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Volume 12
Issue 8
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Viruses, Volume 12, Issue 8 (August 2020) – 119 articles

Cover Story (view full-size image): Viral protein VP24 (VP24) from Ebola virus (EBOV) has been termed a minor matrix protein but its lipid-binding properties have not been investigated. Here, we found that VP24 (left image) lacks direct lipid-binding properties, regardless of post-translational modification. VP24 interaction with the major matrix protein VP40 (right image) and selective plasma membrane localization was not detected, suggesting VP24 biological functions are not likely dependent on direct lipid binding. View this paper
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24 pages, 1016 KiB  
Review
Enteric Viral Co-Infections: Pathogenesis and Perspective
by Heyde Makimaa, Harshad Ingle and Megan T. Baldridge
Viruses 2020, 12(8), 904; https://doi.org/10.3390/v12080904 - 18 Aug 2020
Cited by 26 | Viewed by 7778
Abstract
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of [...] Read more.
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical. Full article
(This article belongs to the Special Issue Viral Coinfection)
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11 pages, 248 KiB  
Review
Pestivirus K (Atypical Porcine Pestivirus): Update on the Virus, Viral Infection, and the Association with Congenital Tremor in Newborn Piglets
by Alais M. Dall Agnol, Alice F. Alfieri and Amauri A. Alfieri
Viruses 2020, 12(8), 903; https://doi.org/10.3390/v12080903 - 18 Aug 2020
Cited by 14 | Viewed by 3111
Abstract
The atypical porcine pestivirus (APPV) belongs to the species Pestivirus K of the genus Pestivirus and the family Flaviviridae, and it has been associated with congenital tremor (CT) type A-II in newborn piglets. Although APPV was discovered in 2015, evidence shows that [...] Read more.
The atypical porcine pestivirus (APPV) belongs to the species Pestivirus K of the genus Pestivirus and the family Flaviviridae, and it has been associated with congenital tremor (CT) type A-II in newborn piglets. Although APPV was discovered in 2015, evidence shows that APPV has circulated in pig herds for many years, at least since 1986. Due to the frequently reported outbreaks of CT on different continents, the importance of this virus for global pig production is notable. Since 2015, several studies have been conducted to clarify the association between APPV and CT. However, some findings regarding APPV infection and the measures taken to control and prevent the spread of this virus need to be contextualized to understand the infection better. This review attempts to highlight advances in the understanding of APPV associated with type A-II CT, such as etiology, epidemiology, diagnosis, and control and prevention measures, and also describes the pathophysiology of the infection and its consequences for pig production. Further research still needs to be conducted to elucidate the host’s immune response to APPV infection, the control and prevention of this infection, and the possible development of vaccines. Full article
(This article belongs to the Special Issue Bovine Viral Diarrhea Virus and Related Pestiviruses)
16 pages, 2013 KiB  
Article
Tick-Borne Encephalitis Virus Adaptation in Different Host Environments and Existence of Quasispecies
by Renata Helmová, Václav Hönig, Hana Tykalová, Martin Palus, Lesley Bell-Sakyi and Libor Grubhoffer
Viruses 2020, 12(8), 902; https://doi.org/10.3390/v12080902 - 18 Aug 2020
Cited by 7 | Viewed by 3407
Abstract
A highly virulent strain (Hypr) of tick-borne encephalitis virus (TBEV) was serially subcultured in the mammalian porcine kidney stable (PS) and Ixodes ricinus tick (IRE/CTVM19) cell lines, producing three viral variants. These variants exhibited distinct plaque sizes and virulence in a mouse model. [...] Read more.
A highly virulent strain (Hypr) of tick-borne encephalitis virus (TBEV) was serially subcultured in the mammalian porcine kidney stable (PS) and Ixodes ricinus tick (IRE/CTVM19) cell lines, producing three viral variants. These variants exhibited distinct plaque sizes and virulence in a mouse model. Comparing the full-genome sequences of all variants, several nucleotide changes were identified in different genomic regions. Furthermore, different sequential variants were revealed to co-exist within one sample as quasispecies. Interestingly, the above-mentioned nucleotide changes found within the whole genome sequences of the new variants were present alongside the nucleotide sequence of the parental strain, which was represented as a minority quasispecies. These observations further imply that TBEV exists as a heterogeneous population that contains virus variants pre-adapted to reproduction in different environments, probably enabling virus survival in ticks and mammals. Full article
(This article belongs to the Section Animal Viruses)
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13 pages, 3988 KiB  
Article
Combinatorial Treatment of Birinapant and Zosuquidar Enhances Effective Control of HBV Replication In Vivo
by Emma Morrish, Liana Mackiewicz, Natasha Silke, Marc Pellegrini, John Silke, Gabriela Brumatti and Gregor Ebert
Viruses 2020, 12(8), 901; https://doi.org/10.3390/v12080901 - 17 Aug 2020
Cited by 7 | Viewed by 3643
Abstract
Chronic hepatitis B virus (HBV) infection remains a global health threat and affects hundreds of millions worldwide. Small molecule compounds that mimic natural antagonists of inhibitor of apoptosis (IAP) proteins, known as Smac-mimetics (second mitochondria-derived activator of caspases-mimetics), can promote the death of [...] Read more.
Chronic hepatitis B virus (HBV) infection remains a global health threat and affects hundreds of millions worldwide. Small molecule compounds that mimic natural antagonists of inhibitor of apoptosis (IAP) proteins, known as Smac-mimetics (second mitochondria-derived activator of caspases-mimetics), can promote the death of HBV-replicating liver cells and promote clearance of infection in preclinical models of HBV infection. The Smac-mimetic birinapant is a substrate of the multidrug resistance protein 1 (MDR1) efflux pump, and therefore inhibitors of MDR1 increase intracellular concentration of birinapant in MDR1 expressing cells. Liver cells are known to express MDR1 and other drug pump proteins. In this study, we investigated whether combining the clinical drugs, birinapant and the MDR1 inhibitor zosuquidar, increases the efficacy of birinapant in killing HBV expressing liver cells. We showed that this combination treatment is well tolerated and, compared to birinapant single agent, was more efficient at inducing death of HBV-positive liver cells and improving HBV-DNA and HBV surface antigen (HBsAg) control kinetics in an immunocompetent mouse model of HBV infection. Thus, this study identifies a novel and safe combinatorial treatment strategy to potentiate substantial reduction of HBV replication using an IAP antagonist. Full article
(This article belongs to the Special Issue Hepatitis B Virus: From Diagnostics to Treatments)
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20 pages, 4723 KiB  
Article
Characterization of Signal Sequences Determining the Nuclear/Nucleolar Import and Nuclear Export of the Caprine Arthritis-Encephalitis Virus Rev Protein
by Marlène Labrecque, Claude Marchand and Denis Archambault
Viruses 2020, 12(8), 900; https://doi.org/10.3390/v12080900 - 17 Aug 2020
Viewed by 3474
Abstract
Caprine arthritis-encephalitis virus (CAEV), a lentivirus, relies on the action of the Rev protein for its replication. The CAEV Rev fulfills its function by allowing the nuclear exportation of partially spliced or unspliced viral mRNAs. In this study, we characterized the nuclear and [...] Read more.
