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Viral evolution

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https://www.readbyqxmd.com/read/29924875/in-silico-and-ex-vivo-approaches-indicate-immune-pressure-on-capsid-and-non-capsid-regions-of-coxsackie-b-viruses-in-the-human-system
#1
Rhiannon Kundu, Robin Knight, Meenakshi Dunga, Mark Peakman
Coxsackie B Virus (CBV) infection has been linked to the aetiology of type 1 diabetes (T1D) and vaccination has been proposed as prophylaxis for disease prevention. Serum neutralising antibodies and the presence of viral protein and RNA in tissues have been common tools to examine this potential disease relationship, whilst the role of anti-CBV cytotoxic T cell responses and their targets have not been studied. To address this knowledge gap, we augmented conventional HLA-binding predictive algorithm-based epitope discovery by cross-referencing epitopes with sites of positive natural selection within the CBV3 viral genome, identified using mixed effects models of evolution...
2018: PloS One
https://www.readbyqxmd.com/read/29924338/insect-retroelements-provide-novel-insights-into-the-origin-of-hepatitis-b-viruses
#2
Zhen Gong, Guan-Zhu Han
The origin of hepadnaviruses (Hepadnaviridae), a group of reverse-transcribing DNA viruses that infect vertebrates, remains mysterious. All the known retrotransposons are only distantly related to hepadnaviruses. Here we report the discovery of two novel lineages of retroelements, which we designate hepadnavirus-like retroelement (HEART1 and HEART2), within the insect genomes through screening 1,095 eukaryotic genomes. Both phylogenetic and similarity analyses suggest that the HEART retroelements represent the closest non-viral relatives of hepadnaviruses so far...
June 19, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29924261/-resistance-to-ganciclovir-in-cytomegalovirus-infection-after-heart-transplant-case-report
#3
Christian Rojas-Contreras, Gabriel De la Cruz-Ku, Stalin Vilcarromero, Ruben Villacaqui Ayllon, Bryan Valcarcel-Valdivia
Cytomegalovirus infection after a heart transplant is a recurrent medical condition. Its frequency increases when the donors are serum-positive, and the recipients are serum-negative to this virus. In the pediatric population, the infection only develops in a small percentage and the patients rarely present resistance to conventional treatment with ganciclovir and valganciclovir. We presented the first report of a pediatric case of the cytomegalovirus infection resistant to ganciclovir and valganciclovir after a heart transplant in a Peruvian public hospital with an unusual presentation...
January 2018: Revista Peruana de Medicina Experimental y Salud Pública
https://www.readbyqxmd.com/read/29923677/a-panoptic-uncovering-of-the-dynamical-evolution-of-the-zika-virus-ns5-methyltransferase-binding-site-loops-zeroing-in-on-the-molecular-landscape
#4
Nikita Devnarain, Mahmoud E S Soliman
The global threat of the Zika virus to humanity is real. Innovative and potent anti-Zika virus drugs are still at large, due to the lack of anti-Zika virus drugs that have passed phase 1 trials. Experimental research has revealed novel inhibitors of Zika virus NS5 methyltransferase enzyme. This study has taken a step further to provide insight into the molecular dynamics of Zika virus and inhibitor binding, which have not been established experimentally. Movements of the methyltransferase binding site loops have a large role to play in the methylation of the viral mRNA cap, which is essential for Zika virus replication...
