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Virus Evolution

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https://www.readbyqxmd.com/read/29977605/ancient-dna-provides-evidence-of-27-000-year-old-papillomavirus-infection-and-long-term-codivergence-with-rodents
#1
Brendan B Larsen, Kenneth L Cole, Michael Worobey
The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29951250/evaluation-of-global-hiv-siv-envelope-gp120-rna-structure-and-evolution-within-and-among-infected-hosts
#2
Brittany Rife Magalis, Sergei L Kosakovsky Pond, Michael F Summers, Marco Salemi
Lentiviral RNA genomes contain structural elements that play critical roles in viral replication. Although structural features of 5'-untranslated regions have been well characterized, attempts to identify important structures in other genomic regions by Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) have led to conflicting structural and mechanistic conclusions. Previous approaches accounted neither for sequence heterogeneity that is ubiquitous in viral populations, nor for selective constraints operating at the protein level...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29942657/viral-attenuation-by-engineered-protein-fragmentation
#3
Daniel J Garry, Andrew D Ellington, Ian J Molineux, James J Bull
A possible but untested method of viral attenuation is protein fragmentation, engineering wild-type proteins as two or more peptides that self-assemble after translation. Here, the bacteriophage T7 was engineered to encode its essential RNA polymerase as two peptides. Initial fitness was profoundly suppressed. Subjecting the engineered virus to over 100 generations of adaptation by serial transfer resulted in a large fitness increase, still remaining below that of evolved wild-type. The fitness increase was accompanied by three substitutions in the fragmented peptides as well as six mutations in other parts of the genome, but the fragmentation was retained...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29942656/bayesian-phylogenetic-and-phylodynamic-data-integration-using-beast-1-10
#4
Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut
The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29942655/patterns-of-genomic-site-inheritance-in-hiv-1m-inter-subtype-recombinants-delineate-the-most-likely-genomic-sites-of-subtype-specific-adaptation
#5
Marcel Tongo, Tulio de Oliveira, Darren P Martin
Recombination between different HIV-1 group M (HIV-1M) subtypes is a major contributor to the ongoing genetic diversification of HIV-1M. However, it remains unclear whether the different genome regions of recombinants are randomly inherited from the different subtypes. To elucidate this, we analysed the distribution within 82 circulating and 201 unique recombinant forms (CRFs/URFs), of genome fragments derived from HIV-1M Subtypes A, B, C, D, F, and G and CRF01_AE. We found that viruses belonging to the analysed HIV-1M subtypes and CRF01_AE contributed certain genome fragments more frequently during recombination than other fragments...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29942654/selective-constraint-and-adaptive-potential-of-west-nile-virus-within-and-among-naturally-infected-avian-hosts-and-mosquito-vectors
#6
Chase W Nelson, Samuel D Sibley, Sergios-Orestis Kolokotronis, Gabriel L Hamer, Christina M Newman, Tavis K Anderson, Edward D Walker, Uriel D Kitron, Jeffrey D Brawn, Marilyn O Ruiz, Tony L Goldberg
Arthropod-borne viruses are among the most genetically constrained RNA viruses, yet they have a remarkable propensity to adapt and emerge. We studied wild birds and mosquitoes naturally infected with West Nile virus (WNV) in a 'hot spot' of virus transmission in Chicago, IL, USA. We generated full coding WNV genome sequences from spatiotemporally matched bird and mosquito samples using high-throughput sequencing, allowing a molecular evolutionary assessment with deep coverage. Mean F ST among samples was 0...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29942653/chikungunya-virus-evolution-following-a-large-3-utr-deletion-results-in-host-specific-molecular-changes-in-protein-coding-regions
#7
Valerie J Morley, María Gabriela Noval, Rubing Chen, Scott C Weaver, Marco Vignuzzi, Kenneth A Stapleford, Paul E Turner
The 3'untranslated region (UTR) in alphavirus genomes functions in virus replication and plays a role in determining virus host range. However, the molecular evolution of virus UTRs is understudied compared to the evolution of protein-coding regions. Chikungunya virus (CHIKV) has the longest 3'UTR among the alphaviruses (500-700 nt), and 3'UTR length and sequence structure vary substantially among different CHIKV lineages. Previous studies showed that genomic deletions and insertions are key drivers of CHIKV 3'UTR evolution...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29876136/easy-and-accurate-reconstruction-of-whole-hiv-genomes-from-short-read-sequence-data-with-shiver
