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Viruses, Volume 14, Issue 3 (March 2022) – 206 articles

Cover Story (view full-size image): Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne nairovirus that causes hemorrhagic fever in humans. The CCHFV nucleoprotein (NP) is the antigen most used for serological screening of CCHFV infection of animals and humans. In this study, we sought to identify epitopes on the NP molecule. We found that the amino acids at positions 161–320 might include dominant epitopes, whereas IgG cross-reactivity to Nairobi sheep disease virus, which is another nairovirus, was limited. Using CCHFV NP-derived synthetic peptides, some potential epitope peptides were also identified. Our results provide useful information to improve NP-based antibody detection assays as well as antigen detection tests relying on anti-NP monoclonal antibodies. View this paper
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20 pages, 5720 KiB  
Article
Infection of Human Endothelial Cells with Lassa Virus Induces Early but Transient Activation and Low Type I IFN Response Compared to the Closely-Related Nonpathogenic Mopeia Virus
by Othmann Merabet, Natalia Pietrosemoli, Emeline Perthame, Jean Armengaud, Jean-Charles Gaillard, Virginie Borges-Cardoso, Maïlys Daniau, Catherine Legras-Lachuer, Xavier Carnec and Sylvain Baize
Viruses 2022, 14(3), 652; https://doi.org/10.3390/v14030652 - 21 Mar 2022
Cited by 3 | Viewed by 2202
Abstract
Lassa virus (LASV), an Old World arenavirus, is responsible for hemorrhagic fevers in western Africa. The privileged tropism of LASV for endothelial cells combined with a dysregulated inflammatory response are the main cause of the increase in vascular permeability observed during the disease. [...] Read more.
Lassa virus (LASV), an Old World arenavirus, is responsible for hemorrhagic fevers in western Africa. The privileged tropism of LASV for endothelial cells combined with a dysregulated inflammatory response are the main cause of the increase in vascular permeability observed during the disease. Mopeia virus (MOPV) is another arenavirus closely related to LASV but nonpathogenic for non-human primates (NHPs) and has never been described in humans. MOPV is more immunogenic than LASV in NHPs and in vitro in human immune cell models, with more intense type I IFN and adaptive cellular responses. Here, we compared the transcriptomic and proteomic responses of human umbilical vein endothelial cells (HUVECs) to infection with the two viruses to further decipher the mechanisms involved in their differences in immunogenicity and pathogenicity. Both viruses replicated durably and efficiently in HUVECs, but the responses they induced were strikingly different. Modest activation was observed at an early stage of LASV infection and then rapidly shut down. By contrast, MOPV induced a late but more intense response, characterized by the expression of genes and proteins mainly associated with the type I IFN response and antigen processing/presentation. Such a response is consistent with the higher immunogenicity of MOPV relative to LASV, whereas the lack of an innate response induced in HUVECs by LASV is consistent with its uncontrolled systemic dissemination through the vascular endothelium. Full article
(This article belongs to the Section Human Virology and Viral Diseases)
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18 pages, 1390 KiB  
Article
Characterization of Serum and Mucosal SARS-CoV-2-Antibodies in HIV-1-Infected Subjects after BNT162b2 mRNA Vaccination or SARS-CoV-2 Infection
by Katja G. Schmidt, Ellen G. Harrer, Koray Tascilar, Sabrina Kübel, Boutaina El Kenz, Fabian Hartmann, David Simon, Georg Schett, Krystelle Nganou-Makamdop and Thomas Harrer
Viruses 2022, 14(3), 651; https://doi.org/10.3390/v14030651 - 21 Mar 2022
Cited by 16 | Viewed by 3157
Abstract
Only limited data are available regarding the immunogenicity of the BNT162b2 mRNA vaccine in HIV-1+ patients. Therefore, we investigated the humoral immune response after BNT162b2-mRNA vaccination or SARS-CoV-2 infection in HIV-1+ patients on antiretroviral therapy compared to HIV-1-uninfected subjects. Serum and [...] Read more.
Only limited data are available regarding the immunogenicity of the BNT162b2 mRNA vaccine in HIV-1+ patients. Therefore, we investigated the humoral immune response after BNT162b2-mRNA vaccination or SARS-CoV-2 infection in HIV-1+ patients on antiretroviral therapy compared to HIV-1-uninfected subjects. Serum and saliva samples were analysed by SARS-CoV-2 spike-specific IgG and IgA ELISAs and a surrogate neutralization assay. While all subjects developed anti-spike IgG and IgA and neutralizing antibodies in serum after two doses of BNT162b2 mRNA vaccine, the HIV-1+ subjects displayed significantly lower neutralizing capacity and anti-spike IgA in serum compared to HIV-1-uninfected subjects. Serum levels of anti-spike IgG and neutralizing activity were significantly higher in vaccinees compared to SARS-CoV-2 convalescents irrespective of HIV-1 status. Among SARS-CoV-2 convalescents, there was no significant difference in spike-specific antibody response between HIV-1+ and uninfected subjects. In saliva, anti-spike IgG and IgA antibodies were detected both in vaccinees and convalescents, albeit at lower frequencies compared to the serum and only rarely with detectable neutralizing activity. In summary, our study demonstrates that the BNT162b2 mRNA vaccine induces SARS-CoV-2-specific antibodies in HIV-1-infected patients on antiretroviral therapy, however, lower vaccine induced neutralization activity indicates a lower functionality of the humoral vaccine response in HIV-1+ patients. Full article
(This article belongs to the Section SARS-CoV-2 and COVID-19)
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9 pages, 257 KiB  
Brief Report
Effects of Casirivimab/Imdevimab Monoclonal Antibody Treatment among Vaccinated Patients Infected by SARS-CoV-2 Delta Variant
by Gaetano Cicchitto, Lorena Cardillo, Claudio de Martinis, Paola Sabatini, Rosita Marchitiello, Giovanna Abate, Adele Rovetti, Antonietta Cavallera, Camillo Apuzzo, Francesco Ferrigno and Giovanna Fusco
Viruses 2022, 14(3), 650; https://doi.org/10.3390/v14030650 - 21 Mar 2022
Cited by 11 | Viewed by 2118
Abstract
There is a growing interest in using monoclonal antibodies (mAbs) in the early stages of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection to prevent disease progression. Little is known about the efficacy of mAbs against the delta variant of concern and its [...] Read more.
