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Journal of Virology, November 2005, p. 13572-13578, Vol. 79, No. 21
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.21.13572-13578.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Stochastic Interplay between Mutation and Recombination during the Acquisition of Drug Resistance Mutations in Human Immunodeficiency Virus Type 1
Christian L. Althaus
and
Sebastian Bonhoeffer*
Ecology & Evolution, ETH Zürich, ETH Zentrum CHN, CH-8092 Zürich, Switzerland
Received 15 April 2005/
Accepted 4 August 2005

ABSTRACT
The emergence of drug resistance mutations in human immunodeficiency
virus (HIV) has been a major setback in the treatment of infected
patients. Besides the high mutation rate, recombination has
been conjectured to have an important impact on the emergence
of drug resistance. Population genetic theory suggests that
in populations limited in size recombination may facilitate
the acquisition of beneficial mutations. The viral population
in an infected patient may indeed represent such a population
limited in size, since current estimates of the effective population
size range from 500 to 10
5. To address the effects of limited
population size, we therefore expand a previously described
deterministic population genetic model of HIV replication by
incorporating the stochastic processes that occur in finite
populations of infected cells. Using parameter estimates from
the literature, we simulate the evolution of drug-resistant
viral strains. The simulations show that recombination has only
a minor effect on the rate of acquisition of drug resistance
mutations in populations with effective population sizes as
small as 1,000, since in these populations, viral strains typically
fix beneficial mutations sequentially. However, for intermediate
effective population sizes (10
4 to 10
5), recombination can accelerate
the evolution of drug resistance by up to 25%. Furthermore,
a reduction in population size caused by drug therapy can be
overcome by a higher viral mutation rate, leading to a faster
evolution of drug resistance.

INTRODUCTION
Human immunodeficiency virus (HIV) infection is characterized
by a high genetic diversity and a remarkable capacity of the
virus to evolve rapidly in response to novel selection pressures
such as drug therapy. These properties are mediated, at least
in part, by the high mutation rate (3.4
x 10
5 per base
pair) (
27) and the fast turnover of actively infected cells
(1 to 2 days) (
18,
42). In addition, recombination has been
conjectured as a further contributing factor (
7). The capacity
of recombination is common to all retroviruses and is due to
template switching between the two genomic RNA strands during
reverse transcription. Recombination can occur when the infecting
virion is heterozygous (i.e., carries two distinct genomic strains).
Such heterozygous virions are produced by cells that are coinfected
by two distinct proviruses.
In vitro experiments show that recombination can lead to the rapid emergence of drug resistance (14, 21, 29). In these experiments, recombinant virus is typically produced by infecting cells with equal mixtures of two mutant strains at a high multiplicity of infection. These conditions favor the production of heterozygous virions and thus lead to the rapid emergence of multiple drug resistance through recombination. However, in vivo the conditions may be less favorable for recombination. First, recombination events will occur between the predominating wild type and the mutants, while recombination events between two mutants will be rare. Thus, it is not clear a priori whether recombination in vivo would more often combine than break up favorable combinations of mutations. Second, the multiplicity of infection may be considerably lower in vivo. Hence, fewer heterozygous virions may be produced.
To investigate the effect of recombination on the evolution of drug resistance, we recently developed a population genetic model of recombination in HIV (6). The model showed that whether recombination facilitates the evolution of drug resistance depends on how mutations interact to determine viral fitness. In particular the model suggested that if mutations conferring resistance interact synergistically (i.e., the combination of resistance mutations results in a higher fitness benefit than expected from the product of the benefits of single resistance mutations) recombination will break down these favorable combinations of mutations and therefore slow down the evolution of drug resistance. In population genetic theory, this interaction of single mutations is called positive epistasis. A recent large-scale data analysis of the fitness effects of drug resistance mutations gave evidence for a predominance of positive epistasis between resistance mutations in HIV-1 in the absence of drugs (3). These findings support the idea that recombination is unlikely to facilitate the preexistence of drug-resistant virus types prior to therapy. However, what type of epistatic interaction predominates between resistance mutations during therapy remains to be established.
