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Viral evolution

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https://www.readbyqxmd.com/read/29450759/gene-expression-and-population-polymorphism-of-maize-iranian-mosaic-virus-in-zea-mays-and-intracellular-localization-and-interactions-of-viral-n-p-and-m-proteins-in-nicotiana-benthamiana
#1
Abozar Ghorbani, Keramatollah Izadpanah, Ralf G Dietzgen
Maize Iranian mosaic virus (MIMV; Mononegavirales, Rhabdoviridae, Nucleorhabdovirus) infects maize and several other poaceous plants. MIMV encodes six proteins, i.e., nucleocapsid protein (N), polymerase cofactor phosphoprotein (P), putative movement protein (P3), matrix protein (M), glycoprotein (G), and large RNA-dependent RNA polymerase (L). In the present study, MIMV gene expression and genetic polymorphism of an MIMV population in maize were determined. N, P, P3, and M protein genes were more highly expressed than the 5' terminal G and L genes...
February 15, 2018: Virus Genes
https://www.readbyqxmd.com/read/29449843/insights-into-the-structural-basis-of-antibody-affinity-maturation-from-next-generation-sequencing
#2
REVIEW
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29447150/life-cycle-synchronization-is-a-viral-drug-resistance-mechanism
#3
Iulia A Neagu, Jason Olejarz, Mark Freeman, Daniel I S Rosenbloom, Martin A Nowak, Alison L Hill
Viral infections are one of the major causes of death worldwide, with HIV infection alone resulting in over 1.2 million casualties per year. Antiviral drugs are now being administered for a variety of viral infections, including HIV, hepatitis B and C, and influenza. These therapies target a specific phase of the virus's life cycle, yet their ultimate success depends on a variety of factors, such as adherence to a prescribed regimen and the emergence of viral drug resistance. The epidemiology and evolution of drug resistance have been extensively characterized, and it is generally assumed that drug resistance arises from mutations that alter the virus's susceptibility to the direct action of the drug...
February 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29446492/bayesian-reconstruction-of-the-evolutionary-history-and-cross-species-transition-of-variola-virus-and-orthopoxviruses
#4
Gianguglielmo Zehender, Alessia Lai, Carla Veo, Annalisa Bergna, Massimo Ciccozzi, Massimo Galli
Variola virus (VARV), the causative agent of smallpox, is an exclusively human virus belonging to the genus Orthopoxvirus, which includes many other viral species covering a wide range of mammal hosts, such as vaccinia, cowpox, camelpox, taterapox, ectromelia and monkeypox virus. The tempo and mode of evolution of Orthopoxviruses were reconstructed using a Bayesian phylodynamic framework by analysing 80 hemagglutinin sequences retrieved from public databases. Bayesian phylogeography was used to estimate their putative ancestral hosts...
February 15, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29445361/a-quasi-steady-state-approximation-to-the-basic-target-cell-limited-viral-dynamics-model-with-a-non-cytopathic-effect
#5
Richard A Cangelosi, Elissa J Schwartz, David J Wollkind
Analysis of previously published target-cell limited viral dynamic models for pathogens such as HIV, hepatitis, and influenza generally rely on standard techniques from dynamical systems theory or numerical simulation. We use a quasi-steady-state approximation to derive an analytic solution for the model with a non-cytopathic effect, that is, when the death rates of uninfected and infected cells are equal. The analytic solution provides time evolution values of all three compartments of uninfected cells, infected cells, and virus...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29444939/single-cell-analysis-of-the-impact-of-host-cell-heterogeneity-on-infection-with-foot-and-mouth-disease-virus
#6
Xiu Xin, Hailong Wang, Lingling Han, Mingzhen Wang, Hui Fang, Yao Hao, Jiadai Li, Hu Zhang, Congyi Zheng, Chao Shen
Viral infection and replication are affected by host-cell heterogeneity, but the mechanisms underlying the effects remain unclear. Using single-cell analysis, we investigated the effects of host-cell heterogeneity, including cell size, inclusion, and cell cycle, on foot and mouth disease virus (FMDV) infection (acute and persistent infections) and replication. We detected variable viral genome replication levels in FMDV-infected cells. Larger cells and cells with a greater number of inclusions generated more viral RNA copies, viral protein, and a higher proportion of infectious cells...
