Viruses

14 pages, 3112 KiB

Open AccessEditor’s ChoiceArticle

Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection

by Austen Terwilliger, Justin Clark, Maile Karris, Haroldo Hernandez-Santos, Sabrina Green, Saima Aslam and Anthony Maresso

Viruses 2021, 13(10), 2049; https://doi.org/10.3390/v13102049 - 12 Oct 2021

Cited by 44 | Viewed by 9546

Abstract

We rationally designed a bacteriophage cocktail to treat a 56-year-old male liver transplant patient with complex, recurrent prostate and urinary tract infections caused by an extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) (UCS1). We screened our library for phages that killed [...] Read more.

We rationally designed a bacteriophage cocktail to treat a 56-year-old male liver transplant patient with complex, recurrent prostate and urinary tract infections caused by an extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) (UCS1). We screened our library for phages that killed UCS1, with four promising candidates chosen for their virulence, mucolytic properties, and ability to reduce bacterial resistance. The patient received 2 weeks of intravenous phage cocktail with concomitant ertapenem for 6 weeks. Weekly serum and urine samples were collected to track the patient’s response. The patient tolerated the phage therapy without any adverse events with symptom resolution. The neutralization of the phage activity occurred with sera collected 1 to 4 weeks after the first phage treatment. This was consistent with immunoassays that detected the upregulation of immune stimulatory analytes. The patient developed asymptomatic recurrent bacteriuria 6 and 11 weeks following the end of phage therapy—a condition that did not require antibiotic treatment. The bacteriuria was caused by a sister strain of E. coli (UCS1.1) that remained susceptible to the original phage cocktail and possessed putative mutations in the proteins involved in adhesion and invasion compared to UCS1. This study highlights the utility of rationally designed phage cocktails with antibiotics at controlling E. coli infection and suggests that microbial succession, without complete eradication, may produce desirable clinical outcomes. Full article

(This article belongs to the Special Issue State-of-the-Art Phage Therapy Development in Europe)

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18 pages, 1903 KiB

Open AccessEditor’s ChoiceArticle

Reduced Infection Efficiency of Phage NCTC 12673 on Non-Motile Campylobacter jejuni Strains Is Related to Oxidative Stress

by Jessica C. Sacher, Muhammad Afzal Javed, Clay S. Crippen, James Butcher, Annika Flint, Alain Stintzi and Christine M. Szymanski

Viruses 2021, 13(10), 1955; https://doi.org/10.3390/v13101955 - 29 Sep 2021

Cited by 5 | Viewed by 3716

Abstract

Campylobacter jejuni is a Gram-negative foodborne pathogen that causes diarrheal disease and is associated with severe post-infectious sequelae. Bacteriophages (phages) are a possible means of reducing Campylobacter colonization in poultry to prevent downstream human infections. However, the factors influencing phage-host interactions must be [...] Read more.

Campylobacter jejuni is a Gram-negative foodborne pathogen that causes diarrheal disease and is associated with severe post-infectious sequelae. Bacteriophages (phages) are a possible means of reducing Campylobacter colonization in poultry to prevent downstream human infections. However, the factors influencing phage-host interactions must be better understood before this strategy can be predictably employed. Most studies have focused on Campylobacter phage binding to the host surface, with all phages classified as either capsule- or flagella-specific. Here we describe the characterization of a C. jejuni phage that requires functional flagellar glycosylation and motor genes for infection, without needing the flagella for adsorption to the cell surface. Through phage infectivity studies of targeted C. jejuni mutants, transcriptomic analysis of phage-resistant mutants, and genotypic and phenotypic analysis of a spontaneous phage variant capable of simultaneously overcoming flagellar gene dependence and sensitivity to oxidative stress, we have uncovered a link between oxidative stress, flagellar motility, and phage infectivity. Taken together, our results underscore the importance of understanding phage-host interactions beyond the cell surface and point to host oxidative stress state as an important and underappreciated consideration for future phage-host interaction studies. Full article

(This article belongs to the Special Issue Phage-Host Interactions 2021)

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19 pages, 6076 KiB

Open AccessEditor’s ChoiceArticle

VP8, the Major Tegument Protein of Bovine Herpesvirus-1, Is Partially Packaged during Early Tegument Formation in a VP22-Dependent Manner

by Soumya Sucharita, Kuan Zhang and Sylvia van Drunen Littel-van den Hurk

Viruses 2021, 13(9), 1854; https://doi.org/10.3390/v13091854 - 17 Sep 2021

Cited by 4 | Viewed by 3030

Abstract

Bovine herpesvirus-1 (BoHV-1) is a major cause of rhinotracheitis and vulvovaginitis in cattle. VP8, the major tegument protein of BoHV-1, is essential for viral replication in the host. VP8 is phosphorylated by the viral kinase US3, mediating its translocation to the cytoplasm. VP8 [...] Read more.

