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https://www.readbyqxmd.com/read/28822699/extent-and-evolution-of-gene-duplication-in-dna-viruses
#1
Yuxia Gao, Huayao Zhao, Yin Jin, Xiaoyu Xu, Guan-Zhu Han
Gene duplication is the main source of genomic novelties and complexities for both eukaryotes and prokaryotes. In contrast, gene duplication appears to be infrequent in the RNA viruses. However, the extent and evolution of gene duplication in DNA viruses remains obscure. Here we perform a genome-wide analysis of gene duplication in the genomes of 250 DNA viruses that represent all known DNA viral genera. While no gene duplication event is identified in single stranded DNA (ssDNA) or reverse transcribing DNA viruses, gene duplication is frequent among double stranded DNA (dsDNA) viruses...
August 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28818736/co-option-of-endogenous-viral-sequences-for-host-cell-function
#2
REVIEW
John A Frank, Cédric Feschotte
Eukaryotic genomes are littered with sequences of diverse viral origins, termed endogenous viral elements (EVEs). Here we used examples primarily drawn from mammalian endogenous retroviruses to document how the influx of EVEs has provided a source of prefabricated coding and regulatory sequences that were formerly utilized for viral infection and replication, but have been occasionally repurposed for cellular function. While EVE co-option has benefited a variety of host biological functions, there appears to be a disproportionate contribution to immunity and antiviral defense...
August 14, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28815119/extracting-geographic-locations-from-the-literature-for-virus-phylogeography-using-supervised-and-distant-supervision-methods
#3
Davy Weissenbacher, Abeed Sarker, Tasnia Tahsin, Matthew Scotch, Graciela Gonzalez
The field of phylogeography allows researchers to model the spread and evolution of viral genetic sequences. Phylogeography plays a major role in infectious disease surveillance, viral epidemiology and vaccine design. When conducting viral phylogeographic studies, researchers require the location of the infected host of the virus, which is often present in public databases such as GenBank. However, the geographic metadata in most GenBank records is not precise enough for many phylogeographic studies; therefore, researchers often need to search the articles linked to the records for more information, which can be a tedious process...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814646/the-intracellular-immune-receptor-sw-5b-confers-broad-spectrum-resistance-to-tospoviruses-through-recognition-of-a-conserved-21-amino-acid-viral-effector-epitope
#4
Min Zhu, Lei Jiang, Baohui Bai, Wenyang Zhao, Xiaojiao Chen, Jia Li, Yong Liu, Zhengqiang Chen, Boting Wang, Chunli Wang, Qian Wu, Qian-Hua Shen, Savithramma P Dinesh-Kumar, Xiaorong Tao
Plants use both cell surface-resident pattern-recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat (NLR) receptors to detect various pathogens. Plant PRRs typically recognize conserved pathogen-associated molecular patterns (PAMPs) to provide broad-spectrum resistance. By contrast, plant NLRs generally detect pathogen strain-specific effectors and confer race-specific resistance. Here, we demonstrate that the tomato NLR Sw-5b confers broad-spectrum resistance against American type tospoviruses by recognizing a conserved 21-amino-acid peptide region within viral movement protein NSm (NSm21)...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28814525/structure-guided-functional-annotation-of-the-influenza-a-virus-ns1-protein-reveals-dynamic-evolution-of-the-p85%C3%AE-binding-site-during-circulation-in-humans
#5
Antonio M Lopes, Patricia Domingues, Roland Zell, Benjamin G Hale
Rational characterization of virulence and host-adaptive markers in the multifunctional influenza A virus NS1 protein is hindered by a lack of comprehensive knowledge about NS1-host protein-protein interfaces. Here, we surveyed the impact of amino-acid variation in NS1 at its structurally-defined binding site for host p85β, a regulator of phosphoinositide-3 kinase (PI3K) signaling. Structure-guided alanine-scanning of all viral residues at this interface defined 10 positions contributing to the interaction, with residues 89, 95, 98, 133, 145 and 162 being most important...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28814516/baculovirus-molecular-evolution-via-gene-turnover-and-recurrent-positive-selection-of-key-genes
#6
Tom Hill, Robert L Unckless
Hosts and viruses are locked in an evolutionary arms race. Hosts are constantly evolving to suppress virulence and replication, while viruses, reliant on host machinery for survival and reproduction, develop counter-strategies to escape this immune defense. Viruses must also adapt to novel conditions when establishing themselves in a host species. Both processes provide strong selection for viral adaptation. Understanding adaptive evolution in insect viruses can help us better understand adaptive evolution in general, and is important due to their use as biocontrol agents, and for protecting ecologically or economically important species from outbreaks...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28812721/predicting-evolution
#7
Michael Lässig, Ville Mustonen, Aleksandra M Walczak
The face of evolutionary biology is changing: from reconstructing and analysing the past to predicting future evolutionary processes. Recent developments include prediction of reproducible patterns in parallel evolution experiments, forecasting the future of individual populations using data from their past, and controlled manipulation of evolutionary dynamics. Here we undertake a synthesis of central concepts for evolutionary predictions, based on examples of microbial and viral systems, cancer cell populations, and immune receptor repertoires...