There is a growing interest in using monoclonal antibodies (mAbs) in the early stages of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection to prevent disease progression. Little is known about the efficacy of mAbs against the delta variant of concern and its clinical presentations. We evaluated the effect of casirivimab/imdevimab treatment among five delta vaccine breakthrough patients. Symptomatic non-hospitalized vaccinated patients were submitted to nasopharyngeal swabs for the detection of SARS-CoV-2 and Next-Generation Sequencing (NGS). Blood analysis and chest Computed Tomography were also performed. A cocktail of casirivimab/imdevimab was administrated, and patients were monitored weekly. Clinical evolution was evaluated by the regression of the symptoms, negative results by real-time RT-PCR, and by the need of hospitalization: these aspects were considered as significant outcomes. In four cases, symptom reversion and viral load reduction were observed within 2 days and 7 days after mAbs treatment, respectively. Only one case, suffering from thymoma, was hospitalized 2 days later because of respiratory failure, which reverted within 18 days. mAbs treatment seems to be safe and effective against the delta variant and its clinical manifestations. Full article
(This article belongs to the Special Issue State-of-the-Art SARS-CoV-2 Research in Italy)
17 pages, 5243 KiB  
Article
Transcriptomics Reveal Several Novel Viruses from Canegrubs (Coleoptera: Scarabaeidae) in Central Queensland, Australia
by Kayvan Etebari, Pauline Lenancker, Kevin S. Powell and Michael J. Furlong
Viruses 2022, 14(3), 649; https://doi.org/10.3390/v14030649 - 21 Mar 2022
Cited by 5 | Viewed by 2318
Abstract
Canegrubs (Coleoptera: Scarabaeidae) are major pests of sugarcane crops in Australia, but despite long-term and intensive research, no commercially viable biological control agents have been identified. We used the RNA-Seq approach to explore the viriomes of three different species of canegrubs from central [...] Read more.
Canegrubs (Coleoptera: Scarabaeidae) are major pests of sugarcane crops in Australia, but despite long-term and intensive research, no commercially viable biological control agents have been identified. We used the RNA-Seq approach to explore the viriomes of three different species of canegrubs from central Queensland, Australia to identify potential candidates for biological control. We identified six novel RNA viruses, characterized their genomes, and inferred their evolutionary relationships with other closely related viruses. These novel viruses showed similarity to other known members from picornaviruses, benyviruses, sobemoviruses, totiviruses, and reoviruses. The abundance of viral reads varied in these libraries; for example, Dermolepida albohirtum picorna-like virus (9696 nt) was built from 83,894 assembled reads while only 1350 reads mapped to Lepidiota negatoria beny-like virus (6371 nt). Future studies are essential to determine their natural incidence in different life stages of the host, biodiversity, geographical distributions, and potential as biological control agents for these important pests of sugarcane. Full article
(This article belongs to the Special Issue Insect Virus Discovery)
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14 pages, 2831 KiB  
Review
Applications of Atomic Force Microscopy in HIV-1 Research
by Itay Rousso and Akshay Deshpande
Viruses 2022, 14(3), 648; https://doi.org/10.3390/v14030648 - 21 Mar 2022
Cited by 5 | Viewed by 5373
Abstract
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is [...] Read more.
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is a relatively new technique with unique capabilities, has been utilized to study HIV-1 biology. Atomic force microscopy can generate high-resolution images at the nanometer-scale and analyze the mechanical properties of individual HIV-1 virions, virus components (e.g., capsids), and infected live cells under near-physiological environments. This review describes the working principles and various imaging and analysis modes of atomic force microscopy, and elaborates on its distinctive contributions to HIV-1 research in areas such as mechanobiology and the physics of infection. Full article
(This article belongs to the Special Issue State-of-the-Art Virology Research in Israel)
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15 pages, 3097 KiB  
Article
Risk Factors for Norovirus Infections and Their Association with Childhood Growth: Findings from a Multi-Country Birth Cohort Study
by Parag Palit, Rina Das, Md. Ahshanul Haque, Md. Mehedi Hasan, Zannatun Noor, Mustafa Mahfuz, Abu Syed Golam Faruque and Tahmeed Ahmed
Viruses 2022, 14(3), 647; https://doi.org/10.3390/v14030647 - 21 Mar 2022
Cited by 4 | Viewed by 2422
Abstract
The prevalence of norovirus infections in different geographical locations and their attribution to childhood diarrhea is well established. However, there are no reports showing possible relationships of different norovirus genogroups with subsequent childhood malnutrition. In this study, we attempted to establish a potential [...] Read more.
The prevalence of norovirus infections in different geographical locations and their attribution to childhood diarrhea is well established. However, there are no reports showing possible relationships of different norovirus genogroups with subsequent childhood malnutrition. In this study, we attempted to establish a potential association between asymptomatic norovirus infections with childhood growth faltering during. Non-diarrheal stools were collected from 1715 children enrolled in locations in a multi-county birth cohort study across eight different geographical locations and were assessed for norovirus genogroup I (GI) and norovirus genogroup II (GII). Asymptomatic norovirus GI infections were negatively associated with monthly length-for-age Z score/LAZ (β = −0.53, 95% CI: −0.73, −0.50) and weight-for-age Z score/WAZ (β = −0.39, 95% CI: −0.49, −0.28), respectively. The burden of asymptomatic norovirus GI infections was negatively associated with LAZ (β = −0.46, 95% CI: −0.67, −0.41) and WAZ (β = −0.66, 95% CI: −0.86, −0.53) at 2 years of age, whilst the burden of asymptomatic norovirus GII infections was negatively associated with WAZ (β = −0.27, 95% CI: −0.45, −0.25) at 2 years of age. Our findings warrant acceleration in attempts to develop vaccines against norovirus GI and norovirus GII, with the aim of minimizing the long-term sequelae on childhood growth. Full article
(This article belongs to the Special Issue Pathogenesis and Immunity of Enteric Virus Infections)
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17 pages, 1807 KiB  
Article
TREC/KREC Levels and T and B Lymphocyte Subpopulations in COVID-19 Patients at Different Stages of the Disease
by Andrei A. Savchenko, Elena Tikhonova, Igor Kudryavtsev, Dmitry Kudlay, Ilya Korsunsky, Vasily Beleniuk and Alexandr Borisov
Viruses 2022, 14(3), 646; https://doi.org/10.3390/v14030646 - 21 Mar 2022
Cited by 18 | Viewed by 2984
Abstract
Background: T and B cell-mediated immunity can be assessed using T cell receptor excision circle (TREC) and Kappa-deleting recombination excision circle (KREC) analysis, respectively, and successful implementation of this method requires evaluation of the correlation between the TREC frequencies and T cell subsets [...] Read more.
