Patterns of Human Immunodeficiency Virus Type 1 Recombination
            <i>Ex Vivo</i>
            Provide Evidence for Coadaptation of Distant Sites, Resulting in Purifying Selection for Intersubtype Recombinants during Replication

HIV-1 infection is characterized by the rapid generation of genetic diversity that facilitates viral escape from immune selection and antiretroviral therapy. Despite recombination's crucial role in viral diversity and evolution, little is known about the genomic factors that influence recombination between highly similar genomes. In this study, we use a minimally modified fulllength HIV-1 genome and high-throughput sequence analysis to study recombination in gag and pol in T cells. We find that recombination is favored at a number of recombination hot spots, where recombination occurs six times more frequently than at corresponding cold spots. Interestingly, these hot spots occur near important features of the HIV-1 genome but do not occur at sites immediately around protease inhibitor or reverse transcriptase inhibitor drug resistance mutations. We show that the recombination hot and cold spots are consistent across five blood donors and are independent of coreceptor-mediated entry. Finally, we check common experimental confounders and find that these are not driving the location of recombination hot spots. This is the first study to identify the location of recombination hot spots between two similar viral genomes with great statistical power and under conditions that closely reflect natural recombination events among HIV-1 quasispecies. IMPORTANCEThe ability of HIV-1 to evade the immune system and antiretroviral therapy depends on genetic diversity within the viral quasispecies. Retroviral recombination is an important mechanism that helps to generate and maintain this genetic diversity, but little is known about how recombination rates vary within the HIV-1 genome. We measured recombination rates in gag and pol and identified recombination hot and cold spots, demonstrating that recombination is not random but depends on the underlying gene sequence. The strength and location of these recombination hot and cold spots can be used to improve models of viral dynamics and evolution, which will be useful for the design of robust antiretroviral therapies.

Section: Discussionsupporting

confidence: 58%

Identifying Recombination Hot Spots in the HIV-1 Genome

Smyth

Schlub

Grimm

et al. 2014

“…Instead, many recombination events yield dysfunctional proteins that are presumably strongly selected against under natural infection conditions. In addition, the probability that a recombinant is functional varies significantly with the position at which recombination occurs within a gene (14,43). The clustering of breakpoints, as observed in natural group M HIV-1 recombinants, appears to be linked to the structure of the encoded protein.…”

Section: Resultsmentioning

confidence: 99%

“…A pair of recent studies focusing on intersubtype HIV-1 group M recombination emphasized that breakpoints falling within certain regions of env or pol yield chimeric proteins that have a higher probability of being dysfunctional than when breakpoints occur in other parts of these genes (14,43). In the case of env, two factors-the mechanistic tendency for recombination to occur more frequently at certain genome sites and selection against dysfunctional recombinants-were shown to account almost entirely for recombination patterns observed in naturally sampled sequences (43).…”

mentioning

confidence: 99%

RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

Simon‐Lorière

Martin

Weeks

et al. 2010

Many viruses, including retroviruses, undergo frequent recombination, a process which can increase their rate of adaptive evolution. In the case of HIV, recombination has been responsible for the generation of numerous intersubtype recombinant variants with epidemiological importance in the AIDS pandemic. Although it is known that fragments of genetic material do not combine randomly during the generation of recombinant viruses, the mechanisms that lead to preferential recombination at specific sites are not fully understood. Here we reanalyze recent independent data defining (i) the structure of a complete HIV-1 RNA genome and (ii) favorable sites for recombination. We show that in the absence of selection acting on recombinant genomes, regions harboring RNA structures in the NL4-3 model strain are strongly predictive of recombination breakpoints in the HIV-1 env genes of primary isolates. In addition, we found that breakpoints within recombinant HIV-1 genomes sampled from human populations, which have been acted upon extensively by natural selection, also colocalize with RNA structures. Critically, junctions between genes are enriched in structured RNA elements and are also preferred sites for generating functional recombinant forms. These data suggest that RNA structure-mediated recombination allows the virus to exchange intact genes rather than arbitrary subgene fragments, which is likely to increase the overall viability and replication success of the recombinant HIV progeny.Recombination is a vital source of genetic diversity for many RNA viruses (15,18,37,38,48,49). By combining polymorphisms present in distinct genomes into a new genome in a single round of replication, recombination enables viruses to more rapidly access greater sequence space than is possible by the stepwise accumulation of point mutations. The net effect is to facilitate both the combination of advantageous mutations within individual highly fit genomes and the removal of deleterious mutations from viral populations. In the case of human immunodeficiency virus (HIV), these processes contribute to the dynamic evasion of immune responses and to the evolution of drug resistance (20,27,34,45).In addition to encoding information necessary for protein production, the genomes of RNA viruses, including HIV, convey functional information through their secondary and tertiary structures. These structures regulate many stages of the viral replication cycle, including genome replication, genome packaging into new viral particles, and intracellular trafficking (5,6,30,36,42). Studies on recombination in RNA viruses in general and in retroviruses in particular have indicated that RNA secondary structures play a potentially important role in genetic recombination (8,9,12,13,16,21,23,24,41).In retroviruses, recombination results primarily from template switching during reverse transcription between the two RNA genomes that are present in the same viral particle (22,50). If these two copies are genetically different, as in a heterozygous virus, templat...

“…The degree to which such recombination is deleterious is expected to increase with both decreasing parental relatedness and the extent to which transferred genome sequences interact with other viral genome sequences (12,16,17). Specifically, it is apparent that viral genome regions that have few genetic interactions with other viral genome regions tend to continue functioning better in foreign genetic backgrounds than do those with extensive interaction networks (12,(18)(19)(20).…”

mentioning

confidence: 99%

Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events

Monjane

Martin

Lakay

et al. 2014

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own "lethally recombinant." Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. IMPORTANCERecombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.