Caprine arthritis-encephalitis virus (CAEV), a lentivirus, relies on the action of the Rev protein for its replication. The CAEV Rev fulfills its function by allowing the nuclear exportation of partially spliced or unspliced viral mRNAs. In this study, we characterized the nuclear and nucleolar localization signals (NLS and NoLS, respectively) and the nuclear export signal (NES) of the CAEV Rev protein. These signals are key actors in the nucleocytoplasmic shuttling of a lentiviral Rev protein. Several deletion and alanine substitution mutants were generated from a plasmid encoding the CAEV Rev wild-type protein that was fused to the enhanced green fluorescent protein (EGFP). Following cell transfection, images were captured by confocal microscopy and the fluorescence was quantified in the different cell compartments. The results showed that the NLS region is localized between amino acids (aa) 59 to 75, has a monopartite-like structure and is exclusively composed of arginine residues. The NoLS was found to be partially associated with the NLS. Finally, the CAEV Rev protein’s NES mapped between aa 89 to 101, with an aa spacing between the hydrophobic residues that was found to be unconventional as compared to that of other retroviral Rev/Rev-like proteins. Full article
(This article belongs to the Special Issue Non-Primate Lentiviruses 2021)
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15 pages, 648 KiB  
Article
Oral Infection by Mucosal and Cutaneous Human Papillomaviruses in the Men Who Have Sex with Men from the OHMAR Study
by Tarik Gheit, Francesca Rollo, Rosario N Brancaccio, Alexis Robitaille, Luisa Galati, Massimo Giuliani, Alessandra Latini, Barbara Pichi, Maria Benevolo, Cyrille Cuenin, Sandrine McKay-Chopin, Raul Pellini, Antonio Cristaudo, Aldo Morrone, Massimo Tommasino and Maria Gabriella Donà
Viruses 2020, 12(8), 899; https://doi.org/10.3390/v12080899 - 17 Aug 2020
Cited by 11 | Viewed by 2636
Abstract
Both mucosal and cutaneous Human Papillomaviruses (HPVs) can be detected in the oral cavity, but investigations regarding the epidemiology of cutaneous HPVs at this site are scarce. We assessed mucosal (alpha) and cutaneous (beta and gamma) HPV infection in oral samples of HIV-infected [...] Read more.
Both mucosal and cutaneous Human Papillomaviruses (HPVs) can be detected in the oral cavity, but investigations regarding the epidemiology of cutaneous HPVs at this site are scarce. We assessed mucosal (alpha) and cutaneous (beta and gamma) HPV infection in oral samples of HIV-infected and uninfected men who have sex with men (MSM). Oral rinse-and-gargles were collected from 310 MSM. Alpha HPVs were detected using the Linear Array, whereas beta and gamma HPVs were detected using multiplex PCR and Luminex technology. An amplicon-based next-generation sequencing (NGS) protocol was applied to a subset of samples collected from 30 HIV-uninfected and 30 HIV-infected MSM. Beta HPVs were significantly more common than alpha types (53.8% vs. 23.9% for HIV-infected subjects, p < 0.0001; 50.3% vs. 17.1% for HIV-uninfected subjects, p < 0.0001). Gamma HPVs were also frequently detected (30.8% and 25.9% in HIV-infected and uninfected MSM, respectively). NGS produced 2,620,725 reads representative of 146 known HPVs (16 alpha-PVs, 53 beta-PVs, 76 gamma-PVs, one unclassified) and eight putative new HPVs, taxonomically assigned to the beta genus. The oral cavity contains a wide spectrum of HPVs, with beta types representing the predominant genus. The prevalence of beta and gamma HPVs is high even in immunorestored HIV-infected individuals. NGS confirmed the abundance of cutaneous HPVs and identified some putative novel beta HPVs. This study confirms that cutaneous HPVs are frequently present at mucosal sites and highlights that their pathological role deserves further investigation since it may not be limited to skin lesions. Full article
(This article belongs to the Section Animal Viruses)
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25 pages, 2836 KiB  
Article
Phylogenetic Analysis of South African Bovine Leukaemia Virus (BLV) Isolates
by Akiko Suzuki, Rosamund Chapman, Nicola Douglass, Olivia Carulei, Johan van Rensburg and Anna-Lise Williamson
Viruses 2020, 12(8), 898; https://doi.org/10.3390/v12080898 - 17 Aug 2020
Cited by 5 | Viewed by 3478
Abstract
Bovine leukaemia virus (BLV) causes chronic lymphoproliferative disorder and fatal lymphosarcoma in cattle, leading to significant economic losses in the beef and dairy industries. BLV is endemic globally and eleven genotypes have been identified. To date, only Zambian isolates have been genotyped from [...] Read more.
