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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/30010059/tracing-the-emerging-genotypes-of-human-respiratory-syncytial-virus-in-beijing-by-evolution-analysis-of-the-attachment-glycoprotein-g-gene
#1
Tuohui Zhang, Yuan Qian, Jie Deng, Runan Zhu, Fang Wang, Yu Sun, Yaxin Ding, Run Tian, Linqing Zhao
BACKGROUND: Emerging human respiratory syncytial virus (HRSV) genotypes, such as ON1 and BA9, are becoming the dominant genotypes prevailing worldwide. Objective To trace the emerging HRSV genotypes in Beijing. METHODS: HRSV-positive specimens as determined by direct immunofluorescence, collected from children diagnosed with bronchiolitis from July 2006 to June 2016, were typed by real-time PCR, then genotyped by phylogenetic analyses of the full attachment glycoprotein (G) gene...
July 16, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30016714/analysis-of-genetic-polymorphisms-and-tropism-in-east-african-leishmania-donovani-by-amplified-fragment-length-polymorphism-and-kdna-minicircle-sequencing
#2
Hanan T Jaber, Asrat Hailu, Francine Pratlong, Patrick Lami, Patrick Bastien, Charles L Jaffe
Visceral leishmaniasis (VL), the most severe form of leishmaniasis, is caused by Leishmania donovani. In addition to fatal VL, these parasites also cause skin diseases in immune-competent and -suppressed people, post-kala azar dermal leishmaniasis (PKDL) and HIV/VL co-infections, respectively. Genetic polymorphism in 36 Ethiopian and Sudanese L. donovani strains from VL, PKDL and HIV/VL patients was examined using Amplified Fragment Length Polymorphism (AFLP), kDNA minicircle sequencing and Southern blotting...
July 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30016713/variation-in-intronic-microsatellites-and-exon-2-of-the-plasmodium-falciparum-chloroquine-resistance-transporter-gene-during-modification-of-artemisinin-combination-therapy-in-thailand
#3
Sunee Seethamchai, Pattakorn Buppan, Napaporn Kuamsab, Phairote Teeranaipong, Chaturong Putaporntip, Somchai Jongwutiwes
The amino acid substitution at residue 76 of the food vacuolar transmembrane protein encoded by the chloroquine resistance transporter gene of Plasmodium falciparum (Pfcrt) is an important, albeit imperfect, determinant of chloroquine susceptibility status of the parasite. Other mutations in Pfcrt can modulate susceptibility of P. falciparum to other antimalarials capable of interfering with heme detoxification process, and may exert compensatory effect on parasite growth rate. To address whether nationwide implementation of artemisinin combination therapy (ACT) in Thailand could affect sequence variation in exon 2 and introns of Pfcrt, we analyzed 136 P...
July 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30010060/interleukin-4-and-stat6-promoter-polymorphisms-but-not-interleukin-10-or-13-are-essential-for-schistosomiasis-and-associated-disease-burden-among-nigerian-children
#4
Samuel A Adedokun, Brooke N Seamans, Natalya T Cox, Gialeigh Liou, Akeem A Akindele, Yi Li, Olusola Ojurongbe, Bolaji N Thomas
Schistosomiasis is endemic in many parts of rural Africa, with previous reports showing interleukin-13 polymorphisms as drivers of infectivity and disease severity in West Africa while IL-13/IL-4 polymorphisms contributes to patterns of reinfection in East Africa. We have shown that there is a genetic delineation in susceptibility to and severity of infectious diseases in Africa, in addition to sub-continental differences in disease pattern. Therefore, which immunoregulatory biomarkers are essential in driving S...
July 12, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30017847/enterovirus-b74-associated-with-hand-foot-and-mouth-disease
#5
Ivanildo P Sousa, Fernanda M Burlandy, Fernando N Tavares, Edson E da Silva
Enterovirus 74 (EV-B74) has been associated with cases of acute flaccid paralysis (AFP) but it is not a commonly found enterovirus. In this work, we present the characterization of an EV-B74 detected from the serum sample of a one-year-old boy presenting with signs and symptoms clinically compatible with hand, foot and mouth disease (HFMD). This is the first report of EV-B74 in Brazil.
