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Viral population genetics

Luiza Guimarães Fabreti, Diogo Castro, Bruno Gorzoni, Luiz Mario Ramos Janini, Fernando Antoneli
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversity is generated and maintained is fundamental when approaching viral persistence and pathobiology in infected hosts. In this paper, we access quasispecies theory through a mathematical model based on the theory of multitype branching processes, to better understand the roles of mechanisms resulting in viral diversity, persistence and extinction...
December 14, 2018: Bulletin of Mathematical Biology
Rebecca M Johnson, Jason L Rasgon
Mosquito specific viruses such as densonucleosis viruses ('densoviruses') have long been suggested as alternative mosquito control agents in the face of increasing insecticide resistance. Densoviruses are very species-specific and have been found to infect many important mosquito species. While some strains are highly pathogenic, other strains are more benign. Densoviruses have been proposed as a way to reduce mosquito populations through pathogenic interactions, but genetic strategies such as viral paratrangenesis offer new approaches...
August 2018: Current Opinion in Insect Science
Zicong Xie, Daxin Pang, Hongming Yuan, Huping Jiao, Chao Lu, Kankan Wang, Qiangbing Yang, Mengjing Li, Xue Chen, Tingting Yu, Xinrong Chen, Zhen Dai, Yani Peng, Xiaochun Tang, Zhanjun Li, Tiedong Wang, Huancheng Guo, Li Li, Changchun Tu, Liangxue Lai, Hongsheng Ouyang
Classical swine fever (CSF) caused by classical swine fever virus (CSFV) is one of the most detrimental diseases, and leads to significant economic losses in the swine industry. Despite efforts by many government authorities to stamp out the disease from national pig populations, the disease remains widespread. Here, antiviral small hairpin RNAs (shRNAs) were selected and then inserted at the porcine Rosa26 (pRosa26) locus via a CRISPR/Cas9-mediated knock-in strategy. Finally, anti-CSFV transgenic (TG) pigs were produced by somatic nuclear transfer (SCNT)...
December 2018: PLoS Pathogens
Joel O Wertheim, Alexandra M Oster, Ben Murrell, Neeraja Saduvala, Walid Heneine, William M Switzer, Jeffrey A Johnson
Understanding genetic variation in human immunodeficiency virus (HIV) is clinically and immunologically important for patient treatment and vaccine development. We investigated the longitudinal intra-host genetic variation of HIV in over 3,000 individuals in the US National HIV Surveillance System with at least four reported HIV-1 polymerase ( pol ) sequences. In this population, we identified 149 putative instances of superinfection (i.e. an individual sequentially infected with genetically divergent, polyphyletic viruses)...
July 2018: Virus Evolution
Swati Kumari, P K Ray, Rahul Singh, P A Desingu, Rajat Varshney, G Saikumar
The aim of the present study was to pathological and molecular investigation of porcine sapelovirus (PSV) in naturally infected Indian pigs of various age groups. Eight samples (16%) out of 49 necropsied animals were positive for PSV on the basis of pathological and molecular investigation. Major lesions of PSV positive cases were thickening and clouding of meninges, congestion in brain, severe to moderate congestion in lungs along with froathy exudates in trachea, thickening of intestinal mucosa, especially mucosal folds of ileum...
December 5, 2018: Microbial Pathogenesis
Jemma L Geoghegan, Edward C Holmes
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically...
December 2018: Genetics
Srinivas Thaduri, Barbara Locke, Fredrik Granberg, Joachim R de Miranda
The parasitic mite, Varroa destructor, in combination with the viruses it vectors, is the main cause for global colony losses of the European honeybee, Apis mellifera. However, an isolated honeybee population established in 1999 on the Island of Gotland, Sweden has naturally acquired resistance to the mite, and has survived without mite control treatment for more than 18 years. A recent study has shown that this mite resistant (MR) population also appears to be resistant to Black queen cell virus (BQCV) and Sacbrood virus (SBV) and tolerant to Deformed wing virus (DWV), relative to nearby mite susceptible (MS) honeybee populations...
