Reassortment in segmented RNA viruses: mechanisms and outcomes

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.

Figure 1. Reassortment, sexual reproduction and recombination

a | Reassortment in non-multipartite RNA viruses. Two virus particles are shown, each with a full complement of three viral genome segments. Following reassortment, hybrid progeny can be formed that contain segments derived from both parents. b | Sexual reproduction. Two parent gamete cells are shown, each with a haploid genome of three chromosomal segments. Following sex between the two parents, a hybrid diploid progeny is produced that contains one copy of each chromosome from each parent. c | Recombination in non-segmented, single-stranded RNA viruses. Following recombination between two virus particles, chimeric genomes are produced that have regions derived from each parent.

Figure 2. Pseudomonas phage φ6, influenza A virus and rotavirus genome organization and assortment

a | The Pseudomonas phage φ6 genome consists of three double-stranded RNA (dsRNA) segments: small (S), medium (M) and large (L). Blue indicates ORFs, and grey represents intergenic regions; lines at the 5′ and 3′ termini represent UTRs. Sequences that are known to be important for the selective packaging of φ6 single-stranded positive-sense RNA ((+)RNA) replication intermediates are shown in red. b | A model of φ6 genome segment assortment and packaging. φ6 (+)RNAs are packaged sequentially. Initially, the procapsid has a binding site only for the S (+)RNA segment, enabling it to be inserted. Following the packaging of the S segment, a binding site for the M (+)RNA segment is revealed in the procapsid, enabling that segment to be inserted. Finally, a binding site for the L (+)RNA segment is revealed, the segment is inserted, and the entire complement of φ6 (+)RNAs are encapsidated. Following packaging of all three (+)RNA segments, the procapsid core expands, which triggers the conversion of the three (+)RNAs into double-stranded RNA (dsRNA) genome segments by viral polymerases. c | The influenza A virus genome comprises eight negative-sense RNA ((−)RNA) segments. A representative segment is shown as a linear (−)RNA molecule (top) and as a ribonucleoprotein (RNP; bottom), in which the (−)RNA is bound by a heterotrimeric polymerase complex and nucleocapsid protein (NP). The ORF, UTRs and sequences that are important for selective genome packaging are coloured as in part a. d | A model of genome segment assortment and packaging in influenza A viruses. Eight influenza A virus RNPs are synthesized in the nucleus and individually exported into the cytosol, where they pair up with each other. While en route to the plasma membrane, the eight RNPs form a supramolecular complex that is encapsidated by a lipid envelope during budding to form the virion. e | The genome of rotavirus A is composed of 11 dsRNA segments, one of which is shown as a (+)RNA precursor in linear form (top) and folded into a putative panhandle shape (bottom). The ORF, UTRs and sequences that are important for selective packaging are coloured as in part a and part b. A polymerase–capping enzyme complex is thought to be bound to the 3′-terminal UGUGACC sequence. A putative stem–loop structure may act as an assortment and/or packaging signal. f | A model of genome segment assortment and packaging in rotaviruses. The 11 (+)RNAs, each with a bound polymerase–capping enzyme complex, are thought to pair up and eventually form a supramolecular complex that is encapsidated by a forming virion particle. During or immediately after encapsidation, the (+)RNAs are converted into dsRNA genome segments by their dedicated polymerase. The polymerases function while tethered to the viral capsid (not shown).

Figure 3. Direct restrictions on the generation of reassortants

a | Incompatibility of RNA–RNA interactions. Two influenza A virus genome segments are shown as ribonucleoproteins (RNPs), each derived from a parent strain (strain A is shown in red and strain B is shown in blue). If the packaging signals are compatible (left), the RNA molecules can interact, which leads to co-packaging and reassortment. However, if the packaging signals are not compatible, the RNA molecules will interact suboptimally, thereby preventing their co-packaging. b | Incompatibility of protein–RNA interactions. A rotavirus A positive-sense RNA ((+)RNA) molecule from one strain may be recognized only by the polymerase from that same strain. If the polymerase in the virion is from a different strain and is unable to recognize the (+)RNA molecule, replication does not occur, thus restricting the generation of reassortants.

Figure 4. Fitness consequences of reassortment

a | Increase in viral fitness. Following reassortment, hybrid progeny can be formed that contain segments derived from both parents. In some cases, the new allelic combination confers phenotypic changes to the reassortant. For example, reassortment can produce an antigenically novel variant that is not recognized by the host immune system. This more-fit reassortant emerges in the host, whereas the less-fit parental strains are eliminated. b | Decrease in viral fitness. In some cases, reassortment can uncouple essential cognate protein sets that interact optimally when kept together. If non-cognate proteins do not interact, the reassortant would be less fit than parental strains and would therefore be eliminated from the population. c | Post-reassortment adaptations. A less-fit reassortant can accumulate mutations that restore the interaction interface between the non-cognate proteins. Such post-reassortment adaptive changes will enable the reassortant to regain fitness and emerge.