Background: T and B cell-mediated immunity can be assessed using T cell receptor excision circle (TREC) and Kappa-deleting recombination excision circle (KREC) analysis, respectively, and successful implementation of this method requires evaluation of the correlation between the TREC frequencies and T cell subsets as well as KREC levels and B lymphocyte subsets. The aim of the present study was to evaluate the correlation between the TREC/KREC concentrations and T/B lymphocyte subsets at different stages of COVID-19. Methods: We examined 33 patients in the acute stage of COVID-19 (including 8 patients with poor outcomes) and 33 COVID-19 survivors. TREC/KREC concentrations were measured using quantitative real-time PCR. T/B lymphocyte subsets were determined using flow cytometry. Results: Blood TREC and KREC levels were found to be significantly lower in the acute stage of COVID-19 compared to control values. Moreover, a zero blood TREC level was a predictor of a poor disease outcome. Reductions in CD3+CD4+CD45ROCD62L and CD3+CD8+CD45ROCD62L T cell counts (as well as in the main fractions of B1 and B2 B cells) indicated a favorable outcome in COVID-19 patients in the acute stage of the disease. Decreased CD3+CD4+CD45ROCD62L+ and CD3+CD8+CD45ROCD62L+ T cell frequencies and increased CD3+CD8+CD45ROCD62L cell counts were found to indicate a poor outcome in patients with acute COVID-19. These patients were also found to have increased B1 cell counts while demonstrating no changes in B2 cell counts. The levels of effector T cell subsets an naïve B cells were normal in COVID-19 survivors. The most pronounced correlations between TREC/KREC levels and T/B cell subsets counts were observed in COVID-19 survivors: there were positive correlations with naïve T and B lymphocytes and negative correlations with central and effector memory T cell subsets. Conclusions: The assessment of correlations between TREC and T cell subsets as well as KREC levels and B cell subset counts in patients with acute COVID-19 and COVID-19 survivors has shown that blood concentrations of TREC and KREC are sensitive indicators of the stage of antigen-independent differentiation of adaptive immunity cells. The results of the TREC and KREC analysis correlated with the stages of COVID-19 and differed depending on the outcome of COVID-19. Full article
(This article belongs to the Special Issue Viruses Research in Russia 2022)
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2 pages, 182 KiB  
Editorial
Special Issue “Endemic Arboviruses”
by Didier Musso, Dominique Rousset and Christophe Peyrefitte
Viruses 2022, 14(3), 645; https://doi.org/10.3390/v14030645 - 21 Mar 2022
Cited by 1 | Viewed by 1696
Abstract
Arthropod-borne viruses (Arbovirus) is an ecological term defining viruses that are maintained in nature through biological transmission between a susceptible vertebrate host and a hematophagous arthropod such as a mosquito [...] Full article
(This article belongs to the Special Issue Endemic Arboviruses)
14 pages, 910 KiB  
Conference Report
The 32nd Brazilian Society of Virology (SBV) 2021 Annual Meeting
by Maite Freitas Silva Vaslin, Alessandra Alevato Leal, Larissa Mayumi Bueno, Cíntia Bittar, Gabriela Fabiano de Souza, Karine Lourenço, Gustavo Peixoto Duarte da Silva, Maria Isabel Maldonado Coelho Guedes, José Luiz Proença-Módena, João Pessoa Araújo Junior, Helena Lage Ferreira and Flávio Guimarães da Fonseca
Viruses 2022, 14(3), 644; https://doi.org/10.3390/v14030644 - 20 Mar 2022
Cited by 1 | Viewed by 1840
Abstract
The Brazilian Society of Virology has been organizing annual meetings for 32 years now. The 32nd annual meeting, which occurred in 2021, was once again an online meeting in consequence of the issues imposed by COVID-19, even with the vaccination advances. As in [...] Read more.
The Brazilian Society of Virology has been organizing annual meetings for 32 years now. The 32nd annual meeting, which occurred in 2021, was once again an online meeting in consequence of the issues imposed by COVID-19, even with the vaccination advances. As in the 2020 meeting, the number of attendees was high, with considerable participation by undergraduate, graduate, and postdoc students. Distinguished scientists from different countries offered high-quality conferences, and oral presentation sessions were presented by young scientists showing their newest research results. For almost five hours a day during five days, attendees discussed high-quality science related to all areas of virology. Even with the difficulties imposed by another pandemic year, the 32nd SBV annual meeting achieved its most important goal—to inspire young scientists and discuss high-quality virology research. Full article
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12 pages, 7890 KiB  
Article
Prevalence, Genetics and Evolutionary Properties of Eurasian Avian-like H1N1 Swine Influenza Viruses in Liaoning
by Hailing Li, Haoyu Leng, Siqi Tang, Chaofan Su, Yina Xu, Yongtao Wang, Jiaming Lv, Shiwei Zhang, Yali Feng, Shaokang Song and Ying Zhang
Viruses 2022, 14(3), 643; https://doi.org/10.3390/v14030643 - 20 Mar 2022
Cited by 5 | Viewed by 2441
Abstract
Swine influenza virus (SIV) is an important zoonosis pathogen. The 2009 pandemic of H1N1 influenza A virus (2009/H1N1) highlighted the importance of the role of pigs as intermediate hosts. Liaoning province, located in northeastern China, has become one of the largest pig-farming areas [...] Read more.
Swine influenza virus (SIV) is an important zoonosis pathogen. The 2009 pandemic of H1N1 influenza A virus (2009/H1N1) highlighted the importance of the role of pigs as intermediate hosts. Liaoning province, located in northeastern China, has become one of the largest pig-farming areas since 2016. However, the epidemiology and evolutionary properties of SIVs in Liaoning are largely unknown. We performed systematic epidemiological and genetic dynamics surveillance of SIVs in Liaoning province during 2020. In total, 33,195 pig nasal swabs were collected, with an SIV detection rate of 2%. Our analysis revealed that multiple subtypes of SIVs are co-circulating in the pig population in Liaoning, including H1N1, H1N2 and H3N2 SIVs. Furthermore, 24 H1N1 SIVs were confirmed to belong to the EA H1N1 lineage and divided into two genotypes. The two genotypes were both triple reassortant, and the predominant one with polymerase, nucleoprotein (NP), and matrix protein (M) genes originating from 2009/H1N1; hemagglutinin (HA) and neuraminidase (NA) genes originating from EA H1N1; and the nonstructural protein (NS) gene originating from triple reassortant H1N2 (TR H1N2) was detected in Liaoning for the first time. According to our evolutionary analysis, the EA H1N1 virus in Liaoning will undergo further genome variation. Full article
(This article belongs to the Topic Veterinary Infectious Diseases)
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12 pages, 472 KiB  
Article
Risk of Seven-Day Worsening and Death: A New Clinically Derived COVID-19 Score
by Alessia Cruciata, Lorenzo Volpicelli, Silvia Di Bari, Giancarlo Iaiani, Bruno Cirillo, Francesco Pugliese, Daniela Pellegrino, Gioacchino Galardo and Gloria Taliani
Viruses 2022, 14(3), 642; https://doi.org/10.3390/v14030642 - 20 Mar 2022
Cited by 1 | Viewed by 2034
Abstract
This monocentric, retrospective, two-stage observational study aimed to recognize the risk factors for a poor outcome in patients hospitalized with SARS-CoV-2 infection, and to develop and validate a risk score that identifies subjects at risk of worsening, death, or both. The data of [...] Read more.
This monocentric, retrospective, two-stage observational study aimed to recognize the risk factors for a poor outcome in patients hospitalized with SARS-CoV-2 infection, and to develop and validate a risk score that identifies subjects at risk of worsening, death, or both. The data of patients with SARS-CoV-2 infection during the first wave of the pandemic were collected and analyzed as a derivation cohort. Variables with predictive properties were used to construct a prognostic score, which was tried out on a validation cohort enrolled during the second wave. The derivation cohort included 494 patients; the median age was 62 and the overall fatality rate was 22.3%. In a multivariable analysis, age, oxygen saturation, neutrophil-to-lymphocyte ratio, C-reactive protein and lactate dehydrogenase were independent predictors of death and composed the score. A cutoff value of 3 demonstrated a sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) of 93.5%, 68.5%, 47.4% and 97.2% for death, and 84.9%, 84.5%, 79.6% and 87.9% for worsening, respectively. The validation cohort included 415 subjects. The score application showed a Se, Sp, PPV and NPV of 93.4%, 61.6%, 29.5% and 98.1% for death, and 81%, 76.3%, 72.1% and 84.1% for worsening, respectively. We propose a new clinical, easy and reliable score to predict the outcome in hospitalized SARS-CoV-2 patients. Full article
(This article belongs to the Topic Infectious Diseases)
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9 pages, 1634 KiB  
Article
Norovirus Genogroup II Epidemics and the Potential Effect of Climate Change on Norovirus Transmission in Taiwan
by Shu-Chun Chiu, Szu-Chieh Hu, Ling-Min Liao, Yu-Hua Chen and Jih-Hui Lin
Viruses 2022, 14(3), 641; https://doi.org/10.3390/v14030641 - 20 Mar 2022
Viewed by 2371
Abstract
The activity of norovirus varies from season to season, and the effect of climate change on the incidence of norovirus outbreaks is a widely recognized yet poorly understood phenomenon. Investigation of the possible association between climatic factors and the incidence of norovirus is [...] Read more.