A key assumption of our previous model was that the population size of infected cells is infinite and therefore that the transitions during a viral life cycle can be calculated deterministically (6). In agreement with population genetic theory (2, 34), the model showed that for infinite populations the effect of recombination depends critically on epistasis. However, in populations limited in size population genetic theory suggests that stochastic processes may play an important role in the outcome of recombination (34). The main difference in finite populations is that not all combinations of mutations are present at the same time in the viral population. If N < 1/µ, with N being the population size and µ being the mutation rate per base pair, there will be less than one mutation on average per generation at a certain base pair and hence the presence or absence of any single-point mutant is governed by stochastic effects. However if N > 1/µ, the dynamics of single-point mutants can be approximated deterministically (38).
Whether the dynamics of recombination can be approximated by deterministic models depends on a different population size, because it is important whether combinations of mutations are already present in the population. For the simplest case that a certain double mutant is produced each generation, the condition N > 1/µ2 must be met. Given a mutation rate of µ = 3.4 x 105 per base pair (27), this corresponds to a population size of 8.7 x 108. The total size of HIV RNA-positive cells is large and estimates range from 107 to 108 (15). However, the number of infected cells that contribute their viral genetic information to successive generations is likely to be smaller. For example, not all RNA-producing cells may produce virions that can infect a new target cell. Therefore, the appropriate measure of population size is that of a genetically idealized population with which the actual population can be equated genetically, e.g., an idealized population that experiences the same amount of genetic drift. This population genetic concept is called the effective population size, Ne (17).
Current estimates of the effective population size of HIV in vivo range from 500 to 105 with most estimates between 103 and 104 (see Table 1). These estimates have been obtained both for treated and untreated patients. Moreover, the estimates are based on different genes. Since the difference between the total number of infected cells (107 to 108) and the estimated effective population size (500 to 105) is likely due to selection, differences between selection pressures in treated versus untreated patients or between different genes could in principle explain the discrepancies between these estimates. However, so far no clear trends have emerged from the currently available data. A further important point is that the effective population size is a concept that only has a well-defined meaning in the context of a chosen process of interest. In particular, the effective population size with regard to neutral or nearly neutral genetic variations will be different from the effective population size in terms of rare beneficial or deleterious mutations. Hence, the current estimates of Ne, based on env and gag-pol, may underestimate Ne with regard to rare selected mutations. Another factor affecting effective population size is population structure. Frost et al. (10) used a metapopulation model to show that the population structure can lead to an effective population size that is considerably smaller than the total size of infected cells. However, this study was not able to account for effective population sizes as low as 103 and 104. Hence, further research will be needed to resolve discrepancies between current estimates of Ne.
As we are interested in the effect of stochasticity on the evolution
of drug resistance, we focus here primarily on small population
sizes (i.e., 1,000 to 10,000). A large body of population genetic
literature has shown that stochastic effects can have an important
influence on the effect of recombination in small or even large
but finite populations (
8,
9,
19,
28,
30,
33). These results
prompt the consideration of finite population sizes in population
genetic studies of HIV evolution. Leigh Brown and Richman (
23)
discussed the influence of a low effective population number
on the evolution of drug resistance, and another study used
a simple stochastic model to calculate the relative frequency
of drug-resistant mutants prior to therapy (
11). However, to
our knowledge, there is currently no population genetic model
of stochastic viral evolution that incorporates the combined
effects of mutation and recombination. To this end, we expand
a previously published deterministic model of HIV recombination
(
6) to study the stochastic effects resulting from finite populations
of infected cells.

MATERIALS AND METHODS
Model.
A virus contains two RNA strands that are transcribed into double-stranded
DNA, called a provirus, which is then inserted into the cell
nucleus. In our model, we consider proviruses consisting of
two loci with two alleles (
a/A and
b/B). Thus, we have four
types of proviruses,
ab,
Ab,
aB, and
AB, where lowercase letters
denote drug-sensitive wild-type alleles and uppercase letters
denote drug-resistant mutant alleles. There is a constant population
of target cells,
N, that are infected. These cells are either
singly or doubly infected and therefore carry one or two proviruses.
