bluuebunny/crossref_metadata_2025_split huggingface dataset:
African Great Apes Are Naturally Infected with Roseoloviruses Closely Related to Human Herpesvirus 7
Authors: Lavergne Anne , Donato Damien , Gessain Antoine , Niphuis Henk , Nerrienet Eric , Verschoor Ernst J. , Lacoste Vincent 
Published: September 2014

ABSTRACT

Primates are naturally infected with herpesviruses. During the last 15 years, the search for homologues of human herpesviruses in nonhuman primates allowed the identification of numerous viruses belonging to the different herpesvirus subfamilies and genera. No simian homologue of human herpesvirus 7 (HHV7) has been reported to date. To investigate the putative existence of HHV7-like viruses in African great apes, we applied the consensus-degenerate hybrid oligonucleotide primers (CODEHOP) program-mediated PCR strategy to blood DNA samples from the four common chimpanzee subspecies (
Pan troglodytes verus
,
P. t. ellioti
,
P. t. troglodytes
, and
P. t. schweinfurthii
), pygmy chimpanzees (
Pan paniscus
), as well as lowland gorillas (
Gorilla gorilla gorilla
). This study led to the discovery of a novel roseolovirus close to HHV7 in each of these nonhuman primate species and subspecies. Generation of the partial glycoprotein B (1,111-bp) and full-length DNA polymerase (3,036/3,042-bp) gene sequences allowed the deciphering of their evolutionary relationships. Phylogenetic analyses revealed that HHV7 and its African great ape homologues formed well-supported monophyletic lineages whose topological resemblance to the host phylogeny is suggestive of virus-host codivergence. Notably, the evolutionary branching points that separate HHV7 from African great ape herpesvirus 7 are remarkably congruent with the dates of divergence of their hosts. Our study shows that African great apes are hosts of human herpesvirus homologues, including HHV7 homologues, and that the latter, like other DNA viruses that establish persistent infections, have cospeciated with their hosts.

IMPORTANCE
Human herpesviruses are known to possess simian homologues. However, surprisingly, none has been identified to date for human herpesvirus 7 (HHV7). This study is the first to describe simian homologues of HHV7. The extensive search performed on almost all African great ape species and subspecies, i.e., common chimpanzees of the four subspecies, bonobos, and lowland gorillas, has allowed characterization of a specific virus in each. Genetic characterization of the partial glycoprotein B and full-length DNA polymerase gene sequences, followed by their phylogenetic analysis and estimation of divergence times, has shed light on the evolutionary relationships of these viruses. In this respect, we conclusively demonstrate the cospeciation between these new viruses and their hosts and report cases of cross-species transmission between two common chimpanzee subspecies in both directions.
Recent Population Expansions of Hepatitis B Virus in the United States
Authors: Ramachandran Sumathi , Purdy Michael A. , Xia Guo-liang , Campo David S. , Dimitrova Zoya E. , Teshale Eyasu H. , Teo Chong Gee , Khudyakov Yury E. 
Published: September 2014

ABSTRACT

The recent epidemic history of hepatitis B virus (HBV) infections in the United States is complex, as indicated by current disparity in HBV genotype distribution between acute and chronic hepatitis B cases and the rapid decline in hepatitis B incidence since the 1990s. We report temporal changes in the genetic composition of the HBV population using whole-genome sequences (
n
= 179) from acute hepatitis B cases (
n
= 1,206) identified through the Sentinel County Surveillance for Acute Hepatitis (1998 to 2006). HBV belonged mainly to subtypes A2 (75%) and D3 (18%), with times of their most recent common ancestors being 1979 and 1987, respectively. A2 underwent rapid population expansions in ca. 1995 and ca. 2002, coinciding with transient rises in acute hepatitis B notification rates among adults; D3 underwent expansion in ca. 1998. A2 strains from cases identified after 2002, compared to those before 2002, tended to cluster phylogenetically, indicating selective expansion of specific strains, and were significantly reduced in genetic diversity (
P
= 0.001) and frequency of drug resistance mutations (
P
= 0.001). The expansion of genetically close HBV A2 strains was associated with risk of infection among male homosexuals (
P
= 0.03). Incident HBV strains circulating in the United States were recent in origin and restricted in genetic diversity. Disparate transmission dynamics among phylogenetic lineages affected the genetic composition of HBV populations and their capacity to maintain drug resistance mutations. The tendency of selectively expanding HBV strains to be transmitted among male homosexuals highlights the need to improve hepatitis B vaccination coverage among at-risk adults.

