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Viruses
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State-of-the-Art Emerging Respiratory Viruses in Europe
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State-of-the-Art Emerging Respiratory Viruses in Europe

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 55747

Special Issue Editor

Prof. Dr. Vittorio Sambri

E-Mail Website
Guest Editor
Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
Interests: emerging viral infections; spirochetes; molecular applications for the microbiological diagnosis of infections. application of artificial intelligence to the microbiological diagnosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The year 2020 saw an unprecedented pandemic outbreak worldwide, caused by a novel member of the viral family Coronaviridae, identified as SARS CoV-2. This novel virus, likely of animal origin, acquired the capability to efficiently infect humans causing a severe acute respiratory syndrome identified by WHO as COVID-19 (coronavirus disease-19). The very first episodes of COVID-19 were reported in December 2019 in the Chinese city of Wuhan (the province of Hubei), Europe, and, in particular, Italy was among the first areas that this novel infection spread with hundreds of thousands of people affected. By the end of 2020, the infection had reached millions of people worldwide, thus becoming the most relevant and devastating pandemic since the Spanish Flu that occurred a century ago. All of this prompted an enormous scientific effort worldwide to increase our knowledge of the virus and the possibility to set up an efficient laboratory and territorial diagnostics workflows, the pathogenesis of COVD-19, the possibility to use effective therapies for COVID-19, and the development of effective strategies to control the diffusion of the pandemic outbreak.

This Special Issue will provide a tool for peer-reviewed dissemination of cutting-edge scientific results obtained in all of the fields related to the identification, clinical picture, treatment, and epidemic control of the infection caused by SARS CoV-2 and related potential emerging respiratory viruses in Europe.

Prof. Dr. Vittorio Sambri
Guest Editor

Manuscript Submission Information

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

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

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

Keywords

  • COVID-19 (including pathogenesis and clinical picture), virology of SARS CoV-2 and other emerging respiratory viruses
  • laboratory diagnosis of COVID-19
  • treatment for SARS CoV-2 infection
  • strategies and modeling for the control of COVID-19 and other potential epidemic viral infections
  • genetics of SARS CoV-2
  • environment and diffusion of SARS CoV-2

Related Special Issue

Published Papers (6 papers)

