bluuebunny/crossref_metadata_2025_split huggingface dataset:
Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity to Historical Virulent Isolates from the 1940s
Authors: Dimitrov Kiril M. , Lee Dong-Hun , Williams-Coplin Dawn , Olivier Timothy L. , Miller Patti J. , Afonso Claudio L. 
Published: February 2016

ABSTRACT

Virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), a devastating disease of poultry and wild birds. Phylogenetic analyses clearly distinguish historical isolates (obtained prior to 1960) from currently circulating viruses of class II genotypes V, VI, VII, and XII through XVIII. Here, partial and complete genomic sequences of recent virulent isolates of genotypes II and IX from China, Egypt, and India were found to be nearly identical to those of historical viruses isolated in the 1940s. Phylogenetic analysis, nucleotide distances, and rates of change demonstrate that these recent isolates have not evolved significantly from the most closely related ancestors from the 1940s. The low rates of change for these virulent viruses (7.05 × 10
−5
and 2.05 × 10
−5
per year, respectively) and the minimal genetic distances existing between these and historical viruses (0.3 to 1.2%) of the same genotypes indicate an unnatural origin. As with any other RNA virus, Newcastle disease virus is expected to evolve naturally; thus, these findings suggest that some recent field isolates should be excluded from evolutionary studies. Furthermore, phylogenetic analyses show that these recent virulent isolates are more closely related to virulent strains isolated during the 1940s, which have been and continue to be used in laboratory and experimental challenge studies. Since the preservation of viable viruses in the environment for over 6 decades is highly unlikely, it is possible that the source of some of the recent virulent viruses isolated from poultry and wild birds might be laboratory viruses.
Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture
Authors: Hughes Heather Y. , Conlan Sean P. , Lau Anna F. , Dekker John P. , Michelin Angela V. , Youn Jung-Ho , Henderson David K. , Frank Karen M. , Segre Julia A. , Palmore Tara N. 
Published: February 2016

ABSTRACT

Perirectal surveillance cultures and a stool culture grew
Aeromonas
species from three patients over a 6-week period and were without epidemiological links. Detection of the
bla
KPC-2
gene in one isolate prompted inclusion of non-
Enterobacteriaceae
in our surveillance culture workup. Whole-genome sequencing confirmed that the isolates were unrelated and provided data for
Aeromonas
reference genomes.
Prospective Evaluation of a New Aspergillus IgG Enzyme Immunoassay Kit for Diagnosis of Chronic and Allergic Pulmonary Aspergillosis
Authors: Dumollard C. , Bailly S. , Perriot S. , Brenier-Pinchart M. P. , Saint-Raymond C. , Camara B. , Gangneux J. P. , Persat F. , Valot S. , Grenouillet F. , Pelloux H. , Pinel C. , Cornet M. 
Published: February 2016

ABSTRACT

Anti-
Aspergillus
IgG antibodies are important biomarkers for the diagnosis of chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA). We compared the performance of a new commercial enzyme immunoassay (EIA) (Bordier Affinity Products) with that of the Bio-Rad and Virion\Serion EIAs. This assay is novel in its association of two recombinant antigens with somatic and metabolic antigens of
Aspergillus fumigatus
. In a prospective multicenter study, 436 serum samples from 147 patients diagnosed with CPA (136 samples/104 patients) or ABPA (94 samples/43 patients) and from 205 controls (206 samples) were tested. We obtained sensitivities of 97%, 91.7%, and 86.1%, and specificities of 90.3%, 91.3%, and 81.5% for the Bordier, Bio-Rad, and Virion\Serion tests, respectively. The Bordier kit was more sensitive than the Bio-Rad kit (
P
< 0.01), which was itself more sensitive than the Virion\Serion kit (
P
= 0.04). The Bordier and Bio-Rad kits had similar specificity (
P
= 0.8), both higher than that of the Virion\Serion kit (
P
= 0.02). The area under the receiver operating characteristic (ROC) curves confirmed the superiority of the Bordier kit over the Bio-Rad and the Virion\Serion kits (0.977, 0.951, and 0.897, respectively;
P
< 0.01 for each comparison). In a subset analysis of 279 serum samples tested with the Bordier and Bio-Rad kits and an in-house immunoprecipitin assay (IPD), the Bordier kit had the highest sensitivity (97.7%), but the IPD tended to be more specific (71.2 and 84.7%, respectively;
P
= 0.10). The use of recombinant, somatic, and metabolic antigens in a single EIA improved the balance of sensitivity and specificity, resulting in an assay highly suitable for use in the diagnosis of chronic and allergic aspergillosis.
Expression of Oncogenic Alleles Induces Multiple Blocks to Human Cytomegalovirus Infection
Authors: Xu Shihao , Schafer Xenia , Munger Joshua 
Published: February 2016