Bovine herpesvirus-1 (BoHV-1) is a major cause of rhinotracheitis and vulvovaginitis in cattle. VP8, the major tegument protein of BoHV-1, is essential for viral replication in the host. VP8 is phosphorylated by the viral kinase US3, mediating its translocation to the cytoplasm. VP8 remains nuclear when not phosphorylated. Interestingly, VP8 has a significant presence in mature BoHV-1YmVP8, in which the VP8 phosphorylation sites are mutated. This suggests that VP8 might be packaged during primary envelopment of BoHV-1. This was investigated by mass spectrometry and Western blotting, which showed VP8, as well as VP22, to be constituents of the primary enveloped virions. VP8 and VP22 were shown to interact via co-immunoprecipitation experiments, in both BoHV-1-infected and VP8-transfected cells. VP8 and VP22 also co-localised with one another and with nuclear lamin-associated protein 2 in BoHV-1-infected cells, suggesting an interaction between VP8 and VP22 in the perinuclear region. In cells infected with VP22-deleted BoHV-1 (BoHV-1ΔUL49), VP8 was absent from the primary enveloped virions, implying that VP22 might be critical for the early packaging of VP8. In conclusion, a novel VP22-dependent mechanism for packaging of VP8 was identified, which may be responsible for a significant amount of VP8 in the viral particle. Full article

(This article belongs to the Special Issue Animal Herpesviruses Pathogenesis and Immunity)

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18 pages, 1864 KiB

Open AccessEditor’s ChoiceArticle

The Pathobiology of H7N3 Low and High Pathogenicity Avian Influenza Viruses from the United States Outbreak in 2020 Differs between Turkeys and Chickens

by Miriã F. Criado, Christina M. Leyson, Sungsu Youk, Suzanne DeBlois, Tim Olivier, Mary Lea Killian, Mia L. Torchetti, Darren J. Parris, Erica Spackman, Darrell R. Kapczynski, David L. Suarez, David E. Swayne and Mary J. Pantin-Jackwood

Viruses 2021, 13(9), 1851; https://doi.org/10.3390/v13091851 - 16 Sep 2021

Cited by 11 | Viewed by 4688

Abstract

An outbreak caused by H7N3 low pathogenicity avian influenza virus (LPAIV) occurred in commercial turkey farms in the states of North Carolina (NC) and South Carolina (SC), United States in March of 2020. Subsequently, H7N3 high pathogenicity avian influenza virus (HPAIV) was detected [...] Read more.

An outbreak caused by H7N3 low pathogenicity avian influenza virus (LPAIV) occurred in commercial turkey farms in the states of North Carolina (NC) and South Carolina (SC), United States in March of 2020. Subsequently, H7N3 high pathogenicity avian influenza virus (HPAIV) was detected on a turkey farm in SC. The infectivity, transmissibility, and pathogenicity of the H7N3 HPAIV and two LPAIV isolates, including one with a deletion in the neuraminidase (NA) protein stalk, were studied in turkeys and chickens. High infectivity [<2 log₁₀ 50% bird infectious dose (BID₅₀)] and transmission to birds exposed by direct contact were observed with the HPAIV in turkeys. In contrast, the HPAIV dose to infect chickens was higher than for turkeys (3.7 log₁₀ BID₅₀), and no transmission was observed. Similarly, higher infectivity (<2–2.5 log₁₀ BID₅₀) and transmissibility were observed with the H7N3 LPAIVs in turkeys compared to chickens, which required higher virus doses to become infected (5.4–5.7 log₁₀ BID₅₀). The LPAIV with the NA stalk deletion was more infectious in turkeys but did not have enhanced infectivity in chickens. These results show clear differences in the pathobiology of AIVs in turkeys and chickens and corroborate the high susceptibility of turkeys to both LPAIV and HPAIV infections. Full article

(This article belongs to the Special Issue Highly Pathogenic Avian Influenza Virus Emergence)

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15 pages, 1096 KiB

Open AccessEditor’s ChoiceArticle

Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses

by Bert Vanmechelen, Zafeiro Zisi, Sophie Gryseels, Joëlle Goüy de Bellocq, Bram Vrancken, Philippe Lemey, Piet Maes and Magda Bletsa

Viruses 2021, 13(9), 1842; https://doi.org/10.3390/v13091842 - 15 Sep 2021

Cited by 5 | Viewed by 4286

Abstract

Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several [...] Read more.

Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses. Full article

(This article belongs to the Section Animal Viruses)

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17 pages, 2201 KiB

Open AccessEditor’s ChoiceArticle

The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants

by Daniel Udenze, Ivan Trus, Henry Munyanduki, Nathalie Berube and Uladzimir Karniychuk

Viruses 2021, 13(9), 1827; https://doi.org/10.3390/v13091827 - 14 Sep 2021

Cited by 5 | Viewed by 3701

Abstract

The host’s immune status may affect virus evolution. Little is known about how developing fetal and placental immune milieus affect virus heterogeneity. This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge. The goal of our study [...] Read more.

