HIV was transmitted from apes to humans multiple times before the virus began to spread among humans some time in the early 20^th century. The virus is now found around the globe and has evolved into several different subtypes. Also, HIV continues to evolve inside each infected individual so that different variations of the virus are often present in the same person at any given time.

When a person initially becomes infected, immune cells called killer T-cells seek out and destroy infected cells. However, HIV quickly acquires genetic mutations that allow it to escape the immune system and multiply in the body. There is a cost to this evasion strategy: the mutant forms of the virus often don’t multiply as rapidly as the variant that first infected the individual. This may explain why the virus often mutates back to its previous form in newly infected people. But many questions remain about how these pressures influence the evolution of the virus in individuals and in populations over time.

Now, Zanini et al. have sequenced the genomes of HIV samples collected from nine people with HIV in Sweden over the course of five to eight years. These individuals were diagnosed between 1990 and 2003 – when HIV medications were not as widely used as they are now – and did not receive any treatment during the course of the study. Therefore, the study provides a rare opportunity to look at how HIV evolves in the absence of drugs that target the virus.

Zanini et al. sequenced the entire genetic code of each form of the virus identified in the samples. The data show that HIV follows predictable patterns of evolution within individuals as well as across human populations. Mutations happen frequently all over the HIV genome. However, the mutant viruses often revert to a common or “optimal” form of the virus throughout the course of infection. This suggests that there is a tradeoff between the benefits of acquiring new mutations and maintaining a set of traits that have enabled the virus to spread so successfully in humans.

To make it easier for other researchers to explore the data, Zanini et al. created a web application that allows others to access and create visual representations of viral evolution.

Together these findings suggest that it will be possible to achieve a fuller understanding of RNA virus evolution that integrates the molecular biology of the virus and the immune response of the host with the evolutionary changes.

The human immunodeficiency virus 1 (HIV-1) is a paradigmatic example of a rapidly adapting population characterized by high diversity, strong selection, and recombination. HIV-1 has originated from multiple zoonotic transmissions from apes in the early part of the 20th century (Sharp and Hahn, 2011), one of which gave rise to the worldwide pandemic. This lineage is called group M and has diversified into different subtypes at a rate of about 1 in 1000 substitutions per year (Lemey et al., 2005; Li et al., 2015). Tens of thousand of HIV-1 group M variants are available in the Los Alamos National Laboratories HIV database (LANL) (Foley et al., 2013).

The evolution of HIV-1 ultimately takes place within infected individuals and can be observed directly in longitudinal samples of virus populations from the same individual. The detailed knowledge of HIV-1 biology paired with historical samples makes HIV-1 an ideal system to study general features of evolution at high mutation rates and strong selection that are otherwise only accessible in evolution experiments (Elena and Lenski, 2003; Miralles et al., 1999).

During the first few months of an HIV-1 infection, the viral population typically acquires several mutations that mediate escape from cytotoxic T-cells (CTL). The properties and dynamics of these mutations and their effect on epitope presentation and virus control have been extensively studied (Bernardin et al., 2005; Goonetilleke et al., 2009; Jones et al., 2004; Kearney et al., 2009; Liu et al., 2011). Such escape variants often compromise virus replication and have been shown to revert upon transmission of the virus to a human leukocyte antigen (HLA) mismatched host (Brockman et al., 2010; Leslie et al., 2004; Li et al., 2007). However, the quantitative contribution of escape and reversion to HIV-1 evolution and the degree to which costly mutations are compensated by additional mutations is less well understood (Lythgoe and Fraser, 2012; Schneidewind et al., 2009). Similar to CTL escape mutations, drug resistance mutations can spread through the viral population within weeks and longitudinal sequence data has been used to study emergence and fitness cost of resistance mutations (Hedskog et al., 2010; Little et al., 2008; Paredes et al., 2009).

Longitudinal sequence data has also been used to track evolution driven by the humoral immune response against HIV-1 which occurs throughout infection and results in high rates of evolution in the variable loops of HIV-1 surface proteins (Bar et al., 2012; Richman et al., 2003; Shankarappa et al., 1999). In a pioneering study, Shankarappa et al. (1999) characterized HIV-1 evolution of parts of the gp120 envelope protein over approximately 6–12 years in 11 patients, demonstrating consistent patterns of diversity and divergence. While this early study was limited to about 10 sequences per sample, next-generation sequencing technology today allows deep characterization of intrapatient HIV-1 variability including rare mutations (Fischer et al., 2010; Hedskog et al., 2010; Henn et al., 2012; Tsibris et al., 2009).

