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PCR primers matched to normal and hypermutated sequences were used in conjunction with an agarose gel ccah system incorporating an AT-binding dye to visualize, separate, clone, and sequence hypermutated and normal sequences in the bp HIV-1 protease gene amplified from patient PBMC. Sixty-nine of 70 hypermutated and 3 of normal sequences had in-frame stop codons. Hypermutated sequences generated in culture corresponded exactly in all parameters to those obtained from patient PBMC.
Ccah survival of species depends on a favorable balance between the beneficial and harmful aspects of mutation.
There is loss of the information content of nucleotide sequences once mutation rates are increased beyond a tolerable error threshold Some RNA viruses seem to tolerate mutation rates near this threshold, existing, not as a specific sequence, but as a quasispecies 1215 When viral mutation rates approach the maximum value compatible with viability 14what results is an intolerance to even small increases in mutation rates How surprising, then, that for some of the same viruses with the highest mutation rates, another mutation process has been described in which remarkable levels of one specific type of nucleotide substitution are observed.
These sequences are referred to as hypermutants and are a product of one specific mutation at rates far beyond viability. Two main types of hypermutation, which differ with respect to the type of substitution observed, have been described for viral sequences. A-to-G hypermutation occurs mostly in measles virus and vesicular stomatitis virus 8949and three cases in nonlentiviral retroviruses avian leukosis virus and spleen necrosis virus have been reported 1623 G-to-A hypermutation is found primarily in the lentivirus family of retroviruses, along with two other examples in satellite tobacco mosaic virus 37 and hepatitis B virus G-to-A hypermutation in the lentivirus human immunodeficiency virus type 1 HIV-1 is the subject of this report.
G-to-A hypermutation is defined as a mutational process in which G-to-A transitions far exceed all other mutations in viral sequences The susceptibility of lentiviruses to hypermutation is thought to be a property of their reverse transcriptase RTwhich, compared to nonlentiviral RTs, has a great capacity to elongate beyond nucleotide mismatches 51 and an increased ability to hypermutate in the presence of unbalanced nucleotide pools in vitro This susceptibility is further evidenced by the elevated A content of lentivirus genomes 7.
Retroviral genomes form a bimodal distribution with respect to base composition that follows taxonomic groups Since then, several groups have recovered hypermutated HIV-1 sequences from clinical samples, confirming that they occur in vivo 41840 Typically, mixtures of hypermutated and normal sequences are found, with hypermutated sequences in the minority 41819303952 Some progress has been made in elucidating the biochemical basis for hypermutation.
First thought to be the work of a mutant RT 1850hypermutation has now been shown to be a property of wild-type RT 42 operating under suboptimal conditions. Attempts have been made to generate hypermutants in a cell-free system in vitro with RNA, purified RT, and strongly biased deoxynucleoside triphosphate dNTP pools 434459 While G-to-A hypermutants were produced, they lacked the marked preference for the GpA and GpG dinucleotide contexts that typify hypermutants produced in vivo or during virus cultivation in vitro.
An intermediate approach where RT in virus particles was allowed to complete first-strand DNA synthesis in the presence of exogenously provided, highly biased dNTP pools also resulted in loss of the GpA and GpG dinucleotide preference Hypermutants were also recovered at low frequency 0.
The cell-free experiments described above were conducted using relative concentrations of dTTP and dCTP that differed by 3 to 4 orders of magnitude. More subtle perturbations in the intracellular environment may trigger dNTP pool biases sufficient to generate hypermutation while maintaining the proper dinucleotide context Imbalanced and fluctuating nucleotide pools are a key element of many types of mutation, including hypermutation. Normal dNTP pools are highly asymmetric in mammalian cells reviewed in reference Since the composition of dNTP pools changes as cells progress through the cell cycle 52045the timing of HIV-1 infection with respect to T-cell activation and entry into the cell cycle could be an important factor determining the generation of hypermutants.
In a retrovirus-based shuttle vector, G-to-A transitions predominated 3132 and were presumably a result of even these modest fluctuations in pools during the cell cycle. At this point understanding of hypermutation is still limited, in part because of the lack of a successful systematic screening method. Indeed, many hypermutated sequences have been submitted to databases without being perceived as such Given the lack of a specific genome location for hypermutation, the fact that hypermutants are almost always buried in a large excess of normal sequences, and the difficulty of precisely reproducing hypermutation in vitro, it is not surprising that this mutational process has been regarded as erratic, rare, and of minor importance in the HIV-1 life cycle.
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Here we describe the design and application of powerful new methods for systematic detection and recovery of hypermutants and their application to clinical samples and to the products ccqg HIV-1 infection in cell culture. The results call for a reassessment of the frequency of hypermutation in vivo, clarify the conditions that generate hypermutants in cell culture, and importantly, highlight a vulnerability of HIV-1 that could be exploited for clinical benefit.
Twenty-six samples were from patients hospitalized in Tanzania in with symptoms compatible with AIDS Fourteen others were from individuals who seroconverted to HIV-1 while in the U. Military between and 6. Thirteen people were participants in the San Francisco Men’s Health Study between and 38 The latter two groups were in the early, asymptomatic stage of HIV-1 infection, and the sample was typically drawn within 6 months of HIV-1 seroconversion.
