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Viruses, Volume 12, Issue 7 (July 2020) – 94 articles

Cover Story (view full-size image): The large capsids, or heads, of giant phages are unusual, containing not only their long genomes, but in many instances a large amount of protein that is ejected into the host bacterial cell. How giant phage heads form is mostly undefined. In this study, the proteolysis of head proteins by the prohead protease was shown to be essential for head maturation of giant Salmonella virus SPN3US. In the absence of proteolysis, precursor head structures remained anchored to the Salmonella inner membrane, thus preventing packaging of the genomic DNA and addition of the tail. View this paper
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Article
Oropouche Virus Infects, Persists and Induces IFN Response in Human Peripheral Blood Mononuclear Cells as Identified by RNA PrimeFlow™ and qRT-PCR Assays
Viruses 2020, 12(7), 785; https://doi.org/10.3390/v12070785 - 21 Jul 2020
Cited by 1 | Viewed by 1758
Abstract
Oropouche orthobunyavirus (OROV) is an emerging arbovirus with a high potential of dissemination in America. Little is known about the role of peripheral blood mononuclear cells (PBMC) response during OROV infection in humans. Thus, to evaluate human leukocytes susceptibility, permissiveness and immune response [...] Read more.
Oropouche orthobunyavirus (OROV) is an emerging arbovirus with a high potential of dissemination in America. Little is known about the role of peripheral blood mononuclear cells (PBMC) response during OROV infection in humans. Thus, to evaluate human leukocytes susceptibility, permissiveness and immune response during OROV infection, we applied RNA hybridization, qRT-PCR and cell-based assays to quantify viral antigens, genome, antigenome and gene expression in different cells. First, we observed OROV replication in human leukocytes lineages as THP-1 monocytes, Jeko-1 B cells and Jurkat T cells. Interestingly, cell viability and viral particle detection are maintained in these cells, even after successive passages. PBMCs from healthy donors were susceptible but the infection was not productive, since neither antigenome nor infectious particle was found in the supernatant of infected PBMCs. In fact, only viral antigens and small quantities of OROV genome were detected at 24 hpi in lymphocytes, monocytes and CD11c+ cells. Finally, activation of the Interferon (IFN) response was essential to restrict OROV replication in human PBMCs. Increased expression of type I/III IFNs, ISGs and inflammatory cytokines was detected in the first 24 hpi and viral replication was re-established after blocking IFNAR or treating cells with glucocorticoid. Thus, in short, our results show OROV is able to infect and remain in low titers in human T cells, monocytes, DCs and B cells as a consequence of an effective IFN response after infection, indicating the possibility of leukocytes serving as a trojan horse in specific microenvironments during immunosuppression. Full article
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Review
Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins
Viruses 2020, 12(7), 784; https://doi.org/10.3390/v12070784 - 21 Jul 2020
Cited by 2 | Viewed by 1447
Abstract
Endemic to West Africa and South America, mammalian arenaviruses can cross the species barrier from their natural rodent hosts to humans, resulting in illnesses ranging from mild flu-like syndromes to severe and fatal haemorrhagic zoonoses. The increased frequency of outbreaks and associated high [...] Read more.
Endemic to West Africa and South America, mammalian arenaviruses can cross the species barrier from their natural rodent hosts to humans, resulting in illnesses ranging from mild flu-like syndromes to severe and fatal haemorrhagic zoonoses. The increased frequency of outbreaks and associated high fatality rates of the most prevalent arenavirus, Lassa, in West African countries, highlights the significant risk to public health and to the socio-economic development of affected countries. The devastating impact of these viruses is further exacerbated by the lack of approved vaccines and effective treatments. Differential immune responses to arenavirus infections that can lead to either clearance or rapid, widespread and uncontrolled viral dissemination are modulated by the arenavirus multifunctional proteins, NP and Z. These two proteins control the antiviral response to infection by targeting multiple cellular pathways; and thus, represent attractive targets for antiviral development to counteract infection. The interplay between the host immune responses and viral replication is a key determinant of virus pathogenicity and disease outcome. In this review, we examine the current understanding of host immune defenses against arenavirus infections and summarise the host protein interactions of NP and Z and the mechanisms that govern immune evasion strategies. Full article
(This article belongs to the Special Issue Arenaviruses 2020)
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Article
Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice
Viruses 2020, 12(7), 783; https://doi.org/10.3390/v12070783 - 21 Jul 2020
Cited by 2 | Viewed by 1533
Abstract
Insertions of endogenous retroviruses cause a significant fraction of mutations in inbred mice but not all strains are equally susceptible. Notably, most new Intracisternal A particle (IAP) ERV mutagenic insertions have occurred in C3H mice. We show here that strain-specific insertional polymorphic IAPs [...] Read more.
Insertions of endogenous retroviruses cause a significant fraction of mutations in inbred mice but not all strains are equally susceptible. Notably, most new Intracisternal A particle (IAP) ERV mutagenic insertions have occurred in C3H mice. We show here that strain-specific insertional polymorphic IAPs accumulate faster in C3H/HeJ mice, relative to other sequenced strains, and that IAP transcript levels are higher in C3H/HeJ embryonic stem (ES) cells compared to other ES cells. To investigate the mechanism for high IAP activity in C3H mice, we identified 61 IAP copies in C3H/HeJ ES cells enriched with H3K4me3 (a mark of active promoters) and, among those tested, all are unmethylated in C3H/HeJ ES cells. Notably, 13 of the 61 are specific to C3H/HeJ and are members of the non-autonomous 1Δ1 IAP subfamily that is responsible for nearly all new insertions in C3H. One copy is full length with intact open reading frames and hence potentially capable of providing proteins in trans to other 1Δ1 elements. This potential “master copy” is present in other strains, including 129, but its 5’ long terminal repeat (LTR) is methylated in 129 ES cells. Thus, the unusual IAP activity in C3H may be due to reduced epigenetic repression coupled with the presence of a master copy. Full article
(This article belongs to the Special Issue Endogenous Retroviruses in Development and Disease)
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Communication
High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Viruses 2020, 12(7), 782; https://doi.org/10.3390/v12070782 - 21 Jul 2020
Viewed by 1208
Abstract
Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from [...] Read more.
Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Full article
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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Article
Human Metapneumovirus Escapes NK Cell Recognition through the Downregulation of Stress-Induced Ligands for NKG2D
Viruses 2020, 12(7), 781; https://doi.org/10.3390/v12070781 - 20 Jul 2020
Viewed by 1029
Abstract
The Pneumoviridae family includes human metapneumovirus (HMPV) and human orthopneumovirus, which is also known as a respiratory syncytial virus (HRSV). These are large enveloped, negative single-strand RNA viruses. HMPV and HRSV are the human members, which commonly infect children. HMPV, which was discovered [...] Read more.
The Pneumoviridae family includes human metapneumovirus (HMPV) and human orthopneumovirus, which is also known as a respiratory syncytial virus (HRSV). These are large enveloped, negative single-strand RNA viruses. HMPV and HRSV are the human members, which commonly infect children. HMPV, which was discovered in 2001, infects most children until the age of five, which causes an influenza-like illness. The interaction of this virus with immune cells is poorly understood. In this study, we show that HMPV evades natural killer (NK) cell attack by downregulating stress-induced ligands for the activating receptor NKG2D including: Major histocompatibility complex (MHC) class I polypeptide-related sequences A and B (MICA, MICB), UL16 binding proteins ULBP2, and ULBP3, but not ULBP1. Mechanistically, we show that the viral protein G is involved in the downregulation of ULBP2 and that the viral protein M2.2 is required for MICA and MICB downregulation. These findings emphasize the importance of NK cells, in general, and NKG2D, in particular, in controlling HMPV infection, which opens new avenues for treating HMPV. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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Article
Comparative Analyses of the Antiviral Activities of IgG and IgA Antibodies to Influenza A Virus M2 Protein
Viruses 2020, 12(7), 780; https://doi.org/10.3390/v12070780 - 20 Jul 2020
Cited by 2 | Viewed by 1118
Abstract
The influenza A virus (IAV) matrix-2 (M2) protein is an antigenically conserved viral envelope protein that plays an important role in virus budding together with another envelope protein, hemagglutinin (HA). An M2-specific mouse monoclonal IgG antibody, rM2ss23, which binds to the ectodomain of [...] Read more.
The influenza A virus (IAV) matrix-2 (M2) protein is an antigenically conserved viral envelope protein that plays an important role in virus budding together with another envelope protein, hemagglutinin (HA). An M2-specific mouse monoclonal IgG antibody, rM2ss23, which binds to the ectodomain of the M2 protein, has been shown to be a non-neutralizing antibody, but inhibits plaque formation of IAV strains. In this study, we generated chimeric rM2ss23 (ch-rM2ss23) IgG and IgA antibodies with the same variable region and compared their antiviral activities. Using gel chromatography, ch-rM2ss23 IgA were divided into three antibody subsets: monomeric IgA (m-IgA), dimeric IgA (d-IgA), and trimeric and tetrameric IgA (t/q-IgA). We found that t/q-IgA had a significantly higher capacity to reduce the plaque size of IAVs than IgG and m-IgA, most likely due to the decreased number of progeny virus particles produced from infected cells. Interestingly, HA-M2 colocalization was remarkably reduced on the infected cell surface in the presence of ch-rM2ss23 antibodies. These results indicate that anti-M2 polymeric IgA restricts IAV budding more efficiently than IgG and suggest a role of anti-M2 IgA in cross-protective immunity to IAVs. Full article
(This article belongs to the Special Issue Influenza Virus Vaccines)
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Communication
Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters
Viruses 2020, 12(7), 779; https://doi.org/10.3390/v12070779 - 20 Jul 2020
Cited by 52 | Viewed by 4297
Abstract
In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the [...] Read more.
In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals. Since age-dependent differences of COVID-19 were identified in humans, we compared the course of SARS-CoV-2 infection in young and aged Syrian hamsters. We show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. However, older hamsters exhibited more pronounced and consistent weight loss. In situ hybridization in the lungs identified viral RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. The latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Full article
(This article belongs to the Special Issue Pathogenesis of Human and Animal Coronaviruses)
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Review
Putative Role of Arthropod Vectors in African Swine Fever Virus Transmission in Relation to Their Bio-Ecological Properties
Viruses 2020, 12(7), 778; https://doi.org/10.3390/v12070778 - 20 Jul 2020
Cited by 9 | Viewed by 1528
Abstract
African swine fever (ASF) is one of the most important diseases in Suidae due to its significant health and socioeconomic consequences and represents a major threat to the European pig industry, especially in the absence of any available treatment or vaccine. In fact, [...] Read more.
African swine fever (ASF) is one of the most important diseases in Suidae due to its significant health and socioeconomic consequences and represents a major threat to the European pig industry, especially in the absence of any available treatment or vaccine. In fact, with its high mortality rate and the subsequent trade restrictions imposed on affected countries, ASF can dramatically disrupt the pig industry in afflicted countries. In September 2018, ASF was unexpectedly identified in wild boars from southern Belgium in the province of Luxembourg, not far from the Franco-Belgian border. The French authorities rapidly commissioned an expert opinion on the risk of ASF introduction and dissemination into metropolitan France. In Europe, the main transmission routes of the virus comprise direct contact between infected and susceptible animals and indirect transmission through contaminated material or feed. However, the seasonality of the disease in some pig farms in Baltic countries, including outbreaks in farms with high biosecurity levels, have led to questions on the possible involvement of arthropods in the transmission of the virus. This review explores the current body of knowledge on the most common arthropod families present in metropolitan France. We examine their potential role in spreading ASF—by active biological or mechanical transmission or by passive transport or ingestion—in relation to their bio-ecological properties. It also highlights the existence of significant gaps in our knowledge on vector ecology in domestic and wild boar environments and in vector competence for ASFV transmission. Filling these gaps is essential to further understanding ASF transmission in order to thus implement appropriate management measures. Full article
Article
Covid-19 Transmission Trajectories–Monitoring the Pandemic in the Worldwide Context
Viruses 2020, 12(7), 777; https://doi.org/10.3390/v12070777 - 20 Jul 2020
Cited by 9 | Viewed by 2000
Abstract
The Covid-19 pandemic is developing worldwide with common dynamics but also with marked differences between regions and countries. These are not completely understood, but presumably, provide a clue to find ways to mitigate epidemics until strategies leading to its eradication become available. We [...] Read more.
