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Virus Evolution

Lei Zhao, Christopher J R Illingworth
Viruses exist within hosts at large population sizes and are subject to high rates of mutation. As such, viral populations exhibit considerable sequence diversity. A variety of summary statistics have been developed which describe, in a single number, the extent of diversity in a viral population; such measurements allow the diversities of different populations to be compared, and the effect of evolutionary forces on a population to be assessed. Here we highlight statistical artefacts underlying some common measures of sequence diversity, whereby variation in the depth of genome sequencing may substantially affect the extent of diversity measured in a viral population, making comparisons of population diversity invalid...
January 2019: Virus Evolution
Robin N Thompson, Chris Wymant, Rebecca A Spriggs, Jayna Raghwani, Christophe Fraser, Katrina A Lythgoe
Understanding which HIV-1 variants are most likely to be transmitted is important for vaccine design and predicting virus evolution. Since most infections are founded by single variants, it has been suggested that selection at transmission has a key role in governing which variants are transmitted. We show that the composition of the viral population within the donor at the time of transmission is also important. To support this argument, we developed a probabilistic model describing HIV-1 transmission in an untreated population, and parameterised the model using both within-host next generation sequencing data and population-level epidemiological data on heterosexual transmission...
January 2019: Virus Evolution
Abayomi S Olabode, Mariano Avino, Garway T Ng, Faisal Abu-Sardanah, David W Dick, Art F Y Poon
Reconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories...
January 2019: Virus Evolution
My V T Phan, Tue Ngo Tri, Pham Hong Anh, Stephen Baker, Paul Kellam, Matthew Cotten
The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains...
July 2018: Virus Evolution
David A Rasmussen, Eduan Wilkinson, Alain Vandormael, Frank Tanser, Deenan Pillay, Tanja Stadler, Tulio de Oliveira
Despite increasing access to antiretrovirals, HIV incidence in rural KwaZulu-Natal remains among the highest ever reported in Africa. While many epidemiological factors have been invoked to explain such high incidence, widespread human mobility and viral movement suggest that transmission between communities may be a major source of new infections. High cross-community transmission rates call into question how effective increasing the coverage of antiretroviral therapy locally will be at preventing new infections, especially if many new cases arise from external introductions...
July 2018: Virus Evolution
Joel O Wertheim, Alexandra M Oster, Ben Murrell, Neeraja Saduvala, Walid Heneine, William M Switzer, Jeffrey A Johnson
Understanding genetic variation in human immunodeficiency virus (HIV) is clinically and immunologically important for patient treatment and vaccine development. We investigated the longitudinal intra-host genetic variation of HIV in over 3,000 individuals in the US National HIV Surveillance System with at least four reported HIV-1 polymerase ( pol ) sequences. In this population, we identified 149 putative instances of superinfection (i.e. an individual sequentially infected with genetically divergent, polyphyletic viruses)...
July 2018: Virus Evolution
Greg Fedewa, Sheli R Radoshitzky, Xiǎolì Chī, Lián Dǒng, Xiankun Zeng, Melissa Spear, Nicolas Strauli, Melinda Ng, Kartik Chandran, Mark D Stenglein, Ryan D Hernandez, Peter B Jahrling, Jens H Kuhn, Joseph L DeRisi
Ebola virus (EBOV) disease is a viral hemorrhagic fever with a high case-fatality rate in humans. This disease is caused by four members of the filoviral genus Ebolavirus , including EBOV. The natural hosts reservoirs of ebolaviruses remain to be identified. Glycoprotein 2 of reptarenaviruses, known to infect only boa constrictors and pythons, is similar in sequence and structure to ebolaviral glycoprotein 2, suggesting that EBOV may be able to infect reptilian cells. Therefore, we serially passaged EBOV and a distantly related filovirus, Marburg virus (MARV), in boa constrictor JK cells and characterized viral infection/replication and mutational frequency by confocal imaging and sequencing...
July 2018: Virus Evolution
Steven M Goodreau, Sarah E Stansfield, James T Murphy, Kathryn C Peebles, Geoffrey S Gottlieb, Neil F Abernethy, Joshua T Herbeck, John E Mittler
HIV viral load (VL) predicts both transmission potential and rate of disease progression. For reasons that are still not fully understood, the set point viral load (SPVL) established after acute infection varies across individuals and populations. Previous studies have suggested that population mean SPVL (MSPVL) has evolved near an optimum that reflects a trade-off between transmissibility and host survival. Sexual network structures affect rates of potential exposure during different within-host phases of infection marked by different transmission probabilities, and thus affect the number and timing of transmission events...
July 2018: Virus Evolution
J R Otieno, E M Kamau, J W Oketch, J M Ngoi, A M Gichuki, Š Binter, G P Otieno, M Ngama, C N Agoti, P A Cane, P Kellam, M Cotten, P Lemey, D J Nokes
[This corrects the article DOI: 10.1093/ve/vey027.][This corrects the article DOI: 10.1093/ve/vey027.].
July 2018: Virus Evolution
Judit J Pénzes, Soledad Marsile-Medun, Mavis Agbandje-McKenna, Robert James Gifford
Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus ) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole ( Ellobius lutescens )...