ABSTRACT
In contrast to many viruses, human cytomegalovirus (HCMV) is unable to productively infect most cancer-derived cell lines. The mechanisms of this restriction are unclear. To explore this issue, we tested whether defined oncogenic alleles, including the simian virus 40 (SV40) T antigen (TAg) and oncogenic H-Ras, inhibit HCMV infection. We found that expression of SV40 TAg blocks HCMV infection in human fibroblasts, whereas the replication of a related herpesvirus, herpes simplex virus 1 (HSV-1), was not impacted. The earliest restriction of HCMV infection involves a block of viral entry, as TAg expression prevented the nuclear delivery of viral DNA and pp65. Subsequently, we found that TAg expression reduces the abundance of platelet-derived growth factor receptor α (PDGFRα), a host protein important for HCMV entry. Viral entry into TAg-immortalized fibroblasts could largely be rescued by PDGFRα overexpression. Similarly, PDGFRα overexpression in HeLa cells markedly increased the levels of HCMV gene expression and DNA replication. However, the robust production of viral progeny was not restored by PDGFRα overexpression in either HeLa cells or TAg-immortalized fibroblasts, suggesting additional restrictions associated with transformation and TAg expression. In TAg-expressing fibroblasts, expression of the immediate early 2 (IE2) protein was not rescued to the same extent as that of the immediate early 1 (IE1) protein, suggesting that TAg expression impacts the accumulation of major immediate early (MIE) transcripts. Transduction of IE2 largely rescued HCMV gene expression in TAg-expressing fibroblasts but did not rescue the production of infectious virions. Collectively, our data indicate that oncogenic alleles induce multiple restrictions to HCMV replication.

IMPORTANCE
HCMV cannot replicate in most cancerous cells, yet the causes of this restriction are not clear. The mechanisms that restrict viral replication in cancerous cells represent viral vulnerabilities that can potentially be exploited therapeutically in other contexts. Here we found that SV40 T antigen-mediated transformation inhibits HCMV infection at multiple points in the viral life cycle, including through inhibition of proper viral entry, normal expression of immediate early genes, and viral DNA replication. Our results suggest that the SV40 T antigen could be a valuable tool to dissect cellular activities that are important for successful infection, thereby potentially informing novel antiviral development strategies. This is an important consideration, given that HCMV is a leading cause of birth defects and causes severe infection in immunocompromised individuals.
Molluscum Contagiosum Virus Transcriptome in Abortively Infected Cultured Cells and a Human Skin Lesion
Authors: Mendez-Rios Jorge D. , Yang Zhilong , Erlandson Karl J. , Cohen Jeffrey I. , Martens Craig A. , Bruno Daniel P. , Porcella Stephen F. , Moss Bernard 
Published: February 2016

ABSTRACT

Molluscum contagiosum virus (MOCV), the only circulating human-specific poxvirus, has a worldwide distribution and causes benign skin lesions that may persist for months in young children and severe infections in immunosuppressed adults. Studies of MOCV are restricted by the lack of an efficient animal model or a cell culture replication system. We used next-generation sequencing to analyze and compare polyadenylated RNAs from abortive MOCV infections of several cell lines and a human skin lesion. Viral RNAs were detected for 14 days after MOCV infection of cultured cells; however, there was little change in the RNA species during this time and a similar pattern occurred in the presence of an inhibitor of protein synthesis, indicating a block preventing postreplicative gene expression. Moreover, a considerable number of MOCV RNAs mapped to homologs of orthopoxvirus early genes, but few did so to homologs of intermediate or late genes. The RNAs made during
in vitro
infections represent a subset of RNAs detected in human skin lesions which mapped to homologs of numerous postreplicative as well as early orthopoxvirus genes. Transfection experiments using fluorescent protein and luciferase reporters demonstrated that vaccinia virus recognized MOCV intermediate and late promoters, indicating similar gene regulation. The specific recognition of the intermediate promoter in MOCV-infected cells provided evidence for the synthesis of intermediate transcription factors, which are products of early genes, but not for late transcription factors. Transcriptome sequencing (RNA-seq) and reporter gene assays may be useful for testing engineered cell lines and conditions that ultimately could provide an
in vitro
replication system.