The earlier studies discussed above have either focused on early infection or particular regions of the HIV-1 genome. However, most virus evolution happens during chronic infection simultaneously at many locations in the genome. To develop a comprehensive and quantitative understanding of the evolution and diversification of HIV-1 populations, we generated a whole-genome, deep-sequencing data set covering nine patients over 5–8 years with 6–12 time points per patient. Importantly, the data set covers the entire genome such that no substitution is missed and includes early samples defining the initial population. To our knowledge, this is the only whole-genome deep sequencing data set with long follow-up of multiple patients. We provide interactive and intuitive web-based access to the data set and hope it will become a resource for many future studies, like the data set by Shankarappa et al. (1999) has been in the last years.

Below, we first describe the methodology we developed to sequence the entire HIV-1 genome at great depth. We then analyze the intrapatient evolution of HIV-1 and show that the minor variants in the virus population explore sequence space in predictable fashion at the single site level. At the same time, we observe a strong tendency for reversion towards the global HIV-1 consensus that is not limited to early infection but occurs at an approximately constant rate throughout chronic infection. Reversion is more frequent at sites that are more conserved at the global level, suggesting a direct relationship between intrapatient fitness cost and global conservation. Together with reproducible patterns of intrapatient variation, this link explains why HIV-1 fitness landscapes can be inferred from cross-sectional data (Dahirel et al., 2011; Ferguson et al., 2013; Mann et al., 2014). We further find frequent recombination, which allows the viral population to evolve independently in different regions of the genome. Nevertheless, recombination is not frequent enough to decouple mutations closer than 100 base pairs and we observe signatures of hitch-hiking at short distances (Maynard Smith and Haigh, 1974).

The study included nine HIV-1-infected patients who were diagnosed in Sweden between 1990 and 2003. Data from two additional patients (p4 and p7) were excluded from analysis because of suspected superinfection and failure to amplify early samples with low virus levels, respectively. The patients were selected to have a relatively well-defined time of infection and to have been treatment-naive for a minimum of 5 years. Patients diagnosed in recent years rarely fulfill these inclusion criteria because therapy is almost universally recommended, but this was not the case when the study patients were diagnosed. Basic characteristics of the patients are presented in Table 1. Additional data on the patients are presented in Supplementary file 1 and Figure 1—figure supplement 1. All patients progressed to moderate-to-severe immunosuppression during the study period. The final CD4 count within the study period for patients 1–3, 5–6 and 8–11 were 340, 369, 140, 228, 287, 378, 158, 200 and 251, respectively. Of the nine patients, eight were males, seven were men who have sex with men (MSM), two were heterosexually infected (HET), and eight were infected in Sweden. The method to estimate the date of infection (EDI) is described in Materials and methods. We retrieved longitudinal biobank plasma samples covering the time period from early infection (time since EDI 33–209 days) until end of study follow-up, which usually coincided with start of antiretroviral therapy (time since EDI 5.5–8.3 years). The number of samples per patient ranged between 6 and 12 and, in total, we investigated 73 samples. The median plasma HIV-1 RNA level was 12,000 copies/ml for the samples with available data on RNA levels. Some samples had low RNA levels, which partly is explained by the study design that required that the patients were treatment-naive for at least 5 years. For detailed information about each individual sample see Supplementary file 1. For a phylogenetic tree of minor variants from all patients see Figure 1—figure supplement 2.

HIV-1 whole-genome deep sequencing

The basic steps of our amplification and sequencing pipeline are illustrated in Figure 1 and explained in detail in Materials and methods. Briefly, viral RNA was extracted from 400 μl patient plasma and used for one-step RT-PCR amplification with six overlapping primer sets that span almost the complete HIV-1 genome, similar to the strategy developed by Gall et al. (2012). Sequencing libraries were made starting from 0.1–1.5 ng of DNA with a stringent size selection for long inserts (>400 bp). Sequencing was performed on the Illumina MiSeq platform and sequence reads were quality filtered and assembled using an in-house data processing pipeline. In total, approximately 100 million reads passed the quality filtering. The coverage varied considerably between samples and amplicons, but was mostly of the order of several thousands or more, see Figure 1B.

