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Reassortment in segmented RNA viruses: mechanisms and outcomes

Key Points

  • Segmented RNA viruses are important pathogens of humans, animals and plants. An understanding of how these viruses replicate and evolve during their spread in nature is expected to inform disease treatment and prevention strategies.

  • A shared feature of all segmented RNA viruses is their capacity to exchange genome segments during co-infection by a process called reassortment. Specifically, when two or more viruses infect a single host cell, they can each package genome segments from the other virus into a nascent hybrid virion.

  • Several factors constrain the generation of reassortants during co-infection, including incompatible RNA–RNA interactions between different gene segments, and incompatible protein–RNA interactions between molecules from different viral strains.

  • Multiple selection pressures can promote or prevent the emergence of reassortant viruses in the population. For example, reassortment can increase viral fitness by enabling the reassortant to escape immune recognition, but it can also decrease viral fitness by uncoupling essential cognate protein sets that interact optimally when kept together.

Abstract

Segmented RNA viruses are widespread in nature and include important human, animal and plant pathogens, such as influenza viruses and rotaviruses. Although the origin of RNA virus genome segmentation remains elusive, a major consequence of this genome structure is the capacity for reassortment to occur during co-infection, whereby segments are exchanged among different viral strains. Therefore, reassortment can create viral progeny that contain genes that are derived from more than one parent, potentially conferring important fitness advantages or disadvantages to the progeny virus. However, for segmented RNA viruses that package their multiple genome segments into a single virion particle, reassortment also requires genetic compatibility between parental strains, which occurs in the form of conserved packaging signals, and the maintenance of RNA and protein interactions. In this Review, we discuss recent studies that examined the mechanisms and outcomes of reassortment for three well-studied viral families — Cystoviridae, Orthomyxoviridae and Reoviridae — and discuss how these findings provide new perspectives on the replication and evolution of segmented RNA viruses.

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Figure 1: Reassortment, sexual reproduction and recombination.
Figure 2: Pseudomonas phage ϕ6, influenza A virus and rotavirus genome organization and assortment.
Figure 3: Direct restrictions on the generation of reassortants.
Figure 4: Fitness consequences of reassortment.

References

  1. Tate, J. E. et al. 2008 estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes: a systematic review and meta-analysis. Lancet Infect. Dis. 12, 136–141 (2012).

    PubMed  Article  Google Scholar 

  2. Klepser, M. E. Socioeconomic impact of seasonal (epidemic) influenza and the role of over-the-counter medicines. Drugs 74, 1467–1479 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  3. GBD 2013 Mortality and Causes of Death Collaborators. Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 385, 117–171 (2015).

  4. Maclachlan, N. J. & Mayo, C. E. Potential strategies for control of bluetongue, a globally emerging, Culicoides-transmitted viral disease of ruminant livestock and wildlife. Antiviral Res. 99, 79–90 (2013).

    CAS  PubMed  Article  Google Scholar 

  5. Mahgoub, H. A., Bailey, M. & Kaiser, P. An overview of infectious bursal disease. Arch. Virol. 157, 2047–2057 (2012).

    CAS  PubMed  Article  Google Scholar 

  6. Hanssen, I. M., Lapidot, M. & Thomma, B. P. Emerging viral diseases of tomato crops. Mol. Plant Microbe Interact. 23, 539–548 (2010).

    CAS  PubMed  Article  Google Scholar 

  7. Bernstein, H. et al. Genetic damage, mutation, and the evolution of sex. Science 229, 1277–1281 (1985).

    CAS  PubMed  Article  Google Scholar 

  8. Bernstein, M. E. Does variation in the testosterone level of the seminal plasma affect the primary sex ratio? J. Theor. Biol. 126, 377–378 (1987).

    CAS  PubMed  Article  Google Scholar 

  9. Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  10. Chao, L. Evolution of sex in RNA viruses. J. Theor. Biol. 133, 99–112 (1988). This seminal article describes how segment reassortment in RNA viruses is conceptually similar to sexual reproduction in eukaryotes and theorizes about the role of such genetic exchange mechanisms during viral evolution.

    CAS  PubMed  Article  Google Scholar 

  11. Chao, L. Levels of selection, evolution of sex in RNA viruses, and the origin of life. J. Theor. Biol. 153, 229–246 (1991).

