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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/28427935/the-manifolded-dynamics-of-hiv-1-transmission-in-northern-alberta-a-combined-analysis-of-virus-genetic-and-public-health-data
#1
B Vrancken, D Adachi, M Benedet, A Singh, R Read, S Shafran, G D Taylor, S Houston, K Simmonds, S Plitt, C Sikora, P Lemey, C L Charlton, J W Tang
Molecular epidemiology has become a key tool for tracking infectious disease epidemics. Here, the spread of the most prevalent HIV-1 subtypes in Northern Alberta, Canada, was characterized with a Bayesian phylogenetic approach using 1146 HIV-1 pol sequences collected between 2007 and 2013 for routine clinical management purposes. Available patient metadata were qualitatively interpreted and correlated with onwards transmission using Fisher exact tests and logistic regression. Most infections were from subtypes A (n=36), B (n=815) and C (n=211)...
April 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28414106/molecular-evolution-of-the-fusion-protein-f-gene-in-human-respiratory-syncytial-virus-subgroup-b
#2
Hirokazu Kimura, Koo Nagasawa, Ryusuke Kimura, Hiroyuki Tsukagoshi, Yuki Matsushima, Kiyotaka Fujita, Eiko Hirano, Naruhiko Ishiwada, Takako Misaki, Kazunori Oishi, Makoto Kuroda, Akihide Ryo
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes...
April 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28412525/liver-microbiome-of-peromyscus-leucopus-a-key-reservoir-host-species-for-emerging-infectious-diseases-in-north-america
#3
A André, A Mouton, V Millien, J Michaux
Microbiome studies generally focus on the gut microbiome, which is composed of a large proportion of commensal bacteria. Here we propose a first analysis of the liver microbiome using next generation sequencing as a tool to detect potentially pathogenic strains. We used Peromyscus leucopus, the main reservoir host species of Lyme disease in eastern North America, as a model and sequenced V5-V6 regions of the 16S gene from 18 populations in southern Quebec (Canada). The Lactobacillus genus was found to dominate the liver microbiome...
April 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28412524/antimicrobial-resistance-and-genetic-diversity-of-the-sxt-element-in-vibrio-cholerae-from-clinical-and-environmental-water-samples-in-northeastern-thailand
#4
Wanida Mala, Kiatichai Faksri, Kittipan Samerpitak, Umaporn Yordpratum, Wanlop Kaewkes, Unchalee Tattawasart, Chariya Chomvarin
Multidrug resistance in V. cholerae has been increasing around the world including northeastern Thailand. The aquatic environment is a reservoir of V. cholerae and might be an important source of resistant strains. The aims of this study were to investigate the phylogenetic relationships of intSXT gene sequences from 31 clinical and 14 environmental V. cholerae O1 and non-O1/non-O139 isolates and 11 sequences amplified directly from environmental water samples. We also amplified class 1 integrons, the SXT elements (targeting the intSXT gene) and antimicrobial resistance genes directly from water samples...
April 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28412523/progenitor-strain-introduction-of-mycobacterium-bovis-at-the-wildlife-livestock-interface-can-lead-to-clonal-expansion-of-the-disease-in-a-single-ecosystem
#5
Anzaan Dippenaar, Sven David Charles Parsons, Michele Ann Miller, Tiny Hlokwe, Nicolaas Claudius Gey van Pittius, Sabir Abdu Adroub, Abdallah Musa Abdallah, Arnab Pain, Robin Mark Warren, Anita Luise Michel, Paul David van Helden
Mycobacterium bovis infects multiple wildlife species and domesticated cattle across South Africa, and negatively impacts on livestock trade and movement of wildlife for conservation purposes. M. bovis infection was first reported in the Kruger National Park (KNP) in South Africa during the 1990s, and has since spread to infect numerous animal host species throughout the park and across South Africa. Whole genome sequencing data of 17 M. bovis isolates were analyzed to investigate the genomic diversity among M...