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Importantly, sequencing depth is determined not only by coverage but also by template availability and sequencing errors (Iyer et al., 2015). We performed a number of control experiments to quantify templates and assess the accuracy of estimates of frequencies of single nucleotide polymorphism (SNP). The results are summarized in the following section and described in detail in Materials and methods.

We quantified the number of HIV-1 genomes that contributed to each sequencing library by PCR-limiting dilution (median: 120 quartiles: 50–500). Hence template availability, rather than coverage, determined the sequencing depth, see Figure 1B. Comparison with routine plasma HIV-1 RNA level measurements performed at time of sampling showed that the median template complementary DNA (cDNA) recovery efficiency was 30%.

We estimated the error rate of the PCR and sequencing pipeline by amplifying and sequencing a plasmid clone. Figure 1C compares the SNP frequencies observed in a clone to those observed in a patient sample. After quality filtering, PCR and sequencing errors never exceeded 0.3% of reads covering a particular position. To detect and control for variation in PCR efficiency among fragments and skewed amplification of different variants, we compared frequencies of variants in overlaps between the six amplicons. A SNP in the overlap is amplified and sequenced twice independently and the concordance of the two measurements of variant frequencies was used to estimate the fragment specific depth, which is limited both by template input and PCR efficiency, see Materials and methods. Frequency estimates were often reproducible to within a few percent. Sometimes, however, variant recovery was poor (mostly in fragment 5) and frequency estimates less accurate. Those fragments are flagged on the website and can be excluded from analyses requiring large depth.

We minimized PCR recombination by reducing the number of PCR cycles and optimizing the reaction protocol (see Materials and methods, Di Giallonardo et al. (2013); Mild et al. (2011)). Control experiments using mixtures of two cultured virus populations showed that less than 10% of reads had experienced RT-PCR recombination.

Taken together, our control experiments show that depending on the sample and fragment, we could estimate frequencies of SNPs down to 1% accuracy (corresponding to several hundred effective templates). In some cases, however, the template number was low or template recovery poor such that only presence or absence of a variant could be called. Furthermore, SNPs remained linked through cDNA synthesis, PCR and sequencing.

Consistent evolution across the entire genome

In most patients, the virus populations were initially homogeneous and diversified over the years, as expected for an infection with a single or small number of similar founder viruses (Keele et al., 2008; Salazar-Gonzalez et al., 2009). In two patients, p3 and p10, the first sample displayed diversity consistent with the transmission of several variants from the same donor, see Figure 3—figure supplement 1. For each of the nine patients, we reconstructed the HIV-1 genome sequence of the first sample by an iterative mapping procedure described in Materials and methods. We use this initial consensus sequence to approximate the sequence of the transmitted founder virus(es). Our first sample is estimated to be between 1 and 7 months into infection and a few mutations (likely CTL escape mutations) had probably spread through the viral population by that time. Thus, the initial consensus sequence probably will differ slightly from the true founder virus. The number of differences, however, will be small compared to the sequence divergence in the 5 or more years of follow-up such that this initial consensus sequence is a useful approximation of the founder virus(es).

Figure 2 shows an example of the dynamics of frequencies of SNP relative to the founder sequence over time, where each dot (top) or line (bottom) represents the frequency of a nucleotide different from the founder sequence. Interactive versions of this graph are available for the entire genome of all patients at hiv.tuebingen.mpg.de.

Figure 2

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To measure the rate at which the virus population accumulates mutations, we calculated the average distance of each sample from the approximate founder sequence in 300 bp windows. Regressing this distance against time yields the rate of divergence in different regions of the genome, see Figure 3A. As expected, some regions such as the variable loops in gp120 and nef evolve faster, while enzymes – protease (PR), reverse transcriptase (RT) – and the rev response element (RRE) evolve more slowly. The rate of divergence varies by about a factor of 10 along the genome, but is consistent with typically about 1.5-fold differences across patients (standard deviation of log2(fold change) 0.6 ± 0.2). The overall pattern of the rate of mutation accumulation agrees with a recent map of HIV genome-wide variation from a population perspective (Li et al., 2015) and correlates well with entropy in a large HIV-1 group M alignment (Spearman’s p = 0.7 after the same smoothing).