Bovine leukaemia virus (BLV) causes chronic lymphoproliferative disorder and fatal lymphosarcoma in cattle, leading to significant economic losses in the beef and dairy industries. BLV is endemic globally and eleven genotypes have been identified. To date, only Zambian isolates have been genotyped from Africa. Although high BLV prevalence has been reported in South Africa, there has been no molecular characterisation of South African BLV isolates. To characterise BLV isolates in South Africa for the first time, we investigated the phylogenetic relationships and compared the genetic variability of eight South African BLV isolates with BLV isolates representing the eleven known genotypes from different geographical regions worldwide. Phylogenetic analyses based on full-length and partial env sequences as well as full-length gag sequences revealed that at least two genotypes, genotypes 1 (G1) and 4 (G4), are present in cattle in South Africa, which is consistent with studies from Zambia. However, our analysis revealed that the G1 South African isolate is more similar to other G1 isolates than the G1 Zambian isolates whereas, the G4 South African isolates are more divergent from other G4 isolates but closely related to the G4 Zambian isolate. Lastly, amino acid sequence alignment identified genotype-specific as well as novel amino acid substitutions in the South African isolates. The detection of two genotypes (G1 and G4) in southern Africa highlights the urgent need for disease management and the development of an efficacious vaccine against local strains. Full article
(This article belongs to the Section Animal Viruses)
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16 pages, 3823 KiB  
Article
Rabbit Hemorrhagic Disease Virus Isolated from Diseased Alpine Musk Deer (Moschus sifanicus)
by Shijun Bao, Kai An, Chunguo Liu, Xiaoyong Xing, Xiaoping Fu, Huiwen Xue, Fengqin Wen, Xijun He and Jingfei Wang
Viruses 2020, 12(8), 897; https://doi.org/10.3390/v12080897 - 17 Aug 2020
Cited by 4 | Viewed by 3865
Abstract
Rabbit hemorrhagic disease virus (RHDV) is the causative agent of rabbit hemorrhagic disease (RHD), and its infection results in mortality of 70–90% in farmed and wild rabbits. RHDV is thought to replicate strictly in rabbits. However, there are also reports showing that gene [...] Read more.
Rabbit hemorrhagic disease virus (RHDV) is the causative agent of rabbit hemorrhagic disease (RHD), and its infection results in mortality of 70–90% in farmed and wild rabbits. RHDV is thought to replicate strictly in rabbits. However, there are also reports showing that gene segments from the RHDV genome or antibodies against RHDV have been detected in other animals. Here, we report the detection and isolation of a RHDV from diseased Alpine musk deer (Moschussifanicus). The clinical manifestations in those deer were sudden death without clinical signs and hemorrhage in the internal organs. To identify the potential causative agents of the disease, we used sequence independent single primer amplification (SISPA) to detect gene segments from viruses in the tissue samples collected from the dead deer. From the obtained sequences, we identified some gene fragments showing very high nucleotide sequence similarity with RHDV genome. Furthermore, we identified caliciviral particles using an electron microscope in the samples. The new virus was designated as RHDV GS/YZ. We then designed primers based on the genome sequence of an RHDV strain CD/China to amplify and sequence the whole genome of the virus. The genome of the virus was determined to be 7437 nucleotides in length, sharing the highest genome sequence identity of 98.7% with a Chinese rabbit strain HB. The virus was assigned to the G2 genotype of RHDVs according to the phylogenetic analyses based on both the full-length genome and VP60 gene sequences. Animal experiments showed that GS/YZ infection in rabbits resulted in the macroscopic and microscopic lesions similar to that caused by the other RHDVs. This is the first report of RHDV isolated from Alpine musk deer, and our findings extended the epidemiology and host range of RHDV. Full article
(This article belongs to the Special Issue Animal and Wildlife Viruses)
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24 pages, 2511 KiB  
Article
Analysis of the Function of the Lymphocytic Choriomeningitis Virus S Segment Untranslated Region on Growth Capacity In Vitro and on Virulence In Vivo
by Satoshi Taniguchi, Tomoki Yoshikawa, Masayuki Shimojima, Shuetsu Fukushi, Takeshi Kurosu, Hideki Tani, Aiko Fukuma, Fumihiro Kato, Eri Nakayama, Takahiro Maeki, Shigeru Tajima, Chang-Kweng Lim, Hideki Ebihara, Shigeru Kyuwa, Shigeru Morikawa and Masayuki Saijo
Viruses 2020, 12(8), 896; https://doi.org/10.3390/v12080896 - 16 Aug 2020
Cited by 5 | Viewed by 3493
Abstract
Lymphocytic choriomeningitis virus (LCMV) is a prototypic arenavirus. The function of untranslated regions (UTRs) of the LCMV genome has not been well studied except for the extreme 19 nucleotide residues of both the 5′ and 3′ termini. There are internal UTRs composed of [...] Read more.
Lymphocytic choriomeningitis virus (LCMV) is a prototypic arenavirus. The function of untranslated regions (UTRs) of the LCMV genome has not been well studied except for the extreme 19 nucleotide residues of both the 5′ and 3′ termini. There are internal UTRs composed of 58 and 41 nucleotide residues in the 5′ and 3′ UTRs, respectively, in the LCMV S segment. Their functional roles have yet to be elucidated. In this study, reverse genetics and minigenome systems were established for LCMV strain WE and the function of these regions were analyzed. It was revealed that nucleotides 20–40 and 20–38 located downstream of the 19 nucleotides in the 5′ and 3′ termini, respectively, were involved in viral genome replication and transcription. Furthermore, it was revealed that the other internal UTRs (nucleotides 41–77 and 39–60 in the 5′ and 3′ termini, respectively) in the S segment were involved in virulence in vivo, even though these regions did not affect viral growth capacity in Vero cells. The introduction of LCMV with mutations in these regions attenuates the virus and may enable the production of LCMV vaccine candidates. Full article
(This article belongs to the Special Issue Arenaviruses 2020)
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13 pages, 1131 KiB  
Article
A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture
by Jalees A. Nasir, Robert A. Kozak, Patryk Aftanas, Amogelang R. Raphenya, Kendrick M. Smith, Finlay Maguire, Hassaan Maan, Muhannad Alruwaili, Arinjay Banerjee, Hamza Mbareche, Brian P. Alcock, Natalie C. Knox, Karen Mossman, Bo Wang, Julian A. Hiscox, Andrew G. McArthur and Samira Mubareka
Viruses 2020, 12(8), 895; https://doi.org/10.3390/v12080895 - 15 Aug 2020
Cited by 65 | Viewed by 10629
Abstract
Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols [...] Read more.
Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts. Full article
(This article belongs to the Collection Coronaviruses)
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16 pages, 3447 KiB  
Article
Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae
by Pasquale Marmo, Maria Cristina Thaller, Gustavo Di Lallo, Lucia Henrici De Angelis, Noemi Poerio, Federica De Santis, Maurizio Fraziano, Luciana Migliore and Marco Maria D’Andrea
Viruses 2020, 12(8), 894; https://doi.org/10.3390/v12080894 - 15 Aug 2020
Cited by 2 | Viewed by 3482
Abstract
Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, [...] Read more.
Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomonas turrisvirgatae MCT13 type strain. Physiological characterization demonstrated that vB_StuS_MMDA13 has a narrow host range, a long latency period, a low burst size, and it is overall stable to both temperature and pH variations. The phage has a double-stranded DNA genome of 63,743 bp, with 89 open reading frames arranged in two opposite arms separated by a 1186 bp non-coding region and shows a very low global similarity to any other known phages. Interestingly, vB_StuS_MMDA13 is endowed with an original nucleotide modification biosynthetic gene cluster, which greatly differs from those of its most closely related phages of the Nipunavirus genus. vB_StuS_MMDA13 is the first characterized lytic bacteriophage of the Siphoviridae family infecting members of the Sphingomonas genus. Full article
(This article belongs to the Section Bacterial Viruses)
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21 pages, 3707 KiB  
Article
Pediatric Enteroviral Central Nervous System Infections in Bialystok, Poland: Epidemiology, Viral Types, and Drivers of Seasonal Variation
by Kacper Toczylowski, Magdalena Wieczorek, Ewa Bojkiewicz, Magdalena Wietlicka-Piszcz, Beata Gad and Artur Sulik
Viruses 2020, 12(8), 893; https://doi.org/10.3390/v12080893 - 15 Aug 2020
Cited by 9 | Viewed by 2903
Abstract
Enteroviruses are common causes of infections of the central nervous system (CNS) that in temperate climates tend to peak in the summer. The aim of the study was to describe epidemiology, drivers of seasonality, and types of enteroviruses causing infections of the CNS [...] Read more.
Enteroviruses are common causes of infections of the central nervous system (CNS) that in temperate climates tend to peak in the summer. The aim of the study was to describe epidemiology, drivers of seasonality, and types of enteroviruses causing infections of the CNS in children in Northeastern Poland. We prospectively collected data on children hospitalized with infection of the CNS attributed to enteroviruses in Bialystok, Poland, from January 2015 to December 2019. In total, 224 children were included. Nineteen different enterovirus types were identified in isolates collected from 188 children. Coxsackie B5 (32%), echovirus 30 (20%), and echovirus 6 (14%) were the three most common types. Enteroviruses were more prevalent during the summer–fall season. Infections caused by echovirus 30 peaked early in June and coxsackievirus B5 in July, whereas echovirus 6 peaked late in October. Phylogenetic analyses of these three enterovirus types showed multiple lineages co-circulating in this region. Mean air temperatures and precipitation rates were independently associated with monthly number of cases. Considering lack of effective treatment or vaccine, easy transmission of enteroviruses between susceptible individuals, their high mutation rate and prolonged time of viral shedding, continued monitoring and surveillance are imperative to recognize enteroviral infections of the CNS and the changes in circulation of enteroviruses in Poland. Full article
(This article belongs to the Section Animal Viruses)
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22 pages, 1414 KiB  
Article
FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae
by Adriano de Bernadi Schneider, Denis Jacob Machado, Sayal Guirales and Daniel A. Janies
Viruses 2020, 12(8), 892; https://doi.org/10.3390/v12080892 - 14 Aug 2020
Cited by 5 | Viewed by 4979
Abstract
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this [...] Read more.
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus, named “Fast Loci Annotation of Viruses” (FLAVi; http://flavi-web.com/), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika. Full article
(This article belongs to the Special Issue Emerging Arboviruses)
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27 pages, 2034 KiB  
Article
Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity
by Ivana Šimić, Tomaž Mark Zorec, Ivana Lojkić, Nina Krešić, Mario Poljak, Florence Cliquet, Evelyne Picard-Meyer, Marine Wasniewski, Vida Zrnčić, Anđela Ćukušić and Tomislav Bedeković
Viruses 2020, 12(8), 891; https://doi.org/10.3390/v12080891 - 14 Aug 2020
Cited by 17 | Viewed by 4197
Abstract
To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, [...] Read more.
To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia. Full article
(This article belongs to the Section Animal Viruses)
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12 pages, 968 KiB  
Article
Nationwide Screening for Bee Viruses and Parasites in Belgian Honey Bees
by Severine Matthijs, Valérie De Waele, Valerie Vandenberge, Bénédicte Verhoeven, Jacqueline Evers, Marleen Brunain, Claude Saegerman, Paul J. J. De Winter, Stefan Roels, Dirk C. de Graaf and Nick De Regge
Viruses 2020, 12(8), 890; https://doi.org/10.3390/v12080890 - 14 Aug 2020
Cited by 13 | Viewed by 3994
Abstract
The health of honey bees is threatened by multiple factors, including viruses and parasites. We screened 557 honey bee (Apis mellifera) colonies from 155 beekeepers distributed all over Belgium to determine the prevalence of seven widespread viruses and two parasites ( [...] Read more.
The health of honey bees is threatened by multiple factors, including viruses and parasites. We screened 557 honey bee (Apis mellifera) colonies from 155 beekeepers distributed all over Belgium to determine the prevalence of seven widespread viruses and two parasites (Varroa sp. and Nosema sp.). Deformed wing virus B (DWV-B), black queen cell virus (BQCV), and sacbrood virus (SBV) were highly prevalent and detected by real-time RT-PCR in more than 95% of the colonies. Acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV) and deformed wing virus A (DWV-A) were prevalent to a lower extent (between 18 and 29%). Most viruses were only present at low or moderate viral loads. Nevertheless, about 50% of the colonies harbored at least one virus at high viral load (>107 genome copies/bee). Varroa mites and Nosema sp. were found in 81.5% and 59.7% of the honey bee colonies, respectively, and all Nosema were identified as Nosema ceranae by real time PCR. Interestingly, we found a significant correlation between the number of Varroa mites and DWV-B viral load. To determine the combined effect of these and other factors on honey bee health in Belgium, a follow up of colonies over multiple years is necessary. Full article
(This article belongs to the Special Issue Novel Concepts in Virology)
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14 pages, 2296 KiB  
Article
Phylogenetic Characterization of Arboviruses in Patients Suffering from Acute Fever in Rondônia, Brazil
by Jackson Alves da Silva Queiroz, Luan Felipo Botelho-Souza, Felipe Souza Nogueira-Lima, Rita de Cássia Pontello Rampazzo, Marco Aurélio Krieger, Miriam Ribas Zambenedetti, Fabricio Klerinton Marchini, Ivo Alberto Borghetti, Dhelio Batista Pereira, Juan Miguel Vilalobos Salcedo, Deusilene Souza Vieira and Alcione de Oliveira dos Santos
Viruses 2020, 12(8), 889; https://doi.org/10.3390/v12080889 - 14 Aug 2020
Cited by 9 | Viewed by 3266
Abstract
The purpose of the study was to classify, through phylogenetic analyses, the main arboviruses that have been isolated in the metropolitan region of Porto Velho, Rondônia, Brazil. Serum samples from patients with symptoms suggesting arboviruses were collected and tested by One Step RT-qPCR [...] Read more.