#8
Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Nicholas J Croucher, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle Gourlay, M Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger Kouyos, Oliver Laeyendecker, Kirsi Liitsola, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Marion Cornelissen, Paul Kellam, Peter Reiss, Christophe Fraser
Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29657837/inter-and-intracontinental-migrations-and-local-differentiation-have-shaped-the-contemporary-epidemiological-landscape-of-canine-parvovirus-in-south-america
#9
Sofía Grecco, Gregorio Iraola, Nicola Decaro, Alice Alfieri, Amauri Alfieri, Marina Gallo Calderón, Ana Paula da Silva, Daniela Name, Jaime Aldaz, Lucía Calleros, Ana Marandino, Gonzalo Tomás, Leticia Maya, Lourdes Francia, Yanina Panzera, Ruben Pérez
Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29644097/the-virome-of-drosophila-suzukii-an-invasive-pest-of-soft-fruit
#10
Nathan C Medd, Simon Fellous, Fergal M Waldron, Anne Xuéreb, Madoka Nakai, Jerry V Cross, Darren J Obbard
Drosophila suzukii (Matsumura) is one of the most damaging and costly pests to invade temperate horticultural regions in recent history. Conventional control of this pest is challenging, and an environmentally benign microbial biopesticide is highly desirable. A thorough exploration of the pathogens infecting this pest is not only the first step on the road to the development of an effective biopesticide, but also provides a valuable comparative dataset for the study of viruses in the model family Drosophilidae ...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29644096/cameroonian-fruit-bats-harbor-divergent-viruses-including-rotavirus-h-bastroviruses-and-picobirnaviruses-using-an-alternative-genetic-code
#11
Claude Kwe Yinda, Stephen Mbigha Ghogomu, Nádia Conceição-Neto, Leen Beller, Ward Deboutte, Emiel Vanhulle, Piet Maes, Marc Van Ranst, Jelle Matthijnssens
Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29593882/low-fidelity-venezuelan-equine-encephalitis-virus-polymerase-mutants-to-improve-live-attenuated-vaccine-safety-and-efficacy
#12
Tiffany F Kautz, Mathilde Guerbois, Kamil Khanipov, Edward I Patterson, Rose M Langsjoen, Ruimei Yun, Kelsey L Warmbrod, Yuriy Fofanov, Scott C Weaver, Naomi L Forrester
During RNA virus replication, there is the potential to incorporate mutations that affect virulence or pathogenesis. For live-attenuated vaccines, this has implications for stability, as replication may result in mutations that either restore the wild-type phenotype via reversion or compensate for the attenuating mutations by increasing virulence (pseudoreversion). Recent studies have demonstrated that altering the mutation rate of an RNA virus is an effective attenuation tool. To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29511572/estimating-evolutionary-rates-in-giant-viruses-using-ancient-genomes
#13
Sebastián Duchêne, Edward C Holmes
Pithovirus sibericum is a giant (610 Kpb) double-stranded DNA virus discovered in a purportedly 30,000-year-old permafrost sample. A closely related virus, Pithovirus massiliensis , was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. sibericum was directly ancestral to P. massiliensis and gave a maximum evolutionary rate of 2.60 × 10-5 nucleotide substitutions per site per year (subs/site/year). If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29511571/private-collection-high-correlation-of-sample-collection-and-patient-admission-date-in-clinical-microbiological-testing-complicates-sharing-of-phylodynamic-metadata
#14
Ryan C Shean, Alexander L Greninger
Infectious pathogens are known for their rapid evolutionary rates with new mutations arising over days to weeks. The ability to rapidly recover whole genome sequences and analyze the spread and evolution of pathogens using genetic information and pathogen collection dates has lead to interest in real-time tracking of infectious transmission and outbreaks. However, the level of temporal resolution afforded by these analyses may conflict with definitions of what constitutes protected health information (PHI) and privacy requirements for de-identification for publication and public sharing of research data and metadata...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29484203/unravelling-the-complicated-evolutionary-and-dissemination-history-of-hiv-1m-subtype-a-lineages