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Minor variants reproducibly explore global HIV-1 diversity

Having found that coarse patterns of divergence are comparable among patients, we asked whether intrapatient diversity at individual sites in the viral genome follows general and predictable patterns. To this end, we compared diversity at each position to the diversity observed in HIV-1 group M (see Materials and methods).

Figure 4A shows the rank correlation between the site-by-site diversity in each patient and a global collection of HIV-1 sequences, both measured by Shannon entropy (see Materials and methods). In all cases, correlation with cross-sectional diversity was initially low, as expected for largely homogeneous populations. As diversity increases within patients, it tends to accumulate at positions that are not conserved, resulting in a rank correlation of about 0.4–0.5 after about 8 years. These correlations are individually significant and reproducible among different genomic regions (error bars in Figure 4).

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Figure 4B offers an alternative perspective on the exploration of sequence space by the HIV-1 populations. We classified nucleotide positions in the genome into four categories ranging from highly conserved positions to less conserved positions within group M (Q1–Q4) using the same alignment as above. Next we asked what fraction of sites within these categories show intrapatient variation at a level of at least 1%. For the least conserved positions, this fraction increased steadily to about 20% after 8 years, while less than 1% of the most conserved sites shows variation above the 1% level. This latter fraction rapidly saturates and does not increase over time. Since variant amplification, sequencing and variant calling does not use any information on cross-sectional conservations, the absence of variation above 1% at conserved sites is further evidence that our amplification and sequencing pipeline does not generate spurious variation. Other thresholds yield similar results.

Taken together, the observations in Figure 4 show that variation is not limited by the mutational input, but that HIV-1 populations accumulate diversity wherever mutations do not severely compromise virus replication. At the single nucleotide level, the spectrum of mutational possibilities is explored reproducibly and the level of within-host diversity is predicted by time since infection and cross-sectional diversity. Conserved positions are typically monomorphic even in deeply sequenced samples with high RNA template input.

The majority of nonsynonymous substitutions are positively selected

In addition to the reproducible patterns of minor diversity, virus evolution is characterized by adaptations that are specific to the host. Immune selection results in escape mutations that rapidly spread through the population (Richman et al., 2003; Walker and McMichael, 2012). Such mutations tend to be nonsynonymous, i.e., change the viral proteins, while evolution at synonymous sites is expected to be conservative. Nevertheless, synonymous mutations can be affected by ‘selective sweeps’ of linked nonsynonymous mutations (Maynard Smith and Haigh, 1974).

To quantify the degree at which the evolutionary dynamics of HIV-1 is dominated by selective sweeps, we calculated divergence and diversity separately at nonsynonymous and synonymous sites in different parts of the HIV-1 genome. Figure 5A compares nonsynonymous (solid lines) and synonymous divergence (dashed lines) in different regions of the genome. In agreement with the results presented in Figure 3, the observed rate of evolution at nonsynonymous sites differed substantially between genomic regions, with env being the fastest and pol the slowest. Divergence at synonymous sites, however, varied very little between different genomic regions indicating random accumulation of synonymous mutations (rather than positive selection).

Figure 5

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Figure 5B shows the corresponding plot for diversity, i.e., the distances between sequences from the same sample. Diversity at nonsynonymous sites (solid lines) saturates after about 2–4 years, suggesting that nonsynonymous SNPs either stay at low frequency because they are deleterious or rapidly increase in frequency and fix without contributing much to diversity. Synonymous diversity increases steadily in the 5’ part of the genome (structural and enzymes), while it saturates in the 3’ half of the genome after a few years – the exact opposite of nonsynonymous divergence.

Indeed, we observe a strong anti-correlation between synonymous diversity and nonsynonymous divergence, which is further quantified in Figure 5C. This suggests that frequent non-synonymous substitutions limit synonymous diversity because they drive linked synonymous mutations to fixation or to extinction (Maynard Smith and Haigh, 1974). We will quantify linkage and recombination below, but the differences in diversity accumulation already suggest that linkage is restricted to short distances.