February 21, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28805638/nonretroviral-integrated-rna-viruses-in-arthropod-vectors-an-occasional-event-or-something-more
#8
REVIEW
Ken E Olson, Mariangela Bonizzoni
With few exceptions, all arthropod-borne viruses (arboviruses) are nonretroviral RNA viruses (NRVs). Despite NRVs do not encode reverse transcriptases and integrases, NRVs-DNA fragments are detected in mosquito cells and mosquitoes at early stages of infection as episomal DNA forms. Additionally, next generation sequencing and bioinformatics analyses have convincingly shown NRVs-vDNA integrated in vector genomes. We hypothesize vDNA role may be linked to host immunity and viral persistence. Key questions remain about nonretroviral integrated RNA virus sequences (NIRVS) in mosquitoes such as what is driving vDNA synthesis from NRVs, how does integration occur and what is their biological function...
August 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28803141/the-poly-proline-tail-of-sivmac-vpx-provides-gain-of-function-for-resistance-to-a-cryptic-proteasome-dependent-degradation-pathway
#9
Nannan Zhang, Haoran Guo, Jiaxin Yang, Guanchen Liu, Shuang Li, Siying Li, Dongyin Wang, Rui Li, Chang Shu, Hongmei Xu, Zhentong Wei, Honglan Huang, Songling Zhang, Pujun Gao, Shan Cen, Richard Markham, Yongsheng Wang, Xiao-Fang Yu, Wei Wei
The lentiviral accessory protein Vpx is critical for viral infection of myeloid cells and acts by hijacking CRL4(DCAF1) E3 ubiquitin ligase to induce the degradation of the host restriction factor SAMHD1. It has been observed that the sequences from HIV-2 and SIVsmm/SIVmac Vpx contain a poly-proline tail which is distinct from other SIV Vpx proteins. However, the role of this region in Vpx function is controversial. Herein, we found proteasome-dependent degradation of a Vpx mutant lacking the poly-proline tail in the nucleus in a CRL4(DCAF1) E3 ligase-independent fashion...
August 10, 2017: Virology
https://www.readbyqxmd.com/read/28802713/detecting-exact-breakpoints-of-deletions-with-diversity-in-hepatitis-b-viral-genomic-dna-from-next-generation-sequencing-data
#10
Ji-Hong Cheng, Wen-Chun Liu, Ting-Tsung Chang, Sun-Yuan Hsieh, Vincent S Tseng
Many studies have suggested that deletions of Hepatitis B Viral (HBV) are associated with the development of progressive liver diseases, even ultimately resulting in hepatocellular carcinoma (HCC). Among the methods for detecting deletions from next-generation sequencing (NGS) data, few methods considered the characteristics of virus, such as high evolution rates and high divergence among the different HBV genomes. Sequencing high divergence HBV genome sequences using the NGS technology outputs millions of reads...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28800954/a-tim-3-oligonucleotide-aptamer-enhances-t-cell-functions-and-potentiates-tumor-immunity-in-mice
#11
Tal Gefen, Iris Castro, Darija Muharemagic, Yvonne Puplampu-Dove, Shradha Patel, Eli Gilboa
T cell immunoglobulin-3 (TIM-3) is a negative regulator of interferon-γ (IFN-γ) secreting CD4(+) T cells and CD8(+) T cytotoxic cells. Recent studies have highlighted the role of TIM-3 as an important mediator of CD8(+) T cell exhaustion in the setting of chronic viral infections and cancer. In murine tumor models, antibody blockade of TIM-3 with anti-TIM-3 antibodies as monotherapy has no or minimal antitumor activity, suggesting that TIM-3 signaling exerts an accessory or amplifying effect in keeping immune responses in check...
August 8, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28800289/viral-master-circuits-from-discovery-to-new-therapy-targets
#12
Anand Pai, Leor S Weinberger
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates)...
August 11, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28798064/accurate-rna-consensus-sequencing-for-high-fidelity-detection-of-transcriptional-mutagenesis-induced-epimutations
#13
Kate S Reid-Bayliss, Lawrence A Loeb
Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing...
