Synthesizing Methuselah: The Question of Artificial Agelessness.

As biological organisms, we age and, eventually, die. However, age's deteriorating effects may not be universal. Some theoretical entities, due to their synthetic composition, could exist independently from aging-artificial general intelligence (AGI). With adequate resource access, an AGI could theoretically be ageless and would be, in some sense, immortal. Yet, this need not be inevitable. Designers could imbue AGIs with artificial mortality via an internal shut-off point. The question, though, is, should they? Should researchers curtail an AGI's potentially endless lifespan by deliberately making it mortal? It is this question that this article explores. First, it considers what type of AGI is under discussion before outlining how such beings could be ageless. Then, after clarifying the type of immortality under discussion and arguing that imbuing an AGI with synthetic aging would be person-affecting, the article explores four core conundrums: (i) deliberately causing a morally significant being's death; (ii) immortality's associated harms; (iii) concerns about immortality's unequal assignment; and (iv) the danger of immortal AGI overlords. The article concludes that while prudence requires we create an aging AGI, in the face of the material harm such an action would constitute, this is an insufficient reason to justify doing so.

Enhancement of CD4 Binding, Host Cell Entry, and Sensitivity to CD4bs Antibody Inhibition Conferred by a Natural but Rare Polymorphism in the HIV-1 Envelope.

A rare but natural polymorphism in the HIV-1 envelope (Env) glycoprotein, lysine at position 425 was selected as a mutation conferring resistance to maraviroc (MVC) in vitro. N425K has not been identified in HIV-infected individuals failing an MVC-based treatment. This study reports that the rare K425 polymorphism in an HIV-1 subtype A Env has increased affinity for CD4, resulting in faster host cell entry kinetics and the ability to scavenge for low cell surface expression of CD4 to mediate entry. Whereas the subtype A wild-type isolate-74 Env (N425) is inhibited by soluble (s) CD4, HIV-1 with K425 A74 Env shows enhanced infection and the ability to infect CCR5+ cells when pretreated with sCD4. Upon adding K425 or N425 HIV-1 to CD4+/CCR5+ cells along with RANTES/CCL3, only K425 HIV-1 was able to infect cells when CCR5 recycled/returned to the cell surface at 12 h post-treatment. These findings suggest that upon binding to CD4, K425 Env may maintain a stable State 2 "open" conformation capable of engaging CCR5 for entry. Only K425 was significantly more sensitivity than wild-type N425 A74 to inhibition by the CD4 binding site (bs) compound, BMS-806, the CD4bs antibody, VRC01 and N6, and the single-chain CD4i antibody, SCm9. K425 A74 was also capable of activating B cells expressing the VRC01 surface immunoglobulin. In summary, despite increased replicative fitness, we propose that K425 HIV-1 may be counterselected within infected individuals if K425 HIV-1 is rapidly eliminated by CD4bs-neutralizing antibodies. IMPORTANCE Typically, a natural amino acid polymorphism is found as the wild-type sequence in the HIV-1 population if it provides a selective advantage to the virus. The natural K425 polymorphism in HIV-1 Env results in higher host cell entry efficiency and greater replicative fitness by virtue of its high binding affinity to CD4. The studies presented herein suggest that the rare K425 HIV-1, compared to the common N425 HIV-1, may be more sensitive to inhibition by CD4bs-neutralizing antibodies (i.e., antibodies that bind to the CD4 binding pocket on the HIV-1 envelope glycoprotein). If CD4bs antibodies did emerge in an infected individual, the K425 HIV-1 may be hypersensitive to inhibition, and thus this K425 virus variant may be removed from the HIV-1 swarm despite its higher replication fitness. Studies are now underway to determine whether addition of the K425 polymorphism into the Envelope-based HIV-1 vaccines could enhance protective immunity.

An Amino Acid Polymorphism within the HIV-1 Nef Dileucine Motif Functionally Uncouples Cell Surface CD4 and SERINC5 Downregulation.