The contrasting behavior of synonymous and nonsynonymous SNPs is also seen in the SNP frequency spectrum – the histogram of SNP abundance – shown in Figure 5D. While the spectra agree for frequencies below 20%, synonymous mutations are strongly underrepresented at higher frequencies (Fisher’s exact test at frequency 0.5, p-value <10^-10). This corroborates the interpretation that, due to substantial recombination, sweeping nonsynonymous mutations only occasionally ‘drag’ adjacent synonymous mutations to fixation. Synonymous mutations rarely rise in frequency because of their own effect on fitness, since they usually have small or deleterious phenotypic effects and do not contribute directly in immune evasion (Zanini and Neher, 2013). The about five-fold excess of nonsynonymous over synonymous SNPs at high frequencies (see Figure 5D) shows that the majority of common nonsynonymous mutations spread due to positive selection.

Next, we sought to quantify what fraction of nonsynonymous divergence is driven by escape from cytotoxic T-lymphocytes (CTLs). Four-digit HLA types were determined for all patients and a set of putatively targeted HIV-1 epitopes were determined using the epitope binding prediction tool MHCi (tools.immuneepitope.org/mhci). We then asked whether we observed more nonsynonymous substitutions in epitopes predicted to be targeted than expected by chance (excluding the variable loops of gp120 and the external part of gp41, see Materials and methods). We found a significant enrichment by a factor 1.9 in the putatively targeted region (p-value <3 × 10⁻⁶), corresponding to 5.5 excess nonsynonymous substitutions, whereby the total number of nonsynonymous substitutions per patient is on average 43 (median, quartiles 36–64). The set of predicted epitopes will contain false positives and lack true epitopes, hence the actual number of CTL driven substitutions could be higher as for example suggested by Allen et al. (2005) who report that roughly half of non-envelope mutations are associated with CTL responses.

Extensive reversion towards consensus

Many CTL escape mutations reduce the replicative capacity of the virus and it is known that such escape mutations often revert upon transmission to a host in which the corresponding epitope is not targeted (Friedrich et al., 2004; Herbeck et al., 2006; Leslie et al., 2004). The balance between escape and reversion results in association between specific escape mutations and the HLA types of the hosts (Kawashima et al., 2009; Palmer et al., 2013). In a diverse population of hosts, the most common state at a specific site is likely the preferred state, while rare alleles tend to be escape mutations that reduce viral replicative capacity (Carlson et al., 2014).

To quantify patterns of reversion and fitness cost, we classified sites in the approximate founder sequence of the viral populations in each subject as being identical or different from the HIV-1 group M consensus. Figure 6A shows the fraction of sites where the founder nucleotide is replaced by a mutant during the infection. This fraction is about ten-fold higher if the founder nucleotide differs from the group M consensus than if it is identical to the group M consensus. Reversion towards group M consensus occurs at a roughly constant rate throughout the observation time (5–8 years).

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Of all changes accumulated by the viral populations, 30 ± 2.5% are reversions towards group M consensus (mean and standard deviation of patient bootstraps after 4–7 years). Similar results are found when comparing with the subtype consensus of each patient virus (24 ± 2.5%). Reversions are between 4 and 5 times more frequent than expected in the absence of a reversion bias (7.8 and 4.5%, respectively). These findings agree with results by Allen et al. (2005), who report that about 20% of amino acid substitutions are reversions.

By focusing on sites where the founder virus differed from the group M consensus, we are predominantly looking at weakly conserved sites. To control for conservation, we carried out the same analysis after stratifying sites by overall level of conservation. Figure 6B shows the result of this analysis, focusing on samples after 5–6 years for the sake of clarity. We find that the rate of reversion is highest at the most conserved sites. Almost 50% of all non-consensus positions at highly conserved sites had reverted to consensus after about 5 years – an almost 1000-fold excess. Even at the least conserved sites, divergence towards group M consensus exceeded divergence away from group M consensus by a factor of 3. These results suggest that the global HIV-1 group M consensus sequence represents an ‘optimal’ HIV-1 sequence, which acts as an attractor for the evolutionary dynamics within hosts. This attraction is strongest at conserved sites, but extends to the least conserved sites in the genome.

