Quantitative measures of within-host viral genetic diversity

Current Opinion in Virology - Tập 49 - Trang 157-163 - 2021
Lara Fuhrmann1,2, Kim Philipp Jablonski1,2, Niko Beerenwinkel1,2
1Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
2SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland

Tài liệu tham khảo

Duffy, 2008, Rates of evolutionary change in viruses: patterns and determinants, Nat Rev Genet, 9, 267, 10.1038/nrg2323 Quer, 2017, Deep sequencing in the management of hepatitis virus infections, Virus Res, 239, 115, 10.1016/j.virusres.2016.12.020 Tsibris, 2009, Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo, PLoS One, 4, 10.1371/journal.pone.0005683 Webber, 2017, Viral richness is positively related to group size, but not mating system, in bats, Ecohealth, 14, 652, 10.1007/s10393-017-1276-3 Vignuzzi, 2006, Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population, Nature, 439, 344, 10.1038/nature04388 Puller, 2017, Estimating time of HIV-1 infection from next-generation sequence diversity, PLoS Comput Biol, 13, 10.1371/journal.pcbi.1005775 Nelson, 2015, Within-host nucleotide diversity of virus populations: insights from next-generation sequencing, Infect Genet Evol, 30, 1, 10.1016/j.meegid.2014.11.026 Lauring, 2020, Within-host viral diversity: a window into viral evolution, Annu Rev Virol, 7, 63, 10.1146/annurev-virology-010320-061642 Beerenwinkel, 2012, Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data, Front Microbiol, 3, 329, 10.3389/fmicb.2012.00329 Posada-Cespedes, 2017, Recent advances in inferring viral diversity from high-throughput sequencing data, Virus Res, 239, 17, 10.1016/j.virusres.2016.09.016 Knyazev, 2021, Epidemiological data analysis of viral quasispecies in the next-generation sequencing era, Brief Bioinformatics, 22, 96, 10.1093/bib/bbaa101 Gregori, 2014, Inference with viral quasispecies diversity indices: clonal and NGS approaches, Bioinformatics, 30, 1104, 10.1093/bioinformatics/btt768 Rogers, 2015, Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection, mBio, 6, 10.1128/mBio.02464-14 Sim, 2015, Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission, PLoS Negl Trop Dis, 9, 10.1371/journal.pntd.0004052 Shen, 2020, Genomic diversity of severe acute respiratory syndrome-coronavirus 2 in patients with coronavirus disease 2019, Clin Infect Dis, 71, 713, 10.1093/cid/ciaa203 Poon, 2016, Quantifying influenza virus diversity and transmission in humans, Nat Genet, 48, 195, 10.1038/ng.3479 McCrone, 2018, Stochastic processes constrain the within and between host evolution of influenza virus, eLife, 7, 10.7554/eLife.35962 Xue, 2019, Reconciling disparate estimates of viral genetic diversity during human influenza infections, Nat Genet, 51, 1298, 10.1038/s41588-019-0349-3 Carlisle, 2019, Viral diversity based on next-generation sequencing of HIV-1 provides precise estimates of infection recency and time since infection, J Infect Dis, 220, 254, 10.1093/infdis/jiz094 Zhao, 2019, Measurements of intrahost viral diversity require an unbiased diversity metric, Virus Evol, 5, 10.1093/ve/vey041 Ramírez, 2013, A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model, Antiviral Res, 98, 273, 10.1016/j.antiviral.2013.03.007 Raj, 2017, Identification of HCV resistant variants against direct acting antivirals in plasma and liver of treatment naïve patients, Sci Rep, 7, 10.1038/s41598-017-04931-y Gregori, 2016, Viral quasispecies complexity measures, Virology, 493, 227, 10.1016/j.virol.2016.03.017 Shannon, 1949, Communication theory of secrecy systems*, Bell Syst Tech J, 28, 656, 10.1002/j.1538-7305.1949.tb00928.x Batista, 2011, An entropy-based approach for the identification of phylogenetically informative genomic regions of Papillomavirus, Infect Genet Evol, 11, 2026, 10.1016/j.meegid.2011.09.013 Parra, 2017, Phylogenetic diversity in core region of hepatitis C virus genotype 1a as a factor associated with fibrosis severity in HIV-1-coinfected patients, Biomed Res Int, 2017, 10.1155/2017/1728456 Icer Baykal, 2021, Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections, Virus Evol, 7, 10.1093/ve/veaa103 Wright, 2011, Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing, J Virol, 85, 2266, 10.1128/JVI.01396-10 McCrone, 2016, Measurements of intrahost viral diversity are extremely sensitive to systematic errors in variant calling, J Virol, 90, 6884, 10.1128/JVI.00667-16 Bertels, 2019, Parallel evolution of HIV-1 in a long-term experiment, Mol Biol Evol, 36, 2400, 10.1093/molbev/msz155 Jadhav, 2020, Genomic diversity and evolution of quasispecies in newcastle disease virus infections, Viruses, 12 Montoya, 2015, Differentiation of acute from chronic hepatitis C virus infection by nonstructural 5B deep sequencing: a population-level tool for incidence estimation, Hepatology, 61, 1842, 10.1002/hep.27734 Lequime, 2016, Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes, PLoS Genet, 12, 10.1371/journal.pgen.1006111 Simpson, 1949, Measurement of diversity, Nature, 163, 688, 10.1038/163688a0 Maldarelli, 2013, HIV populations are large and accumulate high genetic diversity in a nonlinear fashion, J Virol, 87, 10313, 10.1128/JVI.01225-12 Dinis, 2016, Deep sequencing reveals potential antigenic variants at low frequencies in influenza A virus-infected humans, J Virol, 90, 3355, 10.1128/JVI.03248-15 Renzette, 2016, On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity, Mol Ecol, 25, 403, 10.1111/mec.13331 Nei, 1987 Faith, 1992, Conservation evaluation and phylogenetic diversity, Biol Conserv, 61, 1, 10.1016/0006-3207(92)91201-3 Nipperess, 2016, The rarefaction of phylogenetic diversity: formulation, extension and application, 197, 10.1007/978-3-319-22461-9_10 Linck, 2019, Minor allele frequency thresholds strongly affect population structure inference with genomic data sets, Mol Ecol Resour, 19, 639, 10.1111/1755-0998.12995 Eliseev, 2020, Evaluation of haplotype callers for next-generation sequencing of viruses, Infect Genet Evol, 82, 10.1016/j.meegid.2020.104277 Giallonardo, 2014, Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations, Nucleic Acids Res, 42, 10.1093/nar/gku537 Eid, 2009, Real-time DNA sequencing from single polymerase molecules, Science, 323, 133, 10.1126/science.1162986 Kumar, 2018, MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol Biol Evol, 35, 1547, 10.1093/molbev/msy096