2018: PloS One
Hanspeter Stalder, Claudia Bachofen, Matthias Schweizer, Reto Zanoni, Dominik Sauerländer, Ernst Peterhans
The first records of smallpox and rabies date back thousands of years and foot-and-mouth disease in cattle was described in the 16th century. These diseases stood out by their distinct signs, dramatic way of transmission from rabid dogs to humans, and sudden appearance in cattle herds. By contrast, infectious diseases that show variable signs and affect few individuals were identified only much later. Bovine viral diarrhea (BVD), endemic in cattle worldwide, was first described in 1946, together with the eponymous RNA virus as its cause...
2018: PloS One
Daniel Rigling, Nora Borst, Carolina Cornejo, Archil Supatashvili, Simone Prospero
Cryphonectria hypovirus 1 (CHV-1) infects the chestnut blight fungus Cryphonectria parasitica and acts as a biological control agent against this harmful tree disease. In this study, we screened the recently characterized C. parasitica population in Eurasian Georgia for the presence of CHV-1. We found 62 CHV-1 infected C. parasitica isolates (9.3%) among a total of 664 isolates sampled in 14 locations across Georgia. The prevalence of CHV-1 at the different locations ranged from 0% in the eastern part of the country to 29% in the western part...
December 3, 2018: Viruses
Michael D Vahey, Daniel A Fletcher
Influenza viruses inhabit a wide range of host environments using a limited repertoire of protein components. Unlike viruses with stereotyped shapes, influenza produces virions with significant morphological variability even within clonal populations. Whether this tendency to form pleiomorphic virions is coupled to compositional heterogeneity and whether it affects replicative fitness remains unclear. Here, we address these questions by developing a strain of influenza A virus amenable to rapid compositional characterization through quantitative, site-specific labeling of viral proteins...
November 27, 2018: Cell
Wan Zhao, Qianshuo Wang, Zhongtian Xu, Renyi Liu, Feng Cui
Persistent plant viruses circulate between host plants and vector insects, possibly leading to the genetic divergence in viral populations. We analyzed the single nucleotide polymorphisms (SNPs) of Rice stripe virus (RSV) when it incubated in the small brown planthopper and rice. Two SNPs, which lead to nonsynonymous substitutions in the disease-specific protein (SP) of RSV, produced three genotypes, i.e., GG, AA and GA. The GG type mainly existed in the early infection period of RSV in the planthoppers and was gradually substituted by the other two genotypes during viral transmission...
November 27, 2018: Virology
Richard Taubert, Jana Diestelhorst, Norman Junge, Martha M Kirstein, Sven Pischke, Arndt Vogel, Heike Bantel, Ulrich Baumann, Michael P Manns, Heiner Wedemeyer, Elmar Jaeckel
Preceding viral infections have mostly been described in autoimmune hepatitis (AIH) in single cases. We aimed to identify viral infections that potentially trigger AIH, as suggested for hepatitis E virus (HEV) infections. Therefore, antibodies against hepatitis A (HAV), B, C and E viruses; hepatotropic herpesviruses; and parvovirus B19 (PVB19) were analyzed retrospectively in 219 AIH patients at diagnosis, 356 patients with other liver diseases and 89 children from our center. Untreated adult AIH (aAIH) patients showed higher anti-HEV seroprevalences at diagnosis than patients with other liver diseases...
November 28, 2018: Scientific Reports
Gregory R Hart, Andrew L Ferguson
Hepatitis C virus (HCV) afflicts 170 million people and kills 700 000 annually. Vaccination offers the most realistic and cost effective hope of controlling this epidemic, but despite 25 years of research, no vaccine is available. A major obstacle is HCV's extreme genetic variability and rapid mutational escape from immune pressure. Coupling maximum entropy inference with population dynamics simulations, we have employed a computational approach to translate HCV sequence databases into empirical landscapes of viral fitness and simulate the intrahost evolution of the viral quasispecies over these landscapes...
November 28, 2018: Physical Biology
Armita Kakavand Hamidi, Nasrin Yazdani, Kimia Haj Seyedjavadi, Nakisa Zarrabi Ahrabi, Ardavan Tajdini, Keivan Aghazadeh, Mahsa M Amoli
HYPOTHESIS: Although the pathogenesis of sudden sensorineural hearing loss (SSNHL) is not clear, however several causes including genetic factors seems to be implicated. We hypothesized that common genetic variants might be involved in SSNHL. BACKGROUND: SSNHL is known to be an idiopathic disease because the causative factors have not been identified. Several causes including genetic and viral infection besides immune system reaction, neurological disorders, medications, etc...
