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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/28528860/purifying-selection-and-concerted-evolution-of-rna-sensing-toll-like-receptors-in-migratory-waders
#1
Nynke Raven, Simeon Lisovski, Marcel Klaassen, Nathan Lo, Thomas Madsen, Simon Y W Ho, Beata Ujvari
Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have typically focused on their adaptive immune gene repertoires. In this study, we examined the evolution of innate immune genes in three long-distance migratory waders (order Charadriiformes). We analysed two parts of the extracellular domains of two Toll-like receptors (TLR3 and TLR7) involved in virus recognition in the Sanderling (Calidris alba), Red-necked Stint (Calidris ruficollis), and Ruddy Turnstone (Arenaria interpres)...
May 18, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28527973/molecular-analysis-of-group-a-rotaviruses-detected-in-hospitalized-children-from-rawalpindi-pakistan-during-2014
#2
Massab Umair, Bilal Haider Abbasi, Nadia Nisar, Muhammad Masroor Alam, Salmaan Sharif, Shahzad Shaukat, Muhammad Suleman Rana, Adnan Khurshid, Ghulam Mujtaba, Uzma Bashir Aamir, Syed Sohail Zahoor Zaidi
As part of strategy to control diarrheal diseases, World Health Organization (WHO) recommends to include rotavirus vaccines in national immunization programs. Sentinel surveillance networks have been established to monitor rotavirus disease burden and genotype distribution in both pre and post vaccine era in many countries. Unfortunately due to lack of proper surveillance programs, data on rotavirus disease burden and genotype distribution from Pakistan is scarce. We investigated 502 stool samples from children (<5years) hospitalized due to gastroenteritis in Rawalpindi, Pakistan during 2014 for the presence of group A rotavirus (RVA) and its genotypic diversity...
May 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28506839/evolutionary-relationships-among-protein-lysine-deacetylases-of-parasites-causing-neglected-diseases
#3
Larissa L S Scholte, Marina M Mourão, Fabiano Sviatopolk-Mirsky Pais, Jelena Melesina, Dina Robaa, Angela C Volpini, Wolfgang Sippl, Raymond J Pierce, Guilherme Oliveira, Laila A Nahum
The availability of the genomic data of diverse parasites provides an opportunity to identify new drug candidates against neglected tropical diseases affecting people worldwide. Histone modifying enzymes (HMEs) are potential candidates since they play key roles in the regulation of chromatin modifications, thus globally regulating gene expression. Furthermore, aberrant epigenetic states are often associated with human diseases, leading to great interest in HMEs as therapeutic targets. Our work focused on two families of protein lysine deacetylases (HDACs and sirtuins)...
May 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28506840/characterization-of-genome-segments-2-3-and-6-of-epizootic-hemorrhagic-disease-virus-strains-isolated-in-japan-in-1985-2013-identification-of-their-serotypes-and-geographical-genetic-types
#4
Hiroaki Shirafuji, Tomoko Kato, Makoto Yamakawa, Toru Tanaka, Yutaka Minemori, Tohru Yanase
We characterized genome segments 2, 3 and 6 (Seg-2, Seg-3 and Seg-6) of 11 Japanese strains of epizootic hemorrhagic disease (EHD) virus (EHDV) isolated in 1985-2013. The Japanese strains were divisible into two groups based on phylogenetic analyses of the nucleotide sequences of Seg-2 and Seg-6. In both of the phylogenetic trees based on Seg-2 and Seg-6, seven of the 11 Japanese strains were grouped together with EHDV-2 and EHDV-7 strains, and the other four Japanese strains were grouped with EHDV-1 strains...
May 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28506838/phylogenomic-analysis-of-the-complete-sequence-of-a-gastroenteritis-associated-cetacean-adenovirus-bottlenose-dolphin-adenovirus-1-reveals-a-high-degree-of-genetic-divergence
#5
Maja Malmberg, Consuelo Rubio-Guerri, Juliette Hayer, Daniel García-Párraga, Elvira Nieto-Pelegrín, Mar Melero, Teresa Álvaro, Mónica Valls, Jose Manuel Sánchez-Vizcaíno, Sándor Belák, Fredrik Granberg
Adenoviruses are common pathogens in vertebrates, infecting a wide range of hosts, but only having rarely been detected and correlated with disease in cetaceans. This article describes the first complete genomic sequence of a cetacean adenovirus, bottlenose dolphin adenovirus 1 (BdAdV-1), detected in captive bottlenose dolphin population (Tursiops truncatus) suffering from self-limiting gastroenteritis. The complete genome sequence of BdAdV-1 was recovered from data generated by high-throughput sequencing and validated by Sanger sequencing...