Lack of long-range linkage due to frequent recombination

To quantify the decoupling of SNPs by recombination, we calculated linkage disequilibrium (LD) between SNPs as a function of distance for each of the six fragments, see Figure 7. For most fragments, we observed a consistent decrease of LD over the first 100–200 bps, with fragment 5 being an exception with linkage of mutations at longer distances. Importantly, our linkage control (a 50/50 mix of two distinct virus isolates and a total of 1250 RNA molecules per PCR fragment) shows no decay of LD with distance, suggesting negligible RT-PCR recombination.

Figure 7

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The observed decay of LD in patient samples is consistent with a recombination rate of 10⁻⁵/bp/day as estimated in (Batorsky et al., 2011; Neher and Leitner, 2010). Our reasoning proceeds as follows. Figure 5B indicates that diversity accumulates over a time frame of 2–4 years, i.e., about 1000 days. Recombination at a rate of 10⁻⁵/bp/day hits a genome on average every 100 bps in 1000 days. Mutations further apart than 100 bps are hence often separated by recombination and retain little linkage consistent with the observed decay length in Figure 7. The longer linkage in fragment 5 (env) might have several reasons that extend beyond our simple argument: (i) homologous recombination might be suppressed in the most variable regions, (ii) the accuracy of SNP frequency estimates is lower in F5 due to poorer amplification, and (iii) the rapid evolution of env due frequent substitutions and sweeps gives less time to break up linkage. In particular, as shown in Figure 5C, frequent and strong selective sweeps affect synonymous diversity in physical proximity along the genome, confirming the presence of linkage at short distances.

For phylogenetic analysis, we can extract haplotypes from the sequencing reads up to 500 bp in length. Only in the more diverse regions are 500 bp sufficient for well-resolved phylogenies (see Figure 8). However, we find that linkage does not extend beyond 100–200 bp. Hence the read length is not a limiting factor. Only during rapid population shifts such as drug resistance evolution, long read technologies such as PacBio would be necessary to capture the evolutionary dynamics (Nijhuis et al., 1998).

Figure 8

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We have presented a comprehensive portrait of intrapatient evolution of HIV-1 that covers almost the entire genome of the virus, characterizes minor genetic variants, and tracks the fate and dynamics of these variants over a follow-up period of up to 8 years in nine patients. We find that, during the infection, HIV-1 explores the sequence space surrounding the founder virus systematically; similar mutational patterns are observed within different, unrelated patients. Linkage between mutations is limited to approximately 100 bp, so the virus population can accumulate substitutions independently in different regions of the genome as suggested by theoretical models (Mostowy et al., 2011; Rouzine and Coffin, 2005). Nonetheless, local dynamics of SNPs is often dominated by hitch-hiking between neighboring mutations, resulting in an anticorrelation between nonsynonymous divergence and synonymous diversity. A large fraction of all substitutions are reversions towards the global HIV-1 consensus sequence, and these reversions steadily accumulate throughout infection.

The evolutionary dynamics of HIV-1 populations is the result of stochastic forces like mutation and frequent bottlenecks, deterministic fixation of favorable mutations, and recombination. The relative importance of these forces remains unclear (Brown, 1997; Frost et al., 2000; Kouyos et al., 2006; Maldarelli et al., 2013; Pennings et al., 2014; Rouzine and Coffin, 1999). Our observation that intrapatient diversity recapitulates diversity seen across HIV-1 group M and the strong tendency to revert towards consensus suggest that, in chronic infection, selection determines diversity. The reproducible exploration of sequence space can coexist with frequent adaptation only in frequently recombining large populations (Neher et al., 2013). We observe that mutations further apart than 100 bp are effectively shuffled by recombination in most parts of genome, consistent with previous estimates of the HIV-1 recombination rate (Batorsky et al., 2011; Neher and Leitner, 2010). Linkage and stochastic effects become stronger with increasing frequency of strength of selection, consistent with lower synonymous diversity and more LD in env.