July 2018: Virus Evolution
Sarah K Hilton, Jesse D Bloom
Molecular phylogenetics is often used to estimate the time since the divergence of modern gene sequences. For highly diverged sequences, such phylogenetic techniques sometimes estimate surprisingly recent divergence times. In the case of viruses, independent evidence indicates that the estimates of deep divergence times from molecular phylogenetics are sometimes too recent. This discrepancy is caused in part by inadequate models of purifying selection leading to branch-length underestimation. Here we examine the effect on branch-length estimation of using models that incorporate experimental measurements of purifying selection...
July 2018: Virus Evolution
Jemma L Geoghegan, Francesca Di Giallonardo, Kate Cousins, Mang Shi, Jane E Williamson, Edward C Holmes
Aquaculture is the fastest growing industry worldwide. Aquatic diseases have had enormous economic and environmental impacts in the recent past and the emergence of new aquatic pathogens, particularly viruses, poses a continuous threat. Nevertheless, little is known about the diversity, abundance and evolution of fish viruses. We used a meta-transcriptomic approach to help determine the virome of seemingly healthy fish sold at a market in Sydney, Australia. Specifically, by identifying and quantifying virus transcripts we aimed to determine (i) the abundance of viruses in market fish, (ii) test a key component of epidemiological theory that large and dense host populations harbour a greater number of viruses compared to their more solitary counterparts and (iii) reveal the relative roles of virus-host co-divergence and cross-species transmission in the evolution of fish viruses...
July 2018: Virus Evolution
Eva Bons, Frederic Bertels, Roland R Regoes
The evolution of HIV during acute infection is often considered a neutral process. Recent analysis of sequencing data from this stage of infection, however, showed high levels of shared mutations between independent viral populations. This suggests that selection might play a role in the early stages of HIV infection. We adapted an existing model for random evolution during acute HIV-infection to include selection. Simulations of this model were used to fit a global mutational fitness effects distribution to previously published sequencing data of the env gene of individuals with acute HIV infection...
July 2018: Virus Evolution
Asher Leeks, Ernesto A Segredo-Otero, Rafael Sanjuán, Stuart A West
In many viral infections, a large number of different genetic variants can coexist within a host, leading to more virulent infections that are better able to evolve antiviral resistance and adapt to new hosts. But how is this diversity maintained? Why do faster-growing variants not outcompete slower-growing variants, and erode this diversity? One hypothesis is if there are mutually beneficial interactions between variants, with host cells infected by multiple different viral genomes producing more, or more effective, virions...
July 2018: Virus Evolution
J R Otieno, E M Kamau, J W Oketch, J M Ngoi, A M Gichuki, Š Binter, G P Otieno, M Ngama, C N Agoti, P A Cane, P Kellam, M Cotten, P Lemey, D J Nokes
The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen...
July 2018: Virus Evolution
Katharina Kusejko, Claus Kadelka, Alex Marzel, Manuel Battegay, Enos Bernasconi, Alexandra Calmy, Matthias Cavassini, Matthias Hoffmann, Jürg Böni, Sabine Yerly, Thomas Klimkait, Matthieu Perreau, Andri Rauch, Huldrych F Günthard, Roger D Kouyos
Age-mixing patterns are of key importance for understanding the dynamics of human immunodeficiency virus (HIV)-epidemics and target public health interventions. We use the densely sampled Swiss HIV Cohort Study (SHCS) resistance database to study the age difference at infection in HIV transmission pairs using phylogenetic methods. In addition, we investigate whether the mean age difference of pairs in the phylogenetic tree is influenced by sampling as well as by additional distance thresholds for including pairs...
July 2018: Virus Evolution
Michelle Wille, Neus Latorre-Margalef, Conny Tolf, Rebecca Halpin, David Wentworth, Ron A M Fouchier, Jayna Raghwani, Oliver G Pybus, Björn Olsen, Jonas Waldenström
Influenza A virus (IAV) is ubiquitous in waterfowl. In the northern hemisphere IAV prevalence is highest during the autumn and coincides with a peak in viral subtype diversity. Although haemagglutinin subtypes H1-H12 are associated with waterfowl hosts, subtypes H8-H12 are detected very infrequently. To better understand the role of waterfowl in the maintenance of these rare subtypes, we sequenced H8-H12 viruses isolated from Mallards ( Anas platyrhynchos ) from 2002 to 2009. These rare viruses exhibited varying ecological and phylodynamic features...
July 2018: Virus Evolution
Simon Dellicour, Bram Vrancken, Nídia S Trovão, Denis Fargette, Philippe Lemey
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations...
July 2018: Virus Evolution
David A Goodman, Kenneth M Stedman
Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses-which infect members of the order Sulfolobales , growing optimally at 80 °C and pH 3-are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. Nonetheless, much remains to be learned about these viruses. In order to investigate fusellovirus evolution, we have isolated and characterized a novel fusellovirus, Sulfolobus spindle-shaped virus 10 (formerly SSV-L1)...
July 2018: Virus Evolution
R Klitting, T Riziki, G Moureau, G Piorkowski, E A Gould, X de Lamballerie
Virus attenuation by genome re-encoding is a pioneering approach for generating effective live-attenuated vaccine candidates. Its core principle is to introduce a large number of synonymous substitutions into the viral genome to produce stable attenuation of the targeted virus. Introduction of large numbers of mutations has also been shown to maintain stability of the attenuated phenotype by lowering the risk of reversion and recombination of re-encoded genomes. Identifying mutations with low fitness cost is pivotal as this increases the number that can be introduced and generates more stable and attenuated viruses...
July 2018: Virus Evolution
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