The host’s immune status may affect virus evolution. Little is known about how developing fetal and placental immune milieus affect virus heterogeneity. This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge. The goal of our study was to find out whether the isolated in utero environment—an environment with specialized placental immunity and developing fetal immunity—supports the emergence of RNA and DNA virus variants. We used well-established porcine models for isolated Zika virus (RNA virus) and porcine circovirus 2 (DNA virus) fetal infections. We found that the isolated in utero environment was conducive to the emergence of RNA and DNA virus variants. Next-generation sequencing of nearly whole virus genomes and validated bioinformatics pipelines identified both unique and convergent single nucleotide variations in virus genomes isolated from different fetuses. Zika virus and PCV2 in utero evolution also resulted in single nucleotide variations previously reported in the human and porcine field samples. These findings should encourage further studies on virus evolution in placenta and fetuses, to better understand how virus variants emerge and how in utero viral evolution affects congenital virus transmission and pathogenicity. Full article

(This article belongs to the Section Animal Viruses)

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11 pages, 902 KiB

Open AccessEditor’s ChoiceArticle

Histotype-Dependent Oligodendroglial PrP Pathology in Sporadic CJD: A Frequent Feature of the M2C “Strain”

by Ellen Gelpi, Sigrid Klotz, Nuria Vidal-Robau, Gerda Ricken, Günther Regelsberger, Thomas Ströbel, Ognian Kalev, Marlene Leoni, Herbert Budka and Gabor G. Kovacs

Viruses 2021, 13(9), 1796; https://doi.org/10.3390/v13091796 - 9 Sep 2021

Cited by 3 | Viewed by 2746

Abstract

In sporadic Creutzfeldt-Jakob disease, molecular subtypes are neuropathologically well identified by the lesioning profile and the immunohistochemical PrP^d deposition pattern in the grey matter (histotypes). While astrocytic PrP pathology has been reported in variant CJD and some less frequent histotypes (e.g., MV2K), [...] Read more.

In sporadic Creutzfeldt-Jakob disease, molecular subtypes are neuropathologically well identified by the lesioning profile and the immunohistochemical PrP^d deposition pattern in the grey matter (histotypes). While astrocytic PrP pathology has been reported in variant CJD and some less frequent histotypes (e.g., MV2K), oligodendroglial pathology has been rarely addressed. We assessed a series of sCJD cases with the aim to identify particular histotypes that could be more prone to harbor oligodendroglial PrP^d. Particularly, the MM2C phenotype, in both its more “pure” and its mixed MM1+2C or MV2K+2C forms, showed more frequent oligodendroglial PrP pathology in the underlying white matter than the more common MM1/MV1 and VV2 histotypes, and was more abundant in patients with a longer disease duration. We concluded that the MM2C strain was particularly prone to accumulate PrP^d in white matter oligodendrocytes. Full article

(This article belongs to the Special Issue Prion Disease)

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12 pages, 1043 KiB

Open AccessEditor’s ChoiceArticle

Report of One-Year Prospective Surveillance of SARS-CoV-2 in Dogs and Cats in France with Various Exposure Risks: Confirmation of a Low Prevalence of Shedding, Detection and Complete Sequencing of an Alpha Variant in a Cat

by Emilie Krafft, Solène Denolly, Bertrand Boson, Sophie Angelloz-Pessey, Sophie Levaltier, Nicolas Nesi, Sandrine Corbet, Bryce Leterrier, Matthieu Fritz, Eric M. Leroy, Meriadeg Ar Gouilh, François-Loïc Cosset, Angeli Kodjo and Vincent Legros

Viruses 2021, 13(9), 1759; https://doi.org/10.3390/v13091759 - 3 Sep 2021

Cited by 15 | Viewed by 3889

Abstract

Despite the probable zoonotic origin of SARS-CoV-2, only limited research efforts have been made to understand the role of companion animals in SARS-CoV-2 epidemiology. According to recent serological prevalence studies, human-to-companion animal transmission is quite frequent, which led us to consider that the [...] Read more.

Despite the probable zoonotic origin of SARS-CoV-2, only limited research efforts have been made to understand the role of companion animals in SARS-CoV-2 epidemiology. According to recent serological prevalence studies, human-to-companion animal transmission is quite frequent, which led us to consider that the risk of SARS-CoV-2 transmission from animal to human, albeit negligible in the present context, may have been underestimated. In this study, we provide the results of a prospective survey that was conducted to evaluate the SARS-CoV-2 isolation rate by qRT-PCR in dogs and cats with different exposure risks and clinical statuses. From April 2020 to April 2021, we analyzed 367 samples and investigated the presence of SARS-CoV-2 RNA using qRT-PCR. Only four animals tested positive, all of them being cats. Three cats were asymptomatic and one presented a coryza-like syndrome. We describe in detail the infection in two cats and the associated clinical characteristics. Importantly, we obtained SARS-CoV-2 genomes from one infected animal and characterized them as Alpha variants. This represents the first identification of the SARS-CoV-2 Alpha variant in an infected animal in France. Full article

(This article belongs to the Special Issue Enteric and Respiratory Viruses in Animals)

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17 pages, 21140 KiB

Open AccessEditor’s ChoiceArticle

Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL^®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

by Janice Mayne, Xu Zhang, James Butcher, Krystal Walker, Zhibin Ning, Ewelina Wójcik, Jarosław Dastych, Alain Stintzi and Daniel Figeys

Viruses 2021, 13(9), 1734; https://doi.org/10.3390/v13091734 - 31 Aug 2021

Cited by 6 | Viewed by 3924

Abstract

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments [...] Read more.

