1. Aviner, R. et al. SARS-CoV-2 Nsp1 cooperates with initiation factors EIF1 and 1A to selectively enhance translation of viral RNA. PLOS Pathog. 20, e1011535 (2024).
2. Catching, A., Yeh, M. T., Bianco, S., Capponi, S. & Andino, R. A tradeoff between enterovirus A71 particle stability and cell entry. Nat. Commun. 14, 7450 (2023).
3. Deyoe, J. E. et al. Association of culturable-virus detection and household transmission of SARS-CoV-2 – California and Tennessee, 2020–2022. J Infect Dis (2023) doi:10.1093/infdis/jiad018.
4. Yang, J. et al. Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2. Nat Microbiol 8, 121–134 (2023).
5. Yeh, M. T. et al. Genetic stabilization of attenuated oral vaccines against poliovirus types 1 and 3. Nature 1–8 (2023) doi:10.1038/s41586-023-06212-3.
6. Rangel, M. A. et al. High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution. Proc. Natl. Acad. Sci. 120, e2304667120 (2023).
7. Thompson, K. M. et al. Polio eradication: Addressing the hurdles on the last mile. Cell 186, 1–4 (2023).
8. Lidsky, P. V., Yuan, J. & Andino, R. Reconsidering life history theory amid infectious diseases. Trends Ecol. Evol. (2023) doi:10.1016/j.tree.2023.05.004.
9. Wu, C.-T. et al. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell 186, 112-130.e20 (2023).
10. Andino, R., Kirkegaard, K., Macadam, A., Racaniello, V. R. & Rosenfeld, A. B. The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens. J. Infect. Dis. 228, S427–S445 (2023).
11. Lidsky, P. V. & Andino, R. Could aging evolve as a pathogen control strategy? Trends Ecol Evol 37, 1046–1057 (2022).
12. Wahid, R. et al. Evaluating stability of attenuated Sabin and two novel type 2 oral poliovirus vaccines in children. Npj Vaccines 7, 19 (2022).
13. Wahid, R. et al. Genetic and phenotypic stability of poliovirus shed from infants who received novel type 2 or Sabin type 2 oral poliovirus vaccines in Panama: an analysis of two clinical trials. Lancet Microbe (2022) doi:10.1016/s2666-5247(22)00254-3.
14. Garcia-Knight, M. et al. Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study. Plos Pathog 18, e1010802 (2022).
15. Servellita, V. et al. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell 185, 1539-1548.e5 (2022).
16. Xiao, Y. et al. A defective viral genome strategy elicits broad protective immunity against respiratory viruses. Cell 184, 6037-6051.e14 (2021).
17. Aviner, R., Li, K. H., Frydman, J. & Andino, R. Cotranslational prolyl hydroxylation is essential for flavivirus biogenesis. Nature 596, 558–564 (2021).
18. Li, X. et al. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles. Plos Pathog 17, e1009898 (2021).
19. Shirogane, Y. et al. Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. Plos Pathog 17, e1009277 (2021).
20. Dolan, P. T. et al. Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. Elife 10, e61921 (2021).
21. Wu, C.-T. et al. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Cell Metab 33, 1565-1576.e5 (2021).
22. Deng, X. et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 184, 3426-3437.e8 (2021).
23. Konopka-Anstadt, J. L. et al. Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization. Npj Vaccines 5, 26 (2020).
24. Yeh, M. T. et al. Engineering the Live-Attenuated Polio Vaccine to Prevent Reversion to Virulence. Cell Host Microbe 27, 736-751.e8 (2020).
25. Lidsky, P. V. & Andino, R. Epidemics as an adaptive driving force determining lifespan setpoints. P Natl Acad Sci Usa 117, 17937–17948 (2020).
26. Tassetto, M. et al. Control of RNA viruses in mosquito cells through the acquisition of vDNA and endogenous viral elements. Elife 8, e41244 (2019).
27. Diep, J. et al. Enterovirus pathogenesis requires the host methyltransferase SETD3. Nat Microbiol 4, 2523–2537 (2019).