Serine incorporator 5 (SERINC5) reduces the infectivity of progeny HIV-1 virions by incorporating into the outer host-derived viral membrane during egress. To counter SERINC5, the HIV-1 accessory protein Nef triggers SERINC5 internalization by engaging the adaptor protein 2 (AP-2) complex using the [D/E]xxxL[L/I]167 Nef dileucine motif. Nef also engages AP-2 via its dileucine motif to downregulate the CD4 receptor. Although these two Nef functions are related, the mechanisms governing SERINC5 downregulation are incompletely understood. Here, we demonstrate that two primary Nef isolates, referred to as 2410 and 2391 Nef, acquired from acutely HIV-1 infected women from Zimbabwe, both downregulate CD4 from the cell surface. However, only 2410 Nef retains the ability to downregulate cell surface SERINC5. Using a series of Nef chimeras, we mapped the region of 2391 Nef responsible for the functional uncoupling of these two antagonistic pathways to the dileucine motif. Modifications of the first and second x positions of the 2410 Nef dileucine motif to asparagine and aspartic acid residues, respectively (ND164), impaired cell surface SERINC5 downregulation, which resulted in reduced infectious virus yield in the presence of SERINC5. The ND164 mutation additionally partially impaired, but did not completely abrogate, Nef-mediated cell surface CD4 downregulation. Furthermore, the patient infected with HIV-1 encoding 2391 Nef had stable CD4+ T cell counts, whereas infection with HIV-1 encoding 2410 Nef resulted in CD4+ T cell decline and disease progression. IMPORTANCE A contributing factor to HIV-1 persistence is evasion of the host immune response. HIV-1 uses the Nef accessory protein to evade the antiviral roles of the adaptive and intrinsic innate immune responses. Nef targets SERINC5, a restriction factor which potently impairs HIV-1 infection by triggering SERINC5 removal from the cell surface. The molecular determinants underlying this Nef function remain incompletely understood. Recent studies have found a correlation between the extent of Nef-mediated SERINC5 downregulation and the rate of disease progression. Furthermore, single-residue polymorphisms outside the known Nef functional motifs can modulate SERINC5 downregulation. The identification of a naturally occurring Nef polymorphism impairing SERINC5 downregulation in this study supports a link between Nef downregulation of SERINC5 and the rate of plasma CD4+ T cell decline. Moreover, the observed functional impairments of this polymorphism could provide clues to further elucidate unknown aspects of the SERINC5 antagonistic pathway via Nef.

The Desirability of Difference: Georges Canguilhem and Body Integrity Identity Disorder.

Opponents of the provision of therapeutic, healthy limb amputation in Body Integrity Identity Disorder cases argue that such surgeries stand in contrast to the goal of medical practice - that of health restoration and maintenance. This paper refutes such a conclusion via an appeal to the nuanced and reflective model of health proposed by Georges Canguilhem. The paper examines the conceptual entanglement of the statistically common with the normatively desirable, arguing that a healthy body can take multiple forms, including that of an amputee, provided that such a form enables the continuing ability to initiate new norms of existence. It concludes that the practice of healthy limb amputation in cases of Body Integrity Identity Disorder is not only compatible with the goal of medicine but is potentially the only method of achieving this goal in the face of a complex and often mischaracterized disorder.

Differential diagnosis of acute traumatic hip pain in the elderly.

Elderly patients who present with an inability to weight bear following a fall, with normal radiographs, should be appropriately investigated to rule out an occult hip fracture (OHF). We aim to identify both the range and incidence of the differential diagnosis of acute traumatic hip pain in a large series of patients investigated for OHF. A retrospective analysis of consecutive patients investigated for an OHF with magnetic resonance imaging (MRI) was performed. Dedicated musculo- skeletal radiologists reported the MRI scans. All diagnoses including hip fractures, other fractures and soft tissue injuries were recorded. Case notes were reviewed for all patients to identify subsequent complications, management and outcomes. A total of 157 patients fulfilled the inclusion criteria. 52 (33%) patients had a fracture of the proximal femur. The majority of patients with proximal femoral fractures required surgical intervention. 9 patients who had fractures of the greater trochanter of the femur without fracture extension across the femoral neck were managed non-operatively. 40 (25%) patients had fractures of the pelvis, with a combined pubic rami and sacral fracture occurring frequently. The most common diagnosis was a soft tissue injury alone that was seen in 60 (38%) patients imaged. Injuries to the gluteal muscle group, iliopsaos complex and trochanteric bursa were most prevalent. All patients with soft tissue injuries or fractures of the pelvis were successfully managed non-operatively. This study highlights a wide range of differential diagnoses in elderly patients presenting with acute traumatic hip pain. The proximal femur was fractured in 33% of patients imaged for OHFs in our series. The most common diagnosis was a soft tissue injury around the hip and pelvis ; these injuries can be successfully managed without surgery.

Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda.

BACKGROUND: Increasing first-line treatment failures in low- and middle-income countries (LMICs) have led to increased use of integrase strand transfer inhibitors (INSTIs) such as dolutegravir. However, HIV-1 susceptibility to INSTIs in LMICs, especially with previous raltegravir exposure, is poorly understood due to infrequent reporting of INSTI failures and testing for INSTI drug resistance mutations (DRMs). METHODS: A total of 51 non-subtype B HIV-1 infected patients failing third-line (raltegravir-based) therapy in Uganda were initially selected for the study. DRMs were detected using Sanger and deep sequencing. HIV integrase genes of 13 patients were cloned and replication capacities (RCs) and phenotypic susceptibilities to dolutegravir, raltegravir and elvitegravir were determined with TZM-bl cells. Spearman's correlation coefficient was used to determine cross-resistance between INSTIs. RESULTS: INSTI DRMs were detected in 47% of patients. HIV integrase-recombinant virus carrying one primary INSTI DRM (N155H or Y143R/S) was susceptible to dolutegravir but highly resistant to raltegravir and elvitegravir (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to raltegravir, elvitegravir and even dolutegravir. The former multi-DRM virus had WT RC whereas the latter had lower RCs than WT. CONCLUSIONS: In HIV-1 subtype A- and D-infected patients failing raltegravir and harbouring INSTI DRMs, there is high-level resistance to elvitegravir and raltegravir. More routine monitoring of INSTI treatment may be advised in LMICs, considering that multiple INSTI DRMs may have accumulated during prolonged exposure to raltegravir during virological failure, leading to high-level INSTI resistance, including dolutegravir resistance.

Graphic illustration of impairment: science fiction, Transmetropolitan and the social model of disability.

The following paper examines the cyberpunk transhumanist graphic novel Transmetropolitan through the theoretical lens of disability studies to demonstrate how science fiction, and in particular this series, illustrate and can influence how we think about disability, impairment and difference. While Transmetropolitan is most often read as a scathing political and social satire about abuse of power and the danger of political apathy, the comic series also provides readers with representations of impairment and the source of disability as understood by the Social Model of Disability (SMD). Focusing on the setting and fictional world in which Transmetropolitan takes place, as well as key events and illustration styling, this paper demonstrates that the narrative in this work encompasses many of the same theoretical underpinnings and criticisms of society's ignorance of the cause of disability as the SMD does. This paper aims, by demonstrating how Transmetropolitan can be read as an allegory for the disabling potential of society as experienced by individuals with impairments, to prompt readers into thinking more creatively about how narratives, seemingly unconcerned with disability, are informed and can be understood via disability theory.

Evolution-Guided Structural and Functional Analyses of the HERC Family Reveal an Ancient Marine Origin and Determinants of Antiviral Activity.

In humans, homologous to the E6-AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing protein 5 (HERC5) is an interferon-induced protein that inhibits replication of evolutionarily diverse viruses, including human immunodeficiency virus type 1 (HIV-1). To better understand the origin, evolution, and function of HERC5, we performed phylogenetic, structural, and functional analyses of the entire human small-HERC family, which includes HERC3, HERC4, HERC5, and HERC6. We demonstrated that the HERC family emerged >595 million years ago and has undergone gene duplication and gene loss events throughout its evolution. The structural topology of the RCC1-like domain and HECT domains from all HERC paralogs is highly conserved among evolutionarily diverse vertebrates despite low sequence homology. Functional analyses showed that the human small HERCs exhibit different degrees of antiviral activity toward HIV-1 and that HERC5 provides the strongest inhibition. Notably, coelacanth HERC5 inhibited simian immunodeficiency virus (SIV), but not HIV-1, particle production, suggesting that the antiviral activity of HERC5 emerged over 413 million years ago and exhibits species- and virus-specific restriction. In addition, we showed that both HERC5 and HERC6 are evolving under strong positive selection, particularly blade 1 of the RCC1-like domain, which we showed is a key determinant of antiviral activity. These studies provide insight into the origin, evolution, and biological importance of the human restriction factor HERC5 and the other HERC family members.IMPORTANCE Intrinsic immunity plays an important role as the first line of defense against viruses. Studying the origins, evolution, and functions of proteins responsible for effecting this defense will provide key information about virus-host relationships that can be exploited for future drug development. We showed that HERC5 is one such antiviral protein that belongs to an evolutionarily conserved family of HERCs with an ancient marine origin. Not all vertebrates possess all HERC members, suggesting that different HERCs emerged at different times during evolution to provide the host with a survival advantage. Consistent with this, two of the more recently emerged HERC members, HERC5 and HERC6, displayed strong signatures of having been involved in an ancient evolutionary battle with viruses. Our findings provide new insights into the evolutionary origin and function of the HERC family in vertebrate evolution, identifying HERC5 and possibly HERC6 as important effectors of intrinsic immunity in vertebrates.

