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Antiviral drug resistance as an adaptive process

Kristen K. Irwin, Nicholas Renzette, Timothy F. Kowalik and Jeffrey D. Jensen.

in Virus Evolution

P ublished online June 2016 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 7861 words.

Antiviral drug resistance is a matter of great clinical importance that, historically, has been investigated mostly from a virological perspective. Although the proximate mechanisms of...

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Characterizing the multiplicity of HIV founder variants during sexual transmission among MSM

Antoine Chaillon, Sara Gianella, Susan J. Little, Gemma Caballero, Francis Barin, Sergei Kosakovsky Pond, Douglas D. Richman, Davey M. Smith and Sanjay R. Mehta.

in Virus Evolution

P ublished online June 2016 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 3508 words.

Transmission of multiple founder variants has been associated with faster HIV disease progression. Many studies have attempted to determine the number of founder variants, mainly by...

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CodonShuffle: a tool for generating and analyzing synonymously mutated sequences

Daniel Macedo de Melo Jorge, Ryan E. Mills and Adam S. Lauring.

in Virus Evolution

P ublished online October 2015 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 5496 words.

Because synonymous mutations do not change the amino acid sequence of a protein, they are generally considered to be selectively neutral. Empiric data suggest, however, that a significant...

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Coevolutionary Analysis Identifies Protein–Protein Interaction Sites between HIV-1 Reverse Transcriptase and Integrase

Madara Hetti Arachchilage and Helen Piontkivska.

in Virus Evolution

P ublished online February 2016 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 7131 words.

The replication of human immunodeficiency virus-1 (HIV-1) requires reverse transcription of the viral RNA genome and integration of newly synthesized pro-viral DNA into the host genome....

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Co-infection with two strains of Brome mosaic bromovirus reveals common RNA recombination sites in different hosts

Beivy Kolondam, Parth Rao, Joanna Sztuba-Solinska, Philipp H. Weber, Aleksandra Dzianott, Mitrick A. Johns and Jozef J. Bujarski.

in Virus Evolution

P ublished online December 2015 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 7295 words.

We have previously reported intra-segmental crossovers in Brome mosaic virus (BMV) RNAs. In this work, we studied the homologous recombination of BMV RNA in three different hosts: barley (H...

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Connecting within-host dynamics to the rate of viral molecular evolution

Kayla M. Peck, Carmen H. S. Chan and Mark M. Tanaka.

in Virus Evolution

P ublished online October 2015 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 7481 words.

Viruses evolve rapidly, providing a unique system for understanding the processes that influence rates of molecular evolution. Neutral theory posits that the evolutionary rate increases...

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Determinants of taxonomic composition of plant viruses at the Nature Conservancy’s Tallgrass Prairie Preserve, Oklahoma

Vaskar Thapa, Daniel J. McGlinn, Ulrich Melcher, Michael W. Palmer and Marilyn J. Roossinck.

in Virus Evolution

P ublished online August 2015 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 5169 words.

The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test...

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Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses

Christina Kratsch, Thorsten R. Klingen, Linda Mümken, Lars Steinbrück and Alice C. McHardy.

in Virus Evolution

P ublished online February 2016 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 10107 words.

Human influenza viruses are rapidly evolving RNA viruses that cause short-term respiratory infections with substantial morbidity and mortality in annual epidemics. Uncovering the general...

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A diverse group of small circular ssDNA viral genomes in human and non-human primate stools

Terry Fei Fan Ng, Wen Zhang, Jana Sachsenröder, Nikola O. Kondov, Antonio Charlys da Costa, Everardo Vega, Lori R. Holtz, Guang Wu, David Wang, Colin O. Stine, Martin Antonio, Usha S. Mulvaney, Marcus O. Muench, Xutao Deng, Katia Ambert-Balay, Pierre Pothier, Jan Vinjé and Eric Delwart.

in Virus Evolution

P ublished online December 2015 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 6598 words.

Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication...

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Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming

Marta Canuti, Kimberly E. O’Leary, Bruce D. Hunter, Grant Spearman, Davor Ojkic, Hugh G. Whitney and Andrew S. Lang.

in Virus Evolution

P ublished online February 2016 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 12142 words.

Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g.,...

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