    CAS  PubMed  Article  Google Scholar 

  12. Chao, L. Evolution of sex in RNA viruses. Trends Ecol. Evol. 7, 147–151 (1992).

    CAS  PubMed  Article  Google Scholar 

  13. Turner, P. E. Searching for the advantages of virus sex. Orig. Life Evol. Biosph. 33, 95–108 (2003).

    CAS  PubMed  Article  Google Scholar 

  14. Nee, S. On the evolution of sex in RNA viruses. J. Theor. Biol. 138, 407–412 (1989).

    CAS  PubMed  Article  Google Scholar 

  15. Takeda, M. et al. Generation of measles virus with a segmented RNA genome. J. Virol. 80, 4242–4248 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  16. Ojosnegros, S. et al. Viral genome segmentation can result from a trade-off between genetic content and particle stability. PLoS Genet. 7, e1001344 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  17. Lai, M. M. Genetic recombination in RNA viruses. Curr. Top. Microbiol. Immunol. 176, 21–32 (1992).

    CAS  PubMed  Google Scholar 

  18. Boni, M. F. et al. No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene 494, 242–245 (2012).

    CAS  PubMed  Article  Google Scholar 

  19. Boni, M. F. et al. Homologous recombination is very rare or absent in human influenza A virus. J. Virol. 82, 4807–4811 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. Mindich, L. Packaging, replication and recombination of the segmented genome of bacteriophage Φ6 and its relatives. Virus Res. 101, 83–92 (2004).

    CAS  PubMed  Article  Google Scholar 

  21. Onodera, S., Sun, Y. & Mindich, L. Reverse genetics and recombination in Φ8, a dsRNA bacteriophage. Virology 286, 113–118 (2001).

    CAS  PubMed  Article  Google Scholar 

  22. Woods, R. J. Intrasegmental recombination does not contribute to the long-term evolution of group A rotavirus. Infect. Genet. Evol. 32, 354–360 (2015).

    CAS  PubMed  Article  Google Scholar 

  23. Simon-Loriere, E. & Holmes, E. C. Why do RNA viruses recombine? Nat. Rev. Microbiol. 9, 617–626 (2011). This review article compares the mechanism of recombination in non-segmented RNA viruses to that of reassortment in segmented RNA viruses. The authors also describe theories regarding the evolutionary significance of genetic exchange among viruses.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  24. Vidaver, A. K., Koski, R. K. & Van Etten, J. L. Bacteriophage Φ6: a lipid-containing virus of Pseudomonas phaseolicola. J. Virol. 11, 799–805 (1973).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  25. Mindich, L. Precise packaging of the three genomic segments of the double-stranded-RNA bacteriophage Φ6. Microbiol. Mol. Biol. Rev. 63, 149–160 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. Silander, O. K. et al. Widespread genetic exchange among terrestrial bacteriophages. Proc. Natl Acad. Sci. USA 102, 19009–19014 (2005). This first comparative genomics study of members of the Cystoviridae family in nature reveals that reassortment occurs frequently and between highly divergent viral strains. The results of this study suggest that few genetic restrictions to reassortment exist in this family.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  27. O'Keefe, K. J. et al. Geographic differences in sexual reassortment in RNA phage. Evolution 64, 3010–3023 (2010).

    CAS  PubMed  Google Scholar 

  28. Jäälinoja, H. T., Huiskonen, J. T. & Butcher, S. J. Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages Φ6 and Φ8. Structure 15, 157–167 (2007).

    PubMed  Article  CAS  Google Scholar 

  29. Emori, Y., Iba, H. & Okada, Y. Transcriptional regulation of three double-stranded RNA segments of bacteriophage Φ6 in vitro. J. Virol. 46, 196–203 (1983).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  30. Gottlieb, P. et al. In vitro packaging of the bacteriophage Φ6 ssRNA genomic precursors. Virology 181, 589–594 (1991).

    CAS  PubMed  Article  Google Scholar 

  31. Gottlieb, P. et al. In vitro replication, packaging, and transcription of the segmented double-stranded RNA genome of bacteriophage Φ6: studies with procapsids assembled from plasmid-encoded proteins. J. Bacteriol. 172, 5774–5782 (1990).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. Huiskonen, J. T. et al. Structure of the bacteriophage Φ6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 14, 1039–1048 (2006).