October 29, 2018: American Journal of Otolaryngology
Yanlin Zhao, Fang Qin, Rui Zhang, Stephen J Giovannoni, Zefeng Zhang, Jing Sun, Sen Du, Christopher Rensing
The Pelagibacterales order (SAR11) in the Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here we report 11 new pelagiphages in the Podoviridae family. Comparative genomics classified these pelagiphages into the HTVC019Pvirus genus, which includes the previously reported pelagiphages HTVC011P and HTVC019P...
November 26, 2018: Environmental Microbiology
Julia A Beatty, Claire R Sharp, W Paul Duprex, John S Munday
PRACTICAL RELEVANCE: New technologies capable of sequencing the genetic material In any given biological sample, combined with computer-based algorithms for sequence assembly and analysis, have revolutionised infectious disease research. The rate at which novel viruses are being discovered now exceeds our understanding of their clinical relevance. Novel viruses may contribute to diseases that are major causes of feline morbidity and mortality, including cancer and chronic kidney disease...
November 26, 2018: Journal of Feline Medicine and Surgery
Fusheng Zhou, Xuejun Zhang
Major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA) in humans, is one of the most genetically diverse regions in the genome of various species. The human MHC contains about 400 genes in a ∼7.6-Mb span located on the short arm of the chromosomal region 6p21.3. According to the NHGRI-EBI Catalog of published genome-wide association studies ( in HLA region, more than 500 associations have been identified for about 200 traits or phenotypes, including primary immune deficiencies, autoimmune diseases, susceptibility to infections, malignancies, and psychiatric conditions (Welter et al...
December 2018: Journal of Investigative Dermatology. Symposium Proceedings
Serafín Gutiérrez, Mark P Zwart
Multicomponent viral systems face specific challenges when enduring population bottlenecks. These systems can lose coding information due to the lack of co-encapsidation of all the genetic information, at least in a proportion of the capsids in a population. Moreover, bottlenecks can also impact one of the main potential advantages of multicomponent systems: the regulation of gene expression through changes in gene copy frequencies at the population level. How these systems cope with population bottlenecks is far from being clear...
November 21, 2018: Current Opinion in Virology
Claudia Minosse, Marina Selleri, Emanuela Giombini, Barbara Bartolini, Maria Rosaria Capobianchi, Stefano Cerilli, Laura Loiacono, Chiara Taibi, Gianpiero D'Offizi, Fiona McPhee, AnnaRosa Garbuglia
Background: The efficacy of direct-acting antivirals (DAAs) depends on the hepatitis C virus (HCV) genotype 4 (GT4) subtype which are used in the treatment of HCV. We aimed to retrospectively investigate the baseline prevalence of HCV NS5A and NS5B polymorphisms and their impact on virological outcome in GT4-infected patients treated with various DAA regimens. Patients and methods: Available plasma samples from HCV GT4-infected patients treated with different DAA regimens were analyzed at baseline and after treatment failure, where applicable...
2018: Infection and Drug Resistance
Di Xiao, Dandan Liu, Zihao Wen, Xiuxia Huang, Chengli Zeng, Zixing Zhou, Yajing Han, Xiaohong Ye, Jing Wu, Yao Wang, Congcong Guo, Meiling Ou, Shiqi Huang, Chuican Huang, Xiangcai Wei, Guang Yang, Chunxia Jing
Persistent high-risk HPV infection is considered as a major cause of cervical cancer. Nevertheless, only some infected individuals actually develop cervical cancer. The RIG-I pathway in innate immunity plays an important role in antivirus response. Here, we hypothesized that altered function of mitochondrial antiviral signaling protein (MAVS) and mitochondrial TNF receptor-associated factor 3(TRAF3), key molecules downstream of the viral sensors RIG-I, may impair their ability of clearing HPV and thereby influence the risk for cervical precancerous lesions...
November 21, 2018: Cancer Prevention Research
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