The Covid-19 pandemic is developing worldwide with common dynamics but also with marked differences between regions and countries. These are not completely understood, but presumably, provide a clue to find ways to mitigate epidemics until strategies leading to its eradication become available. We describe an iteractive monitoring tool available in the internet. It enables inspection of the dynamic state of the epidemic in 187 countries using trajectories that visualize the transmission and removal rates of the epidemic and in this way bridge epi-curve tracking with modelling approaches. Examples were provided which characterize state of epidemic in different regions of the world in terms of fast and slow growing and decaying regimes and estimate associated rate factors. The basic spread of the disease is associated with transmission between two individuals every two-three days on the average. Non-pharmaceutical interventions decrease this value to up to ten days, whereas ‘complete lock down’ measures are required to stop the epidemic. Comparison of trajectories revealed marked differences between the countries regarding efficiency of measures taken against the epidemic. Trajectories also reveal marked country-specific recovery and death rate dynamics. The results presented refer to the pandemic state in May to July 2020 and can serve as ‘working instruction’ for timely monitoring using the interactive monitoring tool as a sort of ‘seismometer’ for the evaluation of the state of epidemic, e.g., the possible effect of measures taken in both, lock-down and lock-up directions. Comparison of trajectories between countries and regions will support developing hypotheses and models to better understand regional differences of dynamics of Covid-19. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2020)
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Article
Tiotropium Is Predicted to Be a Promising Drug for COVID-19 Through Transcriptome-Based Comprehensive Molecular Pathway Analysis
Viruses 2020, 12(7), 776; https://doi.org/10.3390/v12070776 - 20 Jul 2020
Cited by 7 | Viewed by 2078
Abstract
The coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affects almost everyone in the world in many ways. We previously predicted antivirals (atazanavir, remdesivir and lopinavir/ritonavir) and non-antiviral drugs (tiotropium and rapamycin) that may inhibit the replication [...] Read more.
The coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affects almost everyone in the world in many ways. We previously predicted antivirals (atazanavir, remdesivir and lopinavir/ritonavir) and non-antiviral drugs (tiotropium and rapamycin) that may inhibit the replication complex of SARS-CoV-2 using our molecular transformer–drug target interaction (MT–DTI) deep-learning-based drug–target affinity prediction model. In this study, we dissected molecular pathways upregulated in SARS-CoV-2-infected normal human bronchial epithelial (NHBE) cells by analyzing an RNA-seq data set with various bioinformatics approaches, such as gene ontology, protein–protein interaction-based network and gene set enrichment analyses. The results indicated that the SARS-CoV-2 infection strongly activates TNF and NFκB-signaling pathways through significant upregulation of the TNF, IL1B, IL6, IL8, NFKB1, NFKB2 and RELB genes. In addition to these pathways, lung fibrosis, keratinization/cornification, rheumatoid arthritis, and negative regulation of interferon-gamma production pathways were also significantly upregulated. We observed that these pathologic features of SARS-CoV-2 are similar to those observed in patients with chronic obstructive pulmonary disease (COPD). Intriguingly, tiotropium, as predicted by MT–DTI, is currently used as a therapeutic intervention in COPD patients. Treatment with tiotropium has been shown to improve pulmonary function by alleviating airway inflammation. Accordingly, a literature search summarized that tiotropium reduced expressions of IL1B, IL6, IL8, RELA, NFKB1 and TNF in vitro or in vivo, and many of them have been known to be deregulated in COPD patients. These results suggest that COVID-19 is similar to an acute mode of COPD caused by the SARS-CoV-2 infection, and therefore tiotropium may be effective for COVID-19 patients. Full article
(This article belongs to the Section SARS-CoV-2 and COVID-19)
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Article
Decrypting the Origin and Pathogenesis in Pregnant Ewes of a New Ovine Pestivirus Closely Related to Classical Swine Fever Virus
Viruses 2020, 12(7), 775; https://doi.org/10.3390/v12070775 - 17 Jul 2020
Cited by 5 | Viewed by 1323
Abstract
This study shows the origin and the pathogenic role of a novel ovine pestivirus (OVPV) isolated in 2017 in Italy, as a pathogenic agent causing severe abortions after infection in pregnant ewes and high capacity for virus trans-placental transmission as well as the [...] Read more.
This study shows the origin and the pathogenic role of a novel ovine pestivirus (OVPV) isolated in 2017 in Italy, as a pathogenic agent causing severe abortions after infection in pregnant ewes and high capacity for virus trans-placental transmission as well as the birth of lambs suffering OVPV-persistent infection. The OVPV infection induced early antibody response detected by the specific ELISA against classical swine fever virus (CSFV), another important virus affecting swine. The neutralizing antibody response were similar against CSFV strains from genotype 2 and the OVPV. These viruses showed high identity in the B/C domain of the E2-glycoprotein. Close molecular diagnostics cross-reactivity between CSFV and OVPV was found and a new OVPV molecular assay was developed. The phylodynamic analysis showed that CSFV seems to have emerged as the result of an inter-species jump of Tunisian sheep virus (TSV) from sheep to pigs. The OVPV and the CSFV share the TSV as a common ancestor, emerging around 300 years ago. This suggests that the differentiation of TSV into two dangerous new viruses for animal health (CSFV and OVPV) was likely favored by human intervention for the close housing of multiple species for intensive livestock production. Full article
(This article belongs to the Section Animal Viruses)
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Article
Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018
Viruses 2020, 12(7), 774; https://doi.org/10.3390/v12070774 - 17 Jul 2020
Cited by 4 | Viewed by 1092
Abstract
The complex overlap in waterfowl migratory pathways across the world has established numerous occurrences of genetic reassortment and intercontinental spread of avian influenza virus (AIV) over long distances, thereby calling for huge efforts and targeted surveillance for infection control. During annual surveillance in [...] Read more.