IMPORTANCE
Hepatitis B virus (HBV) remains an important cause of acute and chronic liver disease globally and in the United States. Genetic analysis of HBV whole genomes from cases of acute hepatitis B identified from 1998 to 2006 in the United States showed dominance of genotype A2 (75%), followed by D3 (18%). Strains of both subtypes were recent in origin and underwent rapid population expansions from 1995 to 2000, indicating increase in transmission rate for certain HBV strains during a period of decline in the reported incidence of acute hepatitis B in the United States. HBV A2 strains from a particular cluster that experienced the most recent population expansion were more commonly detected among men who have sex with men. Vaccination needs to be stepped up to protect persons who remain at risk of HBV infection.
Activation of NF-κB by the Kaposi's Sarcoma-Associated Herpesvirus K15 Protein Involves Recruitment of the NF-κB-Inducing Kinase, IκB Kinases, and Phosphorylation of p65
Authors: Hävemeier Anika , Gramolelli Silvia , Pietrek Marcel , Jochmann Ramona , Stürzl Michael , Schulz Thomas F. 
Published: September 2014

ABSTRACT
Kaposi's sarcoma herpesvirus (KSHV) (or human herpesvirus 8) is the cause of Kaposi's sarcoma, primary effusion lymphoma (PEL), and the plasma cell variant of multicentric Castleman's disease (MCD). The transmembrane K15 protein, encoded by KSHV, has been shown to activate NF-κB and the mitogen-activated protein kinases (MAPKs) c-jun-N-terminal kinase (JNK) and extracellular signal-regulated kinase (Erk) as well as phospholipase C gamma (PLCγ) and to contribute to KSHV-induced angiogenesis. Here we investigate how the K15 protein activates the NF-κB pathway. We show that activation of NF-κB involves the recruitment of NF-κB-inducing kinase (NIK) and IKK α/β to result in the phosphorylation of p65/RelA on Ser536. A K15 mutant devoid in NIK/IKK recruitment fails to activate NF-κB but remains proficient in the stimulation of both NFAT- and AP1-dependent promoters, showing that the structural integrity of the mutant K15 protein has not been altered dramatically. Direct recruitment of NIK represents a novel way for a viral protein to activate and manipulate the NF-κB pathway.

IMPORTANCE
KSHV K15 is a viral protein involved in the activation of proinflammatory and angiogenic pathways. Previous studies reported that K15 can activate the NF-κB pathway. Here we show the molecular mechanism underlying the activation of this signaling pathway by K15, which involves direct recruitment of the NF-κB-inducing kinase NIK to K15 as well as NIK-mediated NF-κB p65 phosphorylation on Ser536. K15 is the first viral protein shown to activate NF-κB through direct recruitment of NIK. These results indicate a new mechanism whereby a viral protein can manipulate the NF-κB pathway.
Increased Replicative Fitness of a Dengue Virus 2 Clade in Native Mosquitoes: Potential Contribution to a Clade Replacement Event in Nicaragua
Authors: Quiner Claire A. , Parameswaran Poornima , Ciota Alexander T. , Ehrbar Dylan J. , Dodson Brittany L. , Schlesinger Sondra , Kramer Laura D. , Harris Eva 
Published: September 2014

