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https://www.readbyqxmd.com/read/28818893/complete-genome-sequence-of-a-hobi-like-virus-isolated-from-a-nelore-cow-with-gastroenteric-disease-in-the-state-of-s%C3%A3-o-paulo-brazil
#1
Adriana Cortez, João Pessoa Araújo, Eduardo Furtado Flores, Márcio Garcia Ribeiro, Jane Megid, Antonio Carlos Paes, José Paes de Oliveira Filho, Leila Sabrina Ullmann, Camila Dantas Malossi, Marcos Bryan Heinemann
The Hobi-like virus presents antigenic and molecular differences in relation to bovine virus diarrhea virus 1 and 2. The description of the complete genome of the Hobi-like virus SV757/15, isolated from a Nelore cow with gastroenteric disease in Brazil, will help in understanding the evolution and diversity of pestiviruses.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818750/whole-genome-sequence-phylogenetic-analysis-of-four-mexican-rabies-viruses-isolated-from-cattle
#2
I Bárcenas-Reyes, E Loza-Rubio, G J Cantó-Alarcón, J Luna-Cozar, A Enríquez-Vázquez, R J Barrón-Rodríguez, F Milián-Suazo
Phylogenetic analysis of the rabies virus in molecular epidemiology has been traditionally performed on partial sequences of the genome, such as the N, G, and P genes; however, that approach raises concerns about the discriminatory power compared to whole genome sequencing. In this study we characterized four strains of the rabies virus isolated from cattle in Querétaro, Mexico by comparing the whole genome sequence to that of strains from the American, European and Asian continents. Four cattle brain samples positive to rabies and characterized as AgV11, genotype 1, were used in the study...
August 4, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28818736/co-option-of-endogenous-viral-sequences-for-host-cell-function
#3
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/28818621/codon-usage-bias-in-the-n-gene-of-rabies-virus
#4
Wanting He, Hongyu Zhang, Yuchen Zhang, Ruyi Wang, Sijia Lu, Yanjie Ji, Chang Liu, Pengkun Yuan, Shuo Su
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure...
August 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28818563/-lower-lymphocyte-response-in-severe-cases-of-acute-bronchiolitis-due-to-respiratory-syncytial-virus
#5
José Miguel Ramos-Fernández, David Moreno-Pérez, Cristina Antúnez-Fernández, Guillermo Milano-Manso, Ana María Cordón-Martínez, Antonio Urda-Cardona
INTRODUCTION: Acute bronchiolitis (AB) of the infant has a serious outcome in 6-16% of the hospital admitted cases. Its pathogenesis and evolution is related to the response of the T lymphocytes. The objective of the present study is to determine if the lower systemic lymphocytic response is related to a worse outcome of AB in hospitalised infants. PATIENTS AND METHOD: Retrospective observational-analytical study of cases-controls nested in a cohort of patients admitted due to RSV-AB between the period from October 2010 to March 2015...
August 14, 2017: Anales de Pediatría: Publicación Oficial de la Asociación Española de Pediatría (A.E.P.)
https://www.readbyqxmd.com/read/28815119/extracting-geographic-locations-from-the-literature-for-virus-phylogeography-using-supervised-and-distant-supervision-methods
#6
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/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
#7
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
#8
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/28812422/novel-influenza-d-virus-epidemiology-pathology-evolution-and-biological-characteristics
#9
Shuo Su, Xinliang Fu, Gairu Li, Fiona Kerlin, Michael Veit
In 2011, a new virus was isolated from pigs with influenza-like symptoms and subsequently also from cattle, which are the main reservoir of the virus. It is similar to Influenza C virus (ICV), a (predominantly) human pathogen, causing respiratory disease in children. Since the virus is unable to reassort with ICV (and based on a number of other criteria as discussed in the text) it is now officially named as Influenzavirus D (IDV), a new genus of the Orthomyxoviridae. We summarize the epidemiology, pathology and evolution of IDV and its biological characteristics with emphasis on the only glycoprotein HEF...
August 16, 2017: Virulence
https://www.readbyqxmd.com/read/28805638/nonretroviral-integrated-rna-viruses-in-arthropod-vectors-an-occasional-event-or-something-more
#10
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/28805635/mosquito-specific-and-mosquito-borne-viruses-evolution-infection-and-host-defense
#11
REVIEW
Rebecca Halbach, Sandra Junglen, Ronald P van Rij
Recent virus discovery programs have identified an extensive reservoir of viruses in arthropods. It is thought that arthropod viruses, including mosquito-specific viruses, are ancestral to vertebrate-pathogenic arboviruses. Mosquito-specific viruses are restricted in vertebrate cells at multiple levels, including entry, RNA replication, assembly, and by the inability to replicate at high temperatures. Moreover, it is likely that the vertebrate immune system suppresses replication of these viruses. The evolution from single to dual-host tropism may also require changes in the course of infection in the mosquito host...
August 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28802713/detecting-exact-breakpoints-of-deletions-with-diversity-in-hepatitis-b-viral-genomic-dna-from-next-generation-sequencing-data
#12
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/28800289/viral-master-circuits-from-discovery-to-new-therapy-targets
#13
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/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/28794221/revised-time-scales-of-rna-virus-evolution-based-on-spatial-information
#15
Moritz Saxenhofer, Vanessa Weber de Melo, Rainer G Ulrich, Gerald Heckel
The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographical information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences...
August 16, 2017: Proceedings. Biological Sciences
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/28792064/evidence-of-increasing-diversification-of-zika-virus-strains-isolated-in-the-american-continent
#18
Fabián Aldunate, Fabiana Gámbaro, Alvaro Fajardo, Martín Soñora, Juan Cristina
Zika virus (ZIKV) is a member of the family Flaviviridae. ZIKV emerged in Brazil in 2015, causing an unprecedented epidemic and since then the virus has rapidly spread throughout the Americas. These facts highlight the need of detailed phylogenetic studies to understand the emergence, spread and evolution of ZIKV populations. For these reasons, a Bayesian coalescent Markov Chain Monte Carlo analysis of complete genome sequences of ZIKV strains recently isolated in the American continent was performed. The results of these studies revealed an increasing diversification of ZIKV strains in different genetic lineages and co-circulation of distinct genetic lineages in several countries in the region...
August 9, 2017: Journal of Medical Virology
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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