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Viral evolution

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https://www.readbyqxmd.com/read/28222765/new-h6-influenza-virus-reassortment-strains-isolated-from-anser-fabalis-in-anhui-province-china
#1
Ye Ge, Hongliang Chai, Zhiqiang Fan, Xianfu Wang, Qiucheng Yao, Jian Ma, Si Chen, Yuping Hua, Guohua Deng, Hualan Chen
BACKGROUND: H6 subtype avian influenza viruses are globally distributed and, in recent years, have been isolated with increasing frequency from both domestic and wild bird species as well as infected humans. Many reports have examined the viruses in the context of poultry or several wild bird species, but there is less information regarding their presence in migratory birds. METHODS: Hemagglutination and hemagglutination inhibition tests were used to measure HA activity for different HA subtypes...
February 21, 2017: Virology Journal
https://www.readbyqxmd.com/read/28222327/diversity-evolution-and-population-dynamics-of-avian-influenza-viruses-circulating-in-the-live-poultry-markets-in-china
#2
Liang-Jun Chen, Xian-Dan Lin, Jun-Hua Tian, Yong Liao, Xu-Hua Ying, Jian-Wei Shao, Bin Yu, Jing-Jing Guo, Miao-Ruo Wang, Ying Peng, Mang Shi, Edward C Holmes, Zhan-Qiu Yang, Yong-Zhen Zhang
Live poultry markets (LPMs) are an important source of novel avian influenza viruses (AIV). During 2015-2016 we surveyed AIV diversity in ten LPMs in Hubei, Zhejiang and Jiangxi provinces, China. A high diversity and prevalence of AIVs (totaling 12 subtypes) was observed in LPMs in these provinces. Strikingly, however, the subtypes discovered during 2015-2016 were markedly different to those reported by us in these same localities one year previously, suggesting a dynamic shift in viral genetic diversity over the course of a single year...
February 18, 2017: Virology
https://www.readbyqxmd.com/read/28220254/hiv-1-persistent-viremia-is-frequently-followed-by-episodes-of-low-level-viremia
#3
Marek Widera, Miriam Dirks, Barbara Bleekmann, Robert Jablonka, Martin Däumer, Hauke Walter, Robert Ehret, Jens Verheyen, Stefan Esser
After the start of antiretroviral therapy (ART), plasma HIV-RNA levels should fall below the limit of detection (LOD) within 24 weeks. Hence, the prolonged decline of HIV-RNA after ART initiation is defined as persistent viremia (PV). In this retrospective study, we analyzed factors associated with PV. Next-generation sequencing of viral RNA/DNA was performed to study viral evolution and the emergence of drug-resistance mutations in HIV-infected patients with PV (n = 20). In addition, HIV-DNA species, immunological parameters, and clinical data of the patients were analyzed...
February 20, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28220205/global-properties-of-nested-network-model-with-application-to-multi-epitope-hiv-ctl-dynamics
#4
Cameron Browne
Mathematical modeling and analysis can provide insight on the dynamics of ecosystems which maintain biodiversity in the face of competitive and prey-predator interactions. Of primary interests are the underlying structure and features which stabilize diverse ecological networks. Recently Korytowski and Smith (Theor Ecol 8(1):111-120, 2015) proved that a perfectly nested infection network, along with appropriate life history trade-offs, leads to coexistence and persistence of bacteria-phage communities in a chemostat model...
February 20, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28213477/soft-selective-sweeps-in-evolutionary-rescue
#5
Benjamin A Wilson, Pleuni S Pennings, Dmitri A Petrov
Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28211464/molecular-basis-of-abhd5-lipolysis-activation
#6
Matthew A Sanders, Huamei Zhang, Ljiljana Mladenovic, Yan Yuan Tseng, James G Granneman
Alpha-beta hydrolase domain-containing 5 (ABHD5), the defective gene in human Chanarin-Dorfman syndrome, is a highly conserved regulator of adipose triglyceride lipase (ATGL)-mediated lipolysis that plays important roles in metabolism, tumor progression, viral replication, and skin barrier formation. The structural determinants of ABHD5 lipolysis activation, however, are unknown. We performed comparative evolutionary analysis and structural modeling of ABHD5 and ABHD4, a functionally distinct paralog that diverged from ABHD5 ~500 million years ago, to identify determinants of ABHD5 lipolysis activation...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209121/evolution-of-toll-like-receptors-in-the-context-of-terrestrial-ungulates-and-cetaceans-diversification
#7
Edson Ishengoma, Morris Agaba
BACKGROUND: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined...