The complex overlap in waterfowl migratory pathways across the world has established numerous occurrences of genetic reassortment and intercontinental spread of avian influenza virus (AIV) over long distances, thereby calling for huge efforts and targeted surveillance for infection control. During annual surveillance in South Korea in 2018, a novel avian influenza H6N5 (K6) subtype was isolated from the fecal sample of wild bird. Genomic characterization using a phylogenetic tree indicated the K6 virus to be of North American-origin, with partial homology to an H6N5 strain, A/Aix galericulata/South Korea/K17-1638-5/2017 (K17). A monobasic residue at the HA cleavage site and absence of a notable mutation at the HA receptor-binding site suggested the isolate to be of low pathogenicity. However, molecular analysis revealed the E119V mutation in the NA gene and a human host marker mutation E382D in the polymerase acidic (PA) gene, implying their susceptibility to neuraminidase inhibitors and potential infectivity in humans, respectively. For comparison, K6 and K17 were found to be dissimilar for various mutations, such as A274T of PB2, S375N/T of PB1, or V105M of NP, each concerning the increased virulence of K6 in mammalian system. Moreover, kinetic data presented the highest viral titer of this H6N5 isolate at 106.37 log10TCID50 after 48 h of infection, thus proving efficient adaptability for replication in a mammalian system in vitro. The mouse virus challenge study showed insignificant influence on the total body weight, while viral load shedding in lungs peaked at 1.88 ± 0.21 log10 TICD50/mL, six days post infection. The intercontinental transmission of viruses from North America may continuously be present in Korea, thereby providing constant opportunities for virus reassortment with local resident AIVs; these results hint at the increased potential risk of host jumping capabilities of the new isolates. Our findings reinforce the demand for regular surveillance, not only in Korea but also along the flyways in Alaska. Full article
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Review
Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus
Viruses 2020, 12(7), 773; https://doi.org/10.3390/v12070773 - 17 Jul 2020
Cited by 7 | Viewed by 2108
Abstract
Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus Potyvirus are transmitted by aphids in a non-persistent, non-circulative manner and have been [...] Read more.
Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus Potyvirus are transmitted by aphids in a non-persistent, non-circulative manner and have been extensively studied vis-à-vis their structure, taxonomy, evolution, diagnosis, transmission, and molecular interactions with hosts. This comprehensive review exclusively discusses potyviruses and their transmission by aphid vectors, specifically in the light of several virus, aphid and plant factors, and how their interplay influences potyviral binding in aphids, aphid behavior and fitness, host plant biochemistry, virus epidemics, and transmission bottlenecks. We present the heatmap of the global distribution of potyvirus species, variation in the potyviral coat protein gene, and top aphid vectors of potyviruses. Lastly, we examine how the fundamental understanding of these multi-partite interactions through multi-omics approaches is already contributing to, and can have future implications for, devising effective and sustainable management strategies against aphid-transmitted potyviruses to global agriculture. Full article
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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Review
Brothers in Arms: Structure, Assembly and Function of Arenaviridae Nucleoprotein
Viruses 2020, 12(7), 772; https://doi.org/10.3390/v12070772 - 17 Jul 2020
Cited by 4 | Viewed by 1516
Abstract
Arenaviridae is a family of viruses harbouring important emerging pathogens belonging to the Bunyavirales order. Like in other segmented negative strand RNA viruses, the nucleoprotein (NP) is a major actor of the viral life cycle being both (i) the necessary co-factor of the [...] Read more.
Arenaviridae is a family of viruses harbouring important emerging pathogens belonging to the Bunyavirales order. Like in other segmented negative strand RNA viruses, the nucleoprotein (NP) is a major actor of the viral life cycle being both (i) the necessary co-factor of the polymerase present in the L protein, and (ii) the last line of defence of the viral genome (vRNA) by physically hiding its presence in the cytoplasm. The NP is also one of the major players interfering with the immune system. Several structural studies of NP have shown that it features two domains: a globular RNA binding domain (NP-core) in its N-terminal and an exonuclease domain (ExoN) in its C-terminal. Further studies have observed that significant conformational changes are necessary for RNA encapsidation. In this review we revisited the most recent structural and functional data available on Arenaviridae NP, compared to other Bunyavirales nucleoproteins and explored the structural and functional implications. We review the variety of structural motif extensions involved in NP–NP binding mode. We also evaluate the major functional implications of NP interactome and the role of ExoN, thus making the NP a target of choice for future vaccine and antiviral therapy. Full article
(This article belongs to the Special Issue Function and Structure of Viral Ribonucleoproteins Complexes)
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Article
ZIKV Infection Induces DNA Damage Response and Alters the Proteome of Gastrointestinal Cells
Viruses 2020, 12(7), 771; https://doi.org/10.3390/v12070771 - 17 Jul 2020
Cited by 3 | Viewed by 903
Abstract
The zika virus (ZIKV) is a neurotropic virus that causes congenital abnormalities in babies when they are infected in utero. Some studies have reported these congenital abnormalities result from ZIKV attacking neural progenitor cells within the brain which differentiate into neurons, oligodendrocytes, and [...] Read more.
The zika virus (ZIKV) is a neurotropic virus that causes congenital abnormalities in babies when they are infected in utero. Some studies have reported these congenital abnormalities result from ZIKV attacking neural progenitor cells within the brain which differentiate into neurons, oligodendrocytes, and astrocytes. Each of these glial cells play important roles during development of the fetal brain. In addition to ZIKV-induced congenital abnormalities, infected patients experience gastrointestinal complications. There are presently no reports investigating the role of this virus at the proteomic level in gastrointestinal associated cells, so we conducted an in vitro proteomic study of ZIKV-induced changes in Caco-2, a colon-derived human cell line which is known to be permissive to ZIKV infection. We used SomaScan, a new aptamer-based proteomic tool to identify host proteins that are dysregulated during ZIKV infection at 12, 24, and 48 h post-infection. Bioinformatic analyses predicted that dysregulation of differentially-regulated host proteins results in various gastrointestinal diseases. Validation of the clinical relevance of these promising protein targets will add to the existing knowledge of ZIKV biology. These potential proteins may be useful targets towards the development of therapeutic interventions. Full article
(This article belongs to the Section Animal Viruses)
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Article
The Mutation of the Genes Related to Neurovirulence in HSV-2 Produces an Attenuated Phenotype in Mice
Viruses 2020, 12(7), 770; https://doi.org/10.3390/v12070770 - 17 Jul 2020
Cited by 2 | Viewed by 978
Abstract
HSV-2 (Herpes simplex virus type 2) is a critical viral agent that mainly causes genital herpes and life-long latent infection in the dorsal root ganglia. Gene modification via CRISPR/Cas9 Clustered regularly interspaced short palindromic repeat sequences/CRISPR associated 9) was used here to construct [...] Read more.