While rapid CTL escape at 5–10 sites over the first 2 years of infection has been documented in detail (Allen et al., 2005; Goonetilleke et al., 2009; Herbeck et al., 2006; Jones et al., 2004; Liu et al., 2011) and population level associations between specific HLA types and escape variants suggest widespread CTL escape (Kawashima et al., 2009), the effect of escape and reversion on long-term evolutionary trends is less clear (Lythgoe and Fraser, 2012; Roberts et al., 2015). We find a strong tendency for viral populations to revert towards the global HIV-1 consensus. At sites where the founder sequence differs from the subtype consensus, substitutions are almost five-fold overrepresented: Instead of ≈5% reversions expected based on the fraction of sequence at which the founder virus differs from consensus of the HIV-1 subtype, almost 25% of substitutions are reversions, in agreement with earlier reports on reversion of CTL escapes (Allen et al., 2005; Li et al., 2007). This tendency to revert increases with the level of conservation of the site, suggesting a quantitative relationship between fitness cost and conservation. While reversion is particularly prevalent in acute infection (Li et al., 2007), we show that reversion is not limited to early infection but happens throughout chronic infection.

The bias towards reversion results in a two- to three-fold reduction of the long-term evolutionary rate of HIV, a trend that is reinforced by selection during transmission (Carlson et al., 2014; Sagar et al., 2009). Inter-individual evolutionary rates of HIV-1 are two to six times lower than intra-individual rates, and a number of possible mechanisms have been suggested to explain this discrepancy (Lythgoe and Fraser, 2012). Our results strongly indicate that most of this mismatch can be explained by steady reversion during infection; other factors such as retrieval of ‘stored’ latent variants or stage-specific selection might also contribute to the rate mismatch (Immonen and Leitner, 2014; Lythgoe and Fraser, 2012).

The high rate of reversion has implications for phylogenetic dating. Given the five-fold excess of reverting minor variation, reversion would balance divergence once the typical distance from the consensus sequence equals 17%, corresponding to a nucleotide diversity of about 30%; this is remarkably close to the actual divergence between HIV-1 groups M, N and O (Li et al., 2015). On longer distances, this simple argument will have to be modified due to compensatory mutations resulting in gradual shift of the preferred state at some positions; nonetheless, it indicates a dramatic slowing down of divergence at a scale of the HIV-1-SIVcpz divergence. This apparent deceleration of evolution could explain the contradictory findings of attempts to date the age of HIV-1 and SIV (Worobey et al., 2010). The strong and lasting preference for specific nucleotides needs to be accounted for in phylogenetic analysis, as has recently been shown using experimentally determined fitness landscapes of influenza virus proteins (Bloom, 2014).

Our observations are consistent with results by Ashenberg et al. (2013); Doud et al. (2015), who showed that amino acid preferences are mostly conserved between related influenza strains. Similarly, divergence between HIV-1 subtypes is small enough that epistatic interactions have not yet changed the majority of the preferred states. With increasing evolutionary distance between strains, the molecular context and preferred amino acid at a particular position is more and more likely to differ (Pollock et al., 2012). Nevertheless, a subset of amino acids preferences are conserved almost universally (Risso et al., 2015) and enable sequence based homology search.

The concordance between intrahost variation and patterns of conservation across HIV-1 group M hints at universal fitness costs of mutations. Recently, cross-sectional conservation has been used as a proxy for fitness costs in models of HIV-1 fitness landscapes (Dahirel et al., 2011; Ferguson et al., 2013; Mann et al., 2014). Since reproducible intrapatient diversity likely reflects fitness costs of mutations in vivo, our results provide a direct justification for this approach. However, nine patients are insufficient to extend this analysis to fitness interactions between mutations.

One limitation of this study was the availability of samples from patients with sufficiently long follow-up without therapy after a well-defined time of infection. The majority of patients were MSM infected with subtype B virus. Thus, we cannot exclude that the aspects of HIV-1 evolution that we have investigated may differ between transmission routes or HIV-1 subtypes. While substitution and recombination errors of our optimized protocol for HIV-1 RNA extraction and an RT-PCR are low, the other main limitation was that the number of available template molecules was small in some samples (see also Iyer et al., 2015). In principle, the Primer ID method, which labels and resequences each individual template, allows quantification of templates and almost complete elimination of experimental substitution and recombination errors (Jabara et al., 2011). However, we are not aware of a Primer ID protocol for genome-wide sequencing, which was essential to our study.

