keyword
MENU ▼
Read by QxMD icon Read
search

Viral evolution

keyword
https://www.readbyqxmd.com/read/29029274/mutation-driven-parallel-evolution-during-viral-adaptation
#1
Andrew M Sackman, Lindsey W McGee, Anneliese J Morrison, Jessica Pierce, Jeremy Anisman, Hunter Hamilton, Stephanie Sanderbeck, Cayla Newman, Darin R Rokyta
Convergent evolution has been demonstrated across all levels of biological organization, from parallel nucleotide substitutions to convergent evolution of complex phenotypes, but whether instances of convergence are the result of selection repeatedly finding the same optimal solution to a recurring problem or are the product of mutational biases remains unsettled. We generated 20 replicate lineages allowed to fix a single mutation from each of four bacteriophage genotypes under identical selective regimes to test for parallel changes within and across genotypes at the levels of mutational effect distributions and gene, protein, amino acid, and nucleotide changes...
September 27, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029206/dissecting-hiv-virulence-heritability-of-setpoint-viral-load-cd4-t-cell-decline-and-per-parasite-pathogenicity
#2
Frederic Bertels, Alex Marzel, Gabriel Leventhal, Venelin Mitov, Jacques Fellay, Huldrych F Günthard, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Manuel Battegay, Andri Rauch, Matthias Cavassini, Alexandra Calmy, Enos Bernasconi, Patrick Schmid, Alexandra U Scherrer, Viktor Müller, Sebastian Bonhoeffer, Roger Kouyos, Roland R Regoes
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as" per-parasite pathogenicity". Using viral load and CD4+ T cell measures from 2014 HIV-1 subtype B infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence - measured as the rate of decline of CD4+ T cells - and per-parasite pathogenicity are heritable from donor to recipient...
October 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029128/evolution-and-spatio-temporal-dynamics-of-enterovirus-a71-subgenogroups-in-vietnam
#3
Nguyen Thi Thanh Thao, Celeste Donato, Vu Thi Huyen Trang, Nguyen Trung Kien, Ph M Mai Thuy Trang, Tran Quoc Khanh, Dang Thi Nguyet, October Sessions, Hoang Quoc Cuong, Phan Trong Lan, Vu Thi Que Huong, H Rogier van Doorn, Vijaykrishna Dhanasekaran
Background: Enterovirus A71 (EV-A71) is the major cause of severe hand, foot and mouth disease and viral encephalitis in children across the Asia-Pacific region, including in Vietnam which has experienced a high burden of disease in recent years. Multiple subgenogroups (C1, C4, C5 and B5) concurrently circulate in the region with a large variation in epidemic severity. The relative differences in their evolution and epidemiology were examined within Vietnam and globally. Methods: A total of 752 VP1 gene sequences were analysed (413 generated in this study combined with 339 obtained from GenBank), collected from patients in 36 provinces in Vietnam during 2003-2013 along with epidemiological metadata...
September 23, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029115/whole-genome-next-generation-sequencing-to-study-within-host-evolution-of-chronic-norovirus-infection-among-immunocompromised-patients
#4
J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29027998/temporal-dynamics-of-uncultured-viruses-a-new-dimension-in-viral-diversity
#5
Ksenia Arkhipova, Timofey Skvortsov, John P Quinn, John W McGrath, Christopher Cr Allen, Bas E Dutilh, Yvonne McElarney, Leonid A Kulakov
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29026650/accurate-quantification-of-within-and-between-host-hbv-evolutionary-rates-requires-explicit-transmission-chain-modelling
#6
Bram Vrancken, Marc A Suchard, Philippe Lemey
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-transmission' model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29026649/unique-genome-organization-of-non-mammalian-papillomaviruses-provides-insights-into-the-evolution-of-viral-early-proteins
#7
Koenraad Van Doorslaer, Valeria Ruoppolo, Annie Schmidt, Amelie Lescroël, Dennis Jongsomjit, Megan Elrod, Simona Kraberger, Daisy Stainton, Katie M Dugger, Grant Ballard, David G Ainley, Arvind Varsani
The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds (n = 5), a fish (n = 1), a snake (n = 1), and turtles (n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/29021600/diagnosing-antimicrobial-resistance
#8
REVIEW
Carey-Ann D Burnham, Jennifer Leeds, Patrice Nordmann, Justin O'Grady, Jean Patel
Antimicrobial resistance constitutes a global burden and is one of the major threats to public health. Although the emergence of resistant microorganisms is a natural phenomenon, the overuse or inappropriate use of antimicrobials has had a great effect on resistance evolution. Rapid diagnostic tests that identify drug-resistant bacteria, determine antimicrobial susceptibility and distinguish viral from bacterial infections can guide effective treatment strategies. Moreover, rapid diagnostic tests could facilitate epidemiological surveillance, as emerging resistant infectious agents and transmission can be monitored...