    CAS  PubMed  Article  Google Scholar 

  33. Gottlieb, P., Qiao, X., Strassman, J., Frilander, M. & Mindich, L. Identification of the packaging regions within the genomic RNA segments of bacteriophage Φ6. Virology 200, 42–47 (1994). This study uses an in vitro system to map the location of packaging signals within the ϕ6 RNA segments.

    CAS  PubMed  Article  Google Scholar 

  34. Onodera, S. et al. Construction of a transducing virus from double-stranded RNA bacteriophage Φ6: establishment of carrier states in host cells. J. Virol. 66, 190–196 (1992).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. Onodera, S. et al. Isolation of a mutant that changes genomic packaging specificity in Φ6. Virology 252, 438–442 (1998).

    CAS  PubMed  Article  Google Scholar 

  36. Onodera, S. et al. Directed changes in the number of double-stranded RNA genomic segments in bacteriophage Φ6. Proc. Natl Acad. Sci. USA 95, 3920–3924 (1998). This report describes how the three segments of the ϕ6 genome can be engineered as a single concatenated genome segment, providing insights into the replication advantages of genome segmentation for Cystoviridae family members.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. Palase, P. & Shaw, M. in Fields Virology (eds Howley, P. M. & Knipe D. M.) 1647–1690 (Lippincott Williams & Wilkins, 2007).

    Google Scholar 

  38. Dushoff, J. et al. Mortality due to influenza in the United States — an annualized regression approach using multiple-cause mortality data. Am. J. Epidemiol. 163, 181–187 (2006).

    PubMed  Article  Google Scholar 

  39. Johnson, N. P. & Mueller, J. Updating the accounts: global mortality of the 1918–1920 “Spanish” influenza pandemic. Bull. Hist. Med. 76, 105–115 (2002).

    PubMed  Article  Google Scholar 

  40. Parrish, C. R., Murcia, P. R. & Holmes, E. C. Influenza virus reservoirs and intermediate hosts: dogs, horses, and new possibilities for influenza virus exposure of humans. J. Virol. 89, 2990–2994 (2015).

    CAS  PubMed  Article  Google Scholar 

  41. Gultyaev, A. P., Fouchier, R. A. & Olsthoorn, R. C. Influenza virus RNA structure: unique and common features. Int. Rev. Immunol. 29, 533–556 (2010).

    CAS  PubMed  Article  Google Scholar 

  42. Zheng, W. & Tao, Y. J. Structure and assembly of the influenza A virus ribonucleoprotein complex. FEBS Lett. 587, 1206–1214 (2013).

    CAS  PubMed  Article  Google Scholar 

  43. Noda, T. & Kawaoka, Y. Structure of influenza virus ribonucleoprotein complexes and their packaging into virions. Rev. Med. Virol. 20, 380–391 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  44. Gerber, M. et al. Selective packaging of the influenza A genome and consequences for genetic reassortment. Trends Microbiol. 22, 446–455 (2014). This review article summarizes the genetic, biochemical and structural data supporting the current model of genome segment assortment and packaging in influenza A viruses.

    CAS  PubMed  Article  Google Scholar 

  45. Hutchinson, E. C. & Fodor, E. Transport of the influenza virus genome from nucleus to nucleus. Viruses 5, 2424–2446 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  46. Chou, Y. Y. et al. One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. Proc. Natl Acad. Sci. USA 109, 9101–9106 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  47. Chou, Y. Y. et al. Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis. PLoS Pathog. 9, e1003358 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. Lakdawala, S. S. et al. Influenza A virus assembly intermediates fuse in the cytoplasm. PLoS Pathog. 10, e1003971 (2014). This investigation uses multicolour single-molecule fluorescent in situ hybridization to show that influenza A virus RNAs assort in the cytoplasm while en route to the plasma membrane.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  49. Gavazzi, C. et al. An in vitro network of intermolecular interactions between viral RNA segments of an avian H5N2 influenza A virus: comparison with a human H3N2 virus. Nucleic Acids Res. 41, 1241–1254 (2013).

