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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/30659963/characterization-of-post-pandemic-influenza-virus-circulation-in-southern-region-of-romania-during-2010-2014
#1
George Necula, Odette Popovici, Daniela Manuc, Anca Magdalena Munteanu
No abstract text is available yet for this article.
January 16, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30658215/survival-of-mycobacterium-leprae-and-association-with-acanthamoeba-from-environmental-samples-in-the-inhabitant-areas-of-active-leprosy-cases-a-cross-sectional-study-from-endemic-pockets-of-purulia-west-bengal
#2
Ravindra P Turankar, Mallika Lavania, Joydeepa Darlong, K S R Siva Sai, U Sengupta, Rupendra S Jadhav
BACKGROUND: Mycobacterium leprae being an obligate intracellular parasite cannot be cultured in any artificial culture media but it has been shown to reside in wild armadillos in North America. Many studies suggested that M. leprae could be found in the environment and may have a role in continuing transmission of the disease. The exact role of the environment in the transmission dynamics is still speculative. The present study was undertaken to find out the presence of viable M. leprae around patients' environment like soil and water and association of free living pathogenic protozoa, Acanthamoeba which might play an important role in transmission of the disease...
January 15, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30658214/zika-virus-entry-mechanisms-in-human-cells
#3
REVIEW
Almerinda Agrelli, Ronald Rodrigues de Moura, Sergio Crovella, Lucas André Cavalcanti Brandão
Zika virus (ZIKV) is an enveloped, mosquito-borne Flavivirus, which infects cells through clathrin-mediated endocytosis and fusion employing acidic endosomes. Cell entry is mostly mediated by the viral glycoprotein E, although incomplete particle maturation enables viral protein prM and anionic lipids present in the viral membrane to mediate this process. Incomplete proteolytic maturation results in a set of highly heterogeneous particles. These heterogeneous and dynamic infectious particles offer a variety of possible receptor interaction sites on their surfaces, thus contributing to the wide range of cells susceptible to ZIKV as well as to variation in tissue tropism...
January 15, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30654179/multicentre-investigation-of-carbapenemase-producing-klebsiella-pneumoniae-and-escherichia-coli-in-bulgarian-hospitals-interregional-spread-of-st11-ndm-1-producing-k-pneumoniae
#4
Rumyana Markovska, Temenuga Stoeva, Lyudmila Boyanova, Petya Stankova, Ines Schneider, Emma Keuleyan, Kalina Mihova, Marianna Murdjeva, Mariya Sredkova, Magdalena Lesseva, Gergana Nedelcheva, Atanaska Petrova, Dobrinka Ivanova, Grozdanka Lazarova, Radka Kaneva, Ivan Mitov
AIM: The aim of this study was to investigate the mechanisms of beta-lactam-resistance and the clonal relatedness of carbapenem-nonsusceptible Klebsiella pneumoniae and Escherichia coli isolates, collected consecutively in eight centers in five Bulgarian cities from November 2014 to March 2018. Carbapenemase-producing enterobacteria were detected in all but one centers. Overall, 104 K. pneumoniae and one E. coli were analysed. MATERIALS AND METHODS: Antimicrobial susceptibility and beta-lactamases were analysed...
January 14, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30654178/nontuberculous-mycobacteria-insights-on-taxonomy-and-evolution
#5
Christine Y Turenne
Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others...
January 14, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30654177/a-systematic-deep-sequencing-based-methodology-for-identification-of-mixed-genotype-hepatitis-c-virus-infections
#6
Andrea D Olmstead, Vincent Montoy, Celia K Chui, Winnie Dong, Jeffrey B Joy, Vera Tai, Art F Y Poon, Thuy Nguyen, Chanson J Brumme, Marianne Martinello, Gail V Matthews, P Richard Harrigan, Gregory J Dore, Tanya L Applegate, Jason Grebely, Anita Y M Howe
Hepatitis C virus (HCV) mixed genotype infections can affect treatment outcomes and may have implications for vaccine design and disease progression. Previous studies demonstrate 0-39% of high-risk, HCV-infected individuals harbor mixed genotypes however standardized, sensitive methods of detection are lacking. This study compared PCR amplicon, random primer (RP), and probe enrichment (PE)-based deep sequencing methods coupled with a custom sequence analysis pipeline to detect multiple HCV genotypes. Mixed infection cutoff values, based on HCV read depth and coverage, were identified using receiver operating characteristic curve analysis...