ABSTRACT

The four dengue virus (DENV) serotypes (DENV serotype 1 [DENV-1] to DENV-4) are transmitted by
Aedes aegypti
and
A. albopictus
mosquitoes, causing up to 390 million DENV infections worldwide each year. We previously reported a clade replacement of the DENV-2 Asian-American genotype NI-1 clade by the NI-2B clade in Managua, Nicaragua. Here, we describe our studies of the replicative ability of NI-1 and NI-2B viruses in an
A. aegypti
cell line (Aag2) and
A. aegypti
mosquitoes reared from eggs collected in Managua. In coinfection experiments, several different pairs of NI-1 and NI-2B clinical isolates were used to infect Aag2 cells or blood-fed
A. aegypti
mosquitoes. Results consistently showed a significant replicative advantage of NI-2B over NI-1 viruses early after infection
in vitro
, and in mosquitoes, NI-2B viruses attained a higher replicative index than NI-1 isolates 3 to 7 days postinfection (dpi). At 7 dpi, NI-2B viruses displayed a significantly higher replicative index in legs and salivary glands; however, this advantage was lost by 14 and 21 dpi. We also found that the percentage of mosquitoes in which NI-2B viruses were dominant was significantly higher than that in which NI-1 viruses were dominant on day 7 but not at later time points. Taken together, these data demonstrate that clade NI-2B holds a replicative advantage over clade NI-1 early in infection that wanes at later time points. This early fitness advantage of NI-2B viruses over NI-1 viruses in the native vector,
A. aegypti
, suggests a shorter extrinsic incubation period for NI-2B viruses, which could have contributed to the clade replacement event in Managua.

IMPORTANCE
Dengue virus (DENV), one of the most medically important arthropod-borne viruses, is transmitted to humans by
Aedes aegypti
and
A. albopictus
mosquitoes in tropical and subtropical regions worldwide. Dengue epidemics continue to increase in frequency, geographic range, and severity and are a major public health concern. This is due to globalization, unplanned urbanization, and climate change, as well as host genetics and immune responses and viral genetic changes. DENV consists of four serotypes, in turn composed of genotypes and genetically distinct clades. What drives the frequent replacement of a previously circulating DENV clade by another is unclear. Here, we investigate the replicative fitness of two clades of DENV serotype 2 in
Aedes aegypti
cells and mosquitoes collected from the region where the viruses circulated and conclude that increased replicative fitness could have contributed to a DENV clade replacement event in Nicaragua. These findings provide insight into vector-driven evolution of DENV epidemics.
Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity
Authors: Dziewit Lukasz , Oscik Karolina , Bartosik Dariusz , Radlinska Monika 
Published: September 2014

ABSTRACT

ΦLM21 is a temperate phage isolated from
Sinorhizobium
sp. strain LM21 (
Alphaproteobacteria
). Genomic analysis and electron microscopy suggested that ΦLM21 is a member of the family
Siphoviridae
. The phage has an isometric head and a long noncontractile tail. The genome of ΦLM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, DNA packaging, transcription, replication, and lysis. Virion proteins were characterized using mass spectrometry, leading to the identification of the major capsid and tail components, tape measure, and a putative portal protein. We have confirmed the activity of two gene products, a lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly, the genome of
Sinorhizobium
phage ΦLM21 shows very limited similarity to other known phage genome sequences and is thus considered unique.

IMPORTANCE
Prophages are known to play an important role in the genomic diversification of bacteria via horizontal gene transfer. The influence of prophages on pathogenic bacteria is very well documented. However, our knowledge of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial hosts is still limited. In particular, information on prophages of the agronomically important
Sinorhizobium
species is scarce. In this study, we describe the isolation and molecular characterization of a novel temperate bacteriophage, ΦLM21, of
Sinorhizobium
sp. LM21. Since we have not found any similar sequences, we propose that this bacteriophage is a novel species. We conducted a functional analysis of selected proteins. We have demonstrated that the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host regulatory mechanisms by viruses is quite common in bacteriophages.
Characterization of Simian Immunodeficiency Virus (SIV) That Induces SIV Encephalitis in Rhesus Macaques with High Frequency: Role of TRIM5 and Major Histocompatibility Complex Genotypes and Early Entry to the Brain
Authors: Matsuda Kenta , Dang Que , Brown Charles R. , Keele Brandon F. , Wu Fan , Ourmanov Ilnour , Goeken Robert , Whitted Sonya , Riddick Nadeene E. , Buckler-White Alicia , Hirsch Vanessa M. 
Published: September 2014