February 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28207500/strategic-use-of-dual-regimens-of-boosted-protease-inhibitors-plus-maraviroc-in-poorly-adherent-subjects-in-view-of-long-acting-drugs-a-retrospective-study
#8
Amedeo Ferdinando Capetti, Mariangela Micale, Laura Carenzi, Fosca Niero, Simona Landonio, Stefania Vimercati, Gianfranco Dedivitiis, Giuliano Rizzardini
In view of the forthcoming long-acting antiretrovirals, measures should be taken to prevent the selection of HIV drug resistance mutations. All subjects who had been switched to boosted protease inhibitors plus maraviroc (bPIs/MVC) with baseline HIV-1 RNA >50 copies/mL between June, 2014, and April, 2015, were retrospectively evaluated. HIV-1 RNA, CD4+ T-cells, serum glucose, creatinine, ALT, and adverse events were controlled every 3 to 4 months. We retrospectively analyzed 44 patients: 18 were taking darunavir/ritonavir (DRV/r) and 26 atazanavir/ritonavir (ATV/r) once daily, plus MVC 300 mg once daily...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28202767/genotype-specific-evolution-of-hepatitis-e-virus
#9
Adam B Brayne, Bethany L Dearlove, James S Lester, Sergei L Kosakovsky Pond, Simon D W Frost
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilise this natural case-control study for investigating the evolution of zoonotic viruses compared to single host viruses, using 244 near full length HEV genomes. Genome wide estimates of dN/dS located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype specific evolution of these regions may reflect their fitness...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28194314/evolutionary-and-functional-implications-of-hypervariable-loci-within-the-skin-virome
#10
Geoffrey D Hannigan, Qi Zheng, Jacquelyn S Meisel, Samuel S Minot, Frederick D Bushman, Elizabeth A Grice
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers...
2017: PeerJ
https://www.readbyqxmd.com/read/28191658/interpatient-mutational-spectrum-of-human-coronavirus-oc43-revealed-by-illumina-sequencing
#11
Geoffrey J Gorse, Gira B Patel, Xiaofeng Fan
Human coronaviruses (HCoV) are RNA viruses that cause respiratory tract infections with viral replication of limited duration. The host and viral population heterogeneity could influence clinical phenotypes. Employing long RT-PCR with Illumina sequencing, we quantified the gene mutation load at 0.5% mutation frequency for the 4,529 bp-domain spanning the Spike gene (4,086 bp) of HCoV-OC43 in four upper respiratory clinical specimens obtained during acute illness. There were a total of 121 mutations for all four HCoV samples with the average number of mutations at 30...
February 12, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28185084/-schistosomose-urog%C3%A3-nitale-et-cancer
#12
A Berry, X Iriart, J Fillaux, J-F Magnaval
The existence of a link between urinary schistosomiasis (US) and bladder carcinoma was first suspected by C. Goebel in 1905. In 1911, A.R Ferguson, who was a professor of Pathology and Microbiology at the Faculty of Medicine in Cairo, published a more detailed survey from 40 autopsies, and reported a likely association of bladder carcinoma with granulomas caused by US. Subsequently, published results from several studies reinforced Ferguson's hypothesis. Moreover, in most countries where US was endemic, association of high prevalence of bladder carcinoma with US had been pointed out...
February 10, 2017: Bulletin de la Société de Pathologie Exotique
https://www.readbyqxmd.com/read/28182717/error-baseline-rates-of-five-sample-preparation-methods-used-to-characterize-rna-virus-populations
#13
Jeffrey R Kugelman, Michael R Wiley, Elyse R Nagle, Daniel Reyes, Brad P Pfeffer, Jens H Kuhn, Mariano Sanchez-Lockhart, Gustavo F Palacios
Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses...