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL^®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL^® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment. Full article

(This article belongs to the Special Issue Phage-Bacteria Interplay in Health and Disease)

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18 pages, 21651 KiB

Open AccessEditor’s ChoiceArticle

Structure-Guided Creation of an Anti-HA Stalk Antibody F11 Derivative That Neutralizes Both F11-Sensitive and -Resistant Influenza A(H1N1)pdm09 Viruses

by Osamu Kotani, Yasushi Suzuki, Shinji Saito, Akira Ainai, Akira Ueno, Takuya Hemmi, Kaori Sano, Koshiro Tabata, Masaru Yokoyama, Tadaki Suzuki, Hideki Hasegawa and Hironori Sato

Viruses 2021, 13(9), 1733; https://doi.org/10.3390/v13091733 - 31 Aug 2021

Cited by 3 | Viewed by 3825

Abstract

The stalk domain of influenza virus envelope glycoprotein hemagglutinin (HA) constitutes the axis connecting the head and transmembrane domains, and plays pivotal roles in conformational rearrangements of HA for virus infection. Here we characterized molecular interactions between the anti-HA stalk neutralization antibody F11 [...] Read more.

The stalk domain of influenza virus envelope glycoprotein hemagglutinin (HA) constitutes the axis connecting the head and transmembrane domains, and plays pivotal roles in conformational rearrangements of HA for virus infection. Here we characterized molecular interactions between the anti-HA stalk neutralization antibody F11 and influenza A(H1N1)pdm09 HA to understand the structural basis of the actions and modifications of this antibody. In silico structural analyses using a model of the trimeric HA ectodomain indicated that the F11 Fab fragment has physicochemical properties, allowing it to crosslink two HA monomers by binding to a region near the proteolytic cleavage site of the stalk domain. Interestingly, the F11 binding allosterically caused a marked suppression of the structural dynamics of the HA cleavage loop and flanking regions. Structure-guided mutagenesis of the F11 antibody revealed a critical residue in the F11 light chain for the F11-mediated neutralization. Finally, the mutagenesis led to identification of a unique F11 derivative that can neutralize both F11-sensitive and F11-resistant A(H1N1)pdm09 viruses. These results raise the possibility that F11 sterically and physically disturbs proteolytic cleavage of HA for the ordered conformational rearrangements and suggest that in silico guiding experiments can be useful to create anti-HA stalk antibodies with new phenotypes. Full article

(This article belongs to the Special Issue RNA Viruses: Structure, Adaptation, and Evolution)

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17 pages, 46566 KiB

Open AccessEditor’s ChoiceArticle

An Absolutely Conserved Tryptophan in the Stem of the Envelope Protein E of Flaviviruses Is Essential for the Formation of Stable Particles

by Iris Medits, Franz X. Heinz and Karin Stiasny

Viruses 2021, 13(9), 1727; https://doi.org/10.3390/v13091727 - 30 Aug 2021

Cited by 1 | Viewed by 3356

Abstract

The major envelope protein E of flaviviruses contains an ectodomain that is connected to the transmembrane domain by the so-called “stem” region. In mature flavivirus particles, the stem is composed of two or three mostly amphipathic α-helices and a conserved sequence element (CS) [...] Read more.

The major envelope protein E of flaviviruses contains an ectodomain that is connected to the transmembrane domain by the so-called “stem” region. In mature flavivirus particles, the stem is composed of two or three mostly amphipathic α-helices and a conserved sequence element (CS) with an undefined role in the viral life cycle. A tryptophan is the only residue within this region which is not only conserved in all vector-borne flaviviruses, but also in the group with no known vector. We investigated the importance of this residue in different stages of the viral life cycle by a mutagenesis-based approach using tick-borne encephalitis virus (TBEV). Replacing W421 by alanine or histidine strongly reduced the release of infectious virions and their thermostability, whereas fusion-related entry functions and virus maturation were still intact. Serial passaging of the mutants led to the emergence of a same-site compensatory mutation to leucine that largely restored these properties of the wildtype. The conserved tryptophan in CS (or another big hydrophobic amino acid at the same position) is thus essential for the assembly and infectivity of flaviviruses by being part of a network required for conferring stability to infectious particles. Full article

(This article belongs to the Special Issue Biology of Viral Surface Glycoproteins)

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16 pages, 3886 KiB

Open AccessEditor’s ChoiceArticle

Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

by Lester J. Perez, Gavin A. Cloherty and Michael G. Berg

Viruses 2021, 13(8), 1476; https://doi.org/10.3390/v13081476 - 28 Jul 2021

Cited by 10 | Viewed by 7794

Abstract

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We [...] Read more.