HSV-2 (Herpes simplex virus type 2) is a critical viral agent that mainly causes genital herpes and life-long latent infection in the dorsal root ganglia. Gene modification via CRISPR/Cas9 Clustered regularly interspaced short palindromic repeat sequences/CRISPR associated 9) was used here to construct HSV-2 mutant strains through the deletion of fragments of the RL1 (Repeat Long element 1) and/or LAT (Latency-associated Transcript) genes. The HSV-2 mutant strains LAT-HSV-2 and RL1-LAT-HSV-2 present different biological properties. The proliferation of RL1-LAT-HSV-2 in nerve cells was decreased significantly, and the plaques induced by RL1-LAT-HSV-2 in Vero cells were smaller than those induced by LAT-HSV-2 mutant and wild-type strains. The observation of mice infected with these two mutants compared to mice infected with the wild-type strain indicated that the mutant RL1-LAT-HSV-2 has an attenuated phenotype with reduced pathogenicity during both acute and latent infections and induces a stronger specific immune response than the wild-type strain, whereas the attenuation effect was not found in mice infected with the LAT-HSV-2 mutant containing the LAT gene deletion. However, the simultaneous mutation of both the RL1 and LAT genes did not completely restrict viral proliferation in nerve cells, indicating that multiple HSV genes are involved in viral replication in the neural system. This work suggests that the HSV-2 genes RL1 and/or LAT might be involved in the virulence mechanisms in mouse infections. Full article
(This article belongs to the Special Issue Mechanisms of Viral Fusion and Applications in Antivirals)
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Article
Deploying Machine and Deep Learning Models for Efficient Data-Augmented Detection of COVID-19 Infections
Viruses 2020, 12(7), 769; https://doi.org/10.3390/v12070769 - 16 Jul 2020
Cited by 43 | Viewed by 3515
Abstract
This generation faces existential threats because of the global assault of the novel Corona virus 2019 (i.e., COVID-19). With more than thirteen million infected and nearly 600000 fatalities in 188 countries/regions, COVID-19 is the worst calamity since the World War II. These misfortunes [...] Read more.
This generation faces existential threats because of the global assault of the novel Corona virus 2019 (i.e., COVID-19). With more than thirteen million infected and nearly 600000 fatalities in 188 countries/regions, COVID-19 is the worst calamity since the World War II. These misfortunes are traced to various reasons, including late detection of latent or asymptomatic carriers, migration, and inadequate isolation of infected people. This makes detection, containment, and mitigation global priorities to contain exposure via quarantine, lockdowns, work/stay at home, and social distancing that are focused on “flattening the curve”. While medical and healthcare givers are at the frontline in the battle against COVID-19, it is a crusade for all of humanity. Meanwhile, machine and deep learning models have been revolutionary across numerous domains and applications whose potency have been exploited to birth numerous state-of-the-art technologies utilised in disease detection, diagnoses, and treatment. Despite these potentials, machine and, particularly, deep learning models are data sensitive, because their effectiveness depends on availability and reliability of data. The unavailability of such data hinders efforts of engineers and computer scientists to fully contribute to the ongoing assault against COVID-19. Faced with a calamity on one side and absence of reliable data on the other, this study presents two data-augmentation models to enhance learnability of the Convolutional Neural Network (CNN) and the Convolutional Long Short-Term Memory (ConvLSTM)-based deep learning models (DADLMs) and, by doing so, boost the accuracy of COVID-19 detection. Experimental results reveal improvement in terms of accuracy of detection, logarithmic loss, and testing time relative to DLMs devoid of such data augmentation. Furthermore, average increases of 4% to 11% in COVID-19 detection accuracy are reported in favour of the proposed data-augmented deep learning models relative to the machine learning techniques. Therefore, the proposed algorithm is effective in performing a rapid and consistent Corona virus diagnosis that is primarily aimed at assisting clinicians in making accurate identification of the virus. Full article
(This article belongs to the Special Issue Virus Bioinformatics 2020)
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Article
Minimum Infective Dose of a Lumpy Skin Disease Virus Field Strain from North Macedonia
Viruses 2020, 12(7), 768; https://doi.org/10.3390/v12070768 - 16 Jul 2020
Cited by 5 | Viewed by 928
Abstract
Infection with Lumpy Skin Disease virus (LSDV), as well as infections with other Capripox virus species, are described as the most severe pox diseases of production animals and are therefore listed as notifiable diseases under the guidelines of the World Organization for Animal [...] Read more.
Infection with Lumpy Skin Disease virus (LSDV), as well as infections with other Capripox virus species, are described as the most severe pox diseases of production animals and are therefore listed as notifiable diseases under the guidelines of the World Organization for Animal Health (OIE). To our knowledge there is only a single study examining dose dependency, clinical course, viremia, virus shedding, as well as serological response following experimental LSDV “Neethling” inoculation. Here, we inoculated cattle with four different doses of LSDV strain “Macedonia2016”, a recently characterized virulent LSDV field strain, and examined clinical symptoms, viremia, viral shedding, and seroconversion. Interestingly, around 400 cell culture infectious dose50 (CCID50) of LSDV-“Macedonia2016” were sufficient to induce generalized Lumpy Skin Disease (LSD) in two out of six cattle but with a different incubation time, whereas the other animals of this group showed only a mild course of LSD. However, differences in incubation time, viral loads, serology, and in the clinical scoring could not be observed in the other three groups. In summary, we concluded that experimental LSDV infection of cattle with an infectious virus titer of 105 to 106 CCID50/mL of “Macedonia2016” provides a robust and sufficient challenge model for future studies. Full article
(This article belongs to the Section Animal Viruses)
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Article
Establishment of a Simple and Efficient Reverse Genetics System for Canine Adenoviruses Using Bacterial Artificial Chromosomes
Viruses 2020, 12(7), 767; https://doi.org/10.3390/v12070767 - 16 Jul 2020
Cited by 1 | Viewed by 1359
Abstract
Canine adenoviruses (CAdVs) are divided into pathotypes CAdV1 and CAdV2, which cause infectious hepatitis and laryngotracheitis in canid animals, respectively. They can be the backbones of viral vectors that could be applied in recombinant vaccines or for gene transfer in dogs and in [...] Read more.