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Research

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30 pages, 5217 KiB  
Article
A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic
by Andreas C. Chrysostomou, Bram Vrancken, George Koumbaris, George Themistokleous, Antonia Aristokleous, Christina Masia, Christina Eleftheriou, Costakis Iοannou, Dora C. Stylianou, Marios Ioannides, Panagiotis Petrou, Vasilis Georgiou, Amalia Hatziyianni, Philippe Lemey, Anne-Mieke Vandamme, Philippos P. Patsalis and Leondios G. Kostrikis
Viruses 2021, 13(6), 1098; https://doi.org/10.3390/v13061098 - 09 Jun 2021
Cited by 11 | Viewed by 5119
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial [...] Read more.
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in an extraordinary global public health crisis. In early 2020, Cyprus, among other European countries, was affected by the SARS-CoV-2 epidemic and adopted lockdown measures in March 2020 to limit the initial outbreak on the island. In this study, we performed a comprehensive retrospective molecular epidemiological analysis (genetic, phylogenetic, phylodynamic and phylogeographic analyses) of SARS-CoV-2 isolates in Cyprus from April 2020 to January 2021, covering the first ten months of the SARS-CoV-2 infection epidemic on the island. The primary aim of this study was to assess the transmissibility of SARS-CoV-2 lineages in Cyprus. Whole SARS-CoV-2 genomic sequences were generated from 596 clinical samples (nasopharyngeal swabs) obtained from community-based diagnostic testing centers and hospitalized patients. The phylogenetic analyses revealed a total of 34 different lineages in Cyprus, with B.1.258, B.1.1.29, B.1.177, B.1.2, B.1 and B.1.1.7 (designated a Variant of Concern 202012/01, VOC) being the most prevalent lineages on the island during the study period. Phylodynamic analysis showed a highly dynamic epidemic of SARS-CoV-2 infection, with three consecutive surges characterized by specific lineages (B.1.1.29 from April to June 2020; B.1.258 from September 2020 to January 2021; and B.1.1.7 from December 2020 to January 2021). Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, ΔH69/V70, S898F, ΔY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. Phylogeographic analysis indicated that the majority of imports and exports were to and from the United Kingdom (UK), although many other regions/countries were identified (southeastern Asia, southern Europe, eastern Europe, Germany, Italy, Brazil, Chile, the USA, Denmark, the Czech Republic, Slovenia, Finland, Switzerland and Pakistan). Taken together, these findings demonstrate that the SARS-CoV-2 infection epidemic in Cyprus is being maintained by a continuous influx of lineages from many countries, resulting in the establishment of an ever-evolving and polyphyletic virus on the island. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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9 pages, 671 KiB  
Article
Frontline Screening for SARS-CoV-2 Infection at Emergency Department Admission by Third Generation Rapid Antigen Test: Can We Spare RT-qPCR?
by Valeria Cento, Silvia Renica, Elisa Matarazzo, Maria Antonello, Luna Colagrossi, Federica Di Ruscio, Arianna Pani, Diana Fanti, Chiara Vismara, Massimo Puoti, Francesco Scaglione, Carlo Federico Perno, Claudia Alteri and on behalf of the S.Co.Va Study Group
Viruses 2021, 13(5), 818; https://doi.org/10.3390/v13050818 - 01 May 2021
Cited by 16 | Viewed by 3388
Abstract
To complement RT-qPCR testing for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, many countries have introduced the use of rapid antigen tests. As they generally display lower real-life performances than expected, their correct positioning as frontline screening is still controversial. [...] Read more.
To complement RT-qPCR testing for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, many countries have introduced the use of rapid antigen tests. As they generally display lower real-life performances than expected, their correct positioning as frontline screening is still controversial. Despite the lack of data from daily clinical use, third generation microfluidic assays (such as the LumiraDx SARS-CoV-2 Ag test) have recently been suggested to have similar performances to RT-qPCR and have been proposed as alternative diagnostic tools. By analyzing 960 nasopharyngeal swabs from 960 subjects at the emergency department admissions of a tertiary COVID-19 hospital, LumiraDx assay demonstrated a specificity of 97% (95% CI: 96–98), and a sensitivity of 85% (95% CI: 82–89) in comparison with RT-qPCR, which increases to 91% (95% CI: 86–95) for samples with a cycle threshold ≤ 29. Fifty false-negative LumiraDx-results were confirmed by direct quantification of genomic SARS-CoV-2 RNA through droplet-digital PCR (median (IQR) load = 5880 (1657–41,440) copies/mL). Subgenomic N and E RNAs were detected in 52% (n = 26) and 56% (n = 28) of them, respectively, supporting the presence of active viral replication. Overall, the LumiraDx test complies with the minimum performance requirements of the WHO. Yet, the risk of a misrecognition of patients with active COVID-19 persists, and the need for confirmatory RT-qPCR should not be amended. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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19 pages, 3430 KiB  
Article
Thapsigargin Is a Broad-Spectrum Inhibitor of Major Human Respiratory Viruses: Coronavirus, Respiratory Syncytial Virus and Influenza A Virus
by Sarah Al-Beltagi, Cristian Alexandru Preda, Leah V. Goulding, Joe James, Juan Pu, Paul Skinner, Zhimin Jiang, Belinda Lei Wang, Jiayun Yang, Ashley C. Banyard, Kenneth H. Mellits, Pavel Gershkovich, Christopher J. Hayes, Jonathan Nguyen-Van-Tam, Ian H. Brown, Jinhua Liu and Kin-Chow Chang
Viruses 2021, 13(2), 234; https://doi.org/10.3390/v13020234 - 03 Feb 2021
Cited by 30 | Viewed by 31089
Abstract
The long-term control strategy of SARS-CoV-2 and other major respiratory viruses needs to include antivirals to treat acute infections, in addition to the judicious use of effective vaccines. Whilst COVID-19 vaccines are being rolled out for mass vaccination, the modest number of antivirals [...] Read more.
The long-term control strategy of SARS-CoV-2 and other major respiratory viruses needs to include antivirals to treat acute infections, in addition to the judicious use of effective vaccines. Whilst COVID-19 vaccines are being rolled out for mass vaccination, the modest number of antivirals in use or development for any disease bears testament to the challenges of antiviral development. We recently showed that non-cytotoxic levels of thapsigargin (TG), an inhibitor of the sarcoplasmic/endoplasmic reticulum (ER) Ca2+ ATPase pump, induces a potent host innate immune antiviral response that blocks influenza A virus replication. Here we show that TG is also highly effective in blocking the replication of respiratory syncytial virus (RSV), common cold coronavirus OC43, SARS-CoV-2 and influenza A virus in immortalized or primary human cells. TG’s antiviral performance was significantly better than remdesivir and ribavirin in their respective inhibition of OC43 and RSV. Notably, TG was just as inhibitory to coronaviruses (OC43 and SARS-CoV-2) and influenza viruses (USSR H1N1 and pdm 2009 H1N1) in separate infections as in co-infections. Post-infection oral gavage of acid-stable TG protected mice against a lethal influenza virus challenge. Together with its ability to inhibit the different viruses before or during active infection, and with an antiviral duration of at least 48 h post-TG exposure, we propose that TG (or its derivatives) is a promising broad-spectrum inhibitor against SARS-CoV-2, OC43, RSV and influenza virus. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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Review