July 11, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30006047/genes-under-positive-selection-in-the-core-genome-of-pathogenic-bacillus-cereus-group-members
#6
Jean-Philippe Rasigade, Florian Hollandt, Thierry Wirth
In this comparative genomics study our aim was to unravel genes under positive selection in the core genome of the Bacillus cereus group. Indeed, the members of this group share close genetic relationships but display a rather large phenotypic and ecological diversity, providing a unique opportunity for studying how genomic changes reflect ecological adaptation during the divergence of a bacterial group. For this purpose, we screened ten completely sequenced genomes of four pathogenic Bacillus species, finding that 254 out of 3093 genes have codon sites with dN /dS (ω) values above one...
July 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30006046/population-structure-of-pseudomonas-aeruginosa-through-a-mlst-approach-and-antibiotic-resistance-profiling-of-a-mexican-clinical-collection
#7
F J Castañeda-Montes, M Avitia, O Sepúlveda-Robles, V Cruz-Sánchez, L Kameyama, G Guarneros, A E Escalante
Pseudomonas aeruginosa is one of the most important pathogens worldwide. Population genetics studies have shown that the P. aeruginosa population has an epidemic structure with highly conserved clonal complexes. Nonetheless, epidemiological studies of P. aeruginosa have been historically absent or infrequent in developing countries, in which different medical treatments, conditions and infrastructure may have an impact in population dynamics and evolutionary outcomes, including antibiotic resistance profiles...
July 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30006045/viral-metagenomics-genetic-and-evolutionary-characteristics-of-crimean-congo-hemorrhagic-fever-orthonairovirus-in-humans-kosovo
#8
Petra Emmerich, Xhevat Jakupi, Ronald von Possel, Lindita Berisha, Bahrije Halili, Stephan Günther, Daniel Cadar, Salih Ahmeti, Jonas Schmidt-Chanasit
Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) is a tick-borne virus which causes severe disease in humans with fatality cases up to 30%. We investigated the genetic and evolutionary characteristics of CCHFV in Kosovo, in particular in humans and found that different virus variants of genotype V circulate, with Turkey as a possible origin for the progenitor of southern European CCHF outbreaks. Phylogenetic analyses also revealed a single introduction event and in situ evolution of CCHFV in this country...
July 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30003970/blastocystis-infection-and-subtype-distribution-in-humans-cattle-goats-and-pigs-in-central-and-western-thailand
#9
Ruenruetai Udonsom, Rapeepan Prasertbun, Aongart Mahittikorn, Hirotake Mori, Tanasak Changbunjong, Chalit Komalamisra, Ai-Rada Pintong, Yaowalark Sukthana, Supaluk Popruk
Blastocystis spp. are common gastrointestinal parasites of humans and a variety of animals, with various host-specific subtypes. The aim of this study was to determine the prevalence of Blastocystis infection and identify subtypes in humans and domestic animals. One hundred and thirteen stool samples were collected from pigs, goats, and cattle in Ayutthaya Province (AP; central Thailand) and 218 stool samples were collected from pigs, dogs, cats, chickens, and humans in Kanchanaburi Province (KP; western Thailand)...
July 9, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29981902/unexplored-deep-sea-habitats-in-active-volcanic-barren-island-andaman-and-nicobar-islands-are-sources-of-novel-halophilic-eubacteria
#10
Anburajan Lawrance, Meena Balakrishnan, Rajaprabhu Gunasekaran, Rajaguru Srinivasan, Vinithkumar Nambali Valsalan, Dharani Gopal, Kirubagaran Ramalingam
Deep Sea sediment cores were collected from the surrounding of active volcanic Barren Island, Andaman & Nicobar Islands. A total of 24 halophilic eubacteria were isolated and identified based on their biochemical and 16S rDNA sequences. Three major classes (Gamma-Proteobacteria, Alpha-Proteobacteria and Bacilli) of bacteria were detected in the deep sea sediments of active volcanic Barren Island. Among those, 37% of isolates exhibited antimicrobial activity against all tested Gram positive and Gram negative clinical pathogens...