August 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28797655/n-glycan-profiles-in-h9n-2-avian-influenza-viruses-from-chicken-eggs-and-human-embryonic-lung-fibroblast-cells
#14
Wentian Chen, Yaogang Zhong, Rui Su, Huicai Qi, Weina Deng, Yu Sun, Tianran Ma, Xilong Wang, Hanjie Yu, Xiurong Wang, Zheng Li
N-glycosylation can affect the host specificity, virulence and infectivity of influenza A viruses (IAVs). In this study, the distribution and evolution of N-glycosylation sites in the hemagglutinin (HA) and neuraminidase (NA) of H9N2 virus were explored using phylogenetic analysis. Then, one strain of the H9N2 subtypes was proliferated in the embryonated chicken eggs (ECE) and human embryonic lung fibroblast cells (MRC-5) system. The proliferated viral N-glycan profiles were analyzed by a glycomic method that combined the lectin microarray and MALDI-TOF/TOF-MS...
August 7, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28794047/no-substantial-evidence-for-sexual-transmission-of-minority-hiv-drug-resistance-mutations-in-men-who-have-sex-with-men
#15
Antoine Chaillon, Masato Nakazawa, Joel O Wertheim, Susan J Little, Davey M Smith, Sanjay R Mehta, Sara Gianella
During primary HIV-infection, the presence of minority drug resistant mutations (DRM) may be a consequence of sexual transmission, de novo mutations or technical errors. Baseline blood samples were collected from 24 HIV-infected antiretroviral-naive, genetically- and epidemiologically- linked source and recipient partners, shortly after the recipient's estimated date of infection. An additional 32 longitudinal samples were available from 11 recipients. Deep-sequencing of HIV reverse transcriptase (RT) was performed (Roche/454) and screened for nucleoside and non-nucleoside RT inhibitor DRM...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28794033/ancient-evolution-and-dispersion-of-human-papillomavirus-type-58-variants
#16
Zigui Chen, Wendy C S Ho, Siaw Shi Boon, Priscilla T Y Law, Martin C W Chan, Rob DeSalle, Robert D Burk, Paul K S Chan
Human papillomavirus type 58 is found in 10-18% of cervical cancers in East Asia but rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous since the E7 T20I/G63S variant is more prevalent in East Asia and confers 7-9 fold higher risk for cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28793206/a-model-for-viral-assembly-around-an-explicit-rna-sequence-generates-an-implicit-fitness-landscape
#17
Eric Charles Dykeman
Previously, a stochastic model of single-stranded RNA virus assembly was created to model the cooperative effects between capsid proteins and genomic RNA that would occur in a packaging signal-mediated assembly process. In such an assembly scenario, multiple secondary structural elements from within the RNA, termed "packaging signals" (PS), contact coat proteins and facilitate efficient capsid assembly. In this work, the assembly model is extended to incorporate explicit nucleotide sequence information as well as simple aspects of RNA folding that would be occurring during the RNA/capsid coassembly process...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28791125/nkg2c-memory-like-nk-cells-contribute-to-the-control-of-hiv-viremia-during-primary-infection-optiprim-anrs-147
#18
Françoise Gondois-Rey, Antoine Chéret, Samuel Granjeaud, Françoise Mallet, Ghislain Bidaut, Camille Lécuroux, Mickaël Ploquin, Michaela Müller-Trutwin, Christine Rouzioux, Véronique Avettand-Fenoël, Alessandro Moretta, Gilles Pialoux, Cécile Goujard, Laurence Meyer, Daniel Olive
Natural-killer (NK) cells are important immune effectors during a viral infection. Latent CMV infection is widely spread and was demonstrated to shape the NK cell repertoire through the NKG2C receptor. An expansion of NKG2C(+) NK cells has been reported during primary HIV infection (PHI), but their role is not known. We previously found a correlation between the maturation state of the NK cell compartment and a lower viral load by studying patients from the ANRS 147 Optiprim trial. We investigated here extensively the NKG2C(+) NK cells at the time of PHI and its evolution after 3 months of early antiretroviral therapy (combination antiretroviral therapy (cART))...
July 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/28783091/evolution-of-influenza-a-virus-by-mutation-and-re-assortment
#19
REVIEW
Wenhan Shao, Xinxin Li, Mohsan Ullah Goraya, Song Wang, Ji-Long Chen
Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics...
August 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28772262/evolution-and-emergence-of-pathogenic-viruses-past-present-and-future
#20
Mohammad K Parvez, Shama Parveen
Incidences of emerging/re-emerging deadly viral infections have significantly affected human health despite extraordinary progress in the area of biomedical knowledge. The best examples are the recurring outbreaks of dengue and chikungunya fever in tropical and sub-tropical regions, the recent epidemic of Zika in the Americas and the Caribbean, and the SARS, MERS, and influenza A outbreaks across the globe. The established natural reservoirs of human viruses are mainly farm animals, and, to a lesser extent, wild animals and arthropods...
August 4, 2017: Intervirology
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