The analysis and means of data sharing of next-generation sequencing data from viral populations is still in its infancy. Raw reads require substantial post-processing before the data can be used to answer biological questions and technology is changing rapidly such that no standardized pipelines exist. To facilitate the exploration and further analysis of our data, we have developed a web server that allows to browse characteristics of individual patients, e.g., graph the frequencies of single nucleotide polymorphism through time, and download different aspects of the data in convenient format. It is, for example, possible to select an arbitrary region of the genome with length <500 bp, such as the frequently investigated V3 region, and extract an alignment of haplotypes covering this region along with their frequency from all time points belonging to one patient. We hope that the convenient access to processed data will facilitate follow-up studies on other aspects of viral evolution.

HIV-1 and other microbial populations evolve in a constant struggle between adaptation to a changing environment and maintenance of functionality. Large mutation rates and population sizes generate standing genetic diversity that is limited by the fitness costs rather than mutation rates. Hence the limiting factor for adaptation is not generating the useful mutations, but combining multiple mutations necessary to survive – e.g. escape mutations and reversions – and pruning deleterious mutations. In HIV-1, this process is facilitated by frequent recombination. We expect that the systematic exploration of sequence space, the reproducible patterns of minor variation, and frequent reversion will be characteristic of other RNA viruses. Properties of linkage between mutation will differ since mechanisms of recombination are diverse. But even though selective forces, recombination, and time scales will vary among different microbial populations, theoretical models of rapid adaptation population have shown that many features of the evolutionary dynamics are independent of the specific system (Fisher, 2013; Neher, 2013). Intrapatient evolution of HIV-1 is a unique opportunity to study this evolutionary dynamics directly in vivo.

1. 1. Zanini F
   2. Brodin J
   3. Thebo L
   4. Lanz C
   5. Bratt G
   6. Albert J
   7. Neher RA

   (2015) Whole genome deep sequencing of HIV-1

   Publicly available at the EBI European Nucleotide Archive (Accession no: PRJEB9618).

   http://www.ebi.ac.uk/ena/data/view/PRJEB9618
2. 1. Zanini F
   2. Brodin J
   3. Thebo L
   4. Lanz C
   5. Bratt G
   6. Albert J
   7. Neher RA

   (2015) Population genomics of intrapatient HIV-1 evolution

   Interactive web application facilitating exploration and access to the data.

   http://hiv.tuebingen.mpg.de

1. 1. Allen TM
   2. Altfeld M
   3. Geer SC
   4. Kalife ET
   5. Moore C
   6. O'Sullivan KM
   7. DeSouza I
   8. Feeney ME
   9. Eldridge RL
   10. Maier EL
   11. Kaufmann DE
   12. Lahaie MP
   13. Reyor L
   14. Tanzi G
   15. Johnston MN
   16. Brander C
   17. Draenert R
   18. Rockstroh JK
   19. Jessen H
   20. Rosenberg ES
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Author details

1. Fabio Zanini

   Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany

   Contribution

   FZ, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   Competing interests

   No competing interests declared.

2. Johanna Brodin

   Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden

   Contribution

   JB, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   Competing interests

   No competing interests declared.

3. Lina Thebo

   Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden

   Contribution

   LT, Acquisition of data, Analysis and interpretation of data

   Competing interests

   No competing interests declared.

4. Christa Lanz

   Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany

   Contribution

   CL, Conception and design, Acquisition of data

   Competing interests

   No competing interests declared.

5. Göran Bratt

   Department of Clinical Science and Education, Stockholm South General Hospital, Stockholm, Sweden

   Contribution

   GB, Conception and design, Contributed unpublished essential data or reagents

   Competing interests

   No competing interests declared.

6. Jan Albert

   1. Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
   2. Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden

   Contribution

   JA, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   For correspondence

   Jan.Albert@ki.se

   Competing interests

   No competing interests declared.

7. Richard A Neher

   Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, Tübingen, Germany

   Contribution

   RAN, Conception and design, Analysis and interpretation of data, Drafting or revising the article

   For correspondence

   richard.neher@tuebingen.mpg.de

   Competing interests

   RAN: Reviewing editor, eLife.

   "This ORCID iD identifies the author of this article:" 0000-0003-2525-1407

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