For simplicity we neglect cells that are infected with more
than two proviruses. With
f being the frequency of doubly infected
cells, the total number of proviruses is (1 +
f)
N. We assume
discrete generations and the provirus frequencies change after
the completion of a full replication cycle. We divide the replication
cycle into three steps, which are all formulated as stochastic
processes and are discussed separately below. An illustration
of one generation of the viral population is given in Fig.
1.
The program was written in C++ and run under Linux and Mac OS
X. The source code can be obtained freely on request from the
authors.
Distribution of proviruses in the infected cell population.
A total of (1
f)
N cells are singly infected. Proviruses
are chosen randomly according to their frequencies and distributed
among these cells. The same is done for the
f N doubly infected
cells, except that two proviruses are chosen for each cell.
For two loci with two alleles, there are four different singly
infected cell types and 10 different types of doubly infected
cells. Note that not all of these types may be present at all
times, since the population size of cells,
N, is limited.
Selection of virions that infect target cells.
Single infected cells produce homozygous virions that correspond to the provirus inserted in the cell. In contrast, doubly infected cells can generate heterozygous virions when the inserted proviruses are distinct from each other. We assume that the viral RNA strands are mixed randomly, and therefore half of the virions released from doubly infected cells are heterozygous. The number of virions released by each infected cell depends on the viral proteins produced by the cell and derived from the provirus or proviruses. Virions produced from doubly infected cells can therefore show phenotypic mixing (32) if the proviruses are distinct. We assume that the number of virions produced is proportional to the average fitness of the two proviruses. Since the viral burst size of infected cells is around 103 or higher (13, 41), we calculate the production of virions deterministically. The calculation of virions is best illustrated by an example. Cells that are double infected by two single-resistance viruses, Ab and aB, generate heterozygous virions, AbaB, with a frequency given by
 |
where
CAbaB is the frequency of cells
double infected by the
Ab and
aB strains. The fitness of the
virions is the average of the proviral fitnesses (defined as
wAb and
waB). Half of the produced virions will be heterozygous,
assuming random segregation, and the result is normalized with
Vtot to ensure that all virion frequencies sum up to one. From
the resulting total virus population, (1 +
f)
N virions are selected
randomly to infect target cells (illustrated in Fig.
1), according
to their frequency.
Transcription of inserted virions to proviruses.
After a virion has bound to the surface of a target cell, both genomic RNA strands are released into the cell cytoplasm and the reverse transcriptase (RT) begins to synthesize proviral DNA. During reverse transcription, the RT molecule may jump back and forth between the two genomic RNA strands, thus producing a recombinant provirus. For a given virion, we calculate the probability of producing a certain provirus type as a function of the mutation rate, µ, and the recombination rate, r. To give an example, the probability that the two RNA strands Ab and aB are transcribed into an AB provirus is given by
 | (1) |
The RT attaches to either strand with probability
0.5. At the first strand, it does not mutate the A allele with
probability 1 µ and remains on the same strand
with mutation at the second locus with probability (1
r)µ. Doing this for all four possible pathways of the
RT, we get equation
1. Every single virion transcribes into
one of the four different proviruses according to the calculated
probabilities. This stochastic process generates a total of
(1 +
f)
N proviruses that then are distributed in the total cell
population,
N, as described in the first step.

RESULTS
Emergence of resistant mutants prior to therapy.