May 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28499845/exploring-resistance-pathways-for-first-generation-ns3-4a-protease-inhibitors-boceprevir-and-telaprevir-using-bayesian-network-learning
#6
Lize Cuypers, Pieter Libin, Yoeri Schrooten, Kristof Theys, Velia Chiara Di Maio, Valeria Cento, Maja M Lunar, Frederik Nevens, Mario Poljak, Francesca Ceccherini-Silberstein, Ann Nowé, Kristel Van Laethem, Anne-Mieke Vandamme
Resistance-associated variants (RAVs) have been shown to influence treatment response to direct-acting antivirals (DAAs) and first generation NS3/4A protease inhibitors (PIs) in particular. Interpretation of hepatitis C virus (HCV) genotypic drug resistance remains a challenge, especially in patients who previously failed DAA therapy and need to be retreated with a second DAA based regimen. Bayesian network (BN) learning on HCV sequence data from patients treated with DAAs could provide insight in resistance pathways against PIs for HCV subtypes 1a and 1b, in a similar way as applied before for HIV...
May 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28495649/identification-and-molecular-characterization-of-novel-primate-bocaparvoviruses-from-wild-western-lowland-gorillas-of-moukalaba-doudou-national-park-gabon
#7
Chimene Nze-Nkogue, Masayuki Horie, Shiho Fujita, Eiji Inoue, Etienne-François Akomo-Okoue, Makoto Ozawa, Alfred Ngomanda, Juichi Yamagiwa, Kyoko Tsukiyama-Kohara
Bocaparvoviruses have been studied extensively owing to their ability to cause respiratory illness or gastroenteritis in humans. Some bocaparvoviruses have been detected in non-human primates (gorillas and chimpanzees), but the diversity and evolution of these viruses are not fully understood. In this study, we collected 107 fecal samples from wild western lowland gorillas in Moukalaba-Doudou National Park in Gabon to investigate the presence of bocaparvoviruses. Using a combination of pan-bocaparvovirus PCR and individual identification by microsatellite genotyping, we found that two samples from two apparently healthy infant gorillas were positive for bocaparvovirus...
May 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28495648/complete-genome-sequences-of-two-avian-infectious-bronchitis-viruses-isolated-in-egypt-evidence-for-genetic-drift-and-genetic-recombination-in-the-circulating-viruses
#8
Hassanein H Abozeid, Anandan Paldurai, Sunil K Khattar, Manal A Afifi, Magdy F El-Kady, Ayman H El-Deeb, Siba K Samal
Avian infectious bronchitis virus (IBV) is highly prevalent in chicken populations and is responsible for severe economic losses to poultry industry worldwide. In this study, we report the complete genome sequences of two IBV field strains, CU/1/2014 and CU/4/2014, isolated from vaccinated chickens in Egypt in 2014. The genome lengths of the strains CU/1/2014 and CU/4/2014 were 27,615 and 27,637 nucleotides, respectively. Both strains have a common genome organization in the order of 5'-UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-UTR-poly(A) tail-3'...
May 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28495647/prevalence-of-human-cosavirus-and-saffold-virus-with-an-emergence-of-saffold-virus-genotype-6-in-patients-hospitalized-with-acute-gastroenteritis-in-chiang-mai-thailand-2014-2016
#9
Lucy Menage, Arpaporn Yodmeeklin, Pattara Khamrin, Kattareeya Kumthip, Niwat Maneekarn
Human cosavirus and saffold virus are both newly discovered members of the Picornaviridae family. It has been suggested that these viruses may be the causative agents of acute gastroenteritis. In this study, 1093 stool samples collected from patients with acute gastroenteritis between January 2014 and December 2016, were screened for cosavirus and saffold virus using reverse transcription-polymerase chain reaction. The viral genotypes were then established via nucleotide sequencing. Here, cosavirus was detected in 16 of 1093 stool samples (1...
May 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28495473/genetic-polymorphisms-of-the-p2x7-gene-associated-with-susceptibility-to-and-prognosis-of-pulmonary-tuberculosis
#10
Xianzhi Zheng, Tiecheng Li, Yongzhong Chen, Hongqiu Pan, Zhihai Zhang, Yaoyao Dai, Jianming Wang
In this population-based case control study, we recruited 1601 pulmonary tuberculosis cases and 1526 healthy controls, aiming to investigate the association of genetic polymorphisms of the P2X7 gene with the susceptibility to and prognosis of pulmonary tuberculosis in a Chinese Han population. Five single-nucleotide polymorphisms (SNPs) in the P2X7 gene were genotyped. The odds ratio (OR) or relative risk (RR) together with 95% confidence interval (CI) were used to estimated the effect of genetic polymorphisms on the disease...