The activity of norovirus varies from season to season, and the effect of climate change on the incidence of norovirus outbreaks is a widely recognized yet poorly understood phenomenon. Investigation of the possible association between climatic factors and the incidence of norovirus is key to a better understanding of the epidemiology of norovirus and early prediction of norovirus outbreaks. In this study, clinical stool samples from acute gastroenteritis outbreaks were collected from January 2015 to June 2019 in Taiwan. Data analysis from our study indicated that more than half of the cases were reported in the winter and spring seasons, including those caused by norovirus of genotypes GII (genogroup II).2, GII.3, GII.6, and GII.17, and 45.1% of the patients who tested positive for norovirus were infected by the GII.4 norovirus in autumn. However, GII.6 norovirus accounted for a higher proportion of the cases reported in summer than any other strain. Temperature is a crucial factor influencing patterns of epidemic outbreaks caused by distinct genotypes of norovirus. The results of this study may help experts predict and issue early public warnings of norovirus transmission and understand the effect of climate change on norovirus outbreaks caused by different genotypes and occurring in different locations. Full article
(This article belongs to the Special Issue Noroviruses 2021)
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11 pages, 2297 KiB  
Review
Mutations and Evolution of the SARS-CoV-2 Spike Protein
by Nicholas Magazine, Tianyi Zhang, Yingying Wu, Michael C. McGee, Gianluca Veggiani and Weishan Huang
Viruses 2022, 14(3), 640; https://doi.org/10.3390/v14030640 - 19 Mar 2022
Cited by 89 | Viewed by 10761 | Correction
Abstract
The SARS-CoV-2 spike protein mediates target recognition, cellular entry, and ultimately the viral infection that leads to various levels of COVID-19 severities. Positive evolutionary selection of mutations within the spike protein has led to the genesis of new SARS-CoV-2 variants with greatly enhanced [...] Read more.
The SARS-CoV-2 spike protein mediates target recognition, cellular entry, and ultimately the viral infection that leads to various levels of COVID-19 severities. Positive evolutionary selection of mutations within the spike protein has led to the genesis of new SARS-CoV-2 variants with greatly enhanced overall fitness. Given the trend of variants with increased fitness arising from spike protein alterations, it is critical that the scientific community understand the mechanisms by which these mutations alter viral functions. As of March 2022, five SARS-CoV-2 strains were labeled “variants of concern” by the World Health Organization: the Alpha, Beta, Gamma, Delta, and Omicron variants. This review summarizes the potential mechanisms by which the common mutations on the spike protein that occur within these strains enhance the overall fitness of their respective variants. In addressing these mutations within the context of the SARS-CoV-2 spike protein structure, spike/receptor binding interface, spike/antibody binding, and virus neutralization, we summarize the general paradigms that can be used to estimate the effects of future mutations along SARS-CoV-2 evolution. Full article
(This article belongs to the Special Issue Broad-Spectrum Antivirals of Coronaviruses Replication)
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12 pages, 1013 KiB  
Article
Characterisation of Particle Size and Viability of SARS-CoV-2 Aerosols from a Range of Nebuliser Types Using a Novel Sampling Technique
by Susan Paton, Simon Clark, Antony Spencer, Isobel Garratt, Ikshitaa Dinesh, Katy-Anne Thompson, Allan Bennett and Thomas Pottage
Viruses 2022, 14(3), 639; https://doi.org/10.3390/v14030639 - 19 Mar 2022
Cited by 7 | Viewed by 2701
Abstract
Little is understood about the impact of nebulisation on the viability of SARS-CoV-2. In this study, a range of nebulisers with differing methods of aerosol generation were evaluated to determine SARS-CoV-2 viability following aerosolization. The aerosol particle size distribution was assessed using an [...] Read more.
Little is understood about the impact of nebulisation on the viability of SARS-CoV-2. In this study, a range of nebulisers with differing methods of aerosol generation were evaluated to determine SARS-CoV-2 viability following aerosolization. The aerosol particle size distribution was assessed using an aerosol particle sizer (APS) and SARS-CoV-2 viability was determined after collection into liquid media using All-Glass Impingers (AGI). Viable particles of SARS-CoV-2 were further characterised using the Collison 6-jet nebuliser in conjunction with novel sample techniques in an Andersen size-fractioning sampler to predict lung deposition profiles. Results demonstrate that all the tested nebulisers can generate stable, polydisperse aerosols (Geometric standard deviation (GSD) circa 1.8) in the respirable range (1.2 to 2.2 µm). Viable fractions (VF, units PFU/particle, the virus viability as a function of total particles produced) were circa 5 × 10−3. VF and spray factors were not significantly affected by relative humidity, within this system where aerosols were in the spray tube an extremely short time. The novel Andersen sample collection methods successfully captured viable virus particles across all sizes; with most particle sizes below 3.3 µm. Particle sizes, in MMAD (Mass Median Aerodynamic Diameters), were calculated from linear regression of log10-log10 transformed cumulative PFU data, and calculated MMADs accorded well with APS measurements and did not differ across collection method types. These data will be vital in informing animal aerosol challenge models, and infection prevention and control policies. Full article
(This article belongs to the Special Issue Aerosol Transmission of Viral Disease)
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10 pages, 2563 KiB  
Article
Enteric Viruses Nucleic Acids Distribution along the Digestive Tract of Rhesus Macaques with Idiopathic Chronic Diarrhea
by Eric Delwart, David Merriam, Amir Ardeshir, Eda Altan, Yanpeng Li, Xutao Deng and Dennis J. Hartigan-O’Connor
Viruses 2022, 14(3), 638; https://doi.org/10.3390/v14030638 - 19 Mar 2022
Viewed by 1799
Abstract
Idiopathic chronic diarrhea (ICD) is a little understood common clinical problem in captive rhesus macaques claiming 33% of medical culls unrelated to research. The eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD was characterized using viral metagenomics. [...] Read more.