April 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28411164/high-levels-of-local-inter-and-intra-host-genetic-variation-of-west-nile-virus-and-evidence-of-fine-scale-evolutionary-pressures
#6
Dylan J Ehrbar, Kiet A Ngo, Scott R Campbell, Laura D Kramer, Alexander T Ciota
West Nile virus (WNV; Flaviviridae, Flavivirus) has been endemic in New York State (NYS) since its 1999 introduction, yet prevalence in Culex mosquitoes varies substantially over small spatial and temporal scales. It is unclear if viral genetics plays a role in this variability, as genetic and phenotypic characterization on local scales has generally been lacking. In addition, intrahost diversity of circulating strains have not been fully characterized despite the documented role of minority variants in viral fitness and virulence...
April 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28411163/development-of-a-multi-epitope-peptide-vaccine-inducing-robust-t-cell-responses-against-brucellosis-using-immunoinformatics-based-approaches
#7
Mahdiye Saadi, Ahmad Karkhah, Hamid Reza Nouri
Current investigations have demonstrated that a multi-epitope peptide vaccine targeting multiple antigens could be considered as an ideal approach for prevention and treatment of brucellosis. According to the latest findings, the most effective immunogenic antigens of brucella to induce immune responses are included Omp31, BP26, BLS, DnaK and L7-L12. Therefore, in the present study, an in silico approach was used to design a novel multi-epitope vaccine to elicit a desirable immune response against brucellosis...
April 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28408285/from-epigenetic-landscape-to-phenotypic-fitness-landscape-evolutionary-effect-of-pathogens-on-host-traits
#8
Mark Jayson V Cortez, Jomar F Rabajante, Jerrold M Tubay, Ariel L Babierra
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection...
April 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28404483/anaconda-paramyxovirus-infection-in-an-adult-green-anaconda-after-prolonged-incubation-pathological-characterization-and-whole-genome-sequence-analysis
#9
Patrick C Y Woo, Paolo Martelli, Suk-Wai Hui, Candy C Y Lau, Joseph M Groff, Rachel Y Y Fan, Susanna K P Lau, Kwok-Yung Yuen
From July 2011 to June 2012, 31 out of 33 green anaconda juveniles from an oceanarium in Hong Kong died over a 12-month period. These anacondas were progeny of a female anaconda purchased from Japan and added to the collection in May 2011. The juvenile anacondas were born in July 2011. A novel paramyxovirus, named anaconda paramyxovirus (AnaPV), was isolated from these affected juvenile anacondas. In July 2015, one of the remaining two anacondas, that survived the cluster of fatal infections, died at the age of four...
April 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28404482/plasmid-dynamics-in-vibrio-parahaemolyticus-strains-related-to-shrimp-acute-hepatopancreatic-necrosis-syndrome-ahpns
#10
Chonchanok Theethakaew, Shota Nakamura, Daisuke Motooka, Shigeaki Matsuda, Toshio Kodama, Kaknokrat Chonsin, Orasa Suthienkul, Tetsuya Iida
Vibrio parahaemolyticus is a causative agent of acute hapatopancreatic necrosis syndrome (AHPNS) which causes early mortality in white shrimp. Emergence of AHPNS has caused tremendous economic loss for aquaculture industry particularly in Asia since 2010. Previous studies reported that strains causing AHPNS harbor a 69-kb plasmid with possession of virulence genes, pirA and pirB. However, genetic variation of the 69-kb plasmid among AHPNS related strains has not been investigated. This study aimed to analyze genetic composition and diversity of the 69-kb plasmid in strains isolated from shrimps affected by AHPNS...
