SARS-CoV-2: Epidemiology and Pathogenesis

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 97327

Special Issue Editors

Centro Operativo Veterinario per l'Epidemiologia, Programmazione, Informazione e Analisi del Rischio (COVEPI), National Reference Center for Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale, dell'Abruzzo e del Molise "G. Caporale", Campo Boario, 64100 Teramo, Italy
Interests: epidemiology of animal infectious diseases and zoonoses; risk assessment studies; molecular epidemiology studies on viruses and bacteria; designing surveillance systems for infectious diseases; field epidemiology training; food borne zoonotic diseases
Special Issues, Collections and Topics in MDPI journals
Virology Unit Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”, Teramo, Italy
Interests: diagnosis of viral infectious diseases via innovative molecular methods; coronaviruses; morbilliviruses; reverse genetics; swine influenza viruses; next generations sequencing; arbovirus; orbiviruses; West Nile virus; viral diagnostics; virus discovery; virus evolution; pathogenesis studies
Special Issues, Collections and Topics in MDPI journals
Institute of Pathology and Department of Chemistry, Case Western Reserve University (CWRU), Cleveland, OH 44106, USA
Interests: microbiota–gut–brain axis; gut microbiota; antibiotic treatment; gut health
Special Issues, Collections and Topics in MDPI journals
Food Research & Innovation Centre, College of Science, Engineering and Health, RMIT University, Melbourne, Australia
Interests: gut microbiome; probiotics and prebiotics; fermented foods; food safety; metabolomics; intestinal and respiratory infections and antimicrobials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since its emergence in 2019 in Wuhan City, Hubei Province, China, SARS-CoV-2 has spread across hundreds of countries and all continents. The virus is easily transmitted from person to person. This pandemic is considered the most serious global health threat we have faced from the time of the Spanish flu. In the majority of cases, the disease caused by SARS-CoV-2 (named COVID-19) is asymptomatic or with mild clinical signs, but in a varying percentage of infected patients it may be severe. Patients with severe disease develop pneumonia or acute respiratory distress syndrome (ARDS), thus requiring mechanical ventilation and ICU treatment, and often progress to a fatal outcome. The pandemic caused by SARS-CoV-2 has put the health care systems of the infected countries under enormous stress, determining dramatic economic consequences due to the draconian control measures adopted to reduce virus transmission. SARS-CoV-2 is a new pathogen, and therefore, several aspects related to its epidemiology and pathogenesis are completely unknown. The scientific community is producing a tremendous effort to fill the main knowledge gaps and to develop effective preventive and control tools. This Special Issue aims at highlighting the most recent outcomes of scientific research on the following topics related to SARS-CoV-2:

- Epidemiology of SARS-CoV-2 infection

- Animal reservoirs

- Virulence factors

- Viral evolution and pathogenesis

- Diagnostic findings in humans

- Control measures at local and international level

- Impact on global and local economy

Dr. Paolo Calistri
Dr. Alessio Lorusso
Prof. Dr. Mark E. Obrenovich
Prof. Harsharn Gill
Guest Editors

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Keywords

  • COVID19
  • coronavirus
  • Epidemiology
  • Pathogenesis
  • Infectious diseases
  • One health

Published Papers (23 papers)

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Editorial

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3 pages, 190 KiB  
Editorial
Special Issue “SARS-CoV-2: Epidemiology and Pathogenesis”: Editorial
by Paolo Calistri, Harsharn Gill and Alessio Lorusso
Microorganisms 2023, 11(4), 927; https://doi.org/10.3390/microorganisms11040927 - 03 Apr 2023
Viewed by 820
Abstract
Since its emergence in 2019 in Wuhan City, Hubei Province, China, SARS-CoV-2 has spread across hundreds of countries and all continents [...] Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)