    CAS  PubMed  Article  Google Scholar 

  50. Gavazzi, C. et al. A functional sequence-specific interaction between influenza A virus genomic RNA segments. Proc. Natl Acad. Sci. USA 110, 16604–16609 (2013). This paper describes in vitro experiments that identify direct intermolecular interactions between influenza A virus genomic RNA segments, shedding light on the mechanism of assortment.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. Fournier, E. et al. Interaction network linking the human H3N2 influenza A virus genomic RNA segments. Vaccine 30, 7359–7367 (2012).

    CAS  PubMed  Article  Google Scholar 

  52. Fournier, E. et al. A supramolecular assembly formed by influenza A virus genomic RNA segments. Nucleic Acids Res. 40, 2197–2209 (2012).

    CAS  PubMed  Article  Google Scholar 

  53. Hutchinson, E. C. et al. Genome packaging in influenza A virus. J. Gen. Virol. 91, 313–328 (2010).

    CAS  PubMed  Article  Google Scholar 

  54. Sugita, Y. et al. Configuration of viral ribonucleoprotein complexes within the influenza A virion. J. Virol. 87, 12879–12884 (2013). This study uses electron microscopy to analyse the fine structure of purified RNPs and their configuration within influenza A virions, thereby revealing novel aspects of assortment and packaging.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  55. Enami, M. et al. An influenza virus containing nine different RNA segments. Virology 185, 291–298 (1991).

    CAS  PubMed  Article  Google Scholar 

  56. Gao, Q. et al. A nine-segment influenza a virus carrying subtype H1 and H3 hemagglutinins. J. Virol. 84, 8062–8071 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  57. Brooke, C. B. et al. Most influenza A virions fail to express at least one essential viral protein. J. Virol. 87, 3155–3162 (2013). This article reports experiments showing that the vast majority of influenza A virus particles do not express at least one viral protein. This implies that the genome segment packaging efficiency for influenza A viruses may be lower than previously predicted.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. Brooke, C. B. et al. Influenza A virus nucleoprotein selectively decreases neuraminidase gene-segment packaging while enhancing viral fitness and transmissibility. Proc. Natl Acad. Sci. USA 111, 16854–16859 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. Fonville, J. M. et al. Influenza virus reassortment is enhanced by semi-infectious particles but can be suppressed by defective interfering particles. PLoS Pathog. 11, e1005204 (2015). This work shows that influenza A virus particles that lack a full complement of functional genome segments (that is, semi-infectious particles) can reassort with infectious particles.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  60. Otuka, A. Migration of rice planthoppers and their vectored re-emerging and novel rice viruses in East Asia. Front. Microbiol. 4, 309 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  61. Tate, J. E. & Parashar, U. D. Rotavirus vaccines in routine use. Clin. Infect. Dis. 59, 1291–1301 (2014).

    CAS  PubMed  Article  Google Scholar 

  62. Marthaler, D. et al. Rapid detection and high occurrence of porcine rotavirus A, B, and C by RT-qPCR in diagnostic samples. J. Virol. Methods 209, 30–34 (2014).

    CAS  PubMed  Article  Google Scholar 

  63. Moutelikova, R., Prodelalova, J. & Dufkova, L. Prevalence study and phylogenetic analysis of group C porcine rotavirus in the Czech Republic revealed a high level of VP6 gene heterogeneity within porcine cluster I1. Arch. Virol. 159, 1163–1167 (2014).

    CAS  PubMed  Article  Google Scholar 

  64. Amimo, J. O., Vlasova, A. N. & Saif, L. J. Prevalence and genetic heterogeneity of porcine group C rotaviruses in nursing and weaned piglets in Ohio, USA and identification of a potential new VP4 genotype. Vet. Microbiol. 164, 27–38 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. Park, S. I. et al. Genetically diverse group C rotaviruses cause sporadic infection in Korean calves. J. Vet. Med. Sci. 73, 479–482 (2011).

    PubMed  Article  Google Scholar 

  66. Lobo, P. D. et al. Phylogenetic analysis of human group C rotavirus in hospitalized children with gastroenteritis in Belem, Brazil. J. Med. Virol. 88, 728–733 (2016).

    CAS  Article  Google Scholar 

  67. Luchs, A. & do Carmo Sampaio Tavares Timenetsky, M. Phylogenetic analysis of human group C rotavirus circulating in Brazil reveals a potential unique NSP4 genetic variant and high similarity with Asian strains. Mol. Genet. Genom. 290, 969–986 (2015).