January 14, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30641151/whole-genome-analyses-of-ds-1-like-rotavirus-a-strains-detected-in-children-with-acute-diarrhoea-in-southern-mozambique-suggest-several-reassortment-events
#7
Amy Strydom, Eva Dora João, Lithabiso Motanyane, Martin M Nyaga, A Christiaan Potgieter, Assa Cuamba, Inacio Mandomando, Marta Cassocera, Nilsa de Deus, Hester G O'Neill
We report the first whole genome constellations of Mozambican rotavirus A strains detected between 2012 and 2013 in the Mavalane General Hospital in Maputo city and Manhiça District Hospital in the Manhiça district. Consensus sequences for ten DS-1-like strains (G2P[4] and G8P[4]) were identified with an Illumina Miseq platform using cDNA prepared from dsRNA extracted from stool samples, without genome amplification or prior adaptation to cell culture. Comparison of previously reported genotyping results and the consensus sequences described in this study, indicated that the genotype primers specific for G12 and P[4] might require revision...
January 11, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30641150/the-short-chain-dehydrogenases-reductases-sdr-gene-a-new-specific-target-for-rapid-detection-of-mycobacterium-tuberculosis-complex-by-modified-comparative-genomic-analysis
#8
Reza Kamali Kakhki, Alireza Neshani, Mojtaba Sankian, Kiarash Ghazvini, Amin Hooshyar, Mahsa Sayadi
BACKGROUND: Early detection of tuberculosis is one of the crucial steps for TB control. Although, the sensitivity of conventional methods like Lowenstein Jensen (LJ) culture and direct staining is quite low, molecular techniques like polymerase chain reaction (PCR) are more sensitive and be considered as useful tools for rapid detection of tuberculosis. Various genes like IS6110 and mpb64 have been used as target for detection of M. tuberculosis, but more research is needed to find the most specific targets...
January 11, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639546/astrovirus-evolution-and-emergence
#9
Nicholas Wohlgemuth, Rebekah Honce, Stacey Schultz-Cherry
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown...
January 10, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639545/genetic-diversity-of-trypanosomes-pathogenic-to-livestock-in-tsetse-flies-from-the-nech-sar-national-park-in-ethiopia-a-concern-for-tsetse-suppressed-area-in-southern-rift-valley
#10
Carla M F Rodrigues, Herakles A Garcia, Desie Sheferaw, Adriana C Rodrigues, Carlos L Pereira, Erney P Camargo, Marta M G Teixeira
In Ethiopia, home to the largest African herd of cattle, animal trypanosomiasis is a major constraint to the efforts made for food self-sufficiency. We searched for trypanosomes in tsetse flies caught in the Nech Sar National Park (NSNP), Southern Rifty Valley, Ethiopia, at the district of Arba Minch where intensive tsetse control is successfully improving cattle productivity. Despite narrow geographical and temporal scales of our survey, we found a remarkable diversity of trypanosomes using the sensitive and discriminative method of fluorescent fragment length barcoding...