Research

Jump to: Editorial, Review

13 pages, 1342 KiB  
Article
SARS-CoV-2 Spike Pseudoviruses: A Useful Tool to Study Virus Entry and Address Emerging Neutralization Escape Phenotypes
by Raj Kalkeri, Zhaohui Cai, Shuling Lin, John Farmer, Yury V. Kuzmichev and Fusataka Koide
Microorganisms 2021, 9(8), 1744; https://doi.org/10.3390/microorganisms9081744 - 16 Aug 2021
Cited by 16 | Viewed by 3541
Abstract
SARS-CoV-2 genetic variants are emerging around the globe. Unfortunately, several SARS-CoV-2 variants, especially variants of concern (VOCs), are less susceptible to neutralization by the convalescent and post-vaccination sera, raising concerns of increased disease transmissibility and severity. Recent data suggests that SARS-CoV-2 neutralizing antibody [...] Read more.
SARS-CoV-2 genetic variants are emerging around the globe. Unfortunately, several SARS-CoV-2 variants, especially variants of concern (VOCs), are less susceptible to neutralization by the convalescent and post-vaccination sera, raising concerns of increased disease transmissibility and severity. Recent data suggests that SARS-CoV-2 neutralizing antibody levels are a reliable correlate of vaccine-mediated protection. However, currently used BSL3-based virus micro-neutralization (MN) assays are more laborious, time-consuming, and expensive, underscoring the need for BSL2-based, cost-effective neutralization assays against SARS-CoV-2 variants. In light of this unmet need, we have developed a BSL-2 pseudovirus-based neutralization assay (PBNA) in cells expressing the human angiotensin-converting enzyme-2 (hACE2) receptor for SARS-CoV-2. The assay is reproducible (R2 = 0.96), demonstrates a good dynamic range and high sensitivity. Our data suggest that the biological Anti-SARS-CoV-2 research reagents such as NIBSC 20/130 show lower neutralization against B.1.351 SA (South Africa) and B.1.1.7 UK (United Kingdom) VOC, whereas a commercially available monoclonal antibody MM43 retains activity against both these variants. SARS-CoV-2 spike PBNAs for VOCs would be useful tools to measure the neutralization ability of candidate vaccines in both preclinical models and clinical trials and would further help develop effective prophylactic countermeasures against emerging neutralization escape phenotypes. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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12 pages, 2268 KiB  
Article
Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
by Petr Klempt, Ondřej Brzoň, Martin Kašný, Kateřina Kvapilová, Petr Hubáček, Aleš Briksi, Matěj Bezdíček, Vladimira Koudeláková, Martina Lengerová, Marian Hajdúch, Pavel Dřevínek, Šárka Pospíšilová, Eva Kriegová, Milan Macek and Petr Kvapil
Microorganisms 2021, 9(8), 1671; https://doi.org/10.3390/microorganisms9081671 - 05 Aug 2021
Cited by 7 | Viewed by 3556
Abstract
In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as [...] Read more.
In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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6 pages, 1165 KiB  
Communication
Single-Particle Characterization of SARS-CoV-2 Isoelectric Point and Comparison to Variants of Interest
by Oluwatoyin Areo, Pratik U. Joshi, Mark Obrenovich, Moncef Tayahi and Caryn L. Heldt
Microorganisms 2021, 9(8), 1606; https://doi.org/10.3390/microorganisms9081606 - 28 Jul 2021
Cited by 16 | Viewed by 2858
Abstract
SARS-CoV-2, the cause of COVID-19, is a new, highly pathogenic coronavirus, which is the third coronavirus to emerge in the past 2 decades and the first to become a global pandemic. The virus has demonstrated itself to be extremely transmissible and deadly. Recent [...] Read more.
SARS-CoV-2, the cause of COVID-19, is a new, highly pathogenic coronavirus, which is the third coronavirus to emerge in the past 2 decades and the first to become a global pandemic. The virus has demonstrated itself to be extremely transmissible and deadly. Recent data suggest that a targeted approach is key to mitigating infectivity. Due to the proliferation of cataloged protein and nucleic acid sequences in databases, the function of the nucleic acid, and genetic encoded proteins, we make predictions by simply aligning sequences and exploring their homology. Thus, similar amino acid sequences in a protein usually confer similar biochemical function, even from distal or unrelated organisms. To understand viral transmission and adhesion, it is key to elucidate the structural, surface, and functional properties of each viral protein. This is typically first modeled in highly pathogenic species by exploring folding, hydrophobicity, and isoelectric point (IEP). Recent evidence from viral RNA sequence modeling and protein crystals have been inadequate, which prevent full understanding of the IEP and other viral properties of SARS-CoV-2. We have thus experimentally determined the IEP of SARS-CoV-2. Our findings suggest that for enveloped viruses, such as SARS-CoV-2, estimates of IEP by the amino acid sequence alone may be unreliable. We compared the experimental IEP of SARS-CoV-2 to variants of interest (VOIs) using their amino acid sequence, thus providing a qualitative comparison of the IEP of VOIs. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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8 pages, 1412 KiB  
Communication