June 20, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29922300/iron-overload-is-associated-with-oxidative-stress-and-nutritional-immunity-during-viral-infection-in-fish
#5
Estefanía Tarifeño-Saldivia, Andrea Aguilar, David Contreras, Luis Mercado, Byron Morales-Lange, Katherine Márquez, Adolfo Henríquez, Camila Riquelme-Vidal, Sebastian Boltana
Iron is a trace element, essential to support life due to its inherent ability to exchange electrons with a variety of molecules. The use of iron as a cofactor in basic metabolic pathways is essential to both pathogenic microorganisms and their hosts. During evolution, the shared requirement of micro- and macro-organisms for this important nutrient has shaped the pathogen-host relationship. Infectious pancreatic necrosis virus (IPNv) affects salmonids constituting a sanitary problem for this industry as it has an important impact on post-smolt survival...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29915597/effects-of-experimental-terrestrialization-on-the-skin-mucus-proteome-of-african-lungfish-protopterus-dolloi
#6
Ryan D Heimroth, Elisa Casadei, Irene Salinas
Animal mucosal barriers constantly interact with the external environment, and this interaction is markedly different in aquatic and terrestrial environments. Transitioning from water to land was a critical step in vertebrate evolution, but the immune adaptations that mucosal barriers such as the skin underwent during that process are essentially unknown. Vertebrate animals such as the African lungfish have a bimodal life, switching from freshwater to terrestrial habitats when environmental conditions are not favorable...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29914091/identification-of-bacteriophage-virion-proteins-using-multinomial-na%C3%A3-ve-bayes-with-g-gap-feature-tree
#7
Yanyuan Pan, Hui Gao, Hao Lin, Zhen Liu, Lixia Tang, Songtao Li
Bacteriophages, which are tremendously important to the ecology and evolution of bacteria, play a key role in the development of genetic engineering. Bacteriophage virion proteins are essential materials of the infectious viral particles and in charge of several of biological functions. The correct identification of bacteriophage virion proteins is of great importance for understanding both life at the molecular level and genetic evolution. However, few computational methods are available for identifying bacteriophage virion proteins...
June 15, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29912912/new-insights-into-the-genetic-diversity-of-leishmania-rna-virus-1-and-its-species-specific-relationship-with-leishmania-parasites
#8
Lilian Motta Cantanhêde, Flavia Gonçalves Fernandes, Gabriel Eduardo Melim Ferreira, Renato Porrozzi, Ricardo de Godoi Mattos Ferreira, Elisa Cupolillo
Cutaneous leishmaniasis is a neglected parasitic disease that manifests in infected individuals under different phenotypes, with a range of factors contributing to its broad clinical spectrum. One factor, Leishmania RNA Virus 1 (LRV1), has been described as an endosymbiont present in different species of Leishmania. LRV1 significantly worsens the lesion, exacerbating the immune response in both experimentally infected animals and infected individuals. Little is known about the composition and genetic diversity of these viruses...
2018: PloS One
https://www.readbyqxmd.com/read/29911108/emerging-application-of-genomics-guided-therapeutics-in-personalized-lung-cancer-treatment
#9
REVIEW
Aubhishek Zaman, Trever G Bivona
In lung cancer, genomics-driven comprehensive molecular profiling has identified novel chemically and immunologically addressable vulnerabilities, resulting in an increasing application of precision medicine by targeted inactivation of tumor oncogenes and immunogenic activation of host anti-tumor surveillance as modes of treatment. However, initially profound response of these targeted therapies is followed by relapse due to therapy-resistant residual disease states. Although distinct mechanisms and frameworks for therapy resistance have been proposed, accounting for and upfront prediction of resistance trajectories has been challenging...
May 2018: Annals of Translational Medicine
https://www.readbyqxmd.com/read/29907741/transmission-clearance-trade-offs-indicate-that-dengue-virulence-evolution-depends-on-epidemiological-context
#10
Rotem Ben-Shachar, Katia Koelle
An extensive body of theory addresses the topic of pathogen virulence evolution, yet few studies have empirically demonstrated the presence of fitness trade-offs that would select for intermediate virulence. Here we show the presence of transmission-clearance trade-offs in dengue virus using viremia measurements. By fitting a within-host model to these data, we further find that the interaction between dengue and the host immune response can account for the observed trade-offs. Finally, we consider dengue virulence evolution when selection acts on the virus's production rate...