Idiopathic chronic diarrhea (ICD) is a little understood common clinical problem in captive rhesus macaques claiming 33% of medical culls unrelated to research. The eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD was characterized using viral metagenomics. We compared the distribution of viral reads in tissues and mucosal scrapings from the stomach, duodenum, jejunum, ileum, and the proximal, transverse, and distal colons. In situ hybridization (ISH) using viral probes were performed on fixed tissues. Deep sequencing revealed multiple viruses in the Parvoviridae and Picornaviridae family. Tissues and mucosal scraping from the same locations showed closely related viral reads contents while different gut tissues from the same animal varied widely. ISH showed punctuated staining for both RNA and DNA viruses in the distal colon. Parvovirus staining was also detected in the stomach/duodenum/jejunum in distinct oval-shaped structures. The location of enteric viral nucleic acid differed widely between different viral families and along the length of the digestive tract. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses 2021)
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15 pages, 2115 KiB  
Article
Persistence of Naturally Acquired and Functional SARS-CoV-2 Antibodies in Blood Donors One Year after Infection
by Verena Nunhofer, Lisa Weidner, Alexandra Domnica Hoeggerl, Georg Zimmermann, Natalie Badstuber, Christoph Grabmer, Christof Jungbauer, Nadja Lindlbauer, Nina Held, Monica Pascariuc, Tuulia Ortner, Eva Rohde and Sandra Laner-Plamberger
Viruses 2022, 14(3), 637; https://doi.org/10.3390/v14030637 - 18 Mar 2022
Cited by 10 | Viewed by 2539
Abstract
The developmental course of antibodies produced after a SARS-CoV-2 infection has been insufficiently investigated so far. Therefore, the aim of this study was to investigate the dynamics of SARS-CoV-2 antibody levels against the viral nucleocapsid- and spike-protein among Austrian blood donors as a [...] Read more.
The developmental course of antibodies produced after a SARS-CoV-2 infection has been insufficiently investigated so far. Therefore, the aim of this study was to investigate the dynamics of SARS-CoV-2 antibody levels against the viral nucleocapsid- and spike-protein among Austrian blood donors as a representative group of a supposedly healthy population within the first year after a SARS-CoV-2 infection. The impact of age, sex, vaccination status, AB0-blood group and awareness about the infection was evaluated. Our study shows that the level of anti-N antibodies is declining, while anti-S antibody levels remain stable. Antibodies detected were functional in vitro. Age, sex and blood group do not influence antibody dynamics. However, blood group AB shows significantly lower antibody levels and in vitro functionality compared to other blood groups. Our data reveal that one out of five individuals was not aware of a previous SARS-CoV-2 infection and that the disease course neither affects the level of antibody production nor the in vitro functionality. We also found that 14% of participants show persisting COVID-19-related symptoms for up to nine months. Our results provide valuable insights into the dynamics of the immune response after a SARS-CoV-2 infection in a representative cohort of adult blood donors in Central Europe. Full article
(This article belongs to the Special Issue Antibodies and B Cell Memory in Viral Immunity)
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16 pages, 2631 KiB  
Article
Transduction of HEK293 Cells with BacMam Baculovirus Is an Efficient System for the Production of HIV-1 Virus-like Particles
by Eduard Puente-Massaguer, Byron Cajamarca-Berrezueta, Aleix Volart, Irene González-Domínguez and Francesc Gòdia
Viruses 2022, 14(3), 636; https://doi.org/10.3390/v14030636 - 18 Mar 2022
Cited by 3 | Viewed by 3786
Abstract
Gag virus-like particles (VLPs) are promising vaccine candidates against infectious diseases. VLPs are generally produced using the insect cell/baculovirus expression vector system (BEVS), or in mammalian cells by plasmid DNA transient gene expression (TGE). However, VLPs produced with the insect cell/BEVS are difficult [...] Read more.
Gag virus-like particles (VLPs) are promising vaccine candidates against infectious diseases. VLPs are generally produced using the insect cell/baculovirus expression vector system (BEVS), or in mammalian cells by plasmid DNA transient gene expression (TGE). However, VLPs produced with the insect cell/BEVS are difficult to purify and might not display the appropriate post-translational modifications, whereas plasmid DNA TGE approaches are expensive and have a limited scale-up capability. In this study, the production of Gag VLPs with the BacMam expression system in a suspension culture of HEK293 cells is addressed. The optimal conditions of multiplicity of infection (MOI), viable cell density (VCD) at infection, and butyric acid (BA) concentration that maximize cell transduction and VLP production are determined. In these conditions, a maximum cell transduction efficiency of 91.5 ± 1.1%, and a VLP titer of 2.8 ± 0.1 × 109 VLPs/mL are achieved. Successful VLP generation in transduced HEK293 cells is validated using super-resolution fluorescence microscopy, with VLPs produced resembling immature HIV-1 virions and with an average size comprised in the 100–200 nm range. Additionally, evidence that BacMam transduction occurs via different pathways including dynamin-mediated endocytosis and macropinocytosis is provided. This work puts the basis for future studies aiming at scaling up the BacMam baculovirus system as an alternative strategy for VLP production. Full article
(This article belongs to the Special Issue Virus-Like Particle Vaccines 2022)
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16 pages, 2903 KiB  
Article
The Feline Calicivirus Leader of the Capsid Protein Has the Functional Characteristics of a Viroporin
by Yoatzin Peñaflor-Téllez, Bibiana Chávez-Munguía, Anel Lagunes-Guillén, Lizbeth Salazar-Villatoro and Ana Lorena Gutiérrez-Escolano
Viruses 2022, 14(3), 635; https://doi.org/10.3390/v14030635 - 18 Mar 2022
Cited by 4 | Viewed by 2592
Abstract
The leader of the capsid (LC) protein is exclusive to the Vesivirus genus, and it is needed for successful feline calicivirus (FCV) replication, as well as an efficient apoptosis induction through the mitochondrial pathway. In this work, we aimed to determine if the [...] Read more.
The leader of the capsid (LC) protein is exclusive to the Vesivirus genus, and it is needed for successful feline calicivirus (FCV) replication, as well as an efficient apoptosis induction through the mitochondrial pathway. In this work, we aimed to determine if the LC protein from the FCV is a viroporin. Although lacking in a transmembrane domain or an amphipathic helix, the LC protein from the FCV is toxic when expressed in bacteria and it oligomerizes through disulfide bonds, which are both key characteristics of viroporins. An electron microscopy analysis of LC-expressing E. coli cells suggest that the protein induces osmotic stress. Moreover, we found that the previously studied C40A LC mutant, that fails to induce apoptosis and that hinders the replication cycle, also oligomerizes but it has a reduced toxicity and fails to induce osmotic stress in bacteria. We propose that the LC protein is a viroporin that acts as a disulfide bond-dependent antimicrobial peptide, similar to the Ebola virus delta peptide. Full article
(This article belongs to the Special Issue Feline Viruses and Viral Diseases 2.0)
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18 pages, 1276 KiB  
Review
Human Brain Organoids as Models for Central Nervous System Viral Infection
by Josse A. Depla, Lance A. Mulder, Renata Vieira de Sá, Morgane Wartel, Adithya Sridhar, Melvin M. Evers, Katja C. Wolthers and Dasja Pajkrt
Viruses 2022, 14(3), 634; https://doi.org/10.3390/v14030634 - 18 Mar 2022
Cited by 18 | Viewed by 4434
Abstract
Pathogenesis of viral infections of the central nervous system (CNS) is poorly understood, and this is partly due to the limitations of currently used preclinical models. Brain organoid models can overcome some of these limitations, as they are generated from human derived stem [...] Read more.