Epidemiological Significance of SARS-CoV-2 RNA Dynamic in Naso-Pharyngeal Swabs
by Paolo Calistri, Maria Luisa Danzetta, Laura Amato, Francesca Cito, Alessandra Di Giuseppe, Valentina Zenobio, Daniela Morelli, Ilaria Puglia, Marialuigia Caporale, Silvia Scialabba, Giovanni Savini, Giacomo Migliorati, Nicola D’Alterio and Alessio Lorusso
Microorganisms 2021, 9(6), 1264; https://doi.org/10.3390/microorganisms9061264 - 10 Jun 2021
Cited by 6 | Viewed by 1827
Abstract
From 16 March to 15 December 2020, 132,357 naso-pharyngeal/oropharyngeal swabs were collected in the province of Teramo, Abruzzo Region, Italy, and tested for the presence of SARS-CoV-2 genomic RNA by a commercially available molecular assay. A total of 12,880 swabs resulted positive. For [...] Read more.
From 16 March to 15 December 2020, 132,357 naso-pharyngeal/oropharyngeal swabs were collected in the province of Teramo, Abruzzo Region, Italy, and tested for the presence of SARS-CoV-2 genomic RNA by a commercially available molecular assay. A total of 12,880 swabs resulted positive. For 8212 positive patients (4.150 women and 4.062 men) the median age was statistically different between women (median: 49.55 ± 23.9 of SD) and men (median: 48.35 ± 23.5 of SD) while no differences were found in the comparison between the cycle threshold for the N protein-encoding gene (CT N) median values and gender. Differences were observed in the CT N gene median values of swabs collected from March to September as well as in the pairwise comparison between September and October and between November and December. The CT N gene median values observed in specific periods characterizing the SARS-CoV-2 epidemic in 2020 were also compared with the incidence of COVID-19 cases; a strong inverse correlation was highlighted (Pearson correlation coefficient = −0.978). Our findings confirm the usefulness of the CT N values as an indirect detection parameter to monitor viral loads in the population. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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Article
SARS-CoV-2 IgG Antibodies Seroprevalence and Sera Neutralizing Activity in MEXICO: A National Cross-Sectional Study during 2020
by José Esteban Muñoz-Medina, Concepción Grajales-Muñiz, Angel Gustavo Salas-Lais, Larissa Fernandes-Matano, Constantino López-Macías, Irma Eloísa Monroy-Muñoz, Andrea Santos Coy-Arechavaleta, Iliana Donají Palomec-Nava, Célida Duque-Molina, Ruth Lizzeth Madera-Sandoval, Vanessa Rivero-Arredondo, Joaquín González-Ibarra, Julio Elías Alvarado-Yaah, Teresita Rojas-Mendoza, Clara Esperanza Santacruz-Tinoco, Cesar Raúl González-Bonilla and Víctor Hugo Borja-Aburto
Microorganisms 2021, 9(4), 850; https://doi.org/10.3390/microorganisms9040850 - 15 Apr 2021
Cited by 17 | Viewed by 7441
Abstract
Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in [...] Read more.
Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in the population. In February 2020, the Mexican Social Security Institute began conducting anonymous unrelated sampling of residual sera from specimens across the country, excluding patients with fever within the previous two weeks and/or patients with an acute respiratory infection. Sampling was carried out weekly and began 17 days before Mexico’s first officially confirmed case. The 24,273 sera obtained were analyzed by chemiluminescent-linked immunosorbent assay (CLIA) IgG S1/S2 and, later, positive cases using this technique were also analyzed to determine the rate of neutralization using the enzyme-linked immunosorbent assay (ELISA). We identified 40 CLIA IgG positive cases before the first official report of SARS-CoV-2 infection in Mexico. The national seroprevalence was 3.5% in February and 33.5% in December. Neutralizing activity among IgG positives patients during overall study period was 86.1%. The extent of the SARS-CoV-2 infection in Mexico is 21 times higher than that reported by molecular techniques. Although the general population is still far from achieving herd immunity, epidemiological indicators should be re-estimated based on serological studies of this type. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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8 pages, 215 KiB  
Communication
Persistence of SARS-CoV-2 Viral RNA in Nasopharyngeal Swabs after Death: An Observational Study
by Francesca Servadei, Silvestro Mauriello, Manuel Scimeca, Bartolo Caggiano, Marco Ciotti, Lucia Anemona, Manuela Montanaro, Erica Giacobbi, Michele Treglia, Sergio Bernardini, Luigi Tonino Marsella, Nicoletta Urbano, Orazio Schillaci and Alessandro Mauriello
Microorganisms 2021, 9(4), 800; https://doi.org/10.3390/microorganisms9040800 - 10 Apr 2021
Cited by 10 | Viewed by 2165
Abstract
The aim of this study was to investigate the persistence of SARS-CoV-2 in post-mortem swabs of subjects who died from SARS-CoV-2 infection. The presence of the virus was evaluated post-mortem from airways of 27 SARS-CoV-2 positive patients at three different time points (T1 [...] Read more.