October 12, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29021409/hiv-1-viral-load-and-resistance-in-genital-secretions-in-patients-taking-protease-inhibitor-based-second-line-therapy-in-africa
#9
Anne Hoppe, Marina Giuliano, Abbas Lugemwa, Jennifer A Thompson, Marco Floridia, Ann S Walker, Ismail Senoga, Mary C Abwola, Maria F Pirillo, Cissy M Kityo, Alejandro Arenas-Pinto, Nicholas I Paton
BACKGROUND: HIV is transmitted primarily through sexual intercourse, and the objective of this study was therefore to assess whether there is occult viral replication and resistance in genital secretions in patients on protease inhibitor (PI)-based second-line therapy. METHODS: HIV-infected adults taking ritonavir-boosted lopinavir with either two NRTIs, raltegravir, or as monotherapy for 96 weeks were enrolled at seven clinical sites in Uganda. Viral load (VL) was measured in cervico-vaginal secretions or semen and in a corresponding plasma sample...
October 11, 2017: Antiviral Therapy
https://www.readbyqxmd.com/read/28994824/single-cell-genomics-of-uncultured-marine-alveolates-shows-paraphyly-of-basal-dinoflagellates
#10
Jürgen F H Strassert, Anna Karnkowska, Elisabeth Hehenberger, Javier Del Campo, Martin Kolisko, Noriko Okamoto, Fabien Burki, Jan Janouškovec, Camille Poirier, Guy Leonard, Steven J Hallam, Thomas A Richards, Alexandra Z Worden, Alyson E Santoro, Patrick J Keeling
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H(+)-pyrophosphatase...
October 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28983731/viral-metagenomics-of-six-bat-species-in-close-contact-with-humans-in-southern-china
#11
Xue-Yan Zheng, Min Qiu, Wei-Jie Guan, Jin-Ming Li, Shao-Wei Chen, Ming-Ji Cheng, Shu-Ting Huo, Zhong Chen, Yi Wu, Li-Na Jiang, Qing Chen
Accumulating studies have shown that bats could harbor various important pathogenic viruses that could be transmitted to humans and other animals. Extensive metagenomic studies of different organs/tissues from bats have revealed a large number of novel or divergent viruses. To elucidate viral diversity and epidemiological and phylogenetic characteristics, six pooled fecal samples from bats were generated (based on bat species and geographic regions characteristic for virome analysis). These contained 500 fecal samples from six bat species, collected in four geographic regions...
October 5, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28982996/long-read-sequencing-reveals-a-gc-pressure-during-the-evolution-of-porcine-endogenous-retrovirus
#12
Attila Szűcs, Norbert Moldován, Dóra Tombácz, Zsolt Csabai, Michael Snyder, Zsolt Boldogkői
Here, we present the complete genome sequence of a porcine endogenous retrovirus determined by Pacific Biosciences sequencing. A comparison of the genome of this isolate with those of other strains revealed the operation of a mechanism resulting in the selective accumulation of G and C bases in the viral DNA.
October 5, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28979293/origin-and-evolution-of-rna-dependent-rna-polymerase
#13
Savio T de Farias, Ariosvaldo P Dos Santos Junior, Thais G Rêgo, Marco V José
RNA-dependent RNA polymerases (RdRp) are very ancient enzymes and are essential for all viruses with RNA genomes. We reconstruct the origin and evolution of this polymerase since the initial stages of the origin of life. The origin of the RdRp was traced back from tRNA ancestors. At the origin of the RdRp the most ancient part of the protein is the cofactor-binding site that had the capacity of binding to simple molecules as magnesium, calcium, and ribonucleotides. Our results suggest that RdRp originated from junctions of proto-tRNAs that worked as the first genes at the emergence of the primitive translation system, where the RNA was the informational molecule...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28978683/multiplex-rt-pcr-for-simultaneous-surveillance-of-influenza-a-and-b-viruses
#14
Bin Zhou, Yi-Mo Deng, John R Barnes, October Sessions, Tsui-Wen Chou, Malania Wilson, Thomas J Stark, Michelle Volk, Natalie Spirason, Rebecca A Halpin, Uma Sangumathi Kamaraj, Tao Ding, Timothy B Stockwell, Mirella Salvatore, Elodie Ghedin, Ian G Barr, David E Wentworth
Influenza A and B viruses are the causative agents of annual influenza epidemics that can be severe; influenza A viruses intermittently cause pandemics. Sequence information from influenza genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance. However, due to sequence diversity and the dynamics of influenza evolution, rapid and high-throughput sequencing of influenza viruses remains a challenge. We developed a single-reaction FluA/B Multiplex RT-PCR method that amplifies the most critical genomic segments (HA, NA, and M) of seasonal influenza A and B viruses for next-generation sequencing, regardless of viral types, subtypes, or lineages...