Pathogenesis of viral infections of the central nervous system (CNS) is poorly understood, and this is partly due to the limitations of currently used preclinical models. Brain organoid models can overcome some of these limitations, as they are generated from human derived stem cells, differentiated in three dimensions (3D), and can mimic human neurodevelopmental characteristics. Therefore, brain organoids have been increasingly used as brain models in research on various viruses, such as Zika virus, severe acute respiratory syndrome coronavirus 2, human cytomegalovirus, and herpes simplex virus. Brain organoids allow for the study of viral tropism, the effect of infection on organoid function, size, and cytoarchitecture, as well as innate immune response; therefore, they provide valuable insight into the pathogenesis of neurotropic viral infections and testing of antivirals in a physiological model. In this review, we summarize the results of studies on viral CNS infection in brain organoids, and we demonstrate the broad application and benefits of using a human 3D model in virology research. At the same time, we describe the limitations of the studies in brain organoids, such as the heterogeneity in organoid generation protocols and age at infection, which result in differences in results between studies, as well as the lack of microglia and a blood brain barrier. Full article
(This article belongs to the Special Issue Advances in Neurovirology)
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12 pages, 2015 KiB  
Article
Protection of Ducklings from Duck Hepatitis A Virus Infection with ELPylated Duck Interferon-α
by Yongjuan Wang, Yanli Guo, Haowei Wang, Zhi Wu, Weiming Hong, Huaichang Sun and Shanyuan Zhu
Viruses 2022, 14(3), 633; https://doi.org/10.3390/v14030633 - 18 Mar 2022
Cited by 1 | Viewed by 2801
Abstract
Duck viral hepatitis type I (DVH I) is a lethal disease in ducklings caused by duck hepatitis A virus (DHAV). Although the commercial vaccine is available for vaccination of one-day-old ducklings or breeder ducks, the disease is still prevalent due to the delayed [...] Read more.
Duck viral hepatitis type I (DVH I) is a lethal disease in ducklings caused by duck hepatitis A virus (DHAV). Although the commercial vaccine is available for vaccination of one-day-old ducklings or breeder ducks, the disease is still prevalent due to the delayed immune response in ducklings and variable maternal antibody levels in breeder duck flocks. To explore the feasibility of duck interferon-α (DuIFN-α) for control of DVH I, DuIFN-α was expressed as an elastin-like polypeptide (ELP) fusion protein (ELP-DuIFN-α) in E. coli and purified by inverse phase transition cycling (ITC). After detection of its cytotoxicity, bioactivity, plasma stability and serum half-life, the protective efficacy of ELP-DuIFN-α against DHAV-1 infection of embryos or ducklings was evaluated using different treatment routes at different infection times. The results show that ELP-DuIFN-α was correctly expressed and purified to more than 90% purity after two cycles of ITC. The purified fusion protein had a specific anti-DHAV-1 activity of 6.0 × 104 IU/mg protein, significantly extended plasma stability and serum half-life without overt cytotoxicity. After allantoic injection with ELP-DuIFN-α pre-infection, co-infection or post-infection with DHAV-1, 5/5, 5/5 or 4/5 embryos survived from the virus challenge. After intramuscular injection or oral administration with ELP-DuIFN-α, 3/5 or 4/5 ducklings survived from co-infection with DHAV-1. After oral administration with ELP-DuIFN-α pre-infection, co-infection or post-infection with DHAV-1, 3/5, 4/5 or 4/5 ducklings survived from the virus challenge, and the relative transcription levels of interferon-stimulated genes were significantly higher than the normal control group and virus challenge control group (p < 0.01). These experimental data suggest that ELP-DuIFN-α can be used as a long-lasting anti-DHAV-1 reagent. Full article
(This article belongs to the Special Issue State-of-the-Art Veterinary Virology Research in China)
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13 pages, 1786 KiB  
Article
Investigation of the Low-Populated Excited States of the HIV-1 Nucleocapsid Domain
by Assia Mouhand, Loussiné Zargarian, Anissa Belfetmi, Marjorie Catala, Marco Pasi, Ewen Lescop, Carine Tisné and Olivier Mauffret
Viruses 2022, 14(3), 632; https://doi.org/10.3390/v14030632 - 18 Mar 2022
Cited by 1 | Viewed by 1570
Abstract
The nucleocapsid domain (NCd), located at the C-terminus of the HIV-1 Gag protein, is involved in numerous stages of the replication cycle, such as the packaging of the viral genome and reverse transcription. It exists under different forms through the viral life cycle, [...] Read more.
The nucleocapsid domain (NCd), located at the C-terminus of the HIV-1 Gag protein, is involved in numerous stages of the replication cycle, such as the packaging of the viral genome and reverse transcription. It exists under different forms through the viral life cycle, depending on the processing of Gag by the HIV-1 protease. NCd is constituted of two adjacent zinc knuckles (ZK1 and ZK2), separated by a flexible linker and flanked by disordered regions. Here, conformational equilibria between a major and two minor states were highlighted exclusively in ZK2, by using CPMG and CEST NMR experiments. These minor states appear to be temperature dependent, and their populations are highest at physiological temperature. These minor states are present both in NCp7, the mature form of NCd, and in NCp9 and NCp15, the precursor forms of NCd, with increased populations. The role of these minor states in the targeting of NCd by drugs and its binding properties is discussed. Full article
(This article belongs to the Special Issue Retroviral Nucleocapsid Proteins)
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22 pages, 3422 KiB  
Article
Infectious Salmon Anemia Virus Infectivity Is Determined by Multiple Segments with an Important Contribution from Segment 5
by Matías Cárdenas, Sofía Michelson, Daniel R. Pérez, Margarita Montoya, Jorge Toledo, Yesseny Vásquez-Martínez and Marcelo Cortez-San Martin
Viruses 2022, 14(3), 631; https://doi.org/10.3390/v14030631 - 18 Mar 2022
Cited by 3 | Viewed by 2559
Abstract
Infectious salmon anemia virus (ISAV) is the etiological agent of infectious salmon anemia. It belongs to the genus isavirus, one of the genera of the Orthomyxoviridae family, as does Influenzavirus A. The ISAV genome comprises eight negative-sense single-stranded RNA segments that code for [...] Read more.
Infectious salmon anemia virus (ISAV) is the etiological agent of infectious salmon anemia. It belongs to the genus isavirus, one of the genera of the Orthomyxoviridae family, as does Influenzavirus A. The ISAV genome comprises eight negative-sense single-stranded RNA segments that code for at least 10 proteins. Although some ISAV strains can reach 100% mortality rates, the factors that determine isavirus infectivity remain unknown. However, some studies suggest that segments 5 and 6 are responsible for the different degrees of virulence and infectivity among ISAV subtypes, unlike the influenza A virus, where most segments are involved in the virus infectivity. In this work, synthetic reassortant viruses for the eight segments of ISAV were generated by reverse genetics, combining a highly virulent virus, ISAV 752_09 (HPR7b), and an avirulent strain, SK779/06 (HPR0). We characterized the rescued viruses and their capacity to replicate and infect different cell lines, produce plaques in ASK cells, and their ability to induce and modulate the cellular immune response in vitro. Our results show that the majority of ISAV segments are involved in at least one of the analyzed characteristics, segment 5 being one of the most important, allowing HPR0 viruses, among other things, to produce plaques and replicate in CHSE-214 cells. We determined that segments 5 and 6 participate in different stages of the viral cycle, and their compatibility is critical for viral infection. Additionally, we demonstrated that segment 2 can modulate the cellular immune response. Our results indicate a high degree of genetic compatibility between the genomic segments of HPR7b and HPR0, representing a latent risk of reassortant that would give rise to a new virus with an unknown phenotype. Full article
(This article belongs to the Special Issue Viruses Affecting Salmonids)
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14 pages, 2106 KiB  
Review
Transport of Prions in the Peripheral Nervous System: Pathways, Cell Types, and Mechanisms
by Sam M. Koshy, Anthony E. Kincaid and Jason C. Bartz
Viruses 2022, 14(3), 630; https://doi.org/10.3390/v14030630 - 18 Mar 2022
Cited by 4 | Viewed by 2858
Abstract
Prion diseases are transmissible protein misfolding disorders that occur in animals and humans where the endogenous prion protein, PrPC, undergoes a conformational change into self-templating aggregates termed PrPSc. Formation of PrPSc in the central nervous system (CNS) leads [...] Read more.