The aim of this study was to investigate the persistence of SARS-CoV-2 in post-mortem swabs of subjects who died from SARS-CoV-2 infection. The presence of the virus was evaluated post-mortem from airways of 27 SARS-CoV-2 positive patients at three different time points (T1 2 h; T2 12 h; T3 24 h) by real-time PCR. Detection of antibodies to SARS-CoV-2 was performed by Maglumi 2019-nCoV IgM/IgG chemiluminescence assay. SARS-CoV-2 viral RNA was still detectable in 70.3% of cases within 2 h after death and in 66,6% of cases up to 24 h after death. Our data showed an increase of the viral load in 78,6% of positive individuals 24 h post-mortem (T3) in comparison to that evaluated 2 h after death (T1). Noteworthy, we detected a positive T3 post-mortem swab (24 h after death) from 4 subjects who were negative at T1 (2 h after death). The results of our study may have an important value in the management of deceased subjects not only with a suspected or confirmed diagnosis of SARS-CoV-2, but also for unspecified causes and in the absence of clinical documentation or medical assistance. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
10 pages, 2098 KiB  
Article
A Study of 3CLpros as Promising Targets against SARS-CoV and SARS-CoV-2
by Seri Jo, Suwon Kim, Jahyun Yoo, Mi-Sun Kim and Dong Hae Shin
Microorganisms 2021, 9(4), 756; https://doi.org/10.3390/microorganisms9040756 - 03 Apr 2021
Cited by 6 | Viewed by 2741
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), results in serious chaos all over the world. In addition to the available vaccines, the development of treatments to cure COVID-19 should be done quickly. One of [...] Read more.
The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), results in serious chaos all over the world. In addition to the available vaccines, the development of treatments to cure COVID-19 should be done quickly. One of the fastest strategies is to use a drug-repurposing approach. To provide COVID-19 patients with useful information about medicines currently being used in clinical trials, twenty-four compounds, including antiviral agents, were selected and assayed. These compounds were applied to verify the inhibitory activity for the protein function of 3CLpros (main proteases) of SARS-CoV and SARS-CoV-2. Among them, viral reverse-transcriptase inhibitors abacavir and tenofovir revealed a good inhibitory effect on both 3CLpros. Intriguingly, sildenafil, a cGMP-specific phosphodiesterase type 5 inhibitor also showed significant inhibitory function against them. The in silico docking study suggests that the active-site residues located in the S1 and S2 sites play key roles in the interactions with the inhibitors. The result indicates that 3CLpros are promising targets to cope with SAR-CoV-2 and its variants. The information can be helpful to design treatments to cure patients with COVID-19. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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10 pages, 958 KiB  
Communication
Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7
by Marek Widera, Barbara Mühlemann, Victor M. Corman, Tuna Toptan, Jörn Beheim-Schwarzbach, Niko Kohmer, Julia Schneider, Annemarie Berger, Talitha Veith, Christiane Pallas, Tobias Bleicker, Udo Goetsch, Julia Tesch, Rene Gottschalk, Terry C. Jones, Sandra Ciesek and Christian Drosten
Microorganisms 2021, 9(4), 748; https://doi.org/10.3390/microorganisms9040748 - 02 Apr 2021
Cited by 11 | Viewed by 7358
Abstract
Background: International travel is a major driver of the introduction and spread of SARS-CoV-2. Aim: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt [...] Read more.
Background: International travel is a major driver of the introduction and spread of SARS-CoV-2. Aim: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020. Methods: In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced. Results and conclusion: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Δ69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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14 pages, 2582 KiB  
Article
SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
by Ana Rita Goncalves Cabecinhas, Tim Roloff, Madlen Stange, Claire Bertelli, Michael Huber, Alban Ramette, Chaoran Chen, Sarah Nadeau, Yannick Gerth, Sabine Yerly, Onya Opota, Trestan Pillonel, Tobias Schuster, Cesar M. J. A. Metzger, Jonas Sieber, Michael Bel, Nadia Wohlwend, Christian Baumann, Michel C. Koch, Pascal Bittel, Karoline Leuzinger, Myrta Brunner, Franziska Suter-Riniker, Livia Berlinger, Kirstine K. Søgaard, Christiane Beckmann, Christoph Noppen, Maurice Redondo, Ingrid Steffen, Helena M. B. Seth-Smith, Alfredo Mari, Reto Lienhard, Martin Risch, Oliver Nolte, Isabella Eckerle, Gladys Martinetti Lucchini, Emma B. Hodcroft, Richard A. Neher, Tanja Stadler, Hans H. Hirsch, Stephen L. Leib, Lorenz Risch, Laurent Kaiser, Alexandra Trkola, Gilbert Greub and Adrian Egliadd Show full author list remove Hide full author list
Microorganisms 2021, 9(4), 677; https://doi.org/10.3390/microorganisms9040677 - 25 Mar 2021
Cited by 27 | Viewed by 5698
Abstract
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the [...] Read more.
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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11 pages, 966 KiB  
Article
Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants
by Esther Viedma, Elias Dahdouh, José María González-Alba, Sara González-Bodi, Laura Martínez-García, Fernando Lázaro-Perona, Raúl Recio, María Rodríguez-Tejedor, María Dolores Folgueira, Rafael Cantón, Rafael Delgado, Julio García-Rodríguez, Juan Carlos Galán, Jesús Mingorance and on behalf of the SARS-CoV-2 Working Groups