May 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28479127/whole-genome-characterization-of-a-naturally-occurring-vancomycin-dependent-enterococcus-faecium-from-a-patient-with-bacteremia
#11
Stephanie L Mitchell, Lisa M Mattei, Kevin Alby
Vancomycin-dependent enterococci are a relatively uncommon phenotype recovered in the clinical laboratory. Recognition and recovery of these isolates are important, to provide accurate identification and susceptibility information to treating physicians. Herein, we describe the recovery of a vancomycin-dependent and revertant E. faecium isolates harboring vanB operon from a patient with bacteremia. Using whole genome sequencing, we found a unique single nucleotide polymorphism (S186N) in the D-Ala-D-Ala ligase (ddl) conferring vancomycin-dependency...
May 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28477974/genetic-and-phylogenetic-characterizations-of-a-novel-genotype-of-highly-pathogenic-avian-influenza-hpai-h5n8-viruses-in-2016-2017-in-south-korea
#12
Young-Il Kim, Su-Jin Park, Hyeok-Il Kwon, Eun-Ha Kim, Young-Jae Si, Ju-Hwan Jeong, In-Won Lee, Hiep Dinh Nguyen, Jin-Jung Kwon, Won Suk Choi, Min-Suk Song, Chul-Joong Kim, Young-Ki Choi
During the outbreaks of highly pathogenic avian influenza (HPAI) H5N6 viruses in 2016 in South Korea, novel H5N8 viruses were also isolated from migratory birds. Phylogenetic analysis revealed that the HA gene of these H5N8 viruses belonged to clade 2.3.4.4, similarly to recent H5Nx viruses, and originated from A/Brk/Korea/Gochang1/14(H5N8), a minor lineage of H5N8 that appeared in 2014 and then disappeared. At least four reassortment events occurred with different subtypes (H5N8, H7N7, H3N8 and H10N7) and a chicken challenge study revealed that they were classified as HPAI viruses according to OIE criteria...
May 3, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28465230/molecular-characterization-and-expression-analysis-of-turtle-protein-in-silkworm-that-is-associated-with-nosema-bombycis-infection
#13
Feng Zhu, Shengyan Xiao, Yonghong Zhang, Yulan Shao, Fenfen Tang, Shiliang Chen, Xingrong Bai
In this report, we describe the cloning and characterization of a member of the immunoglobulin superfamily (IgSF); i.e., Turtle. The cDNA of Turtle was cloned from the silkworm Bombyx mori using the rapid amplification of cDNA ends (RACE) technique. Three isoforms of Bombyx Turtle were obtained, including Bmtutl-464, Bmtutl-519, and Bmtutl-810. The three isoforms had identical 27-amino acid signal peptides and four extracellular immunoglobulin (Ig) domains (IgI-IgIV). Sequence similarity and phylogenic analysis indicated that Bmtutl-810 belongs to the group of insect Turtle isoforms and shares 76...
April 30, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28461205/wide-variety-of-recombinant-strains-of-norovirus-gii-in-pediatric-patients-hospitalized-with-acute-gastroenteritis-in-thailand-during-2005-to-2015
#14
Kanittapon Supadej, Pattara Khamrin, Kattareeya Kumthip, Pakawat Kochjan, Arpaporn Yodmeeklin, Hiroshi Ushijima, Niwat Maneekarn
Norovirus (NoV) has been reported as being a common cause of acute gastroenteritis both in children and adults worldwide. Of the many variants, NoV GII.4 is the most predominant genotype. One of the mechanisms that drives the evolution and emergence of new variants of NoV is homologous recombination. This study describes the genetic recombination involved in cases of NoV GII detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand during 2005 to 2015. From a total of 1938 stool samples, 3 (0...
April 28, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28458032/tracing-the-epidemic-history-of-hepatitis-c-virus-genotypes-in-saudi-arabia
#15
Anis Khan, Mohammed Al Balwi, Latifah AlAyyar, Ibrahim AlAbdulkareem, Abdulkareem Albekairy, Abdulrahman Aljumah
HCV genotype 4 is highly prevalent in many Middle Eastern countries, yet little is known about the genotype's epidemic history at the subtype-level in this region. To address the dearth of data from Saudi Arabia (SA) we genotyped 230 HCV isolates in the core/E- and NS5B-region and analyzed using Bayesian phylogenetic approaches. HCV genotype 4 (HCV/4) was positive in 61.7% (142/230) of isolates belonging to 7 different subtypes with the predominance of 4d (73/142; 51.4%) followed by 4a (51/142; 35.9%). Phylogenetic analysis also revealed a distinct epidemiological cluster of HCV/4d for Saudi Arabia...