Canine adenoviruses (CAdVs) are divided into pathotypes CAdV1 and CAdV2, which cause infectious hepatitis and laryngotracheitis in canid animals, respectively. They can be the backbones of viral vectors that could be applied in recombinant vaccines or for gene transfer in dogs and in serologically naïve humans. Although conventional plasmid-based reverse genetics systems can be used to construct CAdV vectors, their large genome size creates technical difficulties in gene cloning and manipulation. In this study, we established an improved reverse genetics system for CAdVs using bacterial artificial chromosomes (BACs), in which genetic modifications can be efficiently and simply made through BAC recombineering. To validate the utility of this system, we used it to generate CAdV2 with the early region 1 gene deleted. This mutant was robustly generated and attenuated in cell culture. The results suggest that our established BAC-based reverse genetics system for CAdVs would be a useful and powerful tool for basic and advanced practical studies with these viruses. Full article
(This article belongs to the Section Animal Viruses)
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Article
Genotypic Characterization of Epstein Barr Virus in Blood of Patients with Suspected Nasopharyngeal Carcinoma in Ghana
Viruses 2020, 12(7), 766; https://doi.org/10.3390/v12070766 - 16 Jul 2020
Cited by 2 | Viewed by 1007
Abstract
Nasopharyngeal cancer (NPC) is associated with Epstein Barr virus (EBV) infection. However different viral strains have been implicated in NPC worldwide. This study aimed to detect and characterize EBV in patients diagnosed with NPC in Ghana. A total of 55 patients diagnosed with [...] Read more.
Nasopharyngeal cancer (NPC) is associated with Epstein Barr virus (EBV) infection. However different viral strains have been implicated in NPC worldwide. This study aimed to detect and characterize EBV in patients diagnosed with NPC in Ghana. A total of 55 patients diagnosed with NPC by CT scan and endoscopy were age-matched with 53 controls without a known oncological disease. Venous blood was collected from the study participants and DNA extracted from the blood samples. Detection of EBV and genotyping were done by amplifying Epstein Barr nuclear antigen 1 (EBNA-1) and Epstein Barr nuclear antigen 2 (EBNA-2), respectively, using specific primers. Viral load in patients and controls was determined using real-time polymerase chain reaction. EBV positivity in controls (92%) was significantly greater than that of NPC patients (67%) (χ2 = 19.17, p < 0.0001), and viral infection was independent of gender (χ2 = 1.770, p = 0.1834). The predominant EBV genotypes in patients and controls were genotype 2 (52%) and genotype 1 (62%), respectively. Median EBV load was significantly higher in NPC patients than the control group (p < 0.01). In summary, prevalence of EBV genotype 2 infection was higher in NPC patients than the control group. Assessment of EBV load may be used as a biomarker for the diagnosis of NPC. Full article
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Review
The Regulation of Flavivirus Infection by Hijacking Exosome-Mediated Cell–Cell Communication: New Insights on Virus–Host Interactions
Viruses 2020, 12(7), 765; https://doi.org/10.3390/v12070765 - 16 Jul 2020
Cited by 4 | Viewed by 2215
Abstract
The arthropod-borne flaviviruses are important human pathogens, and a deeper understanding of the virus–host cell interaction is required to identify cellular targets that can be used as therapeutic candidates. It is well reported that the flaviviruses hijack several cellular functions, such as exosome-mediated [...] Read more.
The arthropod-borne flaviviruses are important human pathogens, and a deeper understanding of the virus–host cell interaction is required to identify cellular targets that can be used as therapeutic candidates. It is well reported that the flaviviruses hijack several cellular functions, such as exosome-mediated cell communication during infection, which is modulated by the delivery of the exosomal cargo of pro- or antiviral molecules to the receiving host cells. Therefore, to study the role of exosomes during flavivirus infections is essential, not only to understand its relevance in virus–host interaction, but also to identify molecular factors that may contribute to the development of new strategies to block these viral infections. This review explores the implications of exosomes in flavivirus dissemination and transmission from the vector to human host cells, as well as their involvement in the host immune response. The hypothesis about exosomes as a transplacental infection route of ZIKV and the paradox effect or the dual role of exosomes released during flavivirus infection are also discussed here. Although several studies have been performed in order to identify and characterize cellular and viral molecules released in exosomes, it is not clear how all of these components participate in viral pathogenesis. Further studies will determine the balance between protective and harmful exosomes secreted by flavivirus infected cells, the characteristics and components that distinguish them both, and how they could be a factor that determines the infection outcome. Full article
(This article belongs to the Special Issue Viruses and Extracellular Vesicles)
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Article
MAVS Genetic Variation Is Associated with Decreased HIV-1 Replication In Vitro and Reduced CD4+ T Cell Infection in HIV-1-Infected Individuals
Viruses 2020, 12(7), 764; https://doi.org/10.3390/v12070764 - 16 Jul 2020
Cited by 1 | Viewed by 1233
Abstract
The mitochondrial antiviral protein MAVS is a key player in the induction of antiviral responses; however, human immunodeficiency virus 1 (HIV-1) is able to suppress these responses. Two linked single nucleotide polymorphisms (SNPs) in the MAVS gene render MAVS insensitive to HIV-1-dependent suppression, [...] Read more.
The mitochondrial antiviral protein MAVS is a key player in the induction of antiviral responses; however, human immunodeficiency virus 1 (HIV-1) is able to suppress these responses. Two linked single nucleotide polymorphisms (SNPs) in the MAVS gene render MAVS insensitive to HIV-1-dependent suppression, and have been shown to be associated with a lower viral load at set point and delayed increase of viral load during disease progression. Here, we studied the underlying mechanisms involved in the control of viral replication in individuals homozygous for this MAVS genotype. We observed that individuals with the MAVS minor genotype had more stable total CD4+ T cell counts during a 7-year follow up and had lower cell-associated proviral DNA loads. Genetic variation in MAVS did not affect immune activation levels; however, a significantly lower percentage of naïve CD4+ but not CD8+ T cells was observed in the MAVS minor genotype. In vitro HIV-1 infection of peripheral blood mononuclear cells (PBMCs) from healthy donors with the MAVS minor genotype resulted in decreased viral replication. Although the precise underlying mechanism remains unclear, our data suggest that the protective effect of the MAVS minor genotype may be exerted by the initiation of local innate responses affecting viral replication and CD4+ T cell susceptibility. Full article
(This article belongs to the Special Issue Innate Immune Sensing of Viruses and Viral Evasion)
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Article
Rotaviruses Associate with Distinct Types of Extracellular Vesicles
Viruses 2020, 12(7), 763; https://doi.org/10.3390/v12070763 - 16 Jul 2020
Cited by 3 | Viewed by 1206
Abstract
Rotaviruses are the leading cause of viral gastroenteritis among children under five years of age. Rotavirus cell entry has been extensively studied; however, rotavirus cell release is still poorly understood. Specifically, the mechanism by which rotaviruses leave the cell before cell lysis is [...] Read more.