Prion diseases are transmissible protein misfolding disorders that occur in animals and humans where the endogenous prion protein, PrPC, undergoes a conformational change into self-templating aggregates termed PrPSc. Formation of PrPSc in the central nervous system (CNS) leads to gliosis, spongiosis, and cellular dysfunction that ultimately results in the death of the host. The spread of prions from peripheral inoculation sites to CNS structures occurs through neuroanatomical networks. While it has been established that endogenous PrPC is necessary for prion formation, and that the rate of prion spread is consistent with slow axonal transport, the mechanistic details of PrPSc transport remain elusive. Current research endeavors are primarily focused on the cellular mechanisms of prion transport associated with axons. This includes elucidating specific cell types involved, subcellular machinery, and potential cofactors present during this process. Full article
(This article belongs to the Special Issue Prion Neuroinvasion 2.0)
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15 pages, 3581 KiB  
Article
Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry
by Humberto Moreira Hungaro, Pedro Marcus Pereira Vidigal, Edilane Cristina do Nascimento, Felipe Gomes da Costa Oliveira, Marco Túlio Pardini Gontijo and Maryoris Elisa Soto Lopez
Viruses 2022, 14(3), 629; https://doi.org/10.3390/v14030629 - 17 Mar 2022
Cited by 5 | Viewed by 2709
Abstract
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and [...] Read more.
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family. Full article
(This article belongs to the Section Bacterial Viruses)
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24 pages, 3899 KiB  
Article
Sex-Dependent Differences in Predictive Value of the C2HEST Score in Subjects with COVID-19—A Secondary Analysis of the COLOS Study
by Piotr Rola, Adrian Doroszko, Małgorzata Trocha, Katarzyna Giniewicz, Krzysztof Kujawa, Marek Skarupski, Damian Gajecki, Jakub Gawryś, Tomasz Matys, Ewa Szahidewicz-Krupska, Barbara Adamik, Krzysztof Kaliszewski, Katarzyna Kiliś-Pstrusińska, Agnieszka Matera-Witkiewicz, Michał Pomorski, Marcin Protasiewicz, Marcin Madziarski, Urszula Chrostek, Joanna Radzik-Zając, Anna Radlińska, Anna Zaleska, Krzysztof Letachowicz, Wojciech Pisarek, Mateusz Barycki, Janusz Sokołowski, Ewa Anita Jankowska and Katarzyna Madziarskaadd Show full author list remove Hide full author list
Viruses 2022, 14(3), 628; https://doi.org/10.3390/v14030628 - 17 Mar 2022
Cited by 3 | Viewed by 1910
Abstract
Background: Since the outbreak of the COVID-19 pandemic, a growing number of evidence suggests that COVID-19 presents sex-dependent differences in clinical course and outcomes. Nevertheless, there is still an unmet need to stratify the risk for poor outcome at the beginning of hospitalization. [...] Read more.
Background: Since the outbreak of the COVID-19 pandemic, a growing number of evidence suggests that COVID-19 presents sex-dependent differences in clinical course and outcomes. Nevertheless, there is still an unmet need to stratify the risk for poor outcome at the beginning of hospitalization. Since individual C2HEST components are similar COVID-19 mortality risk factors, we evaluated sex-related predictive value of the score. Material and Methods: A total of 2183 medical records of consecutive patients hospitalized due to confirmed SARS-CoV-2 infections were analyzed. Subjects were assigned to one of two of the study arms (male vs. female) and afterward allocated to different stratum based on the C2HEST score result. The measured outcomes included: in-hospital-mortality, three-month- and six-month-all-cause-mortality and in-hospital non-fatal adverse clinical events. Results: The C2HEST score predicted the mortality with better sensitivity in female population regarding the short- and mid-term. Among secondary outcomes, C2HEST-score revealed predictive value in both genders for pneumonia, myocardial injury, myocardial infarction, acute heart failure, cardiogenic shock, and acute kidney injury. Additionally in the male cohort, the C2HEST value predicted acute liver dysfunction and all-cause bleeding, whereas in the female arm-stroke/TIA and SIRS. Conclusion: In the present study, we demonstrated the better C2HEST-score predictive value for mortality in women and illustrated sex-dependent differences predicting non-fatal secondary outcomes. Full article
(This article belongs to the Special Issue Risk Factors for COVID-19 Infection)
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10 pages, 382 KiB  
Case Report
SARS-CoV-2 and Influenza Virus Co-Infection Cases Identified through ILI/SARI Sentinel Surveillance: A Pan-India Report
by Neeraj Aggarwal, Varsha Potdar, Neetu Vijay, Labanya Mukhopadhyay, Biswajyoti Borkakoty, S. Manjusree, Manohar Lal Choudhary, Deepika Chowdhury, Riya Verma, Sumit Dutt Bhardwaj, Neelanjana Sarmah, Sreelatha K. H., Prabhat Kumar and Nivedita Gupta
Viruses 2022, 14(3), 627; https://doi.org/10.3390/v14030627 - 17 Mar 2022
Cited by 13 | Viewed by 2596
Abstract
SARS-CoV-2/influenza virus co-infection studies have focused on hospitalized patients who usually had grave sequelae. Here, we report SARS-CoV-2/influenza virus co-infection cases from both community and hospital settings reported through integrated ILI/SARI (Influenza Like Illness/Severe Acute Respiratory Infection) sentinel surveillance established by the Indian [...] Read more.
