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1 Sanjuan, R., Nebot, M.R., Chirico, N., Mansky, L.M., Belshaw, R., Viral mutation rates. J. Virol. 84 (2010), 9733–9748.
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2 Domingo, E., Sheldon, J., Perales, C., Viral quasispecies evolution. Microbiol. Mol. Biol. Rev. 76 (2012), 159–216.
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Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes
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This paper analyzes and quantifies the initial bottleneck during mosquito infection by DENV, using deep-sequencing and bioinformatics approaches. It nicely illustrates the impact of host genetics on bottleneck size—in this case for four different Aedes aegypti isofemale lines.
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3• Lequime, S., Fontaine, A., Ar Gouilh, M., Moltini-Conclois, I., Lambrechts, L., Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PLoS Genet., 12, 2016, e1006111 This paper analyzes and quantifies the initial bottleneck during mosquito infection by DENV, using deep-sequencing and bioinformatics approaches. It nicely illustrates the impact of host genetics on bottleneck size—in this case for four different Aedes aegypti isofemale lines.
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PLoS Genet.
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Lequime, S.1
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4
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Hepatitis C virus transmission bottlenecks analyzed by deep sequencing
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4 Wang, G.P., Sherrill-Mix, S.A., Chang, K.M., Quince, C., Bushman, F.D., Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J. Virol. 84 (2010), 6218–6228.
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Wang, G.P.1
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5
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5 Bull, R.A., Luciani, F., McElroy, K., Gaudieri, S., Pham, S.T., Chopra, A., Cameron, B., Maher, L., Dore, G.J., White, P.A., et al. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog., 7, 2011, e1002243.
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Bull, R.A.1
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6
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Population genomics of intrapatient HIV-1 evolution
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This work follows the evolution of HIV quasispecies in untreated patients for several years, illustrating the continual evolution of the viral quasispecies and selection of minority variants, shaped by positive selection. Accumulation of mutations comes with a fitness cost that triggers reversion towards consensus.
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6•• Zanini, F., Brodin, J., Thebo, L., Lanz, C., Bratt, G., Albert, J., Neher, R.A., Population genomics of intrapatient HIV-1 evolution. eLife, 4, 2015, e11282 This work follows the evolution of HIV quasispecies in untreated patients for several years, illustrating the continual evolution of the viral quasispecies and selection of minority variants, shaped by positive selection. Accumulation of mutations comes with a fitness cost that triggers reversion towards consensus.
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Zanini, F.1
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7
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Influenza A virus transmission bottlenecks are defined by infection route and recipient host
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By neutrally barcoding IAV, the authors could follow the evolution of an artificial mix of viruses in cell culture as well as in vivo. They demonstrate the existence of a strong transmission bottleneck depending both on the recipient host and the mode of transmission.
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7•• Varble, A., Albrecht, R.A., Backes, S., Crumiller, M., Bouvier, N.M., Sachs, D., García-Sastre, A., tenOever, B.R., Influenza A virus transmission bottlenecks are defined by infection route and recipient host. Cell Host Microbe 16 (2014), 691–700 By neutrally barcoding IAV, the authors could follow the evolution of an artificial mix of viruses in cell culture as well as in vivo. They demonstrate the existence of a strong transmission bottleneck depending both on the recipient host and the mode of transmission.
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Varble, A.1
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8 Stapleford, K.A., Coffey, L.L., Lay, S., Bordería, A.V., Duong, V., Isakov, O., Rozen-Gagnon, K., Arias-Goeta, C., Blanc, H., Beaucourt, S., et al. Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential. Cell Host Microbe 15 (2014), 706–716.
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Stapleford, K.A.1
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9
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Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission
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9 Sim, S., Aw, P.P.K., Wilm, A., Teoh, G., Hue, K.D.T., Nguyen, N.M., Nagarajan, N., Simmons, C.P., Hibberd, M.L., Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission. PLoS Negl. Trop. Dis., 9, 2015, e0004052.
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Sim, S.1
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Circulating virus load determines the size of bottlenecks in viral populations progressing within a host
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10 Gutiérrez, S., Yvon, M., Pirolles, E., Garzo, E., Fereres, A., Michalakis, Y., Blanc, S., Circulating virus load determines the size of bottlenecks in viral populations progressing within a host. PLoS Pathog., 8, 2012, e1003009.
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Gutiérrez, S.1
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11
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The multiplicity of cellular infection changes depending on the route of cell infection in a plant virus
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This elegant study uses Turnip Mosaic virus marked with either GFP or RFP to assess the evolution of the MOI during turnip infection. They show that MOI changes tremendously during infection, in relation with the colonization of the host.
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11• Gutiérrez, S., Pirolles, E., Yvon, M., Baecker, V., Michalakis, Y., Blanc, S., The multiplicity of cellular infection changes depending on the route of cell infection in a plant virus. J. Virol. 89 (2015), 9665–9675 This elegant study uses Turnip Mosaic virus marked with either GFP or RFP to assess the evolution of the MOI during turnip infection. They show that MOI changes tremendously during infection, in relation with the colonization of the host.