    CAS  Article  Google Scholar 

  68. El-Senousy, W. M., Ragab, A. M. & Handak, E. M. Prevalence of rotaviruses groups A and C in Egyptian children and aquatic environment. Food Environ. Virol. 7, 132–141 (2016).

    Article  CAS  Google Scholar 

  69. Lahon, A., Walimbe, A. M. & Chitambar, S. D. Full genome analysis of group B rotaviruses from western India: genetic relatedness and evolution. J. Gen. Virol. 93, 2252–2266 (2012).

    CAS  PubMed  Article  Google Scholar 

  70. Trask, S. D., McDonald, S. M. & Patton, J. T. Structural insights into the coupling of virion assembly and rotavirus replication. Nat. Rev. Microbiol. 10, 165–177 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. Rainsford, E. W. & McCrae, M. A. Characterization of the NSP6 protein product of rotavirus gene 11. Virus Res. 130, 193–201 (2007).

    CAS  PubMed  Article  Google Scholar 

  72. McDonald, S. M. & Patton, J. T. Assortment and packaging of the segmented rotavirus genome. Trends Microbiol. 19, 136–144 (2011).

    CAS  PubMed  Article  Google Scholar 

  73. Lawton, J. A., Estes, M. K. & Prasad, B. V. Mechanism of genome transcription in segmented dsRNA viruses. Adv. Virus Res. 55, 185–229 (2000).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. Gallegos, C. O. & Patton, J. T. Characterization of rotavirus replication intermediates: a model for the assembly of single-shelled particles. Virology 172, 616–627 (1989). This seminal investigation analyses the protein composition and activity of rotavirus replication–assembly intermediates and suggests a model for genome segment assortment.

    CAS  PubMed  Article  Google Scholar 

  75. Patton, J. T. & Gallegos, C. O. Structure and protein composition of the rotavirus replicase particle. Virology 166, 358–365 (1988).

    CAS  PubMed  Article  Google Scholar 

  76. Patton, J. T. & Gallegos, C. O. Rotavirus RNA replication: single-stranded RNA extends from the replicase particle. J. Gen. Virol. 71, 1087–1094 (1990).

    CAS  PubMed  Article  Google Scholar 

  77. Suzuki, Y. A candidate packaging signal of human rotavirus differentiating Wa-like and DS-1-like genomic constellations. Microbiol. Immunol. 59, 567–571 (2015).

    CAS  PubMed  Article  Google Scholar 

  78. Li, W. et al. Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions. Nucleic Acids Res. 38, 7718–7735 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. Burkhardt, C. et al. Structural constraints in the packaging of bluetongue virus genomic segments. J. Gen. Virol. 95, 2240–2250 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  80. Sung, P. Y. & Roy, P. Sequential packaging of RNA genomic segments during the assembly of bluetongue virus. Nucleic Acids Res. 42, 13824–13838 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  81. Roner, M. R. & Steele, B. G. Localizing the reovirus packaging signals using an engineered m1 and s2 ssRNA. Virology 358, 89–97 (2007). This paper describes reverse genetics experiments that enabled the localization of the packaging signals for two viral genome segments of Reoviridae family members.

    CAS  PubMed  Article  Google Scholar 

  82. Roner, M. R., Bassett, K. & Roehr, J. Identification of the 5′ sequences required for incorporation of an engineered ssRNA into the reovirus genome. Virology 329, 348–360 (2004).

    CAS  PubMed  Article  Google Scholar 

  83. Roner, M. R. & Joklik, W. K. Reovirus reverse genetics: incorporation of the CAT gene into the reovirus genome. Proc. Natl Acad. Sci. USA 98, 8036–8041 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  84. Zhang, X. et al. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature 527, 531–534 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  85. Desselberger, U. Genome rearrangements of rotaviruses. Arch. Virol. Suppl. 12, 37–51 (1996).