#15
Marcel Tongo, Gordon W Harkins, Jeffrey R Dorfman, Erik Billings, Sodsai Tovanabutra, Tulio de Oliveira, Darren P Martin
Subtype A is one of the rare HIV-1 group M (HIV-1M) lineages that is both widely distributed throughout the world and persists at high frequencies in the Congo Basin (CB), the site where HIV-1M likely originated. This, together with its high degree of diversity suggests that subtype A is amongst the fittest HIV-1M lineages. Here we use a comprehensive set of published near full-length subtype A sequences and A-derived genome fragments from both circulating and unique recombinant forms (CRFs/URFs) to obtain some insights into how frequently these lineages have independently seeded HIV-1M sub-epidemics in different parts of the world...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29479479/mosquito-bottlenecks-alter-viral-mutant-swarm-in-a-tissue-and-time-dependent-manner-with-contraction-and-expansion-of-variant-positions-and-diversity
#16
Edward I Patterson, Kamil Khanipov, Mark M Rojas, Tiffany F Kautz, Dedeke Rockx-Brouwer, Georgiy Golovko, Levent Albayrak, Yuriy Fofanov, Naomi L Forrester
Viral diversity is theorized to play a significant role during virus infections, particularly for arthropod-borne viruses (arboviruses) that must infect both vertebrate and invertebrate hosts. To determine how viral diversity influences mosquito infection and dissemination Culex taeniopus mosquitoes were infected with the Venezuelan equine encephalitis virus endemic strain 68U201. Bodies and legs/wings of the mosquitoes were collected individually and subjected to multi-parallel sequencing. Virus sequence diversity was calculated for each tissue...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#17
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29403651/the-influence-of-phylodynamic-model-specifications-on-parameter-estimates-of-the-zika-virus-epidemic
#18
Veronika Boskova, Tanja Stadler, Carsten Magnus
Each new virus introduced into the human population could potentially spread and cause a worldwide epidemic. Thus, early quantification of epidemic spread is crucial. Real-time sequencing followed by Bayesian phylodynamic analysis has proven to be extremely informative in this respect. Bayesian phylodynamic analyses require a model to be chosen and prior distributions on model parameters to be specified. We study here how choices regarding the tree prior influence quantification of epidemic spread in an emerging epidemic by focusing on estimates of the parameters clock rate, tree height, and reproductive number in the currently ongoing Zika virus epidemic in the Americas...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29362671/the-global-origins-of-resistance-associated-variants-in-the-non-structural-proteins-5a-and-5b-of-the-hepatitis-c-virus
#19
Bradley R Jones, Anita Y M Howe, P Richard Harrigan, Jeffrey B Joy
New, costly, fast acting, therapies targeting the non-structural proteins 5A and 5B (NS5A and NS5B) regions of the hepatitis C virus (HCV) genome are curative in the majority of cases. Variants with certain mutations in the NS5A and NS5B regions of HCV have been shown to reduce susceptibility to direct-acting NS5A and NS5B therapy and are found in treatment naïve patients. Despite this, the ease with which these variants evolve is poorly known, as are their evolutionary and geographic origins. To address this crucial gap we inferred the evolutionary and geographic origins of resistance-associated variants (RAVs) in the HCV NS5A and NS5B regions of subtypes 1a, 1b, and 3a sequences available from global databases...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29340211/differences-in-adaptive-dynamics-determine-the-success-of-virus-variants-that-propagate-together
#20
María Arribas, Jacobo Aguirre, Susanna Manrubia, Ester Lázaro
Virus fitness is a complex parameter that results from the interaction of virus-specific characters (e.g. intracellular growth rate, adsorption rate, virion extracellular stability, and tolerance to mutations) with others that depend on the underlying fitness landscape and the internal structure of the whole population. Individual mutants usually have lower fitness values than the complex population from which they come from. When they are propagated and allowed to attain large population sizes for a sufficiently long time, they approach mutation-selection equilibrium with the concomitant fitness gains...
January 2018: Virus Evolution
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