The purpose of the study was to classify, through phylogenetic analyses, the main arboviruses that have been isolated in the metropolitan region of Porto Velho, Rondônia, Brazil. Serum samples from patients with symptoms suggesting arboviruses were collected and tested by One Step RT-qPCR for Zika, Dengue (serotypes 1–4), Chikungunya, Mayaro and Oropouche viruses. Positive samples were amplified by conventional PCR and sequenced utilizing the Sanger method. The obtained sequences were aligned, and an evolutionary analysis was carried out using Bayesian inference. A total of 308 samples were tested. Of this total, 20 had a detectable viral load for Dengue, being detected DENV1 (18/20), co-infection DENV1 and DENV2 (1/20) and DENV4 (1/20). For Dengue serotype 3 and for the CHIKV, ZIKV, MAYV and OROV viruses, no individuals with a detectable viral load were found. A total of 9 of these samples were magnified by conventional PCR for sequencing. Of these, 6 were successfully sequenced and, according to the evolutionary profile, 5 corresponded to serotype DENV-1 genotype V, and 1 to serotype DENV-4 genotype II. In the study, we demonstrate co-circulation of the DENV-1 genotype V and the DENV-4 genotype II. Co-circulation of several DENV serotypes in the same city poses a risk to the population and is correlated with the increase of the most severe forms of the disease. Similarly, co-circulation of genetically distinct DENV and the occurrence of simultaneous infections can affect recombination events and lead to the emergence of more virulent isolates. Full article
(This article belongs to the Special Issue Emerging Arboviruses)
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42 pages, 1496 KiB  
Review
How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain
by Jéromine Klingler, Halina Anton, Eléonore Réal, Manon Zeiger, Christiane Moog, Yves Mély and Emmanuel Boutant
Viruses 2020, 12(8), 888; https://doi.org/10.3390/v12080888 - 13 Aug 2020
Cited by 9 | Viewed by 6687
Abstract
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in [...] Read more.
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in HIV-1 replication. Indeed, via its different domains, Gag orchestrates the specific encapsidation of the genomic RNA, drives the formation of the viral particle by its auto-assembly (multimerization), binds multiple viral proteins, and interacts with a large number of cellular proteins that are needed for its functions from its translation location to the plasma membrane, where newly formed virions are released. Here, we review the interactions between HIV-1 Gag and 66 cellular proteins. Notably, we describe the techniques used to evidence these interactions, the different domains of Gag involved, and the implications of these interactions in the HIV-1 replication cycle. In the final part, we focus on the interactions involving the highly conserved nucleocapsid (NC) domain of Gag and detail the functions of the NC interactants along the viral lifecycle. Full article
(This article belongs to the Special Issue Function and Structure of Viral Ribonucleoproteins Complexes)
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23 pages, 714 KiB  
Review
Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention
by Asit Kumar, Sunitha Kodidela, Erene Tadrous, Theodore James Cory, Crystal Martin Walker, Amber Marie Smith, Ahona Mukherjee and Santosh Kumar
Viruses 2020, 12(8), 887; https://doi.org/10.3390/v12080887 - 13 Aug 2020
Cited by 24 | Viewed by 7108
Abstract
Extracellular vesicles (EVs) have shown their potential as a carrier of molecular information, and they have been involved in physiological functions and diseases caused by viral infections. Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from [...] Read more.
Extracellular vesicles (EVs) have shown their potential as a carrier of molecular information, and they have been involved in physiological functions and diseases caused by viral infections. Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. They are released via a direct outward budding and fission of plasma membrane blebs into the extracellular space to either facilitate virus propagation or regulate the immune responses. Moreover, EVs generated by virus-infected cells can incorporate virulence factors including viral protein and viral genetic material, and thus can resemble noninfectious viruses. Interactions of EVs with recipient cells have been shown to activate signaling pathways that may contribute to a sustained cellular response towards viral infections. EVs, by utilizing a complex set of cargos, can play a regulatory role in viral infection, both by facilitating and suppressing the infection. EV-based antiviral and antiretroviral drug delivery approaches provide an opportunity for targeted drug delivery. In this review, we summarize the literature on EVs, their associated involvement in transmission in viral infections, and potential therapeutic implications. Full article
(This article belongs to the Special Issue Viruses and Extracellular Vesicles)
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18 pages, 5476 KiB  
Article
Synthesis of Full-Length cDNA Infectious Clones of Soybean Mosaic Virus and Functional Identification of a Key Amino Acid in the Silencing Suppressor Hc-Pro
by Wenhua Bao, Ting Yan, Xiaoyi Deng and Hada Wuriyanghan
Viruses 2020, 12(8), 886; https://doi.org/10.3390/v12080886 - 13 Aug 2020
Cited by 17 | Viewed by 4267
Abstract
Soybean mosaic virus (SMV), which belongs to the Potyviridae, causes significant reductions in soybean yield and seed quality. In this study, both tag-free and reporter gene green fluorescent protein (GFP)-containing infectious clones for the SMV N1 strain were constructed by [...] Read more.