    CAS  PubMed  Google Scholar 

  86. Troupin, C. et al. Rearranged genomic RNA segments offer a new approach to the reverse genetics of rotaviruses. J. Virol. 84, 6711–6719 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  87. Navarro, A., Trask, S. D. & Patton, J. T. Generation of genetically stable recombinant rotaviruses containing novel genome rearrangements and heterologous sequences by reverse genetics. J. Virol. 87, 6211–6220 (2013). This study uses reverse genetics to show that additional RNA, including heterologous gene sequences, can be packaged into rotavirus virions.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. Tian, Y. et al. Genomic concatemerization/deletion in rotaviruses: a new mechanism for generating rapid genetic change of potential epidemiological importance. J. Virol. 67, 6625–6632 (1993).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. Taniguchi, K., Kojima, K. & Urasawa, S. Nondefective rotavirus mutants with an NSP1 gene which has a deletion of 500 nucleotides, including a cysteine-rich zinc finger motif-encoding region (nucleotides 156 to 248), or which has a nonsense codon at nucleotides 153 to 155. J. Virol. 70, 4125–4130 (1996). This report describes a naturally occurring rotavirus mutant that does not express a functional NSP1 protein but that efficiently incorporates the NSP1-coding gene. The implications of this study are that the NSP1-coding RNA molecule itself is essential for assortment and packaging of the other ten genome segments.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  90. Baker, S. F. et al. Influenza A and B virus intertypic reassortment through compatible viral packaging signals. J. Virol. 88, 10778–10791 (2014). This article presents experiments showing that an influenza A virus can package an influenza B virus genome segment, provided that the segment contains cognate influenza A virus packaging signals.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  91. Essere, B. et al. Critical role of segment-specific packaging signals in genetic reassortment of influenza A viruses. Proc. Natl Acad. Sci. USA 110, E3840–E3848 (2013). This investigation shows the importance of compatible packaging signals for efficient reassortment to occur among divergent influenza A virus strains.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  92. Marshall, N. et al. Influenza virus reassortment occurs with high frequency in the absence of segment mismatch. PLoS Pathog. 9, e1003421 (2013). This paper describes experiments that quantify, for the first time, the efficiency of reassortment between two nearly genetically identical strains of influenza A virus, indicating that reassortment is restricted mainly by genetic incompatibility of strains.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  93. Diaz-Munoz, S. L. et al. Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages. BMC Evol. Biol. 13, 206 (2013).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  94. Qiao, X., Qiao, J., Onodera, S. & Mindich, L. Characterization of Φ13, a bacteriophage related to Φ6 and containing three dsRNA genomic segments. Virology 275, 218–224 (2000).

    CAS  PubMed  Article  Google Scholar 

  95. Ramig, R. F. Genetics of the rotaviruses. Annu. Rev. Microbiol. 51, 225–255 (1997).

    CAS  PubMed  Article  Google Scholar 

  96. Wenske, E. A. et al. Genetic reassortment of mammalian reoviruses in mice. J. Virol. 56, 613–616 (1985).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  97. Nibert, M. L., Margraf, R. L. & Coombs, K. M. Nonrandom segregation of parental alleles in reovirus reassortants. J. Virol. 70, 7295–7300 (1996). This work documents the frequency of reassortment between two strains of the Reoviridae family following experimental co-infection, and provides evidence for genetic linkages among segments.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. Ramig, R. F. et al. Analysis of reassortment and superinfection during mixed infection of Vero cells with bluetongue virus serotypes 10 and 17. J. Gen. Virol. 70, 2595–2603 (1989).

    PubMed  Article  Google Scholar 

  99. Lu, X. et al. Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure 16, 1678–1688 (2008). This article reports the high-resolution X-ray crystal structure of the rotavirus polymerase in the presence and absence of RNA template, informing an understanding of genome segment packaging and replication.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. Ogden, K. M., Johne, R. & Patton, J. T. Rotavirus RNA polymerases resolve into two phylogenetically distinct classes that differ in their mechanism of template recognition. Virology 431, 50–57 (2012).

    CAS  PubMed  Article  Google Scholar 

  101. Yang, H., Makeyev, E. V. & Bamford, D. H. Comparison of polymerase subunits from double-stranded RNA bacteriophages. J. Virol. 75, 11088–11095 (2001).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  102. Nelson, M. I. et al. Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009–2011. J. Virol. 86, 8872–8878 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  103. Dugan, V. G. et al. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. 4, e1000076 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  104. Lindstrom, S. E., Cox, N. J. & Klimov, A. Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957–1972: evidence for genetic divergence and multiple reassortment events. Virology 328, 101–119 (2004).