February 14, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29443761/haemolytic-uremic-syndrome-due-to-infection-with-adenovirus-a-case-report-and-literature-review
#7
Victoria Birlutiu, Rares Mircea Birlutiu
RATIONALE: Haemolytic-uremic syndrome is a rare but serious complication of bacterial and viral infections, which is characterized by the triad of: acute renal failure, microangiopathic haemolytic anemia and thrombocytopenia, sometimes severe, requiring peritoneal dialysis. In Europe, hemolytic-uremic syndrome (HUS) in paediatric pathology is primarily caused by Shiga toxin-producing Escherichia coli (STEC) O157, followed by O26. Beside these etiologies, there are other bacterial and viral infections, and also noninfectious ones that have been associated to lead to HUS as well: in the progression of neoplasia, medication-related, post-transplantation, during pregnancy or associated with the antiphospholipid syndrome, systemic lupus erythematosus or family causes with autosomal dominant or recessive inheritance...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29443656/highlights-for-dengue-immunopathogenesis-antibody-dependent-enhancement-cytokine-storm-and-beyond
#8
Diogo Kuczera, João Paulo Assolini, Fernanda Tomiotto-Pellissier, Wander Rogério Pavanelli, Guilherme Ferreira Silveira
Infection with dengue virus (DENV) can lead to a wide spectrum of clinical presentations, ranging from asymptomatic infection to death. It is estimated that the disease manifests only in 90 million cases out of the total 390 million yearly infections. Even though research has not yet elucidated which are the precise pathophysiological mechanisms that trigger severe forms of dengue, the infection elicits a critical immune response significant for dengue pathogenesis development. Understanding how the immune response to DENV is established and how it can resolve the infection or turn into an immunopathology is of great importance in DENV research...
February 2018: Journal of Interferon & Cytokine Research
https://www.readbyqxmd.com/read/29435919/the-microrna
#9
Shao-Yao Ying, Donald C Chang, Shi-Lung Lin
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29431588/aptamers-in-hiv-research-diagnosis-and-therapy
#10
Jyoti Bala, Srinivasan Chinnapaiyan, Rajib Kumar Dutta, Hoshang Unwalla
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range...
February 12, 2018: RNA Biology
https://www.readbyqxmd.com/read/29430852/insights-into-the-evolution-of-the-new-variant-rabbit-haemorrhagic-disease-virus-gi-2-and-the-identification-of-novel-recombinant-strains
#11
D Silvério, A M Lopes, J Melo-Ferreira, M J Magalhães, P Monterroso, A Serronha, E Maio, P C Alves, P J Esteves, J Abrantes
Rabbit haemorrhagic disease (RHD) is a viral disease that affects the European rabbit. RHD was detected in 1984 in China and rapidly disseminated worldwide causing a severe decline in wild rabbit populations. The aetiological agent, rabbit haemorrhagic disease virus (RHDV), is an RNA virus of the family Caliciviridae, genus Lagovirus. Pathogenic (G1-G6 or variants GI.1a-GI.1d) and non-pathogenic strains (GI.4) have been characterized. In 2010, a new variant of RHDV, RHDV2/RHDVb/GI.2, was detected in France...
February 11, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29425151/liver-transplantation-for-alcoholic-liver-disease-and-hepatocellular-carcinoma
#12
REVIEW
Patrizia Burra, Alberto Zanetto, Giacomo Germani
Hepatocellular carcinoma is one of the main important causes of cancer-related death and its mortality is increasingly worldwide. In Europe, alcohol abuse accounts for approximately half of all liver cancer cases and it will become the leading cause of hepatocellular carcinoma in the next future with the sharp decline of chronic viral hepatitis. The pathophysiology of alcohol-induced carcinogenesis involves acetaldehyde catabolism, oxidative stress and chronic liver inflammation. Genetic background plays also a significant role and specific patterns of gene mutations in alcohol-related hepatocellular carcinoma have been characterized...
February 9, 2018: Cancers
https://www.readbyqxmd.com/read/29422601/no-evidence-of-ongoing-evolution-in-replication-competent-latent-hiv-1-in-a-patient-followed-up-for-two-years
#13
Hoi Ping Mok, Nicholas J Norton, Jack C Hirst, Axel Fun, Mikaila Bandara, Mark R Wills, Andrew M L Lever
The persistence of infected T cells harbouring intact HIV proviruses is the barrier to the eradication of HIV. This reservoir is stable over long periods of time despite antiretroviral therapy. There has been controversy on whether low level viral replication is occurring at sanctuary sites periodically reseeding infected cells into the latent reservoir to account its durability. To study viral evolution in a physiologically relevant population of latent viruses, we repeatedly performed virus outgrowth assays on a stably treated HIV positive patient over two years and sequenced the reactivated latent viruses...