2017: PloS One
https://www.readbyqxmd.com/read/28182609/genetic-polymorphisms-associated-with-liver-disease-progression-in-hiv-hcv-coinfected-patients
#14
Luz M Medrano, María A Jiménez-Sousa, Amanda Fernández-Rodríguez, Salvador Resino
The pathogenic mechanisms of the accelerated progression of liver injury in HIV/HCV coinfection are incompletely understood. The progression of liver disease is variable between individuals having similar risk factors, suggesting that genetic background is an important contributor. The aim of this review is to give a summary of all single nucleotide polymorphisms associated with the severity of liver disease in patients coinfected with HIV and HCV reported in the literature. Therefore, a systematic search for articles published was made, 17 of which were selected for this review...
January 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28178344/comparative-analysis-estimates-the-relative-frequencies-of-co-divergence-and-cross-species-transmission-within-viral-families
#15
Jemma L Geoghegan, Sebastián Duchêne, Edward C Holmes
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28174054/nidovirus-rna-polymerases-complex-enzymes-handling-exceptional-rna-genomes
#16
REVIEW
Clara C Posthuma, Aartjan J W Te Welthuis, Eric J Snijder
Coronaviruses and arteriviruses are distantly related human and animal pathogens that belong to the order Nidovirales. Nidoviruses are characterized by their polycistronic plus-stranded RNA genome, the production of subgenomic mRNAs and the conservation of a specific array of replicase domains, including key RNA-synthesizing enzymes. Coronaviruses (26-34 kilobases) have the largest known RNA genomes and their replication presumably requires a processive RNA-dependent RNA polymerase (RdRp) and enzymatic functions that suppress the consequences of the typically high error rate of viral RdRps...
February 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28171759/viral-evolution-mummy-virus-challenges-presumed-history-of-smallpox
#17
Joel O Wertheim
Despite evidence of smallpox in antiquity, a new study of a 350 year-old Lithuanian child mummy suggests that the global viral genetic diversity circulating during the 20(th) century was only around 200 years old.
February 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28170438/the-effective-rate-of-influenza-reassortment-is-limited-during-human-infection
#18
Ashley Sobel Leonard, Micah T McClain, Gavin J D Smith, David E Wentworth, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, Suman R Das, Anthony S Gilbert, Rob Lambkin-Williams, Geoffrey S Ginsburg, Christopher W Woods, Katia Koelle, Christopher J R Illingworth
We characterise the evolutionary dynamics of influenza infection described by viral sequence data collected from two challenge studies conducted in human hosts. Viral sequence data were collected at regular intervals from infected hosts. Changes in the sequence data observed across time show that the within-host evolution of the virus was driven by the reversion of variants acquired during previous passaging of the virus. Treatment of some patients with oseltamivir on the first day of infection did not lead to the emergence of drug resistance variants in patients...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28167936/small-rna-based-genetic-engineering-for-plant-viral-resistance-application-in-crop-protection
#19
REVIEW
Annum Khalid, Qingling Zhang, Muhammad Yasir, Feng Li
Small RNAs regulate a large set of gene expression in all plants and constitute a natural immunity against viruses. Small RNA based genetic engineering (SRGE) technology had been explored for crop protection against viruses for nearly 30 years. Viral resistance has been developed in diverse crops with SRGE technology and a few viral resistant crops have been approved for commercial release. In this review we summarized the efforts generating viral resistance with SRGE in different crops, analyzed the evolution of the technology, its efficacy in different crops for different viruses and its application status in different crops...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28167595/oropouche-virus-clinical-epidemiological-and-molecular-aspects-of-a-neglected-orthobunyavirus
#20
REVIEW
Jorge Fernando Travassos da Rosa, William Marciel de Souza, Francisco de Paula Pinheiro, Mário Luiz Figueiredo, Jedson Ferreira Cardoso, Gustavo Olszanski Acrani, Márcio Roberto Teixeira Nunes
Oropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal...
February 6, 2017: American Journal of Tropical Medicine and Hygiene
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