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2). Full article

(This article belongs to the Special Issue Viral Genetic Diversity)

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16 pages, 2569 KiB

Open AccessEditor’s ChoiceArticle

Characterization of the Roles of SGT1/RAR1, EDS1/NDR1, NPR1, and NRC/ADR1/NRG1 in Sw-5b-Mediated Resistance to Tomato Spotted Wilt Virus

by Zhengqiang Chen, Qian Wu, Cong Tong, Hongyu Chen, Dan Miao, Xin Qian, Xiaohui Zhao, Lei Jiang and Xiaorong Tao

Viruses 2021, 13(8), 1447; https://doi.org/10.3390/v13081447 - 25 Jul 2021

Cited by 15 | Viewed by 5048

Abstract

The tomato Sw-5b gene confers resistance to tomato spotted wilt virus (TSWV) and encodes a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal Solanaceae-specific domain (SD). Although our understanding of how Sw-5b recognizes the viral NSm elicitor has increased significantly, the process by [...] Read more.

The tomato Sw-5b gene confers resistance to tomato spotted wilt virus (TSWV) and encodes a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal Solanaceae-specific domain (SD). Although our understanding of how Sw-5b recognizes the viral NSm elicitor has increased significantly, the process by which Sw-5b activates downstream defense signaling remains to be elucidated. In this study, we used a tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) system to investigate the roles of the SGT1/RAR1, EDS1/NDR1, NPR1, and NRC/ADR1/NRG1 genes in the Sw-5b-mediated signaling pathway. We found that chaperone SGT1 was required for Sw-5b function, but co-chaperone RAR1 was not. Sw-5b-mediated immune signaling was independent of both EDS1 and NDR1. Silencing NPR1, which is a central component in SA signaling, did not result in TSWV systemic infection in Sw-5b-transgenic N. benthamiana plants. Helper NLR NRCs (NLRs required for cell death) were required for Sw-5b-mediated systemic resistance to TSWV infection. Suppression of NRC2/3/4 compromised the Sw-5b resistance. However, the helper NLRs ADR1 and NRG1 may not participate in the Sw-5b signaling pathway. Silencing ADR1, NRG1, or both genes did not affect Sw-5b-mediated resistance to TSWV. Our findings provide new insight into the requirement for conserved key components in Sw-5b-mediated signaling pathways. Full article

(This article belongs to the Special Issue Plant Immunity to Virus Infections 2021)

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16 pages, 1911 KiB

Open AccessEditor’s ChoiceArticle

A Diverse Viral Community from Predatory Wasps in Their Native and Invaded Range, with a New Virus Infectious to Honey Bees

by Emily J. Remnant, James W. Baty, Mariana Bulgarella, Jana Dobelmann, Oliver Quinn, Monica A. M. Gruber and Philip J. Lester

Viruses 2021, 13(8), 1431; https://doi.org/10.3390/v13081431 - 23 Jul 2021

Cited by 17 | Viewed by 3933

Abstract

Wasps of the genus Vespula are social insects that have become major pests and predators in their introduced range. Viruses present in these wasps have been studied in the context of spillover from honey bees, yet we lack an understanding of the endogenous [...] Read more.

Wasps of the genus Vespula are social insects that have become major pests and predators in their introduced range. Viruses present in these wasps have been studied in the context of spillover from honey bees, yet we lack an understanding of the endogenous virome of wasps as potential reservoirs of novel emerging infectious diseases. We describe the characterization of 68 novel and nine previously identified virus sequences found in transcriptomes of Vespula vulgaris in colonies sampled from their native range (Belgium) and an invasive range (New Zealand). Many viruses present in the samples were from the Picorna-like virus family (38%). We identified one Luteo-like virus, Vespula vulgaris Luteo-like virus 1, present in the three life stages examined in all colonies from both locations, suggesting this virus is a highly prevalent and persistent infection in wasp colonies. Additionally, we identified a novel Iflavirus with similarity to a recently identified Moku virus, a known wasp and honey bee pathogen. Experimental infection of honey bees with this novel Vespula vulgaris Moku-like virus resulted in an active infection. The high viral diversity present in these invasive wasps is a likely indication that their polyphagous diet is a rich source of viral infections. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Virology Research in New Zealand)

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13 pages, 1789 KiB

Open AccessEditor’s ChoiceArticle

Effects of Basic Amino Acids and Their Derivatives on SARS-CoV-2 and Influenza-A Virus Infection

by Ivonne Melano, Li-Lan Kuo, Yan-Chung Lo, Po-Wei Sung, Ni Tien and Wen-Chi Su

Viruses 2021, 13(7), 1301; https://doi.org/10.3390/v13071301 - 4 Jul 2021

Cited by 28 | Viewed by 14328

Abstract

Amino acids have been implicated with virus infection and replication. Here, we demonstrate the effects of two basic amino acids, arginine and lysine, and their ester derivatives on infection of two enveloped viruses, SARS-CoV-2, and influenza A virus. We found that lysine and [...] Read more.