July 5, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29981901/multilocus-sequence-typing-and-population-genetic-structure-of-cryptosporidium-cuniculus-in-rabbits-in-heilongjiang-province-china
#11
Ziyin Yang, Fengkun Yang, Jianguang Wang, Cao Jianping, Wei Zhao, Baiyan Gong, Jiangrong Yan, Weizhe Zhang, Aiqin Liu, Yujuan Shen
Multilocus sequence typing (MLST) tools have been used widely to characterize population genetic structure of some Cryptosporidium species. To understand MLST subtypes and population genetic structure of Cryptosporidium cuniculus from rabbits in Heilongjiang Province, China, 34 C. cuniculus DNA specimens were collected including VbA21 (n = 6), VbA28 (n = 2), VbA29 (n = 18) and VbA32 (n = 8). They were analyzed by nested-PCR amplification and sequencing at seven microsatellite, minisatellite and polymorphic loci including CP47, CP56, ML2, DZ-HRGP, MSC6-5, MSC6-7 and RPGR...
July 5, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30017997/phylodynamics-of-parapoxvirus-genus-in-mexico-2007-2011
#12
Lauro Velazquez-Salinas, Elizabeth Ramirez-Medina, Alexa J Bracht, Kate Hole, Barbara P Brito, Douglas P Gladue, Consuelo Carrillo
In this study we report for the first time the phylodynamics of the parapoxvirus (PPV) genus in Mexico. Based on the analysis by PCR of 124 epithelial samples collected between 2007 and 2011 from naturally infected goats, sheep and cows in Mexico, we found that different PPV were present in 21 out of the 24 states sampled during this study. Our phylogenetic analysis confirmed the presence of different PPV species in Mexico, and their phylogenetic relationship with other PPV circulating in the US and Canada...
July 4, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29991455/the-effects-of-random-taxa-sampling-schemes-in-bayesian-virus-phylogeography
#13
Daniel Magee, Matthew Scotch
Public health researchers are often tasked with accurately and quickly identifying the location and time when an epidemic originated from a representative sample of nucleotide sequences. In this paper, we investigate multiple approaches to subsampling the sequence set when employing a Bayesian phylogeographic generalized linear model. Our results indicate that near-categorical posterior MCC estimates on the root can be obtained with replicate runs using 25-50% of the sequence data, and that including 90% of sequences does not necessarily entail more accurate inferences...
July 4, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30008422/the-association-of-human-papillomavirus-type-16-e2-variations-with-cervical-cancer-in-a-han-chinese-population
#14
Shuying Dai, Yueting Yao, Zhiling Yan, Ziyun Zhou, Li Shi, Xiaona Wang, Le Sun, Rongping Zhang, Yufeng Yao
Human papillomavirus type 16 (HPV16) is considered to be the primary pathogen related to cervical cancer. The HPV16 E2 protein plays an important role in tumourigenicity of cervical carcinoma. In the current study, we enrolled 121 HPV16-positive cervical cancer patients in the case group and 130 HPV16-positive asymptomatic individuals in the control group, and we investigated the association between HPV16 E2 gene variations and cervical cancer. The HPV16 E2 DNA was amplified and sequenced. We identified two HPV variants (EUR and As) in the control group; the As variant was predominant (68...
July 2, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29991456/first-phenotypic-and-genotypic-description-of-fasciola-hepatica-infecting-highland-cattle-in-the-state-of-mexico-mexico
#15
M Adela Valero, M Dolores Bargues, Leticia Calderón, Patricio Artigas, Santiago Mas-Coma
Fascioliasis is a plantborne and zoonotic parasitic disease caused by fasciolid liver flukes. Fasciola hepatica is the only fasciolid species described in the Americas. Human fascioliasis endemic areas are mainly located in high altitude areas of the Americas. Given the necessity to characterize F. hepatica populations involved, the phenotypic and genotypic features of fasciolid adults infecting cattle in the highland area of Toluca, State of Mexico, Mexico, were analyzed and compared to fasciolid materials from the Northern Bolivian Altiplano, representing the altiplanic transmission pattern in a hyperendemic scenario...
July 2, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29966765/analysis-of-reptarenavirus-genomes-indicates-different-selective-forces-acting-on-the-s-and-l-segments-and-recent-expansion-of-common-genotypes
#16
Chiara Pontremoli, Diego Forni, Rachele Cagliani, Manuela Sironi
Reptarenaviruses, a genus of snake-infecting viruses belonging to the family Arenaviridae, have bi-segmented genomes. The long (L) segment encodes the Z and L (RNA polymerase) proteins, whereas the short (S) segment codes for the glycoprotein precursor (GPC) and for the nucleoprotein (NP). Presently, reptarenaviruses have only been described in captive snakes. In these animals, mixed infections are common and most infected reptiles harbor multiple S and/or L segment genotypes. Within single animals, L segments are more genetically diverse than S segments and one S segment genotype (S6) was detected in the majority of snakes...