June 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29899428/patient-derived-avian-influenza-a-h5n6-virus-is-highly-pathogenic-in-mice-but-can-be-effectively-treated-by-anti-influenza-polyclonal-antibodies
#11
Weiqi Pan, Haojun Xie, Xiaobo Li, Wenda Guan, Peihai Chen, Beiwu Zhang, Mincong Zhang, Ji Dong, Qian Wang, Zhixia Li, Shufen Li, Zifeng Yang, Chufang Li, Nanshan Zhong, Jicheng Huang, Ling Chen
Highly pathogenic avian influenza A (H5N6) virus has been circulating in poultry since 2013 and causes sporadic infections and fatalities in humans. Due to the re-occurrence and continuous evolution of this virus subtype, there is an urgent need to better understand the pathogenicity of the H5N6 virus and to identify effective preventative and therapeutic strategies. We established a mouse model to evaluate the virulence of H5N6 A/Guangzhou/39715/2014 (H5N6/GZ14), which was isolated from an infected patient...
June 13, 2018: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29899102/a-dual-motif-in-the-hemagglutinin-of-h5n1-goose-guangdong-like-hpaiv-is-conserved-from-their-early-evolution-and-increases-both-membrane-fusion-ph-and-virulence
#12
Ute Wessels, El-Sayed M Abdelwhab, Jutta Veits, Donata Hoffmann, Svenja Mamerow, Olga Stech, Jan Hellert, Martin Beer, Thomas C Mettenleiter, Jürgen Stech
Zoonotic highly pathogenic avian influenza viruses (HPAIV) have raised serious public health concerns of a novel pandemic. These strains emerge from low-pathogenic precursors by acquisition of a polybasic hemagglutinin (HA) cleavage site, the prime virulence determinant. However, required co-adaptations of the HA early in HPAIV evolution remained uncertain. To address this question, we generated several HA1/HA2 chimeras and point mutants of an H5N1 clade 2.2.2 HPAIV and an H5N1 low-pathogenic strain. Initial surveys of 3385 HPAIV H5 HA sequences revealed frequencies of 0...
June 13, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29899101/porcine-reproductive-and-respiratory-syndrome-virus-infection-induces-both-eif2%C3%AE-phosphorylation-dependent-and-independent-host-translation-shutoff
#13
Yang Li, Liurong Fang, Yanrong Zhou, Ran Tao, Dang Wang, Shaobo Xiao
Porcine reproductive and respiratory syndrome virus (PRRSV) is an Arterivirus that has caused tremendous economic losses in the global swine industry since it was discovered in the late 1980s. Inducing host translation shutoff is a strategy used by many viruses to optimize their replication and spread. Here, we demonstrate that PRRSV infection causes host translation suppression, which is strongly dependent on viral replication. By screening PRRSV-encoded nonstructural proteins (nsps), we found that nsp2 participates in the induction of host translation shutoff and that its transmembrane (TM) domain is required for this process...
June 13, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29898986/ultrasensitive-capture-of-human-herpes-simplex-virus-genomes-directly-from-clinical-samples-reveals-extraordinarily-limited-evolution-in-cell-culture
#14
Alexander L Greninger, Pavitra Roychoudhury, Hong Xie, Amanda Casto, Anne Cent, Gregory Pepper, David M Koelle, Meei-Li Huang, Anna Wald, Christine Johnston, Keith R Jerome
Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29898985/the-unique-phylogenetic-position-of-a-novel-tick-borne-phlebovirus-ensures-an-ixodid-origin-of-the-genus-phlebovirus
#15
Keita Matsuno, Masahiro Kajihara, Ryo Nakao, Naganori Nao, Akina Mori-Kajihara, Mieko Muramatsu, Yongjin Qiu, Shiho Torii, Manabu Igarashi, Nodoka Kasajima, Keita Mizuma, Kentaro Yoshii, Hirofumi Sawa, Chihiro Sugimoto, Ayato Takada, Hideki Ebihara
The recent emergence of novel tick-borne RNA viruses has complicated the epidemiological landscape of tick-borne infectious diseases, posing a significant challenge to public health systems that seek to counteract tick-borne diseases. The identification of two novel tick-borne phleboviruses (TBPVs), severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV), as causative agents of severe illness in humans has accelerated the investigation and discoveries of novel TBPVs. In the present study, we isolated a novel TBPV designated Mukawa virus (MKWV) from host-questing Ixodes persulcatus females captured in Japan...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29898396/co-evolution-of-hiv-envelope-and-apex-targeting-neutralizing-antibody-lineage-provides-benchmarks-for-vaccine-design
#16
Kimmo Rantalainen, Zachary T Berndsen, Sasha Murrell, Liwei Cao, Oluwarotimi Omorodion, Jonathan L Torres, Mengyu Wu, Jeffrey Umotoy, Jeffrey Copps, Pascal Poignard, Elise Landais, James C Paulson, Ian A Wilson, Andrew B Ward
Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes...