Amino acids have been implicated with virus infection and replication. Here, we demonstrate the effects of two basic amino acids, arginine and lysine, and their ester derivatives on infection of two enveloped viruses, SARS-CoV-2, and influenza A virus. We found that lysine and its ester derivative can efficiently block infection of both viruses in vitro. Furthermore, the arginine ester derivative caused a significant boost in virus infection. Studies on their mechanism of action revealed that the compounds potentially disturb virus uncoating rather than virus attachment and endosomal acidification. Our findings suggest that lysine supplementation and the reduction of arginine-rich food intake can be considered as prophylactic and therapeutic regimens against these viruses while also providing a paradigm for the development of broad-spectrum antivirals. Full article

(This article belongs to the Topic Broad-Spectrum Antiviral Agents)

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20 pages, 5239 KiB

Open AccessEditor’s ChoiceArticle

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

by Karol Serwin, Andrzej Ossowski, Maria Szargut, Sandra Cytacka, Anna Urbańska, Adam Majchrzak, Anna Niedźwiedź, Ewa Czerska, Anna Pawińska-Matecka, Joanna Gołąb and Miłosz Parczewski

Viruses 2021, 13(7), 1295; https://doi.org/10.3390/v13071295 - 2 Jul 2021

Cited by 10 | Viewed by 4229

Abstract

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed [...] Read more.

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth–death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland. Full article

(This article belongs to the Section SARS-CoV-2 and COVID-19)

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18 pages, 3166 KiB

Open AccessEditor’s ChoiceArticle

A New Master Donor Virus for the Development of Live-Attenuated Influenza B Virus Vaccines

by Chantelle L. White, Kevin Chiem, Daniel R. Perez, Jefferson Santos, Stivalis Cardenas Garcia, Aitor Nogales and Luis Martínez-Sobrido

Viruses 2021, 13(7), 1278; https://doi.org/10.3390/v13071278 - 30 Jun 2021

Cited by 5 | Viewed by 3591

Abstract

Influenza B viruses (IBV) circulate annually, with young children, the elderly and immunocompromised individuals being at high risk. Yearly vaccinations are recommended to protect against seasonally influenza viruses, including IBV. Live attenuated influenza vaccines (LAIV) provide the unique opportunity for direct exposure to [...] Read more.

Influenza B viruses (IBV) circulate annually, with young children, the elderly and immunocompromised individuals being at high risk. Yearly vaccinations are recommended to protect against seasonally influenza viruses, including IBV. Live attenuated influenza vaccines (LAIV) provide the unique opportunity for direct exposure to the antigenically variable surface glycoproteins as well as the more conserved internal components. Ideally, LAIV Master Donor Viruses (MDV) should accurately reflect seasonal influenza strains. Unfortunately, the continuous evolution of IBV have led to significant changes in conserved epitopes compared to the IBV MDV based on B/Ann Arbor/1/1966 strain. Here, we propose a recent influenza B/Brisbane/60/2008 as an efficacious MDV alternative, as its internal viral proteins more accurately reflect those of circulating IBV strains. We introduced the mutations responsible for the temperature sensitive (ts), cold adapted (ca) and attenuated (att) phenotype of B/Ann Arbor/1/1966 MDV LAIV into B/Brisbane/60/2008 to generate a new MDV LAIV. In vitro and in vivo analysis demonstrated that the mutations responsible of the ts, ca, and att phenotype of B/Ann Arbor/1/1966 MDV LAIV were able to infer the same phenotype to B/Brisbane/60/2008, demonstrating its potential as a new MDV for the development of LAIV to protect against contemporary IBV strains. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

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19 pages, 7021 KiB

Open AccessEditor’s ChoiceArticle

Modular Evolution of Coronavirus Genomes

by Yulia Vakulenko, Andrei Deviatkin, Jan Felix Drexler and Alexander Lukashev

Viruses 2021, 13(7), 1270; https://doi.org/10.3390/v13071270 - 29 Jun 2021

Cited by 26 | Viewed by 4900

Abstract

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and [...] Read more.

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses. Full article

(This article belongs to the Special Issue Recombination as an Evolutionary Force in Animal Viruses)

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13 pages, 1810 KiB

Open AccessEditor’s ChoiceArticle

Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

by Leah D. Brandt, Shuang Guo, Kevin W. Joseph, Jana L. Jacobs, Asma Naqvi, John M. Coffin, Mary F. Kearney, Elias K. Halvas, Xiaolin Wu, Stephen H. Hughes and John W. Mellors

Viruses 2021, 13(7), 1235; https://doi.org/10.3390/v13071235 - 25 Jun 2021

Cited by 9 | Viewed by 4349

Abstract

Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the [...] Read more.