February 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29419684/phylogenetic-and-temporal-dynamics-of-human-immunodeficiency-virus-type-1-crf01_ae-and-crf07_bc-among-recently-infected-antiretroviral-therapy-na%C3%A3-ve-men-who-have-sex-with-men-in-jiangsu-province-china-2012-to-2015-a-molecular-epidemiology-based-study
#14
Yue Yang, Xiu-Ping Zhao, Hua-Chun Zou, Min-Jie Chu, Ping Zhong, Xiao-Shan Li, Xiao-Yan Li, Yu-Hui Yu, Ke-Xin Zhu, Yu-Jia Chen, Fei Xia, Bo-Wen Zhu, Luan-Qi Ruan, Yi-Ning Bao, Xun Zhuang
The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29417240/allexiviruses-may-have-acquired-inserted-sequences-between-the-cp-and-crp-genes-to-change-the-translation-reinitiation-strategy-of-crp
#15
Naoto Yoshida, Hanako Shimura, Chikara Masuta
Allexiviruses are economically important garlic viruses that are involved in garlic mosaic diseases. In this study, we characterized the allexivirus cysteine-rich protein (CRP) gene located just downstream of the coat protein (CP) gene in the viral genome. We determined the nucleotide sequences of the CP and CRP genes from numerous allexivirus isolates and performed a phylogenetic analysis. According to the resulting phylogenetic tree, we found that allexiviruses were clearly divided into two major groups (group I and group II) based on the sequences of the CP and CRP genes...
February 7, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29415432/impact-of-rna-degradation-on-viral-diagnosis-an-understated-but-essential-step-for-the-successful-establishment-of-a-diagnosis-network
#16
Damarys Relova, Liliam Rios, Ana M Acevedo, Liani Coronado, Carmen L Perera, Lester J Pérez
The current global conditions, which include intensive globalization, climate changes, and viral evolution among other factors, have led to an increased emergence of viruses and new viral diseases; RNA viruses are key drivers of this evolution. Laboratory networks that are linked to central reference laboratories are required to conduct both active and passive environmental surveillance of this complicated global viral environment. These tasks require a continuous exchange of strains or field samples between different diagnostic laboratories...
February 6, 2018: Veterinary Sciences
https://www.readbyqxmd.com/read/29412520/socio-economic-status-and-time-trends-associated-with-early-art-initiation-following-primary-hiv-infection-in-montreal-canada-1996-to-2015
#17
Vikram Mehraj, Joseph Cox, Bertrand Lebouché, Cecilia Costiniuk, Wei Cao, Taisheng Li, Rosalie Ponte, Réjean Thomas, Jason Szabo, Jean-Guy Baril, Benoit Trottier, Pierre Côté, Roger LeBlanc, Julie Bruneau, Cécile Tremblay, Jean-Pierre Routy
INTRODUCTION: Guidelines regarding antiretroviral therapy (ART) initiation in HIV infection have varied over time, with the 2015 World Health Organization recommendation suggesting ART initiation at the time of diagnosis regardless of CD4 T-cell counts. Herein, we investigated the influence of socio-demographic and clinical factors in addition to time trends on early ART initiation among participants of the Montreal Primary HIV Infection Study. METHODS: The Montreal Primary HIV Infection Study is a prospective cohort established in three community medical centres (CMCs) and two university medical centres (UMCs)...
February 2018: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/29412184/molecular-epidemiology-evolution-and-phylogeny-of-foot-and-mouth-disease-virus
#18
REVIEW
Syed M Jamal, Graham J Belsham
Foot-and-mouth disease virus (FMDV) is responsible for one of the most economically important infectious diseases of livestock. The virus spreads very easily and continues to affect many countries (mainly in Africa and Asia). The risks associated with the introduction of FMDV result in major barriers to trade in animals and their products. Seven antigenically distinct forms of the virus are known, called serotypes, but serotype C has not been detected anywhere for many years and may now be extinct. The serotypes have been further divided into topotypes (except for serotype Asia-1 viruses, which comprise a single topotype), genotypes, lineages and sub-lineages, which are usually restricted to specific geographical regions...
February 2, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29412047/ptx3-a-humoral-pattern-recognition-molecule-in-innate-immunity-tissue-repair-and-cancer
#19
Cecilia Garlanda, Barbara Bottazzi, Elena Magrini, Antonio Inforzato, Alberto Mantovani
Innate immunity includes a cellular and a humoral arm. PTX3 is a fluid-phase pattern recognition molecule conserved in evolution which acts as a key component of humoral innate immunity in infections of fungal, bacterial, and viral origin. PTX3 binds conserved microbial structures and self-components under conditions of inflammation and activates effector functions (complement, phagocytosis). Moreover, it has a complex regulatory role in inflammation, such as ischemia/reperfusion injury and cancer-related inflammation, as well as in extracellular matrix organization and remodeling, with profound implications in physiology and pathology...
April 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29410443/evolution-of-the-quorum-network-and-the-mobilome-plasmids-and-bacteriophages-in-clinical-strains-of-acinetobacter-baumannii-during-a-decade
#20
M López, A Rueda, J P Florido, L Blasco, L Fernández-García, R Trastoy, F Fernández-Cuenca, L Martínez-Martínez, J Vila, A Pascual, G Bou, M Tomas
In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for blaOXA 24/40 ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins...
February 6, 2018: Scientific Reports
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