Mutant virus types that cause resistance against drugs are constantly
produced from the basal population through mutation. Most of
these mutants carry a cost of resistance compared to the wild-type
population (
3). Therefore, resistant mutants are held in a mutation-selection
balance prior to therapy. If they are already present at the
start of therapy they may contribute to a rapid emergence of
resistance (
4,
5,
36). As an example, we calculated the expected
preexistence frequencies of the M41L and T215Y resistance mutations
against zidovudine. The levels of fitness of the mutants relative
to the wild type are as follows: M41L, 80%; T215Y, 85%; and
M41L/T215Y, 85% (
16). Note that one nucleotide substitution
is sufficient to generate the mutation at position 41, but two
nucleotide substitutions are required to get the mutation at
position 215. The preexistence frequencies that are equivalent
to the probabilities of emergence in finite populations are
shown in Table
2.
View this table:
[in this window]
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|
TABLE 2. Calculated frequencies of the M41L, T215Y, and M41L/T215Y resistance mutations to zidovudine in the absence of drugsa
|
Since the interactions of the deleterious effects of the single
mutants are nonmultiplicative, there is an epistatic interaction
between these two positions. A mathematical definition of epistasis
between two loci is
E =
wabwAB
wAbwaB, where
w denotes
the fitness of the corresponding mutants. Using the estimated
fitness values, we get
E > 0 and therefore positive epistasis.
The T215Y mutant appears to have a compensating effect on the
deleterious effect of the M41L mutant, and therefore the double
mutant should be present at higher frequencies than expected
from the deleterious effect of the single mutants. Recombination
will break up this nonrandom association and thus reduce the
frequency of the double mutant, but increase the frequencies
of the single mutants. As seen in Table
2 the numerical effect
is moderate. For
Ne = 10
4, the total provirus population is
(1 +
f)
Ne = 17, 500. For this effective population size, only
the M41L single mutant is likely to occur before therapy, representing
on average about four proviruses. In contrast, the probability
of T215Y or M41L/T215Y mutants being present prior to therapy
would be very small.
Stochastic evolution of resistance.
We measured the influence of recombination on the acquisition of drug resistance mutations during drug therapy. From our findings of preexistence frequencies, we can assume that at least one single mutant is missing at start of therapy. Recombination cannot generate the double mutant until both single mutants are present, and it is therefore appropriate to start the simulations from a homogenous wild-type population. We follow the dynamics of mutant virus types until the double mutant is fixed in the population. Double resistance can evolve in two different ways, as shown in Fig. 2. If the population size of infected cells is small, it is unlikely that both single mutations are present in the population at the same time. Instead, typically one of the single mutants is produced by mutation and rises to fixation before the second mutation arises in the population. Thus, the double mutation occurs by sequential acquisition of both mutations. In this case, recombination has little effect on the evolution of drug resistance. In contrast, for large populations of infected cells, both single mutants are present at the same time. When one cell is infected by both of them, a double mutant can be produced through recombination. In this scenario, recombination can substantially accelerate the evolution of drug resistance. These findings are in line with classical population genetics theory, which showed that in populations of intermediate size recombination can accelerate the rate of fixation of beneficial alleles (9, 28, 30).
To measure the effect of recombination, we let the simulations
run over different values of
Ne and with different strengths
of selection. The effect of recombination is expressed as the
reduction in the time of fixation of the double-resistance mutant
through recombination, given by 1
Tr = 0.5/
Tr = 0, where
Tr is the average time to fixation for a recombination rate,
r. A reduction in fixation time of 0.2 thus means that recombination
reduces the time to fixation by 20%. Fixation here means that
the double-resistance mutants constitute at least 90% of the
population. A full fixation of 100% is not appropriate since
different virus types can be present due to recurrent mutation.
The average time of fixation is measured in viral generations.
Fitness of the wild type (
wab) was set to 1. The single mutants
are taken to have equal fitnesses,
wAb =
waB = 1
+ s, and the
double mutant is assumed to have fitness
wAB = (1 +
s)
2. Thus,
we assume no epistasis between mutations. Since the mutations
confer resistance, they are beneficial during drug therapy compared
to the wild type. Simulations were done with different strengths
of selection, i.e.,
s was set to 1%, 10%, 100%, and 1,000%.