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Gutiérrez, S.1
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12 Pillai, S.K., Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain 129 (2006), 1872–1883.
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13 Schnell, G., Spudich, S., Harrington, P., Price, R.W., Swanstrom, R., Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia. PLoS Pathog., 5, 2009, e1000395.
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14 van Marle, G., Gill, M.J., Kolodka, D., McManus, L., Grant, T., Church, D.L., Compartmentalization of the gut viral reservoir in HIV-1 infected patients. Retrovirology, 4, 2007, 87.
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Exceptional heterogeneity in viral evolutionary dynamics characterises chronic hepatitis C virus infection
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This study analyzes intrahost evolution in HCV-infected patient, and compares their results with cohort of HIV-infected patients. The authors nicely highlight the differences in quasispecies evolution during these two persistent infections.
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15•• Raghwani, J., Rose, R., Sheridan, I., Lemey, P., Suchard, M.A., Santantonio, T., Farci, P., Klenerman, P., Pybus, O.G., Exceptional heterogeneity in viral evolutionary dynamics characterises chronic hepatitis C virus infection. PLoS Pathog., 12, 2016, e1005894 This study analyzes intrahost evolution in HCV-infected patient, and compares their results with cohort of HIV-infected patients. The authors nicely highlight the differences in quasispecies evolution during these two persistent infections.
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Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication
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17 Abram, M.E., Ferris, A.L., Shao, W., Alvord, W.G., Hughes, S.H., Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication. J. Virol. 84 (2010), 9864–9878.
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Abram, M.E.1
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18 Kim, E.-Y., Lorenzo-Redondo, R., Little, S.J., Chung, Y.-S., Phalora, P.K., Maljkovic Berry, I., Archer, J., Penugonda, S., Fischer, W., Richman, D.D., et al. Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection. PLoS Pathog., 10, 2014, e1004281.
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Kim, E.-Y.1
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19 Vignuzzi, M., Stone, J.K., Arnold, J.J., Cameron, C.E., Andino, R., Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439 (2006), 344–348.
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The authors studied the importance of viral mutation rate by generating low fidelity variants of chikungunya virus and Sindbis virus. Both viruses exhibit significant attenuation in mice, mosquitoes and fruit flies, illustrating the pivotal role of mutation rates in viral pathogenesis.
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20• Rozen-Gagnon, K., Stapleford, K.A., Mongelli, V., Blanc, H., Failloux, A.-B., Saleh, M.-C., Vignuzzi, M., Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models. PLoS Pathog., 10, 2014, e1003877 The authors studied the importance of viral mutation rate by generating low fidelity variants of chikungunya virus and Sindbis virus. Both viruses exhibit significant attenuation in mice, mosquitoes and fruit flies, illustrating the pivotal role of mutation rates in viral pathogenesis.
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Rozen-Gagnon, K.1
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Generation and characterization of influenza A viruses with altered polymerase fidelity
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23 Cheung, P.P.H., Watson, S.J., Choy, K.-T., Fun Sia, S., Wong, D.D.Y., Poon, L.L.M., Kellam, P., Guan, Y., Malik Peiris, J.S., Yen, H.-L., Generation and characterization of influenza A viruses with altered polymerase fidelity. Nat. Commun., 5, 2014, 4794.
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RNA recombination enhances adaptability and is required for virus spread and virulence
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After studies demonstrating the importance of the mutation rate through the generation of fidelity variants, this study goes to analyze a poliovirus recombinant-defective mutant. In combination with mutation modifying fidelity, the authors demonstrate that recombination allows the regrouping of beneficial mutations and the purification of deleterious ones, and is thus a key parameter in viral fitness.
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Low-fidelity polymerases of alphaviruses recombine at higher rates to overproduce defective interfering particles
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26 Poirier, E.Z., Mounce, B.C., Rozen-Gagnon, K., Hooikaas, P.J., Stapleford, K.A., Moratorio, G., Vignuzzi, M., Low-fidelity polymerases of alphaviruses recombine at higher rates to overproduce defective interfering particles. J. Virol. 90 (2016), 2446–2454.
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30 Tapia, K., Kim, W., Sun, Y., Mercado-López, X., Dunay, E., Wise, M., Adu, M., López, C.B., Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity. PLoS Pathog., 9, 2013, e1003703.
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This recent study from the Lopez lab nicely highlights the role of defective genomes in RSV pathogenesis. Defective genomes activate type-I interferon in vitro and thwart viral infection in vivo. A correlation can be found between the expression of antiviral genes and defective genomes amount in RSV-infected patients.
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33• Sun, Y., Jain, D., Koziol-White, C.J., Genoyer, E., Gilbert, M., Tapia, K., Panettieri, R.A., Hodinka, R.L., López, C.B., Immunostimulatory defective viral genomes from respiratory syncytial virus promote a strong innate antiviral response during infection in mice and humans. PLoS Pathog., 11, 2015, e1005122 This recent study from the Lopez lab nicely highlights the role of defective genomes in RSV pathogenesis. Defective genomes activate type-I interferon in vitro and thwart viral infection in vivo. A correlation can be found between the expression of antiviral genes and defective genomes amount in RSV-infected patients.
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