Microorganisms 2021, 9(2), 454; https://doi.org/10.3390/microorganisms9020454 - 22 Feb 2021
Cited by 9 | Viewed by 3539
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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12 pages, 1245 KiB  
Article
Do Blood Eosinophils Predict in-Hospital Mortality or Severity of Disease in SARS-CoV-2 Infection? A Retrospective Multicenter Study
by Pierrick Le Borgne, Laure Abensur Vuillaume, Karine Alamé, François Lefebvre, Sylvie Chabrier, Lise Bérard, Pauline Haessler, Stéphane Gennai, Pascal Bilbault and Charles-Eric Lavoignet
Microorganisms 2021, 9(2), 334; https://doi.org/10.3390/microorganisms9020334 - 08 Feb 2021
Cited by 9 | Viewed by 2360
Abstract
Introduction: Healthcare systems worldwide have been battling the ongoing COVID-19 pandemic. Eosinophils are multifunctional leukocytes implicated in the pathogenesis of several inflammatory processes including viral infections. We focus our study on the prognostic value of eosinopenia as a marker of disease severity and [...] Read more.
Introduction: Healthcare systems worldwide have been battling the ongoing COVID-19 pandemic. Eosinophils are multifunctional leukocytes implicated in the pathogenesis of several inflammatory processes including viral infections. We focus our study on the prognostic value of eosinopenia as a marker of disease severity and mortality in COVID-19 patients. Methods: Between 1 March and 30 April 2020, we conducted a multicenter and retrospective study on a cohort of COVID-19 patients (moderate or severe disease) who were hospitalized after presenting to the emergency department (ED). We led our study in six major hospitals of northeast France, one of the outbreak’s epicenters in Europe. Results: We have collected data from 1035 patients, with a confirmed diagnosis of COVID-19. More than three quarters of them (76.2%) presented a moderate form of the disease, while the remaining quarter (23.8%) presented a severe form requiring admission to the intensive care unit (ICU). Mean circulating eosinophils rate, at admission, varied according to disease severity (p < 0.001), yet it did not differ between survivors and non-survivors (p = 0.306). Extreme eosinopenia (=0/mm3) was predictive of severity (aOR = 1.77, p = 0.009); however, it was not predictive of mortality (aOR = 0.892, p = 0.696). The areas under the Receiver operating characteristics (ROC) curve were, respectively, 58.5% (CI95%: 55.3–61.7%) and 51.4% (CI95%: 46.8–56.1%) for the ability of circulating eosinophil rates to predict disease severity and mortality. Conclusion: Eosinopenia is very common and often profound in cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Eosinopenia was not a useful predictor of mortality; however, undetectable eosinophils (=0/mm3) were predictive of disease severity during the initial ED management. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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12 pages, 1458 KiB  
Communication
SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data
by Tristan Cardon, Isabelle Fournier and Michel Salzet
Microorganisms 2020, 8(12), 2036; https://doi.org/10.3390/microorganisms8122036 - 19 Dec 2020
Cited by 2 | Viewed by 2430
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the [...] Read more.
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this “ghost proteome” was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts, we were interested in finding out their interaction with the viral protein coming from the SARS-CoV-2 virus, responsible for the 2020 COVID-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by affinity purification in co-immunoprecipitation (co-IP) in the perspective of drug repurposing. The initial work revealed the interaction between 332 human cellular reference proteins (RefProts) with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study), plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the ghost proteome for discovering new therapeutic targets, and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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15 pages, 2573 KiB  
Article
HCoV-NL63 and SARS-CoV-2 Share Recognized Epitopes by the Humoral Response in Sera of People Collected Pre- and during CoV-2 Pandemic
by Elena Rita Simula, Maria Antonietta Manca, Seyedsomaye Jasemi, Sergio Uzzau, Salvatore Rubino, Pierangela Manchia, Angela Bitti, Mario Palermo and Leonardo A. Sechi
Microorganisms 2020, 8(12), 1993; https://doi.org/10.3390/microorganisms8121993 - 14 Dec 2020
Cited by 20 | Viewed by 4067