We assume maximal recombination,
r = 0.5, and we set the fraction
of doubly infected cells to
f = 0.75 (
20). Figure
3A shows the
reduction in time caused by recombination for different values
of
Ne and different strengths of selection. Recombination has
a significant effect at population sizes of around 10
4 and at
intermediate selection strengths, with the reduction in fixation
time being approximately 25%. The effect of recombination is
dramatically reduced with decreasing population sizes. At
Ne = 103 the reduction in fixation time is only 5 to 10%. We also
considered the effect of a smaller fraction of doubly infected
cells and lower rates of recombination, since both may in reality
be smaller than the values used so far. Since we use an estimate
for the multiplicity of infection derived from solid tissue
(
20), where target cells are in close proximity to each other,
it is possible that averaged across all infected cells the fraction
of multiply infected cells may be smaller. Moreover, the recombination
rate between two loci depends on the number of nucleotides between
them. Thus, mutations close to each other will have lower recombination
rates than mutations further apart. Plot B in Fig.
3 shows the
effect of recombination on fixation time with parameters
f =
0.25 and
r = 0.1. With these smaller parameter values, the effect
on fixation time is less, with the maximum reduction being between
15 and 20%. For a small population size of 10
3, recombination
will have a minor effect of 1 to 7%.
Epistasis in small population sizes.
So far, we have excluded epistatic interactions between resistance
mutations to examine the effects of recombination that arise
in finite populations, independent of epistasis. However, epistasis
between resistance mutations can generate a linkage disequilibrium
that is reduced by recombination. Since there is evidence for
a predominance of positive epistasis among resistance mutations
in HIV-1 in the absence of therapy (
3), we wanted to determine
how the combined effects of epistasis and finite population
sizes are affected by recombination. To this end, we measured
again the reduction in fixation time compared to no recombination
in two different fitness regimes. The fitness levels of the
wild type and drug-resistant double mutant were set to 1 and
1.2, respectively. In simulations with positive epistasis, the
fitness of each single mutant was set to 1.05. For simulations
with negative epistasis, the fitness of each single mutant was
set to 1.15. Figure
4 shows the reduction in time caused by
recombination over different effective population sizes for
these fitness values. Recombination reduces the time to fixation
in small populations of around 10
3, since beneficial single
mutants that arise after the start of therapy can be combined.
The reduction is larger for negative epistasis because the single
mutants are overrepresented and therefore are more likely to
be combined. The effect of genetic drift decreases in larger
population sizes. For
Ne > 10
5, drift effects are small and
epistatic selection determines the population structure. As
described by Bretscher et al. (
6), recombination only reduces
the time to fixation for negative epistasis. For positive epistasis,
there is a negative reduction, i.e., recombination increases
the time to fixation of the double mutant.
Population size versus mutation rate.
A correlation between the evolution of drug resistance and increased
mutation rate has been observed in HIV (
24). For example, zidovudine-resistant
RT was found to increase the mutation rate 4.3-fold. Zidovudine
itself increases the mutation rate of a wild-type RT by 7.6-fold
(
25). Together, a zidovudine-resistant RT in the presence of
zidovudine led to a 24-fold increase in the virus mutant frequency
(
26). Concomitantly, a rapid decay in virus load over several
orders of magnitude can occur during therapy (
18,
35,
42). It
is unclear whether the decay in virus load affects the effective
population size of virus or infected cells. The estimates of
Ne shown in Table
1 were measured in untreated patients as well
as during therapy. The ranges suggest that the effective population
size can vary by roughly 1 order of magnitude. Therefore, we
investigated the effect of increased mutation rates in populations
with decreased effective population sizes during the acquisition
of drug resistance mutations. Table
3 shows the average time
to fixation in viral generations. The results show that increased
mutation rates caused by drug treatment result in a faster evolution
of drug resistance even if the effective population size is
reduced by the same factor or even more. These results are in
agreement with theoretical studies on the waiting time to produce
a double mutant (
8).