January 10, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639544/differential-interaction-strategies-of-hepatitis-c-virus-genotypes-during-entry-an-in-silico-investigation-of-envelope-glycoprotein-e2-cd81-interaction
#11
Chayan Bhattacharjee, Suman K Nandy, Pratik Das, Aparna Mukhopadhyay
Hepatitis C Virus is a blood borne pathogen responsible for chronic hepatitis in >71 million people. Wide variations across strains and genotypes are one of the major hurdles in therapeutic development. While genotype 1 remains the most extensively studied and abundant strain, genotype 3 is more virulent and second most prevalent. This study aimed to compare differences in the glycoprotein E2 across HCV genotypes at nucleotide, protein and structural levels. Nucleotide sequences of E2 from 29 strains across genotypes 1a, 1b, 3a and 3b revealed a stark preference for C-richness which was attributed to a distinct bias for C-rich codons in genotype 1...
January 10, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639520/vitamin-d-mediated-attenuation-of-mir-155-in-human-macrophages-infected-to-dengue-virus-implications-for-the-cytokine-response
#12
John F Arboleda, Geysson J Fernandez, Silvio Urcuqui-Inchima
Clinical manifestations of dengue disease rely on complex interactions between dengue virus (DENV) and host factors that drive altered immune responses, including excessive inflammation. We have recently established that vitamin D can modulate DENV-induced cytokine responses and restrict infection in human macrophages. Cytokine responses are finely regulated by several homeostatic mechanisms, including microRNAs (miRNAs) that can rapidly target specific genes involved in the control of immune signaling pathways...
January 9, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639519/molecular-evolution-and-characterization-of-novel-seneca-valley-virus-svv-strains-in-south-china
#13
Minmin Wang, Lulu Chen, Shuonan Pan, Chunxiao Mou, Kaichuang Shi, Zhenhai Chen
Seneca Valley virus (SVV) is an emerging swine virus associated with porcine vesicular disease. From June to the end of 2017, five SVV strains were isolated from the swine herds in Guangdong, China. Complete genomic sequences of these newly discovered SVV strains were analyzed by genomic and phylogenetic analysis. The results revealed that these SVV strains could be grouped into five genetic branches together with most of other Chinese strains. Interestingly, it is for the first time that a stretch of 11-nucleotide insertion was found in the 5' UTR region of SVV GD04/2017 strain...
January 9, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30639518/genetic-diversity-of-human-parechoviruses-in-stool-samples-germany
#14
Corinna Pietsch, Uwe G Liebert
Human parechoviruses (HPeV) are ubiquitous and mainly occur in early infancy. They are known to cause various clinical manifestations including acute gastroenteritis. To gain insight into the diversity of circulating HPeV genotypes, stool samples from patients (n = 539) with clinical signs of infectious gastroenteritis which showed negative results for other common viral and bacterial enteric pathogens were obtained during three years, 2008 to 2010. Real-time RT-PCR showed HPeV RNA in 34 (6.3%) of the samples...
January 9, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30634001/monkeypox-virus-phylogenetic-similarities-between-a-human-case-detected-in-cameroon-in-2018-and-the-2017-2018-outbreak-in-nigeria
#15
Serge Alain Sadeuh-Mba, Martial Gide Yonga, Mathieu Els, Christophe Batejat, Sara Eyangoh, Valérie Caro, Etoundi Alain, Elisabeth Carniel, Richard Njouom
A monkeypox virus was detected from a human clinical case in 2018 in Cameroon; a country where no human cases were reported since 1989. The virus exhibited close genetic relatedness with another monkeypox virus isolated in Nigeria during the 2017-2018 outbreak. Although our molecular findings argue in favor of an extension of the monkeypox outbreak from Nigeria into Cameroon, the possibility that the monkeypox virus detected could be indigenous to Cameroon cannot be ruled out.
January 8, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30615950/-1-h-nuclear-magnetic-resonance-based-metabolic-profiling-of-cerebrospinal-fluid-to-identify-metabolic-features-and-markers-for-tuberculosis-meningitis
#16
Peixu Zhang, Weiguanliu Zhang, Yue Lang, Yan Qu, Jiafeng Chen, Li Cui
BACKGROUND: Tuberculosis meningitis (TBM) is the most severe form of tuberculosis, and currently lacks efficient diagnostic approaches. Metabolomics has the potential to differentiate patients with TBM from those with other forms of meningitis and meningitis-negative individuals. However, no systemic metabolomics research has compared the cerebrospinal fluid (CSF) of these patients. METHODS: 1 H nuclear magnetic resonance (NMR) was used for CSF metabolic profiling...