    CAS  PubMed  Article  Google Scholar 

  105. Nelson, M. I. et al. Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. 4, e1000012 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  106. Rambaut, A. et al. The genomic and epidemiological dynamics of human influenza A virus. Nature 453, 615–619 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  107. Holmes, E. C. et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 3, e300 (2005). This first large-scale comparative genomics study of influenza A viruses shows that multiple co-circulating lineages exist and documents reassortment events.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  108. Ghedin, E. et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437, 1162–1166 (2005).

    CAS  PubMed  Article  Google Scholar 

  109. Westgeest, K. B. et al. Genome-wide analysis of reassortment and evolution of human influenza A (H3N2) viruses circulating between 1968 and 2011. J. Virol. 88, 2844–2857 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  110. McDonald, S. M. et al. Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations. PLoS Pathog. 5, 1000634 (2009). This first large-scale comparative genomics study of human rotaviruses shows that multiple co-circulating lineages exist and documents reassortment events.

    Article  CAS  Google Scholar 

  111. McDonald, S. M. et al. Diversity and relationships of cocirculating modern human rotaviruses revealed using large-scale comparative genomics. J. Virol. 86, 9148–9162 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  112. Zhang, S. et al. Analysis of human rotaviruses from a single location over an 18-year time span suggests that protein coadaption influences gene constellations. J. Virol. 88, 9842–9863 (2014). This comparative genomics study of human rotavirus identifies persistent lineages and suggests that co-adaptation of functionally interacting viral proteins may restrict reassortment over time.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  113. Dennis, A. F. et al. Molecular epidemiology of contemporary G2P[4] human rotaviruses cocirculating in a single U.S. community: footprints of a globally transitioning genotype. J. Virol. 88, 3789–3801 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  114. Nomikou, K. et al. Widespread reassortment shapes the evolution and epidemiology of bluetongue virus following European invasion. PLoS Pathog. 11, e1005056 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  115. Nelson, M. I. et al. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog. 3, 1220–1228 (2007).

    CAS  PubMed  Article  Google Scholar 

  116. Simonsen, L. et al. The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol. Biol. Evol. 24, 1811–1820 (2007).

    CAS  PubMed  Article  Google Scholar 

  117. Li, C. et al. Compatibility among polymerase subunit proteins is a restricting factor in reassortment between equine H7N7 and human H3N2 influenza viruses. J. Virol. 82, 11880–11888 (2008). This is the first investigation to reveal how incompatibilities among polymerase subunits can restrict reassortment among divergent influenza A viruses.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  118. Hara, K. et al. Co-incorporation of the PB2 and PA polymerase subunits from human H3N2 influenza virus is a critical determinant of the replication of reassortant ribonucleoprotein complexes. J. Gen. Virol. 94, 2406–2416 (2013).

    CAS  PubMed  Article  Google Scholar 

  119. Octaviani, C. P., Goto, H. & Kawaoka, Y. Reassortment between seasonal H1N1 and pandemic (H1N1) 2009 influenza viruses is restricted by limited compatibility among polymerase subunits. J. Virol. 85, 8449–8452 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  120. McDonald, S. M. et al. Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction. J. Virol. 83, 6135–6148 (2009). This is the first report to demonstrate how incompatibilities between the rotavirus polymerase and core shell protein may restrict reassortment among divergent strains.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  121. McDonald, S. M. & Patton, J. T. Rotavirus VP2 core shell regions critical for viral polymerase activation. J. Virol. 85, 3095–3105 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  122. Taraporewala, Z. F. et al. Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system. J. Virol. 80, 7984–7994 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  123. Ilyushina, N. A. et al. Postreassortment changes in a model system: HA–NA adjustment in an H3N2 avian–human reassortant influenza virus. Arch. Virol. 150, 1327–1338 (2005).

    CAS  PubMed  Article  Google Scholar 

  124. Kaverin, N. V. et al. Postreassortment changes in influenza A virus hemagglutinin restoring HA–NA functional match. Virology 244, 315–321 (1998). This article reports that compensatory mutations can correct mismatched protein interactions that were due to reassortment for influenza A viruses in cell culture experiments.

    CAS  PubMed  Article  Google Scholar 

  125. Kaverin, N. V. et al. Intergenic HA–NA interactions in influenza A virus: postreassortment substitutions of charged amino acid in the hemagglutinin of different subtypes. Virus Res., 66, 123–129 (2000).