Soybean mosaic virus (SMV), which belongs to the Potyviridae, causes significant reductions in soybean yield and seed quality. In this study, both tag-free and reporter gene green fluorescent protein (GFP)-containing infectious clones for the SMV N1 strain were constructed by Gibson assembly and with the yeast homologous recombination system, respectively. Both infectious clones are suitable for agroinfiltration on the model host N. benthamiana and show strong infectivity for the natural host soybean and several other legume species. Both infectious clones were seed transmitted and caused typical virus symptoms on seeds and progeny plants. We used the SMV-GFP infectious clone to further investigate the role of key amino acids in the silencing suppressor helper component-proteinase (Hc-Pro). Among twelve amino acid substitution mutants, the co-expression of mutant 2—with an Asparagine→Leucine substitution at position 182 of the FRNK (Phe-Arg-Asn-Lys) motif—attenuated viral symptoms and alleviated the host growth retardation caused by SMV. Moreover, the Hc-Prom2 mutant showed stronger oligomerization than wild-type Hc-Pro. Taken together, the SMV infectious clones will be useful for studies of host–SMV interactions and functional gene characterization in soybeans and related legume species, especially in terms of seed transmission properties. Furthermore, the SMV-GFP infectious clone will also facilitate functional studies of both virus and host genes in an N. benthamiana transient expression system. Full article
(This article belongs to the Special Issue Plant Virus Pathogenesis and Disease Control)
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32 pages, 5216 KiB  
Article
Low-Level Ionizing Radiation Induces Selective Killing of HIV-1-Infected Cells with Reversal of Cytokine Induction Using mTOR Inhibitors
by Daniel O. Pinto, Catherine DeMarino, Thy T. Vo, Maria Cowen, Yuriy Kim, Michelle L. Pleet, Robert A. Barclay, Nicole Noren Hooten, Michele K. Evans, Alonso Heredia, Elena V. Batrakova, Sergey Iordanskiy and Fatah Kashanchi
Viruses 2020, 12(8), 885; https://doi.org/10.3390/v12080885 - 13 Aug 2020
Cited by 8 | Viewed by 4163
Abstract
HIV-1 infects 39.5 million people worldwide, and cART is effective in preventing viral spread by reducing HIV-1 plasma viral loads to undetectable levels. However, viral reservoirs persist by mechanisms, including the inhibition of autophagy by HIV-1 proteins (i.e., Nef and Tat). HIV-1 reservoirs [...] Read more.
HIV-1 infects 39.5 million people worldwide, and cART is effective in preventing viral spread by reducing HIV-1 plasma viral loads to undetectable levels. However, viral reservoirs persist by mechanisms, including the inhibition of autophagy by HIV-1 proteins (i.e., Nef and Tat). HIV-1 reservoirs can be targeted by the “shock and kill” strategy, which utilizes latency-reversing agents (LRAs) to activate latent proviruses and immunotarget the virus-producing cells. Yet, limitations include reduced LRA permeability across anatomical barriers and immune hyper-activation. Ionizing radiation (IR) induces effective viral activation across anatomical barriers. Like other LRAs, IR may cause inflammation and modulate the secretion of extracellular vesicles (EVs). We and others have shown that cells may secrete cytokines and viral proteins in EVs and, therefore, LRAs may contribute to inflammatory EVs. In the present study, we mitigated the effects of IR-induced inflammatory EVs (i.e., TNF-α), through the use of mTOR inhibitors (mTORi; Rapamycin and INK128). Further, mTORi were found to enhance the selective killing of HIV-1-infected myeloid and T-cell reservoirs at the exclusion of uninfected cells, potentially via inhibition of viral transcription/translation and induction of autophagy. Collectively, the proposed regimen using cART, IR, and mTORi presents a novel approach allowing for the targeting of viral reservoirs, prevention of immune hyper-activation, and selectively killing latently infected HIV-1 cells. Full article
(This article belongs to the Special Issue HIV-1 Latency: Regulation and Reversal)
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22 pages, 753 KiB  
Review
Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview
by Franziska K. Geis and Stephen P. Goff
Viruses 2020, 12(8), 884; https://doi.org/10.3390/v12080884 - 13 Aug 2020
Cited by 86 | Viewed by 10093
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. [...] Read more.
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host. Full article
(This article belongs to the Special Issue Endogenous Retroviruses in Development and Disease)
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18 pages, 5845 KiB  
Article
A Single Mutation in the VP1 Gene of Enterovirus 71 Enhances Viral Binding to Heparan Sulfate and Impairs Viral Pathogenicity in Mice
by Xianliang Ke, Yuan Zhang, Yan Liu, Yuanjiu Miao, Caishang Zheng, Dan Luo, Jianhong Sun, Qinxue Hu, Yi Xu, Hanzhong Wang and Zhenhua Zheng
Viruses 2020, 12(8), 883; https://doi.org/10.3390/v12080883 - 13 Aug 2020
Cited by 12 | Viewed by 3603
Abstract
Enterovirus 71 (EV71) is the major causative pathogen of human hand, foot, and mouth disease (hHFMD) and has evolved to use various cellular receptors for infection. However, the relationship between receptor preference and EV71 virulence has not been fully revealed. By using reverse [...] Read more.
Enterovirus 71 (EV71) is the major causative pathogen of human hand, foot, and mouth disease (hHFMD) and has evolved to use various cellular receptors for infection. However, the relationship between receptor preference and EV71 virulence has not been fully revealed. By using reverse genetics, we identified that a single E98K mutation in VP1 is responsible for rapid viral replication in vitro. The E98K mutation enhanced binding of EV71-GZCII to cells in a heparan sulfate (HS)-dependent manner, and it attenuated the virulence of EV71-GZCII in BALB/c mice, indicating that the HS-binding property is negatively associated with viral virulence. HS is widely expressed in vascular endothelial cells in different mouse tissues, and weak colocalization of HS with scavenger receptor B2 (SCARB2) was detected. The cGZCII-98K virus bound more efficiently to mouse tissue homogenates, and the cGZCII-98K virus titers in mouse tissues and blood were much lower than the cGZCII virus titers. Together, these findings suggest that the enhanced adsorption of the cGZCII-98K virus, which likely occurs through HS, is unable to support the efficient replication of EV71 in vivo. Our study confirmed the role of HS-binding sites in EV71 infection and highlighted the importance of the HS receptor in EV71 pathogenesis. Full article
(This article belongs to the Section Animal Viruses)
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20 pages, 3636 KiB  
Article
Modelling West Nile Virus and Usutu Virus Pathogenicity in Human Neural Stem Cells
by Silvia Riccetti, Alessandro Sinigaglia, Giovanna Desole, Norbert Nowotny, Marta Trevisan and Luisa Barzon
Viruses 2020, 12(8), 882; https://doi.org/10.3390/v12080882 - 12 Aug 2020
Cited by 14 | Viewed by 3599
Abstract
West Nile virus (WNV) and Usutu virus (USUV) are genetically related neurotropic mosquito-borne flaviviruses, which frequently co-circulate in nature. Despite USUV seeming to be less pathogenic for humans than WNV, the clinical manifestations induced by these two viruses often overlap and may evolve [...] Read more.