IMPORTANCE
The inability to propagate molluscum contagiosum virus, which causes benign skin lesions in young children and more extensive infections in immunosuppressed adults, has constrained our understanding of the biology of this human-specific virus. In the present study, we characterized the RNAs synthesized in abortively infected cultured cells and a human skin lesion by next-generation sequencing. These studies provided an initial transcription map of the MOCV genome, suggested temporal regulation of gene expression, and indicated that the
in vitro
replication block occurs prior to intermediate and late gene expression. RNA-seq and reporter assays, as described here, may help to further evaluate MOCV gene expression and define conditions that could enable MOCV replication
in vitro
.
Differential Expression of the Middle East Respiratory Syndrome Coronavirus Receptor in the Upper Respiratory Tracts of Humans and Dromedary Camels
Authors: Widagdo W. , Raj V. Stalin , Schipper Debby , Kolijn Kimberley , van Leenders Geert J. L. H. , Bosch Berend J. , Bensaid Albert , Segalés Joaquim , Baumgärtner Wolfgang , Osterhaus Albert D. M. E. , Koopmans Marion P. , van den Brand Judith M. A. , Haagmans Bart L. 
Published: February 2016

ABSTRACT
Middle East respiratory syndrome coronavirus (MERS-CoV) is not efficiently transmitted between humans, but it is highly prevalent in dromedary camels. Here we report that the MERS-CoV receptor—dipeptidyl peptidase 4 (DPP4)—is expressed in the upper respiratory tract epithelium of camels but not in that of humans. Lack of DPP4 expression may be the primary cause of limited MERS-CoV replication in the human upper respiratory tract and hence restrict transmission.
The C-Terminal Tail of TRIM56 Dictates Antiviral Restriction of Influenza A and B Viruses by Impeding Viral RNA Synthesis
Authors: Liu Baoming , Li Nan L. , Shen Yang , Bao Xiaoyong , Fabrizio Thomas , Elbahesh Husni , Webby Richard J. , Li Kui 
Published: February 2016

ABSTRACT

Accumulating data suggest that tripartite-motif-containing (TRIM) proteins participate in host responses to viral infections, either by acting as direct antiviral restriction factors or through regulating innate immune signaling of the host. Of >70 TRIMs, TRIM56 is a restriction factor of several positive-strand RNA viruses, including three members of the family
Flaviviridae
(yellow fever virus, dengue virus, and bovine viral diarrhea virus) and a human coronavirus (OC43), and this ability invariably depends upon the E3 ligase activity of TRIM56. However, the impact of TRIM56 on negative-strand RNA viruses remains unclear. Here, we show that TRIM56 puts a check on replication of influenza A and B viruses in cell culture but does not inhibit Sendai virus or human metapneumovirus, two paramyxoviruses. Interestingly, the anti-influenza virus activity was independent of the E3 ligase activity, B-box, or coiled-coil domain. Rather, deletion of a 63-residue-long C-terminal-tail portion of TRIM56 abrogated the antiviral function. Moreover, expression of this short C-terminal segment curtailed the replication of influenza viruses as effectively as that of full-length TRIM56. Mechanistically, TRIM56 was found to specifically impede intracellular influenza virus RNA synthesis. Together, these data reveal a novel antiviral activity of TRIM56 against influenza A and B viruses and provide insights into the mechanism by which TRIM56 restricts these medically important orthomyxoviruses.