    CAS  Article  Google Scholar 

  126. Rudneva, I. A. et al. Effect of gene constellation and postreassortment amino acid change on the phenotypic features of H5 influenza virus reassortants. Arch. Virol. 152, 1139–1145 (2007).

    CAS  PubMed  Article  Google Scholar 

  127. Neverov, A. D. et al. Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes. PLoS Genet. 10, e1004037 (2014). This study shows that influenza A virus reassortment in nature causes a temporary increase in the rate of amino acid changes as the viral proteins adapt to a new genetic environment.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  128. Krammer, F., Palese, P. & Steel, J. Advances in universal influenza virus vaccine design and antibody mediated therapies based on conserved regions of the hemagglutinin. Curr. Top. Microbiol. Immunol. 386, 301–321 (2015).

    CAS  PubMed  Google Scholar 

  129. Jin, H. & Subbarao, K. Live attenuated influenza vaccine. Curr. Top. Microbiol. Immunol. 386, 181–204 (2015).

    CAS  PubMed  Google Scholar 

  130. Chandran, A. & Santosham, M. RotaTeq: a three-dose oral pentavalent reassortant rotavirus vaccine. Expert Rev. Vaccines 7, 1475–1480 (2008).

    CAS  PubMed  Article  Google Scholar 

  131. Qin, X. C. et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc. Natl Acad. Sci. USA 11, 6744–6749 (2014).

    Article  CAS  Google Scholar 

  132. Andersson, D. I., Jerlstrom-Hultqvist, J. & Nasvall, J. Evolution of new functions de novo and from preexisting genes. Cold Spring Harb. Perspect. Biol. 7, a017996 (2015).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  133. Shirogane, Y., Watanabe, S. & Yanagi, Y. Cooperation between different RNA virus genomes produces a new phenotype. Nat. Commun. 3, 1235 (2012).

    PubMed  Article  CAS  Google Scholar 

  134. Rager, M. et al. Polyploid measles virus with hexameric genome length. EMBO J. 21, 2364–2372 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  135. Beniac, D. R. et al. The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy. PLoS ONE. 7, e29608 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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Acknowledgements

S.M.M. receives financial support from the Virginia Tech Carilion School of Medicine and Research Institute and the US National Institutes of Health (NIH; grants R01AI116815, R21AI113402 and R21AI119588). P.E.T. receives financial support from the US National Science Foundation BEACON Center for Study of Evolution in Action and the NIH (grant R01AI09164601). J.T.P. is supported by funding from the University of Maryland, College Park, USA.

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Glossary

Segmented RNA viruses

Viruses in which the genome consists of more than one RNA molecule (that is, segments). The genome segments can be packaged within a single virion particle or into separate particles.

Type species

A representative viral strain that is studied to understand the biology of an entire viral genus or family.

Reassortment

A process of genetic exchange whereby two or more parental viruses co-infect a single host cell and exchange genome segments. The outcome is the formation of hybrid viral progeny with genome segments derived from multiple parental strains.

Assortment

The mechanism by which a segmented virus packages one of each genome segment into a virion particle.

Viral fitness

The capacity of an individual virus to generate infectious progeny, relative to other virus genotypes in the population.

Pathovars

Bacterial strains with the same or similar characteristics.

In vitro packaging system

A simplified experimental system in which viral genome segments are incorporated into a virion particle; this occurs in a test tube and outside the context of an infected host cell.

Defective-interfering RNAs

Spontaneously generated mutant RNA molecules that usually contain large gene deletions but maintain sequences that are crucial for their replication and packaging. These RNAs reduce the fitness of full-length viruses during cellular co-infection.

HA–NA subtype

A binomial system of classification for influenza A viruses that is based on the neutralizing antibody response to the virion structural proteins haemagglutinin (HA) and neuraminidase (NA).

Diploidy or polyploidy

In virology: when an individual virus encapsidates two (diploidy) or more (polyploidy) copies of the genome into a single virus particle.

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McDonald, S., Nelson, M., Turner, P. et al. Reassortment in segmented RNA viruses: mechanisms and outcomes. Nat Rev Microbiol 14, 448–460 (2016). https://doi.org/10.1038/nrmicro.2016.46

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