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause serious illness in older adults and people with chronic underlying medical conditions; however, children and young people are often asymptomatic or with mild symptoms. We evaluated the presence of specific antibodies (Abs) response against [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause serious illness in older adults and people with chronic underlying medical conditions; however, children and young people are often asymptomatic or with mild symptoms. We evaluated the presence of specific antibodies (Abs) response against Human coronavirus NL63 (HCoV-NL63) S protein epitopes (NL63-RBM1, NL63-RBM2_1, NL63-RBM2_2, NL63-RBM3, NL63-SPIKE541–554, and NL63-DISC-like) and SARS-CoV-2 epitopes (COV2-SPIKE421–434 and COV2-SPIKE742–759) in plasma samples of pre-pandemic, mid-pandemic, and COVID-19 cohorts by indirect ELISA. Moreover, a competitive assay was performed to check for cross reactivity response between COV2-SPIKE421–434 and NL63-RBM3 among patients with a definitive diagnosis of SARS-CoV-2. Immune reaction against all SARS-CoV-2 and HCoV-NL63 epitopes showed a significantly higher response in pre-pandemic patients compared to mid-pandemic patients. The results indicate that probably antibodies against HCoV-NL63 may be able to cross react with SARS-CoV-2 epitopes and the higher incidence in pre-pandemic was probably due to the timing of collection when a high incidence of HCoV-NL63 is reported. In addition, the competitive assay showed cross-reactivity between antibodies directed against COV2-SPIKE421–434 and NL63-RBM3 peptides. Pre-existing HCoV-NL63 antibody response cross reacting with SARS-CoV-2 has been detected in both pre- and mid-pandemic individual, suggesting that previous exposure to HCoV-NL63 epitopes may produce antibodies which could confer a protective immunity against SARS-CoV-2 and probably reduce the severity of the disease. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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8 pages, 619 KiB  
Communication
Duration of COVID-19: Data from an Italian Cohort and Potential Role for Steroids
by Damiano D’Ardes, Michela Pontolillo, Lucia Esposito, Mara Masciarelli, Andrea Boccatonda, Ilaria Rossi, Marco Bucci, Maria Teresa Guagnano, Claudio Ucciferri, Francesca Santilli, Marta Di Nicola, Katia Falasca, Jacopo Vecchiet, Thomas Schael and Francesco Cipollone
Microorganisms 2020, 8(9), 1327; https://doi.org/10.3390/microorganisms8091327 - 31 Aug 2020
Cited by 18 | Viewed by 2758
Abstract
The diffusion of SARS-CoV-2, starting from China in December 2019, has led to a pandemic, reaching Italy in February 2020. Previous studies in Asia have shown that the median duration of SARS-CoV-2 viral shedding was approximately 12–20 days. We considered a cohort of [...] Read more.
The diffusion of SARS-CoV-2, starting from China in December 2019, has led to a pandemic, reaching Italy in February 2020. Previous studies in Asia have shown that the median duration of SARS-CoV-2 viral shedding was approximately 12–20 days. We considered a cohort of patients recovered from COVID-19 showing that the median disease duration between onset and end of COVID-19 symptoms was 27.5 days (interquartile range (IQR): 17.0–33.2) and that the median duration between onset of symptoms and microbiological healing, defined by two consecutive negative nasopharyngeal swabs, was 38 days (IQR: 31.7–50.2). A longer duration of COVID-19 with delayed clinical healing (symptom-free) occurred in patients presenting at admission a lower PaO2/FiO2 ratio (p < 0.001), a more severe clinical presentation (p = 0.001) and a lower lymphocyte count (p = 0.035). Moreover, patients presenting at admission a lower PaO2/FiO2 ratio and more severe disease showed longer viral shedding (p = 0.031 and p = 0.032, respectively). In addition, patients treated with corticosteroids had delayed clinical healing (p = 0.013). Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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12 pages, 1736 KiB  
Article
Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis
by Martina Rueca, Barbara Bartolini, Cesare Ernesto Maria Gruber, Antonio Piralla, Fausto Baldanti, Emanuela Giombini, Francesco Messina, Luisa Marchioni, Giuseppe Ippolito, Antonino Di Caro and Maria Rosaria Capobianchi
Microorganisms 2020, 8(9), 1302; https://doi.org/10.3390/microorganisms8091302 - 26 Aug 2020
Cited by 35 | Viewed by 4439
Abstract
We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six [...] Read more.
We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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19 pages, 2671 KiB  
Article
Forecasting the Spreading of COVID-19 across Nine Countries from Europe, Asia, and the American Continents Using the ARIMA Models
by Ovidiu-Dumitru Ilie, Roxana-Oana Cojocariu, Alin Ciobica, Sergiu-Ioan Timofte, Ioannis Mavroudis and Bogdan Doroftei
Microorganisms 2020, 8(8), 1158; https://doi.org/10.3390/microorganisms8081158 - 30 Jul 2020
Cited by 34 | Viewed by 5236
Abstract
Since mid-November 2019, when the first SARS-CoV-2-infected patient was officially reported, the new coronavirus has affected over 10 million people from which half a million died during this short period. There is an urgent need to monitor, predict, and restrict COVID-19 in a [...] Read more.