ABSTRACTAlthough nonhuman primate models of neuro-AIDS have made tremendous contributions to our understanding of disease progression in the central nervous system (CNS) of human immunodeficiency virus type 1 (HIV-1)-infected individuals, each model holds advantages and limitations. In this study,in vivopassage of SIVsmE543 was conducted to obtain a viral isolate that can induce neuropathology in rhesus macaques. After a series of fourin vivopassages in rhesus macaques, we have successfully isolated SIVsm804E. SIVsm804E shows efficient replication in peripheral blood mononuclear cells (PBMCs) and monocyte-derived macrophages (MDMs)in vitroand induces neuro-AIDS in high frequenciesin vivo. Analysis of the acute phase of infection revealed that SIVsm804E establishes infection in the CNS during the early phase of the infection, which was not observed in the animals infected with the parental SIVsmE543-3. Comprehensive analysis of disease progression in the animals used in the study suggested that host major histocompatibility complex class I (MHC-I) and TRIM5α genotypes influence the disease progression in the CNS. Taken together, our findings show that we have successfully isolated a new strain of simian immunodeficiency virus (SIV) that is capable of establishing infection in the CNS at early stage of infection and causes neuropathology in infected rhesus macaques at a high frequency (83%) using a single inoculum, when animals with restrictive MHC-I or TRIM5α genotypes are excluded. SIVsm804E has the potential to augment some of the limitations of existing nonhuman primate neuro-AIDS models.IMPORTANCEHuman immunodeficiency virus (HIV) is associated with a high frequency of neurologic complications due to infection of the central nervous system (CNS). Although the use of antiviral treatment has reduced the incidence of severe complications, milder disease of the CNS continues to be a significant problem. Animal models to study development of neurologic disease are needed. This article describes the development of a novel virus isolate that induces neurologic disease in a high proportion of rhesus macaques infected without the need for prior immunomodulation as is required for some other models.
Human Coronavirus NL63 Utilizes Heparan Sulfate Proteoglycans for Attachment to Target Cells
Authors: Milewska Aleksandra , Zarebski Miroslaw , Nowak Paulina , Stozek Karol , Potempa Jan , Pyrc Krzysztof 
Published: September 2014

ABSTRACT
Human coronavirus NL63 (HCoV-NL63) is an alphacoronavirus that was first identified in 2004 in the nasopharyngeal aspirate from a 7-month-old patient with a respiratory tract infection. Previous studies showed that HCoV-NL63 and the genetically distant severe acute respiratory syndrome (SARS)-CoV employ the same receptor for host cell entry, angiotensin-converting enzyme 2 (ACE2), but it is largely unclear whether ACE2 interactions are sufficient to allow HCoV-NL63 binding to cells. The present study showed that directed expression of angiotensin-converting enzyme 2 (ACE2) on cells previously resistant to HCoV-NL63 renders them susceptible, showing that ACE2 protein acts as a functional receptor and that its expression is required for infection. However, comparative analysis showed that directed expression or selective scission of the ACE2 protein had no measurable effect on virus adhesion. In contrast, binding of HCoV-NL63 to heparan sulfates was required for viral attachment and infection of target cells, showing that these molecules serve as attachment receptors for HCoV-NL63.