Rotaviruses are the leading cause of viral gastroenteritis among children under five years of age. Rotavirus cell entry has been extensively studied; however, rotavirus cell release is still poorly understood. Specifically, the mechanism by which rotaviruses leave the cell before cell lysis is not known. Previous works have found rotavirus proteins and viral particles associated with extracellular vesicles secreted by cells. These vesicles have been shown to contain markers of exosomes; however, in a recent work they presented characteristics more typical of microparticles, and they were associated with an increase in the infectivity of the virus. In this work, we purified different types of vesicles from rotavirus-infected cells. We analyzed the association of virus with these vesicles and their possible role in promotion of rotavirus infection. We confirmed a non-lytic rotavirus release from the two cell lines tested, and observed a notable stimulation of vesicle secretion following rotavirus infection. A fraction of the secreted viral particles present in the cell supernatant was protected from protease treatment, possibly through its association with membranous vesicles; the more pronounced association of the virus was with fractions corresponding to cell membrane generated microvesicles. Using electron microscopy, we found different size vesicles with particles resembling rotaviruses associated from both- the outside and the inside. The viral particles inside the vesicles were refractory to neutralization with a potent rotavirus neutralizing monoclonal antibody, and were able to infect cells even without trypsin activation. The association of rotavirus particles with extracellular vesicles suggests these might have a role in virus spread. Full article
(This article belongs to the Special Issue Viruses and Extracellular Vesicles)
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Article
Cocirculation of Swine H1N1 Influenza A Virus Lineages in Germany
Viruses 2020, 12(7), 762; https://doi.org/10.3390/v12070762 - 15 Jul 2020
Cited by 3 | Viewed by 1315
Abstract
The genome analysis of 328 H1N1 swine influenza virus isolates collected in a 13-year long-term swine influenza surveillance in Germany is reported. Viral genomes were sequenced with the Illumina next-generation sequencing technique and conventional Sanger methods. Phylogenetic analyses were conducted with Bayesian tree [...] Read more.
The genome analysis of 328 H1N1 swine influenza virus isolates collected in a 13-year long-term swine influenza surveillance in Germany is reported. Viral genomes were sequenced with the Illumina next-generation sequencing technique and conventional Sanger methods. Phylogenetic analyses were conducted with Bayesian tree inference. The results indicate continued prevalence of Eurasian avian swine H1N1 but also emergence of a novel H1N1 reassortant, named Schneiderkrug/2013-like swine H1N1, with human-like hemagglutinin and avian-like neuraminidase and internal genes. Additionally, the evolution of an antigenic drift variant of A (H1N1) pdm09 was observed, named Wachtum/2014-like swine H1N1. Both variants were first isolated in northwest Germany, spread to neighboring German states and reached greater proportions of the H1N1 isolates of 2014 and 2015. The upsurge of Wachtum/2014-like swine H1N1 is of interest as this is the first documented persistent swine-to-swine spread of A (H1N1) pdm09 in Germany associated with antigenic variation. Present enzootic swine influenza viruses in Germany now include two or more co-circulating, antigenically variant viruses of each of the subtypes, H1N1 and H1N2. Full article
(This article belongs to the Special Issue Endemic and Emerging Swine Viruses)
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Article
Low Host Abundance and High Temperature Determine Switching from Lytic to Lysogenic Cycles in Planktonic Microbial Communities in a Tropical Sea (Red Sea)
Viruses 2020, 12(7), 761; https://doi.org/10.3390/v12070761 - 15 Jul 2020
Cited by 4 | Viewed by 1151
Abstract
The lytic and lysogenic life cycles of marine phages are influenced by environmental conditions such as solar radiation, temperature, and host abundance. Temperature can regulate phage infection, but its role is difficult to discern in oligotrophic waters where there is typically low host [...] Read more.
The lytic and lysogenic life cycles of marine phages are influenced by environmental conditions such as solar radiation, temperature, and host abundance. Temperature can regulate phage infection, but its role is difficult to discern in oligotrophic waters where there is typically low host abundance and high temperatures. Here, we study the temporal variability of viral dynamics and the occurrence of lysogeny using mitomycin C in a eutrophic coastal lagoon in the oligotrophic Red Sea, which showed strong seasonality in terms of temperature (22.1–33.3 °C) and large phytoplankton blooms. Viral abundances ranged from 2.2 × 106 to 1.5 × 107 viruses mL−1 and were closely related to chlorophyll a (chl a) concentration. Observed high virus-to-bacterium ratio (VBR) (4–79; 16 ± 4 (SE)) suggests that phages exerted a tight control of their hosts as indicated by the significant decrease in bacterial abundance with increasing virus concentration. Heterotrophic bacterial abundance also showed a significant decrease with increasing temperature. However, viral abundance was not related to temperature changes and the interaction of water temperature, suggesting an indirect effect of temperature on decreased host abundance, which was observed at the end of the summertime. From the estimated burst size (BS), we observed lysogeny (undetectable to 29.1%) at low percentages of 5.0% ± 1.2 (SE) in half of the incubations with mitomycin C, while it increased to 23.9% ± 2.8 (SE) when the host abundance decreased. The results suggest that lytic phages predominate, switching to a moderate proportion of temperate phages when the host abundance reduces. Full article
(This article belongs to the Special Issue Phage Ecology)
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Article
An Assessment of Secondary Clinical Disease, Milk Production and Quality, and the Impact on Reproduction in Holstein Heifers and Cows from a Single Large Commercial Herd Persistently Infected with Bovine Viral Diarrhea Virus Type 2
Viruses 2020, 12(7), 760; https://doi.org/10.3390/v12070760 - 15 Jul 2020
Cited by 2 | Viewed by 1051
Abstract
The aim of this study was to evaluate secondary clinical disease, milk production efficiency and reproductive performance of heifers and cows persistently infected (PI) with bovine viral diarrhea virus type 2 (BVDV type 2). PI animals (n = 25) were identified using [...] Read more.