January 4, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30611743/genome-wide-analysis-of-the-ovodefensin-gene-family-monophyletic-origin-independent-gene-duplication-and-presence-of-different-selection-patterns
#17
Long Zhang, Dongmei Chen, Lintian Yu, Yi Wei, Juan Li, Caiquan Zhou
Ovodefensins (OvoDs) represent a group of cysteine-rich host defense peptides that are abundant in the egg white. Recent studies have found that ovodefensins are specific to birds and reptiles. However, the entire repertoire and evolutionary relationships of this gene family have not been thoroughly elucidated to date. Following our cross-species and genome-wide computational study, a total of 94 ovodefensin genes with multiple novel cysteine sequence motifs were identified from 22 phylogenetically divergent species...
January 3, 2019: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30597207/genomic-epidemiological-investigation-of-a-streptococcus-suis-outbreak-in-guangxi-china-2016
#18
Wenhua Huang, Mingliu Wang, Huaijie Hao, Ruifu Yang, Jijie Xie, Jinhong Su, Mei Lin, Yujun Cui, Yongqiang Jiang
In June 2016, a Streptococcus suis outbreak occurred in Guangxi, China. We determined the genetic characteristics of six clinically isolated strains by serotyping, PCR, and whole-genome sequencing, performing genome epidemiology analysis on these and 961 public available S. suis genomes. We also classified the first sequence type ST665 human case. Sporadic and outbreak cases were distinguished by whole-genome sequencing and phylogenomics. This approach could help to prevent and control S. suis epidemics in Guangxi and the wider region...
December 28, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30594654/selective-sweep-and-phylogenetic-models-for-the-emergence-and-spread-of-pyrimethamine-resistance-mutations-in-plasmodium-vivax
#19
Ayaz Shaukat, Qasim Ali, Timothy Connelley, Muhammad Azmat Ullah Khan, Mushtaq A Saleem, Mike Evans, Imran Rashid, Neil D Sargison, Umer Chaudhry
Pyrimethamine resistance is a major concern for the control of human haemoprotozoa, especially Plasmodium species. Currently, there is little understanding of how pyrimethamine resistance developed in Plasmodium vivax in the natural field conditions. Here, we present for the first time evidence of positive selection pressure on a dihydrofolate reductase locus and its consequences on the emergence and the spread of pyrimethamine resistance in P. vivax in the Punjab province of Pakistan. First, we examined the dihydrofolate reductase locus in 38 P...
December 27, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30593925/macro-geographical-specificities-of-the-prevailing-tuberculosis-epidemic-as-seen-through-sitvit2-an-updated-version-of-the-mycobacterium-tuberculosis-genotyping-database
#20
David Couvin, Audrey David, Thierry Zozio, Nalin Rastogi
In order to provide a global overview of genotypic, epidemiologic, demographic, phylogeographical, and drug resistance characteristics related to the prevailing tuberculosis (TB) epidemic, we hereby report an update of the 6th version of the international genotyping database SITVIT2. We also make all the available information accessible through a dedicated website (available at http://www.pasteur-guadeloupe.fr:8081/SITVIT2). Thanks to the public release of SITVIT2 which is currently the largest international multimarker genotyping database with a compilation of on 111,635 clinical isolates from 169 countries of patient origin (131 countries of isolation, representing 1032 cities), our major aim is to highlight macro- and micro-geographical cleavages and phylogeographical specificities of circulating Mycobacterium tuberculosis complex (MTBC) clones worldwide...
December 26, 2018: Infection, Genetics and Evolution
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