IMPORTANCE
ACE2 protein was proposed as a receptor for HCoV-NL63 already in 2005, but an in-depth analysis of early events during virus infection had not been performed thus far. Here, we show that the ACE2 protein is required for viral entry but that it is not the primary binding site on the cell surface. Conducted research showed that heparan sulfate proteoglycans function as adhesion molecules, increasing the virus density on cell surface and possibly facilitating the interaction between HCoV-NL63 and its receptor. Obtained results show that the initial events during HCoV-NL63 infection are more complex than anticipated and that a newly described interaction may be essential for understanding the infection process and, possibly, also assist in drug design.
Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM
Authors: Boyd Andrew D , Yang Young Min , Li Jianrong , Kenost Colleen , Burton Mike D , Becker Bryan , Lussier Yves A 
Published: September 2014

Abstract
Reporting of hospital adverse events relies on Patient Safety Indicators (PSIs) using International Classification of Diseases, Ninth Edition, Clinical Modification (ICD-9-CM) codes. The US transition to ICD-10-CM in 2015 could result in erroneous comparisons of PSIs. Using the General Equivalent Mappings (GEMs), we compared the accuracy of ICD-9-CM coded PSIs against recommended ICD-10-CM codes from the Centers for Medicaid/Medicare Services (CMS). We further predict their impact in a cohort of 38 644 patients (1 446 581 visits and 399 hospitals). We compared the predicted results to the published PSI related ICD-10-CM diagnosis codes. We provide the first report of substantial hospital safety reporting errors with five direct comparisons from the 23 types of PSIs (transfusion and anesthesia related PSIs). One PSI was excluded from the comparison between code sets due to reorganization, while 15 additional PSIs were inaccurate to a lesser degree due to the complexity of the coding translation. The ICD-10-CM translations proposed by CMS pose impending risks for (1) comparing safety incidents, (2) inflating the number of PSIs, and (3) increasing the variability of calculations attributable to the abundance of coding system translations. Ethical organizations addressing ‘data-, process-, and system-focused’ improvements could be penalized using the new ICD-10-CM Agency for Healthcare Research and Quality PSIs because of apparent increases in PSIs bearing the same PSI identifier and label, yet calculated differently. Here we investigate which PSIs would reliably transition between ICD-9-CM and ICD-10-CM, and those at risk of under-reporting and over-reporting adverse events while the frequency of these adverse events remain unchanged.
Can paramedics use FRAX (the WHO Fracture Risk Assessment Tool) to help GPs improve future fracture risk in patients who fall? Protocol for a randomised controlled feasibility study
Authors: Clarke Shane , Bradley Rachel , Simmonds Bethany , Salisbury Chris , Benger Jonathan , Marques Elsa , Greenwood Rosemary , Shepstone Lee , Robinson Maria , Appleby-Fleming John , Gooberman-Hill Rachael 
Published: September 2014

IntroductionCurrently identification, and therefore, management of patients at risk of osteoporotic fracture in the UK is suboptimal. As the majority of patients who fracture have fallen, it follows that people who fall can usefully be targeted in any programme that aims to reduce osteoporotic fracture. Targeting vulnerable patients who are likely to benefit from intervention may help shift the management of fracture prevention into primary care, away from emergency departments. Paramedics who attend to patients who have fallen may be well placed to assess future fracture risk, using the Fracture Risk Assessment Tool (FRAX) and communicate that information directly to general practitioners (GPs).Methods and analysisThis feasibility study takes the form of a pragmatic, randomised controlled trial aimed at exploring and refining issues of study design, recruitment, retention, sample size and acceptability preceding a large-scale study with fracture as the end point. Patients (aged >50) who fall, call an ambulance, are attended by a study paramedic and give verbal consent will be asked FRAX and fall questions. Patients who subsequently formally consent to participation will be randomised to control (usual care) or intervention groups. Intervention will constitute transmission of calculated future fracture risk to the patients’ GP with suitable, evidence-based recommendations for investigation or treatment. 3 months after the index fall, data (proportion of patients in each group undergoing investigation or starting new treatment, quality of life and health economic) will be collected and analysed using descriptive statistics. A nested qualitative study will explore issues of acceptability and study design with patients, paramedics and GPs.Ethics and disseminationThis protocol was approved by NRES Committee South Central Oxford C in October 2012. Research Ethics Committee ref.12/SC/0604. The study findings will be disseminated through peer-reviewed journals, conference presentations and local public events. A publication plan and authorship criteria have been preagreed.Trial registration numberISRCTN: 36245726.