April 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28392468/description-of-a-new-species-trichuris-ursinus-n-sp-nematoda-trichuridae-from-papio-ursinus-keer-1792-from-south-africa
#11
Rocío Callejón, Ali Halajian, Cristina Cutillas
In the present work, we carried out a morphological, biometrical and molecular study of whipworms Trichuris Roederer, 1761 (Nematoda: Trichuridae) parasitizing Papio ursinus Keer 1792 (Chacma baboon). Biometrical and molecular data suggest a new species of Trichuris parasitizing baboons. In addition of main morphological features (spicule, spicule sheath, spicule tube, proximal cloacal tube, distal cloacal tube, vulva, vagina), the mean values of individual variables between Trichuris colobae, Trichuris suis, Trichuris trichiura examined by Student's t tests suggest that T...
April 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28392469/susceptibility-and-initial-immune-response-of-tupaia-belangeri-cells-to-dengue-virus-infection
#12
Mohammad Enamul Hoque Kayesh, Bouchra Kitab, Takahiro Sanada, Daisuke Hayasaka, Kouichi Morita, Michinori Kohara, Kyoko Tsukiyama-Kohara
Dengue is an emerging disease of great public health significance worldwide. The lack of a suitable infection model has hampered dengue virus (DENV) pathogenesis study, and developing a suitable small animal model has been a long-standing challenge. The aim of this study was to develop a feasible experimental model of DENV infection using Tupaia belangeri. The susceptibility of tupaia to DENV infection and characteristics of its innate immune response were examined in vitro. We found that tupaia fibroblast cells support replication of DENV serotypes 1-4 with a linear increase in viral load 24-96h post-infection in both cells and culture supernatants...
April 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28392467/predicted-coreceptor-usage-at-end-stage-hiv-disease-in-tissues-derived-from-subjects-on-antiretroviral-therapy-with-an-undetectable-plasma-viral-load
#13
S L Lamers, G B Fogel, E S Liu, D J Nolan, M Salemi, A E Barbier, R Rose, E J Singer, M S McGrath
HIV cure research is increasingly focused on anatomical tissues as sites for residual HIV replication during combined antiretroviral therapy (cART). Tissue-based HIV could contribute to low-level immune activation and viral rebound over the course of infection and could also influence the development of diseases, such as atherosclerosis, neurological disorders and cancers. cART-treated subjects have a decreased and irregular presence of HIV among tissues, which has resulted in a paucity of actual evidence concerning how or if HIV persists, replicates and evolves in various anatomical sites during therapy...
April 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28389387/association-of-cyp2b6-gene-polymorphisms-and-anti-tuberculosis-drug-induced-hepatotoxicity-in-a-chinese-population
#14
Yu Wang, Xi Xiang, Shou-Quan Wu, Guo Chen, Miao-Miao Zhang, Ming-Gui Wang, Feng-Juan Wang, Andrew J Sandford, Jian-Qing He
OBJECTIVES: Antituberculosis drug-induced hepatotoxicity (ATDH) remains a common and severe challenge in tuberculosis (TB) chemotherapy. A growing number of studies have revealed that genetic polymorphisms affect an individual's susceptibility to ATDH. The aim of this study was to explore the role of cytochrome P450 family 2 subfamily B member 6 (CYP2B6) gene polymorphisms in the development of ATDH in Chinese TB patients. METHODS: CYP2B6*6 genotypes were determined in TB patients with and without ATDH...
April 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28366737/mirna-101-1-and-mirna-221-expressions-and-their-polymorphisms-as-biomarkers-for-early-diagnosis-of-hepatocellular-carcinoma
#15
Olfat Shaker, Maha Alhelf, George Morcos, Aisha Elsharkawy
BACKGROUND: Hepatocellular carcinoma (HCC) is the fifth most common malignant tumor with an increasing incidence. Hepatitis C virus (HCV) is one of the major risk factors that lead to HCC development. MicroRNAs are conserved non-coding RNAs which regulate gene expression at the posttranscriptional level. They have been recently identified as important regulators that affect carcinogenesis. Of these miRNAs, are miR-221 and miR-101-1, which their aberrant expressions have been reported to play an important role in HCC...