June 29, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29964191/molecular-epidemiology-of-aminoglycoside-resistance-in-clinical-isolates-of-klebsiella-pneumoniae-collected-from-qazvin-and-tehran-provinces-iran
#17
Gelareh Nasiri, Amir Peymani, Taghi Naserpour Farivar, Peyman Hosseini
Production of aminoglycoside modifying enzymes (AMEs) and 16S rRNA methylases are two main resistance mechanisms against these antibiotics. This study determined the frequency of AMEs and 16 s rRNA methylase genes among aminoglycoside non-susceptible K. pneumoniae isolates and evaluated their clonal relationship by enterobacterial repetitive intergenic consensus (ERIC)-PCR. A total of 177 K. pneumoniae isolates were collected from hospitals of Qazvin and Tehran, Iran. The identification of isolates was done by standard laboratory methods and API 20E strips...
June 28, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29960078/towards-better-prediction-of-mycobacterium-tuberculosis-lineages-from-miru-vntr-data
#18
Nithum Thain, Christopher Le, Aldo Crossa, Shama Desai Ahuja, Jeanne Sullivan Meissner, Barun Mathema, Barry Kreiswirth, Natalia Kurepina, Ted Cohen, Leonid Chindelevitch
The determination of lineages from strain-based molecular genotyping information is an important problem in tuberculosis. Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is a commonly used molecular genotyping approach that uses counts of the number of times pre-specified loci repeat in a strain. There are three main approaches for determining lineage based on MIRU-VNTR data - one based on a direct comparison to the strains in a curated database, and two others, on machine learning algorithms trained on a large collection of labeled data...
June 27, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29940348/first-detection-and-molecular-identification-of-borrelia-species-in-bactrian-camel-camelus-bactrianus-from-northwest-china
#19
Bintao Zhai, Qingli Niu, Zhijie Liu, Jifei Yang, Yuping Pan, Youquan Li, Hongxi Zhao, Jianxun Luo, Hong Yin
Comprehensive epidemiological surveys for Lyme disease have not been conducted for the Bactrian camel in China. In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Species-specificity nested PCR based on the 5S-23S rRNA, OspA, flaB and 16S rRNA genes revealed that the total positive rate of Borrelia spp. was 3.6% (5/138, 95% CI = 0.2-17.9). These results were confirmed by sequence analysis of the positive PCR products or positive colonies...
June 22, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29936039/distinguishing-echinococcus-granulosus-sensu-stricto-genotypes-g1-and-g3-with-confidence-a-practical-guide
#20
Liina Kinkar, Teivi Laurimäe, Gerardo Acosta-Jamett, Vanessa Andresiuk, Ibrahim Balkaya, Adriano Casulli, Robin B Gasser, Luis Miguel González, Karen L Haag, Houria Zait, Malik Irshadullah, Abdul Jabbar, David J Jenkins, Maria Teresa Manfredi, Hossein Mirhendi, Selim M'rad, Mohammad Rostami-Nejad, Myriam Oudni-M'rad, Nora Beatriz Pierangeli, Francisco Ponce-Gordo, Steffen Rehbein, Mitra Sharbatkhori, Eshrat Beigom Kia, Sami Simsek, Silvia Viviana Soriano, Hein Sprong, Viliam Šnábel, Gérald Umhang, Antonio Varcasia, Urmas Saarma
Cystic echinococcosis (CE), a zoonotic disease caused by tapeworms of the species complex Echinococcus granulosus sensu lato, represents a substantial global health and economic burden. Within this complex, E. granulosus sensu stricto (genotypes G1 and G3) is the most frequent causative agent of human CE. Currently, there is no fully reliable method for assigning samples to genotypes G1 and G3, as the commonly used mitochondrial cox1 and nad1 genes are not sufficiently consistent for the identification and differentiation of these genotypes...
June 21, 2018: Infection, Genetics and Evolution
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