West Nile virus (WNV) and Usutu virus (USUV) are genetically related neurotropic mosquito-borne flaviviruses, which frequently co-circulate in nature. Despite USUV seeming to be less pathogenic for humans than WNV, the clinical manifestations induced by these two viruses often overlap and may evolve to produce severe neurological complications. The aim of this study was to investigate the effects of WNV and USUV infection on human induced pluripotent stem cell-derived neural stem cells (hNSCs), as a model of the neural progenitor cells in the developing fetal brain and in adult brain. Zika virus (ZIKV), a flavivirus with known tropism for NSCs, was used as the positive control. Infection of hNSCs and viral production, effects on cell viability, apoptosis, and innate antiviral responses were compared among viruses. WNV displayed the highest replication efficiency and cytopathic effects in hNSCs, followed by USUV and then ZIKV. In these cells, both WNV and USUV induced the overexpression of innate antiviral response genes at significantly higher levels than ZIKV. Expression of interferon type I, interleukin-1β and caspase-3 was significantly more elevated in WNV- than USUV-infected hNSCs, in agreement with the higher neuropathogenicity of WNV and the ability to inhibit the interferon response pathway. Full article
(This article belongs to the Special Issue West Nile Virus 2019)
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31 pages, 8141 KiB  
Review
Femtoplankton: What’s New?
by Jonathan Colombet, Maxime Fuster, Hermine Billard and Télesphore Sime-Ngando
Viruses 2020, 12(8), 881; https://doi.org/10.3390/v12080881 - 12 Aug 2020
Cited by 4 | Viewed by 6882
Abstract
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. [...] Read more.
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010–2020) of high abundances of biomimetic mineral–organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities. Full article
(This article belongs to the Special Issue Viruses of Aquatic Ecosystems)
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26 pages, 1524 KiB  
Review
Of Mice and Men: The Coronavirus MHV and Mouse Models as a Translational Approach to Understand SARS-CoV-2
by Robert W. Körner, Mohamed Majjouti, Miguel A. Alejandre Alcazar and Esther Mahabir
Viruses 2020, 12(8), 880; https://doi.org/10.3390/v12080880 - 12 Aug 2020
Cited by 96 | Viewed by 13070
Abstract
The fatal acute respiratory coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since COVID-19 was declared a pandemic by the World Health Organization in March 2020, infection and mortality rates have been rising steadily worldwide. The lack [...] Read more.
The fatal acute respiratory coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since COVID-19 was declared a pandemic by the World Health Organization in March 2020, infection and mortality rates have been rising steadily worldwide. The lack of a vaccine, as well as preventive and therapeutic strategies, emphasize the need to develop new strategies to mitigate SARS-CoV-2 transmission and pathogenesis. Since mouse hepatitis virus (MHV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2 share a common genus, lessons learnt from MHV and SARS-CoV could offer mechanistic insights into SARS-CoV-2. This review provides a comprehensive review of MHV in mice and SARS-CoV-2 in humans, thereby highlighting further translational avenues in the development of innovative strategies in controlling the detrimental course of SARS-CoV-2. Specifically, we have focused on various aspects, including host species, organotropism, transmission, clinical disease, pathogenesis, control and therapy, MHV as a model for SARS-CoV and SARS-CoV-2 as well as mouse models for infection with SARS-CoV and SARS-CoV-2. While MHV in mice and SARS-CoV-2 in humans share various similarities, there are also differences that need to be addressed when studying murine models. Translational approaches, such as humanized mouse models are pivotal in studying the clinical course and pathology observed in COVID-19 patients. Lessons from prior murine studies on coronavirus, coupled with novel murine models could offer new promising avenues for treatment of COVID-19. Full article
(This article belongs to the Section SARS-CoV-2 and COVID-19)
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20 pages, 5666 KiB  
Article
Tomato Brown Rugose Fruit Virus Contributes to Enhanced Pepino Mosaic Virus Titers in Tomato Plants
by Chen Klap, Neta Luria, Elisheva Smith, Lior Hadad, Elena Bakelman, Noa Sela, Eduard Belausov, Oded Lachman, Diana Leibman and Aviv Dombrovsky
Viruses 2020, 12(8), 879; https://doi.org/10.3390/v12080879 - 11 Aug 2020
Cited by 23 | Viewed by 6502
Abstract
The tobamovirus tomato brown rugose fruit virus (ToBRFV), a major threat to tomato production worldwide, has recently been documented in mixed infections with the potexvirus pepino mosaic virus (PepMV) CH2 strain in traded tomatoes in Israel. A study of greenhouse tomato plants in [...] Read more.
The tobamovirus tomato brown rugose fruit virus (ToBRFV), a major threat to tomato production worldwide, has recently been documented in mixed infections with the potexvirus pepino mosaic virus (PepMV) CH2 strain in traded tomatoes in Israel. A study of greenhouse tomato plants in Israel revealed severe new viral disease symptoms including open unripe fruits and yellow patched leaves. PepMV was only detected in mixed infections with ToBRFV in all 104 tested sites, using serological and molecular analyses. Six PepMV isolates were identified, all had predicted amino acids characteristic of CH2 mild strains excluding an isoleucine at amino acid position 995 of the replicase. High-throughput sequencing of viral RNA extracted from four selected symptomatic plants showed solely the ToBRFV and PepMV, with total aligned read ratios of 40.61% and 11.73%, respectively, indicating prevalence of the viruses. Analyses of interactions between the co-infecting viruses by sequential and mixed viral inoculations of tomato plants, at various temperatures, showed a prominent increase in PepMV titers in ToBRFV pre-inoculated plants and in mixed-infected plants at 18–25 °C, compared to PepMV-single inoculations, as analyzed by Western blot and quantitative RT-PCR tests. These results suggest that Israeli mild PepMV isolate infections, preceded by ToBRFV, could induce symptoms characteristic of PepMV aggressive strains. Full article
(This article belongs to the Special Issue Plant Virus Pathogenesis and Disease Control)
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12 pages, 2444 KiB  
Article
Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism
by Silvia Spinelli, Denise Tremblay, Sylvain Moineau, Christian Cambillau and Adeline Goulet
Viruses 2020, 12(8), 878; https://doi.org/10.3390/v12080878 - 11 Aug 2020
Cited by 7 | Viewed by 3437
Abstract
Virulent phages infecting L. lactis, an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the [...] Read more.