SARS-CoV-2/influenza virus co-infection studies have focused on hospitalized patients who usually had grave sequelae. Here, we report SARS-CoV-2/influenza virus co-infection cases from both community and hospital settings reported through integrated ILI/SARI (Influenza Like Illness/Severe Acute Respiratory Infection) sentinel surveillance established by the Indian Council of Medical Research. We describe the disease progression and outcomes in these cases. Out of 13,467 samples tested from 4 July 2021–31 January 2022, only 5 (0.04%) were of SARS-CoV-2/influenza virus co-infection from 3 different sites in distinct geographic regions. Of these, three patients with extremes of age required hospital admission, but none required ICU admission or mechanical ventilation. No mortality was reported. The other two co-infection cases from community settings were managed at home. This is the first report on SARS-CoV-2/Influenza virus co-infection from community as well as hospital settings in India and shows that influenza viruses are circulating in the community even during COVID-19. The results emphasize the need for continuous surveillance for multiple respiratory pathogens for effective public health management of ILI/SARI cases in line with the WHO (World Health Organization) recommendations. Full article
(This article belongs to the Special Issue Respiratory Viral Coinfection)
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12 pages, 1461 KiB  
Article
Insights into Gene Transcriptional Regulation of Kayvirus Bacteriophages Obtained from Therapeutic Mixtures
by Sara Arroyo-Moreno, Colin Buttimer, Francesca Bottacini, Nina Chanishvili, Paul Ross, Colin Hill and Aidan Coffey
Viruses 2022, 14(3), 626; https://doi.org/10.3390/v14030626 - 17 Mar 2022
Cited by 4 | Viewed by 2224
Abstract
Bacteriophages (phages) of the genus Kayvirus of Staphylococcus aureus are promising agents for therapeutic applications. In this study, we isolated Kayvirus phages, SAM1 and SAM2, from the Fersisi commercial phage cocktail (George Eliava Institute, Tbilisi, Georgia), which exhibits high sequence homology with phage [...] Read more.
Bacteriophages (phages) of the genus Kayvirus of Staphylococcus aureus are promising agents for therapeutic applications. In this study, we isolated Kayvirus phages, SAM1 and SAM2, from the Fersisi commercial phage cocktail (George Eliava Institute, Tbilisi, Georgia), which exhibits high sequence homology with phage K (≥94%, BLASTn). We found that phages SAM1 and SAM2 infected 95% and 86% of 21 MRSA of differing sequence types (MLST, SCCmec type) obtained from the Irish National MRSA collection, respectively. We conducted differential transcriptomic analysis by RNA-Seq on phage SAM1 during host infection, showing differential expression of its genes at different points during host infection. This analysis also allowed the identification of potentially adverse outcomes in the application of these phages to target MRSA as therapy. The interaction of phage SAM1 on the host caused the upregulation of prophage genes. Additionally, phage infection was found to cause the slight upregulation of host genes implicated in virulence factors relating to hemolysins, immune evasion, and adhesion, but also the downregulation of genes associated with enterotoxins. The findings of this study give further insights into the biology of kayviruses and their use as therapeutics. Full article
(This article belongs to the Special Issue Bacteriophages from Biology to Therapy for the 21st Century)
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15 pages, 3756 KiB  
Article
Identifying Country-Level Risk Factors for the Spread of COVID-19 in Europe Using Machine Learning
by Serafeim Moustakidis, Christos Kokkotis, Dimitrios Tsaopoulos, Petros Sfikakis, Sotirios Tsiodras, Vana Sypsa, Theoklis E. Zaoutis and Dimitrios Paraskevis
Viruses 2022, 14(3), 625; https://doi.org/10.3390/v14030625 - 17 Mar 2022
Cited by 1 | Viewed by 1934
Abstract
Coronavirus disease 2019 (COVID-19) has resulted in approximately 5 million deaths around the world with unprecedented consequences in people’s daily routines and in the global economy. Despite vast increases in time and money spent on COVID-19-related research, there is still limited information about [...] Read more.
Coronavirus disease 2019 (COVID-19) has resulted in approximately 5 million deaths around the world with unprecedented consequences in people’s daily routines and in the global economy. Despite vast increases in time and money spent on COVID-19-related research, there is still limited information about the factors at the country level that affected COVID-19 transmission and fatality in EU. The paper focuses on the identification of these risk factors using a machine learning (ML) predictive pipeline and an associated explainability analysis. To achieve this, a hybrid dataset was created employing publicly available sources comprising heterogeneous parameters from the majority of EU countries, e.g., mobility measures, policy responses, vaccinations, and demographics/generic country-level parameters. Data pre-processing and data exploration techniques were initially applied to normalize the available data and decrease the feature dimensionality of the data problem considered. Then, a linear ε-Support Vector Machine (ε-SVM) model was employed to implement the regression task of predicting the number of deaths for each one of the three first pandemic waves (with mean square error of 0.027 for wave 1 and less than 0.02 for waves 2 and 3). Post hoc explainability analysis was finally applied to uncover the rationale behind the decision-making mechanisms of the ML pipeline and thus enhance our understanding with respect to the contribution of the selected country-level parameters to the prediction of COVID-19 deaths in EU. Full article
(This article belongs to the Special Issue State-of-the-Art Virus Research in Greece)
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14 pages, 1751 KiB  
Article
Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19
by Anissa Chouikha, Wasfi Fares, Asma Laamari, Sondes Haddad-Boubaker, Zeineb Belaiba, Kais Ghedira, Wafa Kammoun Rebai, Kaouther Ayouni, Marwa Khedhiri, Samar Ben Halima, Henda Krichen, Henda Touzi, Imen Ben Dhifallah, Fatma Z. Guerfali, Chiraz Atri, Saifeddine Azouz, Oussema Khamessi, Monia Ardhaoui, Mouna Safer, Nissaf Ben Alaya, Ikram Guizani, Rym Kefi, Mariem Gdoura and Henda Trikiadd Show full author list remove Hide full author list
Viruses 2022, 14(3), 624; https://doi.org/10.3390/v14030624 - 17 Mar 2022
Cited by 11 | Viewed by 3137
Abstract
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and [...] Read more.
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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14 pages, 1780 KiB  
Article
Expanding the Medfly Virome: Viral Diversity, Prevalence, and sRNA Profiling in Mass-Reared and Field-Derived Medflies
by Luis Hernández-Pelegrín, Ángel Llopis-Giménez, Cristina Maria Crava, Félix Ortego, Pedro Hernández-Crespo, Vera I. D. Ros and Salvador Herrero
Viruses 2022, 14(3), 623; https://doi.org/10.3390/v14030623 - 17 Mar 2022
Cited by 7 | Viewed by 3835
Abstract
The Mediterranean fruit fly (medfly), Ceratitis capitata, is an agricultural pest of a wide range of fruits. The advent of high-throughput sequencing has boosted the discovery of RNA viruses infecting insects. In this article, we aim to characterize the RNA virome and [...] Read more.
The Mediterranean fruit fly (medfly), Ceratitis capitata, is an agricultural pest of a wide range of fruits. The advent of high-throughput sequencing has boosted the discovery of RNA viruses infecting insects. In this article, we aim to characterize the RNA virome and viral sRNA profile of medfly. By means of transcriptome mining, we expanded the medfly RNA virome to 13 viruses, including two novel positive ssRNA viruses and the first two novel dsRNA viruses reported for medfly. Our analysis across multiple laboratory-reared and field-collected medfly samples showed the presence of a core RNA virome comprised of Ceratitis capitata iflavirus 2 and Ceratitis capitata negev-like virus 1. Furthermore, field-collected flies showed a higher viral diversity in comparison to the laboratory-reared flies. Based on the small RNA sequencing, we detected small interfering RNAs mapping to all the viruses present in each sample, except for Ceratitis capitata nora virus. Although the identified RNA viruses do not cause obvious symptoms in medflies, the outcome of their interaction may still influence the medfly’s fitness and ecology, becoming either a risk or an opportunity for mass-rearing and SIT applications. Full article
(This article belongs to the Special Issue Viruses in Mass-Reared Invertebrates)
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