Since mid-November 2019, when the first SARS-CoV-2-infected patient was officially reported, the new coronavirus has affected over 10 million people from which half a million died during this short period. There is an urgent need to monitor, predict, and restrict COVID-19 in a more efficient manner. This is why Auto-Regressive Integrated Moving Average (ARIMA) models have been developed and used to predict the epidemiological trend of COVID-19 in Ukraine, Romania, the Republic of Moldova, Serbia, Bulgaria, Hungary, USA, Brazil, and India, these last three countries being otherwise the most affected presently. To increase accuracy, the daily prevalence data of COVID-19 from 10 March 2020 to 10 July 2020 were collected from the official website of the Romanian Government GOV.RO, World Health Organization (WHO), and European Centre for Disease Prevention and Control (ECDC) websites. Several ARIMA models were formulated with different ARIMA parameters. ARIMA (1, 1, 0), ARIMA (3, 2, 2), ARIMA (3, 2, 2), ARIMA (3, 1, 1), ARIMA (1, 0, 3), ARIMA (1, 2, 0), ARIMA (1, 1, 0), ARIMA (0, 2, 1), and ARIMA (0, 2, 0) models were chosen as the best models, depending on their lowest Mean Absolute Percentage Error (MAPE) values for Ukraine, Romania, the Republic of Moldova, Serbia, Bulgaria, Hungary, USA, Brazil, and India (4.70244, 1.40016, 2.76751, 2.16733, 2.98154, 2.11239, 3.21569, 4.10596, 2.78051). This study demonstrates that ARIMA models are suitable for making predictions during the current crisis and offers an idea of the epidemiological stage of these regions. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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10 pages, 2391 KiB  
Article
SARS-CoV-2 RNA Persistence in Naso-Pharyngeal Swabs
by Maria Luisa Danzetta, Laura Amato, Francesca Cito, Alessandra Di Giuseppe, Daniela Morelli, Giovanni Savini, Maria Teresa Mercante, Alessio Lorusso, Ottavio Portanti, Ilaria Puglia, Federica Monaco, Claudia Casaccia, Annapia Di Gennaro, Lilia Testa, Giacomo Migliorati, Nicola D’Alterio and Paolo Calistri
Microorganisms 2020, 8(8), 1124; https://doi.org/10.3390/microorganisms8081124 - 26 Jul 2020
Cited by 22 | Viewed by 3462
Abstract
Since February 2020, Italy has been seriously affected by the SARS-CoV-2 pandemic. To support the National Health Care system, naso-pharyngeal/oropharyngeal swabs collected from suspected cases of Teramo province, Abruzzo region, are tested at Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, for [...] Read more.
Since February 2020, Italy has been seriously affected by the SARS-CoV-2 pandemic. To support the National Health Care system, naso-pharyngeal/oropharyngeal swabs collected from suspected cases of Teramo province, Abruzzo region, are tested at Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise G. Caporale, for the presence of SARS-CoV-2 RNA. Out of 12,446 tested individuals, 605 returned positive results at least once, with prevalence significantly higher in men. A reduction of the level of viral RNA in the first swab per each positive patient collected over time was also observed. Moreover, 81 patients had at least one positive sample and two final negative tests: positivity in swabs lasted from 14 to 63 days, with a median value of 30 days. This shows the potential for the virus to coexist with patients for a long time, although we highlighted intermittent positivity in several cases. The evolution of the SARS-CoV-2 epidemiological situation and knowledge on viral shedding should be closely monitored, to interpret the findings correctly and adjust accordingly the surveillance activities. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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21 pages, 7368 KiB  
Article
A Municipality-Based Approach Using Commuting Census Data to Characterize the Vulnerability to Influenza-Like Epidemic: The COVID-19 Application in Italy
by Lara Savini, Luca Candeloro, Paolo Calistri and Annamaria Conte
Microorganisms 2020, 8(6), 911; https://doi.org/10.3390/microorganisms8060911 - 16 Jun 2020
Cited by 11 | Viewed by 3247
Abstract
In February 2020, Italy became the epicenter for COVID-19 in Europe, and at the beginning of March, the Italian Government put in place emergency measures to restrict population movement. Aim of our analysis is to provide a better understanding of the epidemiological context [...] Read more.
In February 2020, Italy became the epicenter for COVID-19 in Europe, and at the beginning of March, the Italian Government put in place emergency measures to restrict population movement. Aim of our analysis is to provide a better understanding of the epidemiological context of COVID-19 in Italy, using commuting data at a high spatial resolution, characterizing the territory in terms of vulnerability. We used a Susceptible–Infectious stochastic model and we estimated a municipality-specific infection contact rate (β) to capture the susceptibility to the disease. We identified in Lombardy, Veneto and Emilia Romagna regions (52% of all Italian cases) significant clusters of high β, due to the simultaneous presence of connections between municipalities and high population density. Local simulated spreading in regions, with different levels of infection observed, showed different disease geographical patterns due to different β values and commuting systems. In addition, we produced a vulnerability map (in the Abruzzi region as an example) by simulating the epidemic considering each municipality as a seed. The result shows the highest vulnerability values in areas with commercial hubs, close to the highest populated cities and the most industrial area. Our results highlight how human mobility can affect the epidemic, identifying particular situations in which the health authorities can promptly intervene to control the disease spread. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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Review