June 12, 2018: Cell Reports
https://www.readbyqxmd.com/read/29895748/long-term-follow-up-of-acute-hepatitis-b-new-insights-in-its-natural-history-and-implications-for-antiviral-treatment
#17
Stefano Menzo, Claudia Minosse, Donatella Vincenti, Laura Vincenzi, Fabio Iacomi, Paola Zaccaro, Gianpiero D'Offizi, Maria R Capobianchi
Acute hepatitis B infection (AHB) is still a common viral acute hepatitis worldwide. As vaccination, antiviral treatment, and immigration are bound to affect the epidemiological landscape of HBV infections, and some of its aspects need to be investigated: (1) the circulation of vaccine escape mutants and of primary drug resistant strains; (2) the change in HBV genotype prevalence; and (3) the clinical implications of AHB and the probability of chronification. The serological, virological, and clinical parameters of 75 patients, acutely infected by HBV, were gathered for a retrospective study...
June 12, 2018: Genes
https://www.readbyqxmd.com/read/29895721/changes-in-the-ev-a71-genome-through-recombination-and-spontaneous-mutations-impact-on-virulence
#18
REVIEW
Madiiha Bibi Mandary, Chit Laa Poh
Enterovirus 71 (EV-A71) is a major etiological agent of hand, foot and mouth disease (HFMD) that mainly affects young children less than five years old. The onset of severe HFMD is due to neurological complications bringing about acute flaccid paralysis and pulmonary oedema. In this review, we address how genetic events such as recombination and spontaneous mutations could change the genomic organization of EV-A71, leading to an impact on viral virulence. An understanding of the recombination mechanism of the poliovirus and non-polio enteroviruses will provide further evidence of the emergence of novel strains responsible for fatal HFMD outbreaks...
June 12, 2018: Viruses
https://www.readbyqxmd.com/read/29895222/novel-roles-for-sm-class-rnas-in-the-regulation-of-gene-expression
#19
Demián Cazalla
Viruses masterfully regulate host gene expression during infection. Many do so, in part, by expressing non-coding RNAs. Recent work has shown that HSUR 2, a viral non-coding RNA expressed by the oncogenic Herpesvirus saimiri, regulates mRNA expression through a novel mechanism. HSUR 2 base pairs with both target mRNAs and host miRNAs in infected cells. This results in HSUR 2-dependent recruitment of host miRNAs and associated Ago proteins to target mRNAs, and the subsequent destabilization of target mRNAs. Using this mechanism, this virus regulates key cellular pathways during viral infection...
June 12, 2018: RNA Biology
https://www.readbyqxmd.com/read/29893205/effective-population-size-differences-in-calomys-musculinus-the-host-of-jun%C3%A3-n-virus-its-relationship-with-the-epidemiological-history-of-argentine-hemorrhagic-fever
#20
Marina B Chiappero, María Florencia Piacenza, María Cecilia Provensal, Gladys E Calderón, Cristina N Gardenal, Jaime J Polop
Argentine hemorrhagic fever (AHF) is a serious endemic disease in Argentina, produced by Junín virus, whose host is the Sigmodontinae rodent Calomys musculinus . Within the endemic area, human incidence and proportion of infected rodents remains high for 5-10 years after the first appearance of the disease (epidemic [E] zone) and then gradually declines to sporadic cases (historic [H] zone). We tested the hypothesis that host populations within the E zone are large and well connected by gene flow, facilitating the transmission and maintenance of the virus, whereas those in the H and nonendemic (NE) zones are small and isolated, with the opposite effect...
June 11, 2018: American Journal of Tropical Medicine and Hygiene
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