DISCUSSION
The results from our simulations show that whether recombination
facilitates the acquisition of drug resistance mutations depends
strongly on the effective population size of the virus. Recombination
will only reduce the fixation time of a drug-resistant double
mutant when both single mutants are present at a sufficiently
high frequency at the same time. Consistent with these results,
in in vitro experiments in which equal mixtures of two single-resistance
viruses are used to infect cells, recombination leads to the
rapid emergence of drug-resistant double mutants (
14,
21,
29).
However, provided the effective population size is small, the
conditions in vivo may be very different, since the single parental
mutants may be rare. Indeed, Nijhuis et al. (
31) have shown
in their study of stochastic processes during HIV-1 evolution
that recombination is not observed in all patients.
Our simulations show that preexistence of resistant mutants is unlikely if the effective population size is indeed as small as 103 and, in particular, when more than one nucleotide substitution is required for resistance. In this scenario, the double-resistance mutations have to be produced during drug therapy. The acquisition of these mutations then occurs sequentially rather than simultaneously, and hence the effect of recombination in reducing the time to fixation of the double mutant is negligible. The effect of recombination is substantially higher for larger effective population sizes and maximal at effective population sizes around 104. Here, single mutants are likely to be present together but the double mutant is likely to be absent. Recombination then generates double mutants and therefore reduces the time to fixation by up to 25%. The effect of recombination decreases with decreasing mutation rate and decreasing fraction of multiply infected cells. The effective mutation rate may be lower than the current estimate of 3.4 x 105 per base pair (27), since deletions, insertions, and frameshift mutations generally do not generate resistance mutations (12). Furthermore, only specific nucleotide substitutions lead to a desired mutation and some resistance mutations need more than one nucleotide substitution as mentioned above. Given that the multiplicity of infection was measured in solid tissue (20), it is possible that the multiplicity of infection averaged across all infected cells is also somewhat lower.
Drug therapy generally decreases the viral population size and therefore likely decreases also the effective population size. On the other hand it is known that for some antiretroviral drugs both the drug and the resistance mutations induce an increase in the mutation rate. We have shown here that a reduction in effective viral population size as a result of drug treatment and the consequent slower evolution of drug resistance can be overcome by higher viral mutation rates.
Epistasis has a minor influence in small effective population sizes of infected cells. Negative epistasis causes a bigger reduction than positive epistasis in the time to fixation. Interestingly, for effective population sizes bigger than 105, the beneficial effect of recombination is cancelled out by positive epistasis. Here, the dynamics resemble the deterministic regime and recombination will break up double mutants rather than create them.
In summary, our simulations show that the effect of recombination on the emergence of drug resistance in HIV is likely to be small if the effective population size is as low as 1,000. However, recombination can increase the rate of evolution of multidrug resistance for larger effective population sizes with a maximum around 104. For very large effective population sizes (>105), the effect of recombination primarily depends on epistasis, which is in agreement with results for deterministic models of recombination. To develop a better quantitative understanding of the effect of recombination on the evolution of multidrug resistance in HIV, we will need more accurate estimates of the underlying biological parameters. In particular we need to resolve the discrepancies between current estimates of the effective population size in vivo, and we need more accurate estimates for the effective population size in terms of rare beneficial or deleterious mutations.

ACKNOWLEDGMENTS
We would like to thank Roger Kouyos, Almut Scherer, Marcel Salathé,
and Martin Ackermann for helpful discussions and Lucy Crooks
for critical readings of the manuscript. Moreover, we thank
an anonymous reviewer for constructive comments.
Funding by the Swiss National Science Foundation is gratefully acknowledged.

FOOTNOTES
* Corresponding author. Mailing address: Ecology & Evolution, ETH Zürich, ETH Zentrum CHN, CH-8092 Zürich, Switzerland. Phone: 41 1 632 7106. Fax: 41 1 632 12 71. E-mail:
sebastian.bonhoeffer{at}env.ethz.ch.

Present address: Theoretical Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. 

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Journal of Virology, November 2005, p. 13572-13578, Vol. 79, No. 21
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.21.13572-13578.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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