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18 pages, 882 KiB  
Review
Potential Diagnostic and Prognostic Biomarkers for Adenovirus Respiratory Infection in Children and Young Adults
by Giovanni Battista Biserni, Sara Scarpini, Arianna Dondi, Carlotta Biagi, Luca Pierantoni, Riccardo Masetti, Sugitha Sureshkumar, Alessandro Rocca and Marcello Lanari
Viruses 2021, 13(9), 1885; https://doi.org/10.3390/v13091885 - 21 Sep 2021
Cited by 10 | Viewed by 4585
Abstract
Human Adenoviruses (HAdV) are known to be potentially associated with strong inflammatory responses and morbidity in pediatric patients. Although most of the primary infections are self-limiting, the severity of clinical presentation, the elevation of the white blood cell count and inflammatory markers often [...] Read more.
Human Adenoviruses (HAdV) are known to be potentially associated with strong inflammatory responses and morbidity in pediatric patients. Although most of the primary infections are self-limiting, the severity of clinical presentation, the elevation of the white blood cell count and inflammatory markers often mimic a bacterial infection and lead to an inappropriate use of antibiotics. In infections caused by HAdV, rapid antigen detection kits are advisable but not employed routinely; costs and feasibility of rapid syndromic molecular diagnosis may limit its use in the in-hospital setting; lymphocyte cultures and two-sampled serology are time consuming and impractical when considering the use of antibiotics. In this review, we aim to describe the principal diagnostic tools and the immune response in HAdV infections and evaluate whether markers based on the response of the host may help early recognition of HAdV and avoid inappropriate antimicrobial prescriptions in acute airway infections. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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14 pages, 746 KiB  
Review
SARS-CoV-2 Infections in Animals: Reservoirs for Reverse Zoonosis and Models for Study
by Tessa Prince, Shirley L. Smith, Alan D. Radford, Tom Solomon, Grant L. Hughes and Edward I. Patterson
Viruses 2021, 13(3), 494; https://doi.org/10.3390/v13030494 - 17 Mar 2021
Cited by 51 | Viewed by 7481
Abstract
The recent SARS-CoV-2 pandemic has brought many questions over the origin of the virus, the threat it poses to animals both in the wild and captivity, and the risks of a permanent viral reservoir developing in animals. Animal experiments have shown that a [...] Read more.
The recent SARS-CoV-2 pandemic has brought many questions over the origin of the virus, the threat it poses to animals both in the wild and captivity, and the risks of a permanent viral reservoir developing in animals. Animal experiments have shown that a variety of animals can become infected with the virus. While coronaviruses have been known to infect animals for decades, the true intermediate host of the virus has not been identified, with no cases of SARS-CoV-2 in wild animals. The screening of wild, farmed, and domesticated animals is necessary to help us understand the virus and its origins and prevent future outbreaks of both COVID-19 and other diseases. There is intriguing evidence that farmed mink infections (acquired from humans) have led to infection of other farm workers in turn, with a recent outbreak of a mink variant in humans in Denmark. A thorough examination of the current knowledge and evidence of the ability of SARS-CoV-2 to infect different animal species is therefore vital to evaluate the threat of animal to human transmission and reverse zoonosis. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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Other

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6 pages, 220 KiB  
Commentary
The Appropriateness of Invasive Ventilation in COVID-19 Positive Cancer Patients: Proposal of a New Prognostic Score
by Michele Ghidini, Alice Indini, Erika Rijavec, Claudia Bareggi, Monica Cattaneo, Gianluca Tomasello, Barbara Galassi, Donatella Gambini and Francesco Grossi
Viruses 2021, 13(3), 508; https://doi.org/10.3390/v13030508 - 19 Mar 2021
Cited by 2 | Viewed by 1958
Abstract
Over the last months, as oncology specialists, we have frequently been contacted for estimating prognosis for cancer patients affected by COVID-19 infection. Until now, there have been no clear markers to guide decision making regarding the appropriateness of invasive ventilation in cancer patients [...] Read more.
Over the last months, as oncology specialists, we have frequently been contacted for estimating prognosis for cancer patients affected by COVID-19 infection. Until now, there have been no clear markers to guide decision making regarding the appropriateness of invasive ventilation in cancer patients affected by COVID-19 infection. We developed a practical tool encompassing a prognostic score, “The Milano Policlinico ONCOVID-ICU score.” The score is composed of three groups of variables: patient’s characteristics such as sex, age, BMI, and comorbidities; oncological variables (treatment intent, life expectancy, on or off-treatment status); and clinical parameters in association with laboratory values (the Sequential Organ Failure Assessment (SOFA) score and D-dimer). The SOFA score includes six different clinical parameters and during the first few days of ICU admissions has an important prognostic role. The oncological history should never represent, per se, a contraindication to intensive care and must be considered together with other variables, such as laboratory values, clinical parameters, and patient characteristics, in order to make the hardest but best possible choice. To our knowledge, “The Milano Policlinico ONCOVID-ICU score” is the first prognostic score proposed in this setting of patients and requires further validation. This tool may be useful to assess the prognosis of cancer patients in critical conditions. Full article
(This article belongs to the Special Issue State-of-the-Art Emerging Respiratory Viruses in Europe)
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