March 30, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28365387/structural-analysis-and-insight-into-zika-virus-ns5-mediated-interferon-inhibition
#16
Hamza Arshad Dar, Tahreem Zaheer, Rehan Zafar Paracha, Amjad Ali
The Zika virus outbreak in 2015-2016 is the largest of its kind for which WHO declared a Public Health Emergency of International Concerns. No FDA approved drug is available for the treatment of the viral infection. The interaction of flavivirus NS5 protein with SIAH2 ubiquitin ligase has been previously known. NS5 of Zika virus has been implicated in the degradation of STAT2 protein, which activates interferon-stimulated antiviral activity. Based on our proposition that NS5 utilizes SIAH2-mediated proteasomal degradation of STAT2, an in-silico study was carried out to characterize the protein-protein interactions between NS5, SIAH2 and STAT2 proteins...
March 30, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28359834/novel-antigenic-shift-in-ha-sequences-of-h1n1-viruses-detected-by-big-data-analysis
#17
Ruiying Zhang, Chongfeng Xu, Ziyuan Duan
The influenza virus H1N1 has been prevalent all over the world for nearly a century. Many studies on its evolutionary history, substitution rate and antigenicity-associated sites have been done with small datasets. To have a complete view, we analysed 3171 full-length HA sequences from human H1N1 viruses sampled from 1918 to 2016, and discovered a new clade has formed with sequences isolated in Iran. Based on genetic distance calculations, we revealed an uneven evolutionary rate among sequences isolated in different years...
March 28, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28359833/first-report-in-africa-of-two-clinical-isolates-of-proteus-mirabilis-carrying-salmonella-genomic-island-sgi1-variants-sgi1-pmabb-and-sgi1-w
#18
Ahmed M Soliman, Ashraf M Ahmed, Toshi Shimamoto, Ramadan A El-Domany, Hirofumi Nariya, Tadashi Shimamoto
Two Proteus mirabilis strains, designated PmTAN59 and PmKAF126, were isolated from two different Egyptian cities in 2014 and 2015, respectively. PmTAN59 was isolated from a sputum swab from a pneumonia patient in Tanta University Teaching Hospital. PmKAF126 was isolated from a patient with a diabetic foot infection in a hospital in the city of Kafr El-Sheikh. The two isolates were identified with bacterial small ribosomal RNA (16S rRNA) gene amplification and sequencing and tested for antimicrobial sensitivity with a Kirby-Bauer disk diffusion assay...
March 28, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28347753/genetic-and-physicochemical-analyses-of-a-novel-ferret-hepatitis-e-virus-and-clinical-signs-of-infection-after-birth
#19
Tian-Cheng Li, Sayaka Yoshizaki, Michiyo Kataoka, Yasushi Ami, Yuriko Suzaki, Yen Hai Doan, Kei Haga, Koji Ishii, Naokazu Takeda, Takaji Wakita
A novel cluster of five ferret hepatitis E virus (HEV) strains was detected from nine laboratory ferrets (Mustela putorius furo) imported from a ferret farm in the U.S. Our detection of ferret HEV RNA and anti-HEV antibodies, and alanine aminotransferase (ALT) value assessment indicated that all of the 9 ferrets were infected with ferret HEV, and that the infection exhibited three patterns: sub-clinical infection (n=2), acute hepatitis (n=6) and persistent infection (n=1). Next-generation sequence analyses of the entire genome sequences of the five strains revealed that their nucleotide sequence identities ranged from 99...
March 25, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28342887/genetic-detection-and-characterization-of-goose-parvovirus-implications-for-epidemiology-and-pathogenicity-in-cherry-valley-pekin-ducks
#20
LETTER
Kang Ning, Te Liang, Minghang Wang, Yunhan Dong, Shenghua Qu, Dabing Zhang
No abstract text is available yet for this article.
March 23, 2017: Infection, Genetics and Evolution
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