The aim of this study was to evaluate secondary clinical disease, milk production efficiency and reproductive performance of heifers and cows persistently infected (PI) with bovine viral diarrhea virus type 2 (BVDV type 2). PI animals (n = 25) were identified using an antigen capture ELISA of ear notch samples. They were distributed into three age groups: ≤ 12 (n = 8), 13 to 24 (n = 6) and 25 to 34 (n = 11) months old. A control group of BVDV antigen ELISA negative female cattle that were age matched to the PI animals was utilized from the same herd. The PI group had a 1.29 higher odds ratio for diarrhea than controls (p = 0.001, IC95% = 1.032–1.623) and 1.615 greater chance of developing bovine respiratory disease (BRD) (p = 0.012, IC95% = 1.155–2.259). The age at first insemination (p = 0.012) and number of insemination attempts required to establish the first pregnancy (p = 0.016) were both higher for PI than controls. Milk production was higher for control cows than PI cows during most of the sampling periods. Somatic cell counts (SCC) were higher in PI cows than the controls at all sampling points across lactation (p ≤ 0.042). PI cattle had a higher incidence of disease, produced less milk, a higher SCC, and poorer reproductive performance than control cattle in this study. Full article
(This article belongs to the Special Issue Bovine Viral Diarrhea Virus and Related Pestiviruses)
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Article
Attach Me If You Can: Murine Norovirus Binds to Commensal Bacteria and Fungi
Viruses 2020, 12(7), 759; https://doi.org/10.3390/v12070759 - 14 Jul 2020
Cited by 5 | Viewed by 1508
Abstract
The presence of commensal bacteria enhances both acute and persistent infection of murine noroviruses. For several enteric viral pathogens, mechanisms by which these bacteria enhance infection involve direct interactions between the virus and bacteria. While it has been demonstrated that human noroviruses bind [...] Read more.
The presence of commensal bacteria enhances both acute and persistent infection of murine noroviruses. For several enteric viral pathogens, mechanisms by which these bacteria enhance infection involve direct interactions between the virus and bacteria. While it has been demonstrated that human noroviruses bind to a variety of commensal bacteria, it is not known if this is also true for murine noroviruses. The goal of this study was to characterize interactions between murine noroviruses and commensal bacteria and determine the impact of bacterial growth conditions, incubation temperature and time, on murine norovirus attachment to microbes that comprise the mammalian microbiome. We show that murine noroviruses bind directly to commensal bacteria and show similar patterns of attachment as human norovirus VLPs examined under the same conditions. Furthermore, while binding levels are not impacted by the growth phase of the bacteria, they do change with time and incubation temperature. We also found that murine norovirus can bind to a commensal fungal species, Candida albicans. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses)
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Article
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses
Viruses 2020, 12(7), 758; https://doi.org/10.3390/v12070758 - 14 Jul 2020
Cited by 1 | Viewed by 1552
Abstract
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, [...] Read more.
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options. Full article
(This article belongs to the Special Issue Computational Biology of Viruses: From Molecules to Epidemics)
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Review
The bZIP Proteins of Oncogenic Viruses
Viruses 2020, 12(7), 757; https://doi.org/10.3390/v12070757 - 14 Jul 2020
Viewed by 1367
Abstract
Basic leucine zipper (bZIP) transcription factors (TFs) govern diverse cellular processes and cell fate decisions. The hallmark of the leucine zipper domain is the heptad repeat, with leucine residues at every seventh position in the domain. These leucine residues enable homo- and heterodimerization [...] Read more.
Basic leucine zipper (bZIP) transcription factors (TFs) govern diverse cellular processes and cell fate decisions. The hallmark of the leucine zipper domain is the heptad repeat, with leucine residues at every seventh position in the domain. These leucine residues enable homo- and heterodimerization between ZIP domain α-helices, generating coiled-coil structures that stabilize interactions between adjacent DNA-binding domains and target DNA substrates. Several cancer-causing viruses encode viral bZIP TFs, including human T-cell leukemia virus (HTLV), hepatitis C virus (HCV) and the herpesviruses Marek’s disease virus (MDV), Epstein–Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV). Here, we provide a comprehensive review of these viral bZIP TFs and their impact on viral replication, host cell responses and cell fate. Full article
(This article belongs to the Special Issue New Advances in Kaposi's Sarcoma-Associated Herpesvirus Research)
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Article
Beclin1 Binds to Enterovirus 71 3D Protein to Promote the Virus Replication
Viruses 2020, 12(7), 756; https://doi.org/10.3390/v12070756 - 14 Jul 2020
Cited by 1 | Viewed by 1051
Abstract
Enterovirus 71 (EV71) is the main pathogen causing hand-foot-mouth disease (HFMD) in infants and children, which can also lead to severe neurological diseases and even death. Therefore, understanding the replication mechanism of EV71 is of great significance for the prevention and control of [...] Read more.
Enterovirus 71 (EV71) is the main pathogen causing hand-foot-mouth disease (HFMD) in infants and children, which can also lead to severe neurological diseases and even death. Therefore, understanding the replication mechanism of EV71 is of great significance for the prevention and control of EV71-induced diseases. Beclin1 (BECN1, a mammalian homologue of ATG6 in yeast) is an important core protein for the initiation and the normal process of autophagy in cells. In addition to its involvement in autophagy, Beclin1 has also been reported to play an important role in cancer and innate immune signaling pathways. However, the role of Beclin1 in EV71 replication remains elusive. Here, we primarily found that Beclin1 facilitates EV71 replication in human rhabdomyosarcoma (RD) cells and the autophagy was actually induced, but Beclin1 was not significantly affected at either mRNA level or protein level during early EV71 infection. Further studies discovered that Beclin1 could interacts with EV71 non-structural protein 3D mainly through its evolutionary conserved domain (ECD) and coiled-coiled domain (CCD), thus promoting the replication of EV71 in human rhabdomyosarcoma (RD) cells and human astroglioma (U251) cells. Collectively, we reveal a novel regulatory mechanism associated with Beclin1 to promote EV71 replication, thus providing a potential therapeutic target for the prevention and control of EV71-associated diseases. Full article
(This article belongs to the Special Issue Gastroenteritis Viruses)
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