Jump to: Editorial, Research

13 pages, 1179 KiB  
Review
Severity, Pathogenicity and Transmissibility of Delta and Lambda Variants of SARS-CoV-2, Toxicity of Spike Protein and Possibilities for Future Prevention of COVID-19
by Mehrnoosh Moghaddar, Ramtin Radman and Ian Macreadie
Microorganisms 2021, 9(10), 2167; https://doi.org/10.3390/microorganisms9102167 - 18 Oct 2021
Cited by 28 | Viewed by 6288
Abstract
The World Health Organization reports that SARS-CoV-2 has infected over 220 million people and claimed over 4.7 million lives globally. While there are new effective vaccines, the differences in behavior of variants are causing challenges in vaccine development or treatment. Here, we discuss [...] Read more.
The World Health Organization reports that SARS-CoV-2 has infected over 220 million people and claimed over 4.7 million lives globally. While there are new effective vaccines, the differences in behavior of variants are causing challenges in vaccine development or treatment. Here, we discuss Delta, a variant of concern, and Lambda, a variant of interest. They demonstrate high infectivity and are less responsive to the immune response in vaccinated individuals. In this review, we briefly summarize the reason for infectivity and the severity of the novel variants. Delta and Lambda variants exhibit more changes in NSPs proteins and the S protein, compared to the original Wuhan strain. Lambda also has numerous amino acid substitutions in NSPs and S proteins, plus a deletion in the NTD of S protein, leading to partial escape from neutralizing antibodies (NAbs) in vaccinated individuals. We discuss the role of furin protease and the ACE2 receptor in virus infection, hotspot mutations in the S protein, the toxicity of the S protein and the increased pathogenicity of Delta and Lambda variants. We discuss future therapeutic strategies, including those based on high stability of epitopes, conservation of the N protein and the novel intracellular antibody receptor, tripartite-motif protein 21 (TRIM21) recognized by antibodies against the N protein. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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19 pages, 356 KiB  
Review
COVID-19: Insights into Potential Vaccines
by Ke-Yan Loo, Vengadesh Letchumanan, Hooi-Leng Ser, Siew Li Teoh, Jodi Woan-Fei Law, Loh Teng-Hern Tan, Nurul-Syakima Ab Mutalib, Kok-Gan Chan and Learn-Han Lee
Microorganisms 2021, 9(3), 605; https://doi.org/10.3390/microorganisms9030605 - 15 Mar 2021
Cited by 50 | Viewed by 6179
Abstract
People around the world ushered in the new year 2021 with a fear of COVID-19, as family members have lost their loved ones to the disease. Millions of people have been infected, and the livelihood of many has been jeopardized due to the [...] Read more.
People around the world ushered in the new year 2021 with a fear of COVID-19, as family members have lost their loved ones to the disease. Millions of people have been infected, and the livelihood of many has been jeopardized due to the pandemic. Pharmaceutical companies are racing against time to develop an effective vaccine to protect against COVID-19. Researchers have developed various types of candidate vaccines with the release of the genetic sequence of the SARS-CoV-2 virus in January. These include inactivated viral vaccines, protein subunit vaccines, mRNA vaccines, and recombinant viral vector vaccines. To date, several vaccines have been authorized for emergency use and they have been administered in countries across the globe. Meanwhile, there are also vaccine candidates in Phase III clinical trials awaiting results and approval from authorities. These candidates have shown positive results in the previous stages of the trials, whereby they could induce an immune response with minimal side effects in the participants. This review aims to discuss the different vaccine platforms and the clinical trials of the candidate vaccines. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
10 pages, 574 KiB  
Review
SARS-CoV-2 Pandemic: Not the First, Not the Last
by Paolo Calistri, Nicola Decaro and Alessio Lorusso
Microorganisms 2021, 9(2), 433; https://doi.org/10.3390/microorganisms9020433 - 19 Feb 2021
Cited by 6 | Viewed by 2554
Abstract
The common trait among the betacoronaviruses that emerged during the past two decades (the severe acute respiratory syndrome coronavirus—SARS-CoV, the Middle East respiratory syndrome coronavirus—MERS-CoV, and the recent SARS coronavirus 2—SARS-CoV-2) is their probable animal origin, all deriving from viruses present in bat [...] Read more.
The common trait among the betacoronaviruses that emerged during the past two decades (the severe acute respiratory syndrome coronavirus—SARS-CoV, the Middle East respiratory syndrome coronavirus—MERS-CoV, and the recent SARS coronavirus 2—SARS-CoV-2) is their probable animal origin, all deriving from viruses present in bat species. Bats have arisen the attention of the scientific community as reservoir of emerging viruses, given their wide geographical distribution, their biological diversity (around 1400 species, 21 different families and over 200 genera), and their peculiar ecological and physiological characteristics which seem to facilitate them in harbouring a high viral diversity. Several human activities may enable the viral spill-over from bats to humans, such as deforestation, land-use changes, increased livestock grazing or intensive production of vegetal cultures. In addition, the globalization of trade and high global human mobility allow these viruses to be disseminated in few hours in many parts of the World. In order to avoid the emergence of new pandemic threats in the future we need to substantially change our global models of social and economic development, posing the conservation of biodiversity and the preservation of natural ecosystems as a pillar for the protection of global human health. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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13 pages, 1015 KiB  
Review
Severe COVID-19 and Sepsis: Immune Pathogenesis and Laboratory Markers
by Mai M. Zafer, Hadir A. El-Mahallawy and Hossam M. Ashour
Microorganisms 2021, 9(1), 159; https://doi.org/10.3390/microorganisms9010159 - 12 Jan 2021
Cited by 37 | Viewed by 9462
Abstract
The ongoing outbreak of the novel coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has taken a significant toll on people and countries all over the world. The pathogenesis of COVID-19 has not been completely elucidated yet. This [...] Read more.
The ongoing outbreak of the novel coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has taken a significant toll on people and countries all over the world. The pathogenesis of COVID-19 has not been completely elucidated yet. This includes the interplay between inflammation and coagulation which needs further investigation. The massive production of proinflammatory cytokines and chemokines results in the so-called cytokine storm, leading to plasma leakage, vascular hyperpermeability, and disseminated vascular coagulation. This is usually accompanied by multiorgan failure. The extensive changes in the serum levels of cytokines are thought to play a crucial role in the COVID-19 pathogenesis. Additionally, the viral load and host inflammation factors are believed to have a significant role in host damage, particularly lung damage, from SARS-CoV-2. Interestingly, patients exhibit quantitative and qualitative differences in their immune responses to the virus, which can impact the clinical manifestation and outcomes of COVID-19. There needs to be a better understanding of the dynamic events that involve immune responses, inflammatory reactions, and viral replication in the context of the COVID-19 infection. Here, we discuss the main aspects of COVID-19 pathogenesis while supporting the hypothesis that inflammatory immune responses are involved in the progression of the disease to a more critical and fatal phase. We also explore the similarities and differences between severe COVID-19 and sepsis. A deeper understanding of the COVID-19 clinical picture as it relates to better-known conditions such as sepsis can provide useful clues for the management, prevention, and therapy of the disease. Full article
(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)
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