Nested PCR primers 28 were used either without modification, for amplification of normal sequences, or with modifications designed to cca their homology to hypermutated sequences. The primers for amplification of hypermutants contained either mixed bases hyp primers or G-to-A replacements hypa primers at some of the sites GpA or GpG susceptible to hypermutation. Each PCR amplification was run in duplicate, once with normal primers and a second time with an equal mixture of hyp and hypa primers.
A touchdown approach, with incremental decreases in annealing temperature, was used in the initial 14 cycles of the first-round PCR 1324 Products were visualized by poststaining with ethidium bromide. We attempted to recover both normal and hypermutated sequences from every sample, but different approaches were used depending on the HA yellow gel profile of the bulk PCR product.
The PCR product was cloned directly if it was separated into normal and hypermutated bands of nearly equal intensity, or if there was only one band. If the hypermutated and normal bands were of unequal intensity, the two populations were excised from the gel, extracted using the Qiaquick Spin Purification Gel Extraction Kit from Qiagen Valencia, Calif.
When hypermutated bands were faint, the two populations were excised and extracted as above, but the hypermutated sequences were reamplified with second-round primers DP16 and DP17 prior to cloning. The G residues susceptible to hypermutation within the recognition sequences underlined are indicated by asterisks. At least one clone, and often several clones, representing all of the different mobilities found within each sample was selected for sequencing.
Sequences were assembled with Sequencher software Applied Biosystems. All of fcag asymptomatic patients from the United States harbored subtype B. One ccga was dually infected with subtypes A and D, and one other harbored an unclassified strain, possibly an AD recombinant data not shown. The PCR product was xcag for the presence of hypermutated sequences on HA yellow gels and by sequencing. All virus stocks were free of hypermutants by these assays. Nine different culture conditions were established see Fig.
Cells and culture supernatants were collected at 6, 12, 24, 48, and 72 h after infection, with the exception of culture condition IX, where collection took place at 6, 12, 24, 48, and 72 h after addition of PHA.
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Relationship of hypermutation to T-cell activation in virus cultures. Cultures were sampled at intervals and assayed for the presence of p24 antigen in the culture supernatant solid lines and for the presence of hypermutated HIV-1 DNA sequences. Filled stars, samples where hypermutated sequences were abundant; open stars, samples with rare hypermutated sequences. Samples a, b, c, d, e, g, and h are bulk PCR products.
Time points not marked by stars or asterisks yielded only normal sequences both before and after enrichment not shown. Parameters of hypermutation were evaluated with the Hypermut Program Package 54 http: This program identifies mutations and their dinucleotide context with respect to a reference sequence that is provided with each alignment. Unless primer mismatching is addressed, the recovery of hypermutants will be severely limited. Thus we addressed the issue of primer mismatching first.
Nested primers which amplify a bp segment encoding HIV-1 protease were examined for GA and GG dinucleotides, which are susceptible to hypermutation. At the same time, a gel electrophoresis system was designed to permit detection of hypermutants. The cloned genes were all of equal length and mobility, as shown in the gel without HA yellow. Calibration of the HA yellow gel system. The GA and GG dinucleotides that are susceptible to hypermutation are shaded.
The gel on the left shows the migration of these PCR products as a single band at bp without HA yellow. On the right, a gel incorporating HA yellow is shown, illustrating the direct relationship between AT content and mobility. PCR products representing the normal and maximally hypermutated sequences were used as migration standards in subsequent HA yellow gels.
Among the 10 samples, 5 showed a substantial increase in hypermutated sequences when primers hyp and hypa were used patients 3, 9177, 5, 6, and 8; Fig.
Patients 2 and 10 yielded a variety of hypermutated bands with both normal and hypermutated primers.
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Patients 1, 7, and 9 showed essentially a single band at the normal position regardless of the primers used. Thus the use of primers hyp and hypa increased the number of samples with detectable hypermutation in the bulk 1797 product on HA yellow gels from 2 of 10 to 7 of Relative recovery of hypermutated sequences with normal and hypermutated PCR primers. Primers were designed to incorporate G-to-A substitutions in GA or GG dinucleotides Materials and Methods and compared to primers matched to normal sequences for their ability to amplify hypermutated sequences from the PBMC of 10 patients.
N, normal primers; H, primers hyp and hypa. Hypermutated bands detected with primers hyp and hypa but not with normal primers are indicated for patients 3, 4, 5, 6, and 8 asterisks.
The positions of normal and fully hypermutated standards are indicated by arrows. Sometimes all of the PCR product migrated at the normal position Fig. Notably, some samples had most of the PCR product retarded in the gel lanes 2, 6, and Other samples migrated mostly at the normal position but were smeared upward without distinct bands Fig. PCR products were compared to normal and hypermutated standards on HA yellow gels. While all products migrated as a single band at bp without HA yellow leftthey were often split into several bands in the presence of HA yellow right.
Products were visualized by staining with ethidium bromide. A combination of approaches was used to recover and sequence a range of normal and hypermutated sequences from each of 53 patient samples. These included use of both normal and hypermutated PCR primers, extraction of PCR products after separation in HA yellow gels, and reamplification of rare sequences extracted from HA yellow gels see Materials and Methods.
Multiple sequences were obtained from each patient, ranging from 1 to 11977 the total number of sequences was For this xcag, we eliminated identical sequences, which were sometimes found in within-patient comparisons, from the data set.
Classification of sequences from patient PBMC.