IMPORTANCE
Options to treat influenza are limited, and drug-resistant influenza virus strains can emerge through minor genetic changes. Understanding novel virus-host interactions that alter influenza virus fitness may reveal new targets/approaches for therapeutic interventions. We show here that TRIM56, a tripartite-motif protein, is an intrinsic host restriction factor of influenza A and B viruses. Unlike its antiviral actions against positive-strand RNA viruses, the anti-influenza virus activity of TRIM56 was independent of the E3 ligase activity. Rather, expression of a short segment within the very C-terminal tail of TRIM56 inhibited the replication of influenza viruses as effectively as that of full-length TRIM56 by specifically targeting viral RNA synthesis. These data reveal the remarkable multifaceted activity of TRIM56, which has developed multiple domains to inhibit multiple viral families. They also raise the possibility of developing a broad-spectrum, TRIM56-based antiviral approach for addition to influenza prophylaxis and/or control strategies.
Single-Particle Tracking Shows that a Point Mutation in the Carnivore Parvovirus Capsid Switches Binding between Host-Specific Transferrin Receptors
Authors: Lee Donald W. , Allison Andrew B. , Bacon Kaitlyn B. , Parrish Colin R. , Daniel Susan 
Published: February 2016

ABSTRACT
Determining how viruses infect new hosts via receptor-binding mechanisms is important for understanding virus emergence. We studied the binding kinetics of canine parvovirus (CPV) variants isolated from raccoons—a newly recognized CPV host—to different carnivore transferrin receptors (TfRs) using single-particle tracking. Our data suggest that CPV may utilize adhesion-strengthening mechanisms during TfR binding and that a single mutation in the viral capsid at VP2 position 300 can profoundly alter receptor binding and infectivity.
Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides
Authors: Weichert Stefan , Koromyslova Anna , Singh Bishal K. , Hansman Satoko , Jennewein Stefan , Schroten Horst , Hansman Grant S. 
Published: February 2016

ABSTRACT
Histo-blood group antigens (HBGAs) are important binding factors for norovirus infections. We show that two human milk oligosaccharides, 2′-fucosyllactose (2′FL) and 3-fucosyllactose (3FL), could block norovirus from binding to surrogate HBGA samples. We found that 2′FL and 3FL bound at the equivalent HBGA pockets on the norovirus capsid using X-ray crystallography. Our data revealed that 2′FL and 3FL structurally mimic HBGAs. These results suggest that 2′FL and 3FL might act as naturally occurring decoys in humans.
Novel Feline Leukemia Virus Interference Group Based on the
env
Gene
Authors: Miyake Ariko , Watanabe Shinya , Hiratsuka Takahiro , Ito Jumpei , Ngo Minh Ha , Makundi Isaac , Kawasaki Junna , Endo Yasuyuki , Tsujimoto Hajime , Nishigaki Kazuo 
Published: February 2016

ABSTRACT

Feline leukemia virus (FeLV) subgroups have emerged in infected cats via the mutation or recombination of the
env
gene of subgroup A FeLV (FeLV-A), the primary virus. We report the isolation and characterization of a novel
env
gene, TG35-2, and report that the TG35-2 pseudotype can be categorized as a novel FeLV subgroup. The TG35-2 envelope protein displays strong sequence identity to FeLV-A Env, suggesting that selection pressure in cats causes novel FeLV subgroups to emerge.
Discovery of a Novel Bat Gammaherpesvirus
Authors: Host Kurtis M. , Damania Blossom 
Published: February 2016

ABSTRACT

Zoonosis is the leading cause of emerging infectious diseases. In a recent article, R. S. Shabman et al. (mSphere 1[1]:e00070-15, 2016,
http://dx.doi.org/10.1128/mSphere.00070-15
) report the identification of a novel gammaherpesvirus in a cell line derived from the microbat
Myotis velifer incautus.
This is the first report on a replicating, infectious gammaherpesvirus from bats. The new virus is named bat gammaherpesvirus 8 (BGHV8), also known as
Myotis
gammaherpesvirus 8, and is able to infect multiple cell lines, including those of human origin. Using next-generation sequencing technology, the authors constructed a full-length annotated genomic map of BGHV8. Phylogenetic analysis of several genes from BGHV8 revealed similarity to several mammalian gammaherpesviruses, including Kaposi’s sarcoma-associated herpesvirus (KSHV).
Perspectives on the provision of GDM screening in general practice versus the hospital setting: a qualitative study of providers and patients
Authors: Tierney Marie , O'Dea Angela , Danyliv Andrii , Carmody Louise , McGuire Brian E , Glynn Liam G , Dunne Fidelma 
Published: February 2016

