Influenza Virus, and Human Immunodeficiency Virus Infections

by Paulina Glowacka, Lidia Rudnicka, Olga Warszawik-Hendzel, Mariusz Sikora, Mohamad Goldust, Patrycja Gajda, Anna Stochmal, Leszek Blicharz, Adriana Rakowska and Malgorzata Olszewska

Biology 2020, 9(8), 192; https://doi.org/10.3390/biology9080192 - 28 Jul 2020

Cited by 28 | Viewed by 7837

Abstract

This review updates current knowledge regarding the risk of viral infections, including COVID-19, in patients treated with cyclosporine. We also shortly refer to bacterial infections and parasitic infestations in patients treated with cyclosporin. Cyclosporine is an immunosuppressive drug, which is widely used in [...] Read more.

This review updates current knowledge regarding the risk of viral infections, including COVID-19, in patients treated with cyclosporine. We also shortly refer to bacterial infections and parasitic infestations in patients treated with cyclosporin. Cyclosporine is an immunosuppressive drug, which is widely used in medicine, including in the treatment of autoimmune skin diseases in dermatology, rheumatology, ophthalmology and nephrology, and in organ transplantation. A usual concern associated with immunosuppressive treatment is the potential risk of infections. Interestingly, several data indicate a relatively low risk of infections, especially viral infections, in patients receiving cyclosporine. It was shown that cyclosporine exerts an inhibitory effect on the replication of some viruses, or may have a potentially beneficial effect on the disease course in infections. These include hepatitis C, influenza virus, rotavirus, human immunodeficiency virus and coronavirus infections. Available data indicate that cyclosporine may have a beneficial effect on COVID-19, which is caused by the coronavirus SARS-COV2. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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Other

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13 pages, 705 KiB

Open AccessOpinion

The Possible Role of Microbial Proteases in Facilitating SARS-CoV-2 Brain Invasion

by Nozethu Mjokane, Olufemi S. Folorunso, Adepemi O. Ogundeji and Olihile M. Sebolai

Biology 2021, 10(10), 966; https://doi.org/10.3390/biology10100966 - 27 Sep 2021

Cited by 6 | Viewed by 3110

Abstract

SARS-CoV-2 has been shown to display proclivity towards organs bearing angiotensin-converting enzyme (ACE2) expression cells. Of interest herein is the ability of the virus to exhibit neurotropism. However, there is limited information on how this virus invades the brain. With this contribution, we [...] Read more.

SARS-CoV-2 has been shown to display proclivity towards organs bearing angiotensin-converting enzyme (ACE2) expression cells. Of interest herein is the ability of the virus to exhibit neurotropism. However, there is limited information on how this virus invades the brain. With this contribution, we explore how, in the context of a microbial co-infection using a cryptococcal co-infection as a model, SARS-CoV-2 could reach the brain. We theorise that the secretion of proteases by disseminated fungal cells might also activate the S2 domain of the viral spike glycoprotein for membrane fusion with brain endothelial cells leading to endocytosis. Understanding this potential invasion mechanism could lead to better SARS-CoV-2 intervention measures, which may also be applicable in instances of co-infection, especially with protease-secreting pathogens. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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7 pages, 1267 KiB

Open AccessPerspective

Alcohol, Cannabis and Crossfading: Concerns for COVID-19 Disease Severity

by Vijay Sivaraman, Morgan M. Richey and ABM Nasir

Biology 2021, 10(8), 779; https://doi.org/10.3390/biology10080779 - 16 Aug 2021

Cited by 2 | Viewed by 2860

Abstract

Risk factors for severe COVID-19 pathology are currently being investigated worldwide. The emergence of this highly infectious respiratory disease has plagued the world, with varying severity across populations of different age, race, and socio-economic level. These data suggest that other environmental or social [...] Read more.

Risk factors for severe COVID-19 pathology are currently being investigated worldwide. The emergence of this highly infectious respiratory disease has plagued the world, with varying severity across populations of different age, race, and socio-economic level. These data suggest that other environmental or social factors may contribute to this disease’s severity. Using a mouse model, we identify heavy alcohol and cannabinoid consumption as risk factors for increased pulmonary pathology in the setting of exposure to a microbial pulmonary pathogen (K. pneumoniae). We present observational evidence that pneumonia patients admitted to North Carolina hospitals have longer lengths of stay when they endorse alcohol use or have conditions considered alcohol attributable. We are concerned that the observed increase in alcohol and legal cannabinoid sales during lockdown and quarantine may contribute to increased pulmonary pathology among patients who become infected with COVID-19. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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5 pages, 765 KiB

Open AccessOpinion

Coronavirus Disease 2019 (COVID-19) Crisis: Losing Our Immunity When We Need It the Most

by Abdelaziz Ghanemi, Mayumi Yoshioka and Jonny St-Amand

Biology 2021, 10(6), 545; https://doi.org/10.3390/biology10060545 - 18 Jun 2021

Cited by 17 | Viewed by 3856

Abstract

The ongoing coronavirus disease 2019 (COVID-19) crisis has led to a new socioeconomic reality with the acquisition of novel habits. Measures imposed by governments and health authorities such as confinement and lockdown have had important consequences, including mental health problems, economic crisis, and [...] Read more.

The ongoing coronavirus disease 2019 (COVID-19) crisis has led to a new socioeconomic reality with the acquisition of novel habits. Measures imposed by governments and health authorities such as confinement and lockdown have had important consequences, including mental health problems, economic crisis, and social isolation. Combined with newly acquired habits such as hand washing, sanitization, and face masks, these have all directly and indirectly led to reduced immunity. Such effects on the immune system not only impact the epidemiological profile with respect to COVID-19 and other infectious diseases but also limit the efficacy of the ongoing anti-COVID-19 vaccination campaign. Therefore, there is a need to review these approaches and optimize measures towards better population immunity, which is much needed during such an epidemic. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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