October 4, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28975628/predictors-of-prolonged-length-of-hospital-stay-or-readmissions-for-acute-viral-lower-respiratory-tract-infections-among-infants-with-a-history-of-bronchopulmonary-dysplasia
#15
Carlos E Rodríguez-Martínez, Ranniery Acuña-Cordero, Monica P Sossa-Briceño
BACKGROUND: Length of hospital stay and readmissions are outcome measures that have been largely overlooked in many studies that have evaluated the clinical evolution of pediatric patients with bronchopulmonary dysplasia (BPD). The aim of the present study was to identify predictors of prolonged hospitalizations or readmissions for acute lower respiratory infections (ALRIs) in infants with BPD. METHODS: In a prospective cohort study, we determined independent predictors of prolonged hospitalizations or readmissions for ALRIs during the first two years of life in a population of infants with BPD living in Bogota, Colombia...
October 3, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28973354/emergence-of-novel-human-norovirus-gii-17-strains-correlates-with-changes-in-blockade-antibody-epitopes
#16
Lisa C Lindesmith, Jacob F Kocher, Eric F Donaldson, Kari Debbink, Michael L Mallory, Excel W Swann, Paul D Brewer-Jenson, Ralph S Baric
Background: Human norovirus is a significant public health burden with >30 genotypes causing endemic levels of disease and strains from the GII.4 genotype causing serial pandemics as the virus evolves new ligand binding and antigenicity features. During 2014-2015, genotype GII.17 cluster IIIb strains emerged as the leading cause of norovirus infection in select global locations. Comparison of capsid sequences indicate that GII.17 is evolving at previously defined GII.4 antibody epitopes...
August 3, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28972144/resistance-to-pyridine-based-inhibitor-kf116-reveals-an-unexpected-role-of-integrase-in-hiv-1-gag-pol-proteolytic-processing
#17
Ashley C Hoyte, Augusta V Jamin, Pratibha C Koneru, Matthew J Kobe, Ross C Larue, James R Fuchs, Alan N Engelman, Mamuka Kvaratskhelia
The pyridine-based multimerization selective HIV-1 integrase (IN) inhibitors (MINIs) are a distinct subclass of allosteric IN inhibitors. MINIs potently inhibit HIV-1 replication during virion maturation by inducing hyper or aberrant IN multimerization, yet are largely ineffective during the early steps of viral replication. Here, we investigated the mechanism for the evolution of a triple IN substitution (T124N/V165I/T174I) that emerges in cell culture with a representative MINI KF116. We show that HIV-1NL4-3 IN(T124N/V165I/T174I) confers marked (>2000-fold) resistance to KF116...
September 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28971485/evolution-of-the-serologic-and-virologic-course-of-occult-hbv-infection-in-therapy-experienced-hiv-co-infected-patients
#18
Edina Amponsah-Dacosta, Selokela G Selabe, M Jeffrey Mphahlele
BACKGROUND: We investigated how the natural course of occult hepatitis B virus (HBV) infection (OBI) may evolve during HIV co-infection and long term HBV-active HAART. METHODS: From a cohort of 181 HIV infected patients who were consecutively recruited over a 5 year period, 28 HBV co-infected patients with sequential sera (n = 98) were identified. Iterative HBV serology and viral loads were determined before and during treatment. The viral HBsAg gene was then serially amplified, directly sequenced and molecularly characterized...
October 2, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28970973/multi-scale-immunoepidemiological-modeling-of-within-host-and-between-host-hiv-dynamics-systematic-review-of-mathematical-models
#19
Nargesalsadat Dorratoltaj, Ryan Nikin-Beers, Stanca M Ciupe, Stephen G Eubank, Kaja M Abbas
OBJECTIVE: The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level. BACKGROUND: While within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels...
2017: PeerJ
https://www.readbyqxmd.com/read/28970295/infectious-and-non-infectious-complications-in-primary-immunodeficiency-disorders-an-autopsy-study-from-north-india
#20
Kirti Gupta, Amit Rawat, Parimal Agrawal, Ankur Jindal, Ritambhra Nada, Biman Saikia, Koon Wing Chan, Yu Lung Lau, Ranjana Walker Minz, Surjit Singh
BACKGROUND: Primary immunodeficiency disorders (PID) include a wide spectrum of inherited disorders characterised by functional abnormalities of one or more components of the immune system. Recent updates from the genomic data have contributed significantly to its better understanding with identification of new entities. Diagnosis is always challenging due to their variable clinical presentation. With the evolution of molecular diagnosis, many of these children are being diagnosed early and offered appropriate therapy...
September 28, 2017: Journal of Clinical Pathology
keyword
keyword
4794
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"