ObjectiveA novel gestational diabetes mellitus (GDM) screening programme which involved offering screening at the patient's general practitioner (GP) compared with the traditional hospital setting was trialled. This study investigates perspectives of involved stakeholders on the provision of GDM screening at both settings.DesignThematic analysis of the perspectives of stakeholders involved in the receiving and provision of GDM screening in both the GP and hospital settings drawn from focus groups and interviews.Participants3 groups of participants are included in this research—patient participants, GP screening providers and hospital screening providers. All were recruited from a larger sample who participated in a randomised controlled screening trial. Purposeful sampling was utilised to select participants with a wide variety of perspectives on the provision of GDM screening.SettingParticipants were recruited from a geographical area covered by 3 hospitals in Ireland.Results4 themes emerged from thematic analysis—namely (1) travel distance, (2) best care provision, (3) sense of ease created and (4) optimal screening.ConclusionsThe influence of travel distance from the screening site is the most important factor influencing willingness to attend for GDM screening among women who live a considerable distance from the hospital setting. For patients who live equidistance from both settings, other factors are important; namely the waiting facilities including parking, perceived expertise of screening provider personnel, access to emergency treatment if necessary, accuracy of tests and access to timely results and treatment. Optimal screening for GDM should be specialist led, incorporate expert advice of GDM screening, treatment and management, should be provided locally, offer adequate parking and comfort levels, provide accurate tests, and timely access to results and treatment. Such a service should result in improved rates of GDM screening uptake.Trial registration numberISRCTN41202110.
Sleep duration and mortality in the elderly: a systematic review with meta-analysis
Authors: Silva Andressa Alves da , Mello Renato Gorga Bandeira de , Schaan Camila Wohlgemuth , Fuchs Flávio D , Redline Susan , Fuchs Sandra C 
Published: February 2016

ObjectiveThe purpose of our study was to evaluate the association between short and long sleep duration and all-cause and cardiovascular mortality among elderly individuals.DesignSystematic review and meta-analysis of population-based cohort studies.SettingArticles were retrieved from international and national electronic databases.Study selectionStudies were identified in PubMed, EMBASE, LILACS (Latin American and Caribbean Health Sciences Literature), IBECS (Bibliographic Index on Health Sciences from Spain) and CAPES (PhD thesis repository) between 1980 and 2015. Studies which met all criteria were eligible: participants aged 60 years or over, assessment of sleep duration as 24 h, nighttime or daytime sleep, evaluation of all-cause or cause-specific mortality, population-based cohort studies conducted on representative samples. There was no language restriction and studies published as abstracts were excluded.Data extractionData were analysed using the Comprehensive Meta-Analysis software (V.3.3.070), and summary estimates (relative risk (RR), 95% CI) were calculated using a random effects model. Heterogeneity and consistency were evaluated through Cochran's Q and the I2statistics, respectively, and sensitivity analyses were conducted.Primary and secondary outcome measuresAll-cause and cardiovascular mortality.ResultsOverall, 27 cohort studies were selected, comprising >70 000 elderly individuals, and followed up from 3.4 to 35 years. In the pooled analysis, long and short sleep duration were associated with increased all-cause mortality (RR 1.33; 95% CI 1.24 to 1.43 and RR 1.07; 95% CI 1.03 to 1.11, respectively), compared with the reference category. For cardiovascular mortality, the pooled relative risks were 1.43 (95% CI 1.15 to 1.78) for long sleep, and 1.18 (95% CI 0.76 to 1.84) for short sleep. Daytime napping ≥30 min was associated with risk of all-cause mortality (RR 1.27; 95% CI 1.08 to 1.49), compared with no daytime sleep, but longer sleep duration (≥2.0 h) was not (RR 1.34; 95% CI 1.95 to 1.90).ConclusionsAmong elderly individuals, long and short sleep duration are associated with increased risk for all-cause mortality. Long sleep duration is associated with cardiovascular mortality.