April 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28456663/comparative-whole-genome-analysis-of-dengue-virus-serotype-2-strains-differing-in-trans-endothelial-cell-leakage-induction-in-vitro
#16
Sneha Singh, M G Anupriya, Easwaran Sreekumar
The role of genetic differences among dengue virus (DENV) in causing increased microvascular permeability is less explored. In the present study, we compared two closely related DENV serotype-2 strains of Cosmopolitan genotype for their in vitro infectivity phenotype and ability to induce trans-endothelial leakage. We found that these laboratory strains differed significantly in infecting human microvascular endothelial cells (HMEC-1) and hepatocytes (Huh7), two major target cells of DENV in in vivo infections...
April 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28456662/new-mitogenome-and-nuclear-evidence-on-the-phylogeny-and-taxonomy-of-the-highly-zoonotic-tapeworm-echinococcus-granulosus-sensu-stricto
#17
Liina Kinkar, Teivi Laurimäe, Mitra Sharbatkhori, Hossein Mirhendi, Eshrat Beigom Kia, Francisco Ponce-Gordo, Vanessa Andresiuk, Sami Simsek, Antti Lavikainen, Malik Irshadullah, Gérald Umhang, Myriam Oudni-M'rad, Gerardo Acosta-Jamett, Steffen Rehbein, Urmas Saarma
Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1-G8 and G10) of which G1-G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that G1-G3 could be regarded as a distinct species E. granulosus sensu stricto (s. s.), the evidence to support this is inconclusive. Most importantly, data from nuclear DNA that provide means to investigate the exchange of genetic material between G1-G3 is lacking as none of the published nuclear DNA studies have explicitly included G2 or G3...
April 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28450084/identification-of-a-novel-canine-norovirus
#18
Livia Bodnar, Eleonora Lorusso, Barbara Di Martino, Cristiana Catella, Gianvito Lanave, Gabriella Elia, Krisztián Bányai, Canio Buonavoglia, Vito Martella
By screening a collection of fecal samples from young dogs from different European countries, noroviruses (NoVs) were found in 13/294 (4.4%) animals with signs of enteritis whilst they were not detected in healthy dogs (0/42). An informative portion of the genome (3.4kb at the 3' end) was generated for four NoV strains. In the capsid protein VP1 region, strains 63.15/2015/ITA and FD53/2007/ITA were genetically related to the canine GVI.2 strain C33/Viseu/2007/PRT (97.4-98.6% nt and 90.3-98.6% aa). Strain FD210/2007/ITA displayed the highest identity to the GVI...
April 24, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28442437/characterization-of-enterotoxigenic-escherichia-coli-strains-isolated-from-the-massive-multi-pathogen-gastroenteritis-outbreak-in-the-antofagasta-region-following-the-chilean-earthquake-2010
#19
David Montero, Maricel Vidal, Mirka Pardo, Alexia Torres, Eduardo Kruger, Mauricio Farfán, Miguel O'Ryan, Qingwei Luo, James Fleckenstein, Felipe Del Canto, Roberto Vidal
In March 2010, a massive outbreak of gastroenteritis started in the region of Antofagasta (northern Chile). The outbreak was mainly attributed to Norovirus genogroup II although ETEC strains were also isolated with high frequency from clinical samples. We review this outbreak and determined that ETEC was an underestimated etiologic agent.
April 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28438670/epidemiological-features-and-genetic-characterization-of-virus-strains-in-rotavirus-associated-gastroenteritis-in-children-of-odisha-in-eastern-india
#20
Eileena Mohanty, Bhagirathi Dwibedi, S K Kar, A S Acharya
We have studied the clinical characteristics, severity and seasonality of rotavirus infection and prevalent genotypes in 652 non-rota vaccinated children in Odisha in eastern India. P genotypes were analysed for their association with host blood group antigens. P type of the virus is determined by the VP8* gene, and specific recognition of A - type of Histo - blood group antigen by P[14]VP8* has been reported. VP4, VP7 and VP6 genes of commonly identified G1P[8] strain were compared with genes of the same strain isolated from other parts of India, elsewhere and strains used for Rotarix and Rotateq vaccines...
April 21, 2017: Infection, Genetics and Evolution
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