Efforts to cure HIV-1 infection require better quantification of the HIV-1 reservoir, particularly the clones of cells harboring replication-competent (intact) proviruses, termed repliclones. The digital droplet PCR assays commonly used to quantify intact proviruses do not differentiate among specific repliclones, thus the dynamics of repliclones are not well defined. The major challenge in tracking repliclones is the relative rarity of the cells carrying specific intact proviruses. To date, detection and accurate quantification of repliclones requires in-depth integration site sequencing. Here, we describe a simplified workflow using integration site-specific qPCR (IS-qPCR) to determine the frequencies of the proviruses integrated in individual repliclones. We designed IS-qPCR to determine the frequencies of repliclones and clones of cells that carry defective proviruses in samples from three donors. Comparing the results of IS-qPCR with deep integration site sequencing data showed that the two methods yielded concordant estimates of clone frequencies (r = 0.838). IS-qPCR is a potentially valuable tool that can be applied to multiple samples and cell types over time to measure the dynamics of individual repliclones and the efficacy of treatments designed to eliminate them. Full article

(This article belongs to the Special Issue Mechanisms of Viral Persistence)

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24 pages, 5294 KiB

Open AccessEditor’s ChoiceArticle

Microglial HIV-1 Expression: Role in HIV-1 Associated Neurocognitive Disorders

by Hailong Li, Kristen A. McLaurin, Jessica M. Illenberger, Charles F. Mactutus and Rosemarie M. Booze

Viruses 2021, 13(5), 924; https://doi.org/10.3390/v13050924 - 17 May 2021

Cited by 19 | Viewed by 4775

Abstract

The persistence of HIV-1 viral reservoirs in the brain, despite treatment with combination antiretroviral therapy (cART), remains a critical roadblock for the development of a novel cure strategy for HIV-1. To enhance our understanding of viral reservoirs, two complementary studies were conducted to [...] Read more.

The persistence of HIV-1 viral reservoirs in the brain, despite treatment with combination antiretroviral therapy (cART), remains a critical roadblock for the development of a novel cure strategy for HIV-1. To enhance our understanding of viral reservoirs, two complementary studies were conducted to (1) evaluate the HIV-1 mRNA distribution pattern and major cell type expressing HIV-1 mRNA in the HIV-1 transgenic (Tg) rat, and (2) validate our findings by developing and critically testing a novel biological system to model active HIV-1 infection in the rat. First, a restricted, region-specific HIV-1 mRNA distribution pattern was observed in the HIV-1 Tg rat. Microglia were the predominant cell type expressing HIV-1 mRNA in the HIV-1 Tg rat. Second, we developed and critically tested a novel biological system to model key aspects of HIV-1 by infusing F344/N control rats with chimeric HIV (EcoHIV). In vitro, primary cultured microglia were treated with EcoHIV revealing prominent expression within 24 h of infection. In vivo, EcoHIV expression was observed seven days after stereotaxic injections. Following EcoHIV infection, microglia were the major cell type expressing HIV-1 mRNA, results that are consistent with observations in the HIV-1 Tg rat. Within eight weeks of infection, EcoHIV rats exhibited neurocognitive impairments and synaptic dysfunction, which may result from activation of the NogoA-NgR3/PirB-RhoA signaling pathway and/or neuroinflammation. Collectively, these studies enhance our understanding of HIV-1 viral reservoirs in the brain and offer a novel biological system to model HIV-associated neurocognitive disorders and associated comorbidities (i.e., drug abuse) in rats. Full article

(This article belongs to the Special Issue Advances in Neurovirology)

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18 pages, 7325 KiB

Open AccessEditor’s ChoiceArticle

Global Metabolic Profiling of Baculovirus Infection in Silkworm Hemolymph Shows the Importance of Amino-Acid Metabolism

by Min Feng, Shigang Fei, Junming Xia, Mengmeng Zhang, Hongyun Wu, Luc Swevers and Jingchen Sun

Viruses 2021, 13(5), 841; https://doi.org/10.3390/v13050841 - 6 May 2021

Cited by 19 | Viewed by 3334

Abstract

Viruses rely on host cell metabolism to provide the necessary energy and biosynthetic precursors for successful viral replication. Infection of the silkworm, Bombyx mori, by Bombyx mori nucleopolyhedrovirus (BmNPV), has been studied extensively in the past to unravel interactions between baculoviruses and [...] Read more.

Viruses rely on host cell metabolism to provide the necessary energy and biosynthetic precursors for successful viral replication. Infection of the silkworm, Bombyx mori, by Bombyx mori nucleopolyhedrovirus (BmNPV), has been studied extensively in the past to unravel interactions between baculoviruses and their lepidopteran hosts. To understand the interaction between the host metabolic responses and BmNPV infection, we analyzed global metabolic changes associated with BmNPV infection in silkworm hemolymph. Our metabolic profiling data suggests that amino acid metabolism is strikingly altered during a time course of BmNPV infection. Amino acid consumption is increased during BmNPV infection at 24 h post infection (hpi), but their abundance recovered at 72 hpi. Central carbon metabolism, on the other hand, particularly glycolysis and glutaminolysis, did not show obvious changes during BmNPV infection. Pharmacologically inhibiting the glycolytic pathway and glutaminolysis also failed to reduce BmNPV replication, revealing that glycolysis and glutaminolysis are not essential during BmNPV infection. This study reveals a unique amino acid utilization process that is implemented during BmNPV infection. Our metabolomic analysis of BmNPV-infected silkworm provides insights as to how baculoviruses induce alterations in host metabolism during systemic infection. Full article