Virulent phages infecting L. lactis, an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca2+. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected. Full article
(This article belongs to the Section Bacterial Viruses)
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17 pages, 3335 KiB  
Article
Genetic and Antigenic Characterization and Retrospective Surveillance of Bovine Influenza D Viruses Identified in Hokkaido, Japan from 2018 to 2020
by Jun Hayakawa, Tomomi Masuko, Tae Takehana and Tohru Suzuki
Viruses 2020, 12(8), 877; https://doi.org/10.3390/v12080877 - 11 Aug 2020
Cited by 9 | Viewed by 3148
Abstract
Influenza D virus (IDV), which is a new member of the Orthomyxoviridae family, is potentially involved in bovine respiratory diseases (BRDs). Bovine IDVs (BIDVs) from Japan have been distributed nationwide since 2010 and are genetically distinct from foreign IDVs. We isolated BIDVs from [...] Read more.
Influenza D virus (IDV), which is a new member of the Orthomyxoviridae family, is potentially involved in bovine respiratory diseases (BRDs). Bovine IDVs (BIDVs) from Japan have been distributed nationwide since 2010 and are genetically distinct from foreign IDVs. We isolated BIDVs from three BRD outbreaks, in Hokkaido during 2018–2020, to understand their genetic and antigenic characteristics. Retrospective surveillance was performed using sera collected throughout the last decade in Hokkaido to investigate BIDV existence. Three BIDVs were isolated using cell culture. Comparative and phylogenetic analyses using sequence data of the three BIDVs and IDVs from Japan and other countries available in GenBank demonstrated that Japanese BIDVs, including the three BIDV isolates, were genetically distinct from other IDVs. Genotype classifications based on the rotavirus genotype classification revealed multiple genotypes of RNA segments 1–7. Two BIDVs were of a new genotype, different from those of other Japanese BIDVs. Neutralization assays against two BIDVs with different genotypes using sera collected in acute and recovery phases of BRD revealed differences in cross-reactivity to heterogenous BIDVs. Retrospective surveillance suggested that BIDV existed in Hokkaido, in 2009. Our findings suggest that BIDVs of different genotypes and antigenicity are distributed and maintained in Hokkaido and provide new insights into molecular characteristics and the evolution of IDVs. Full article
(This article belongs to the Section Animal Viruses)
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14 pages, 3552 KiB  
Article
Gammaherpesvirus in Cervid Species from Norway: Characterization of a New Virus in Wild and Semi-Domesticated Eurasian Tundra Reindeer (Rangifer tarandus tarandus)
by Carlos G. das Neves, Carlos Sacristán, Knut Madslien and Morten Tryland
Viruses 2020, 12(8), 876; https://doi.org/10.3390/v12080876 - 11 Aug 2020
Cited by 9 | Viewed by 4591
Abstract
Gammaherpesvirus infections have been described in cervids worldwide, mainly the genera Macavirus or Rhadinovirus. However, little is known about the gammaherpesviruses species infecting cervids in Norway and Fennoscandia. Blood samples from semi-domesticated (n = 39) and wild (n = 35) [...] Read more.
Gammaherpesvirus infections have been described in cervids worldwide, mainly the genera Macavirus or Rhadinovirus. However, little is known about the gammaherpesviruses species infecting cervids in Norway and Fennoscandia. Blood samples from semi-domesticated (n = 39) and wild (n = 35) Eurasian tundra reindeer (Rangifer tarandus tarandus), moose (Alces alces, n = 51), and red deer (Cervus elaphus, n = 41) were tested using a panherpesvirus DNA polymerase (DPOL) PCR. DPOL-PCR-positive samples were subsequently tested for the presence of glycoprotein B (gB) gene. The viral DPOL gene was amplified in 28.2% (11/39) of the semi-domesticated reindeer and in 48.6% (17/35) of the wild reindeer. All moose and red deer tested negative. Additionally, gB gene was amplified in 4 of 11 semi-domesticated and 15 of 17 wild Eurasian reindeer DPOL-PCR-positive samples. All the obtained DPOL and gB sequences were highly similar among them, and corresponded to a novel gammaherpesvirus species, tentatively named Rangiferine gammaherpesvirus 1, that seemed to belong to a genus different from Macavirus and Rhadinovirus. This is the first report of a likely host-specific gammaherpesvirus in semi-domesticated reindeer, an economic and cultural important animal, and in wild tundra reindeer, the lastpopulation in Europe. Future studies are required to clarify the potential impact of this gammaherpesvirus on reindeer health. Full article
(This article belongs to the Special Issue Animal and Wildlife Viruses)
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16 pages, 1262 KiB  
Review
Cannabinoid-Induced Immunomodulation during Viral Infections: A Focus on Mitochondria
by Cherifa Beji, Hamza Loucif, Roman Telittchenko, David Olagnier, Xavier Dagenais-Lussier and Julien van Grevenynghe
Viruses 2020, 12(8), 875; https://doi.org/10.3390/v12080875 - 11 Aug 2020
Cited by 12 | Viewed by 4292
Abstract
This review examines the impact of cannabinoids on viral infections, as well as its effects on the mitochondria of the nervous and immune system. The paper conveys information about the beneficial and negative impacts of cannabinoids on viral infections, especially HIV-1. These include [...] Read more.
This review examines the impact of cannabinoids on viral infections, as well as its effects on the mitochondria of the nervous and immune system. The paper conveys information about the beneficial and negative impacts of cannabinoids on viral infections, especially HIV-1. These include effects on the inflammatory response as well as neuroprotective effects. We also explore non-apoptotic mitochondrial pathways modulated by the activity of cannabinoids, resulting in modifications to cellular functions. As a large part of the literature derives from studies of the nervous system, we first compile the information related to mitochondrial functions in this system, particularly through the CB1 receptor. Finally, we reflect on how this knowledge could complement what has been demonstrated in the immune system, especially in the context of the CB2 receptor and Ca2+ uptake. The overall conclusion of the review is that cannabinoids have the potential to affect a broad range of cell types through mitochondrial modulation, be it through receptor-specific action or not, and that this pathway has a potential implication in cases of viral infection. Full article
(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)
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