28. Laufman, O., Perrino, J. & Andino, R. Viral Generated Inter-Organelle Contacts Redirect Lipid Flux for Genome Replication. Cell 178, 275-289.e16 (2019).
29. Taguwa, S. et al. Zika Virus Dependence on Host Hsp70 Provides a Protective Strategy against Infection and Disease. Cell Reports 26, 906-920.e3 (2019).
30. Nayak, A. et al. A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability. Cell Host Microbe 24, 542-557.e9 (2018).
31. Shah, P. S. et al. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell 175, 1931-1945.e18 (2018).
32. Geller, R., Pechmann, S., Acevedo, A., Andino, R. & Frydman, J. Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation. Nat Commun 9, 1781 (2018).
33. Dolan, P. T., Whitfield, Z. J. & Andino, R. Mapping the Evolutionary Potential of RNA Viruses. Cell Host Microbe 23, 435–446 (2018).
34. Dolan, P. T., Whitfield, Z. J. & Andino, R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Ann Rev Virol 5, 69–92 (2018).
35. Tassetto, M., Kunitomi, M. & Andino, R. Circulating Immune Cells Mediate a Systemic RNAi-Based Adaptive Antiviral Response in Drosophila. Cell 169, 314-325.e13 (2017).
36. Xiao, Y. et al. Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses. Nat Commun 8, 375 (2017).
37. Xiao, Y. et al. RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell host & microbe 22, 420 (2017).
38. Whitfield, Z. J. et al. The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome. Current Biology 27, 3511-3519.e7 (2017).
39. Stern, A. et al. The Evolutionary Pathway to Virulence of an RNA Virus. Cell 169, 35-46 e19 (2017).
40. Xiao, Y. et al. RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell host & microbe 19, 493–503 (2016).
41. Taguwa, S. et al. Defining Hsp70 Subnetworks in Dengue Virus Replication Reveals Key Vulnerability in Flavivirus Infection. Cell 163, 1108–1123 (2015).
42. Schulte, M. B., Draghi, J. A., Plotkin, J. B. & Andino, R. Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses. eLife 4, e03753 (2015).
43. Andino, R. & Domingo, E. Viral quasispecies. Virology 479–480, 46–51 (2015).
44. Stern, A. et al. Costs and benefits of mutational robustness in RNA viruses. Cell Rep 8, 1026–1036 (2014).
45. Acevedo, A., Brodsky, L. & Andino, R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 505, 686–690 (2014).
46. Gitlin, L., Hagai, T., LaBarbera, A., Solovey, M. & Andino, R. Rapid evolution of virus sequences in intrinsically disordered protein regions. PLoS pathogens 10, e1004529 (2014).
47. Hagai, T., Azia, A., Babu, M. M. & Andino, R. Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Rep 7, 1729–1739 (2014).
48. Lauring, A. S., Frydman, J. & Andino, R. The role of mutational robustness in RNA virus evolution. Nature reviews. Microbiology 11, 327–336 (2013).
49. Lauring, A. S., Acevedo, A., Cooper, S. B. & Andino, R. Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus. Cell host & microbe 12, 623–632 (2012).
50. Saleh, M.-C. et al. Antiviral immunity in Drosophila requires systemic RNA interference spread. Nature 458, 346–350 (2009).
51. Vignuzzi, M., Wendt, E. & Andino, R. Engineering attenuated virus vaccines by controlling replication fidelity. Nature medicine 14, 154–161 (2008).
52. Barnes, D., Kunitomi, M., Vignuzzi, M., Saksela, K. & Andino, R. Harnessing endogenous miRNAs to control virus tissue tropism as a strategy for developing attenuated virus vaccines. Cell host & microbe 4, 239–248 (2008).
53. 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, 344–348 (2006).
54. Rij, R. P. van et al. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes & development 20, 2985–2995 (2006).
55. Rij, R. P. van & Andino, R. Enjoy the Silence. Science 303, 1978–1979 (2004).
56. Gitlin, L., Karelsky, S. & Andino, R. Correction: Corrigendum: Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 423, 197–197 (2003).