(This article belongs to the Section Invertebrate Viruses)

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12 pages, 928 KiB

Open AccessEditor’s ChoiceArticle

Semipersistently Transmitted, Phloem Limited Plant Viruses Are Inoculated during the First Subphase of Intracellular Stylet Penetrations in Phloem Cells

by Jaime Jiménez, Aránzazu Moreno and Alberto Fereres

Viruses 2021, 13(1), 137; https://doi.org/10.3390/v13010137 - 19 Jan 2021

Cited by 6 | Viewed by 3450

Abstract

The green peach aphid Myzus persicae Sulzer is the main vector of the semipersistently transmitted and phloem-limited Beet yellows virus (BYV, Closterovirus). Studies monitoring the M. persicae probing behavior by using the Electrical penetration graphs (EPG) technique revealed that inoculation of BYV [...] Read more.

The green peach aphid Myzus persicae Sulzer is the main vector of the semipersistently transmitted and phloem-limited Beet yellows virus (BYV, Closterovirus). Studies monitoring the M. persicae probing behavior by using the Electrical penetration graphs (EPG) technique revealed that inoculation of BYV occurs during unique brief intracellular punctures (phloem-pds) produced in companion and/or sieve element cells. Intracellular stylet punctures (or pds) are subdivided in three subphases (II-1, II-2 and II-3), which have been related to the delivery or uptake of non-phloem limited viruses transmitted in a non-persistent or semipersistent manner. As opposed to non-phloem limited viruses, the specific pd subphase(s) involved in the successful delivery of phloem limited viruses by aphids remain unknown. Therefore, we monitored the feeding process of BYV-carrying M. persicae individuals in sugar beet plants by the EPG technique and the feeding process was artificially terminated at each phloem-pd subphase. Results revealed that aphids that only performed the subphase II-1 of the phloem-pd transmitted BYV at similar efficiency than those allowed to perform subphase II-2 or the complete phloem-pd. This result suggests that BYV inoculation occurs during the first subphase of the phloem-pd. The specific transmission mechanisms involved in BYV delivery in phloem cells are discussed. Full article

(This article belongs to the Special Issue Closteroviridae)

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9 pages, 905 KiB

Open AccessEditor’s ChoiceCommunication

The Anticoagulant Nafamostat Potently Inhibits SARS-CoV-2 S Protein-Mediated Fusion in a Cell Fusion Assay System and Viral Infection In Vitro in a Cell-Type-Dependent Manner

by Mizuki Yamamoto, Maki Kiso, Yuko Sakai-Tagawa, Kiyoko Iwatsuki-Horimoto, Masaki Imai, Makoto Takeda, Noriko Kinoshita, Norio Ohmagari, Jin Gohda, Kentaro Semba, Zene Matsuda, Yasushi Kawaguchi, Yoshihiro Kawaoka and Jun-ichiro Inoue

Viruses 2020, 12(6), 629; https://doi.org/10.3390/v12060629 - 10 Jun 2020

Cited by 207 | Viewed by 12071

Abstract

Although infection by SARS-CoV-2, the causative agent of coronavirus pneumonia disease (COVID-19), is spreading rapidly worldwide, no drug has been shown to be sufficiently effective for treating COVID-19. We previously found that nafamostat mesylate, an existing drug used for disseminated intravascular coagulation (DIC), [...] Read more.

Although infection by SARS-CoV-2, the causative agent of coronavirus pneumonia disease (COVID-19), is spreading rapidly worldwide, no drug has been shown to be sufficiently effective for treating COVID-19. We previously found that nafamostat mesylate, an existing drug used for disseminated intravascular coagulation (DIC), effectively blocked Middle East respiratory syndrome coronavirus (MERS-CoV) S protein-mediated cell fusion by targeting transmembrane serine protease 2 (TMPRSS2), and inhibited MERS-CoV infection of human lung epithelium-derived Calu-3 cells. Here we established a quantitative fusion assay dependent on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein, angiotensin I converting enzyme 2 (ACE2) and TMPRSS2, and found that nafamostat mesylate potently inhibited the fusion while camostat mesylate was about 10-fold less active. Furthermore, nafamostat mesylate blocked SARS-CoV-2 infection of Calu-3 cells with an effective concentration (EC)₅₀ around 10 nM, which is below its average blood concentration after intravenous administration through continuous infusion. On the other hand, a significantly higher dose (EC₅₀ around 30 μM) was required for VeroE6/TMPRSS2 cells, where the TMPRSS2-independent but cathepsin-dependent endosomal infection pathway likely predominates. Together, our study shows that nafamostat mesylate potently inhibits SARS-CoV-2 S protein-mediated fusion in a cell fusion assay system and also inhibits SARS-CoV-2 infection in vitro in a cell-type-dependent manner. These findings, together with accumulated clinical data regarding nafamostat’s safety, make it a likely candidate drug to treat COVID-19. Full article

(This article belongs to the Special Issue Pathogenesis of Human and Animal Coronaviruses)

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