First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda.

BACKGROUND: Our understanding of HIV-1 and antiretroviral treatment (ART) is strongly biased towards subtype B, the predominant subtype in North America and western Europe. Efforts to characterize the response to first-line treatments in other HIV-1 subtypes have been hindered by the availability of large study cohorts in resource-limited settings. To maximize our statistical power, we combined HIV-1 sequence and clinical data from every available study population associated with the Joint Clinical Research Centre (JCRC) in Uganda. These records were combined with contemporaneous ART-naive records from Uganda in the Stanford HIVdb database. METHODS: Treatment failures were defined by the presence of HIV genotype records with sample collection dates after the ART start dates in the JCRC database. Drug resistances were predicted by the Stanford HIVdb algorithm, and HIV subtype classification and recombination detection was performed with SCUEAL. We used Bayesian network analysis to evaluate associations between drug exposures and subtypes, and binomial regression for associations with recombination. RESULTS: This is the largest database of first-line treatment failures ([Formula: see text]) in Uganda to date, with a predicted statistical power of 80% to detect subtype associations at an odds ratio of [Formula: see text]. In the subset where drug regimen data were available, we observed that use of 3TC was associated with a higher rate of first line treatment failure, whereas regimens containing AZT and TDF were associated with reduced rates of failure. In the complete database, we found limited evidence of associations between HIV-1 subtypes and treatment failure, with the exception of a significantly lower frequency of failures among A/D recombinants that comprised about 7% of the population. First-line treatment failure was significantly associated with reduced numbers of recombination breakpoints across subtypes. CONCLUSIONS: Expanding access to first-line ART should confer the anticipated public health benefits in Uganda, despite known differences in the pathogenesis of HIV-1 subtypes. Furthermore, the impact of ART may actually be enhanced by frequent inter-subtype recombination in this region.

European Nucleotide Archive in 2016.

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.

Accepting new patients who require opioids into family practice: results from the MAAP-NS census survey study.

BACKGROUND: Acceptance to a family practice is key to access and continuity of care. While Canadian patients increasingly report not being able to acquire acceptance to a family practice, little is known about the association between requiring opioids and acceptance. We aim to determine the proportion of family physicians who would accept new patients who require opioids and describe physician and practice characteristics associated with willingness to accept these patients. METHODS: Census telephone survey of family physicians' practices in Nova Scotia, Canada. MEASURES: physician (i.e., age, sex, years in practice) and practice (i.e., number/type of provider in the practice, care hours/week) characteristics and practice-reported willingness to accept new patients who require opioids. RESULTS: The survey was completed for 587 family physicians (83.7% response rate). 354 (60.3%) were taking new patients unconditionally or with conditions; 326 provided a response to whether they would accept new patients who require opioids; 91 (27.9%) reported they would not accept a new patient who requires opioids. Compared to family physicians who would not accept patients who require opioids, in bivariate analysis, those who would, tended to work in larger practices; had fewer years in practice; are female; and provided more patient care. The relationship to number of providers in the practice, having a nurse, and experience persisted in multivariate analysis. CONCLUSIONS: The strongest predictors of willingness to accept patients who require opioids are fewer years in practice (OR = 0.96 [95% CI 0.93, 0.99]) and variables indicating a family physician has support of a larger (OR = 1.19 [95% CI 1.00, 1.42]), interdisciplinary team (e.g., nurses, mental health professionals) (OR = 1.15 [95% CI 1.11, 5.05]). Almost three-quarters (72.1%) of surveyed family physicians would accept patients requiring opioids.

Factors influencing reversion from virus infection in sweetpotato.

Viruses limit sweetpotato (Ipomoea batatas) production worldwide. Many sweetpotato landraces in East Africa are, however, largely virus-free. Moreover, some plants infected by the prevalent Sweet potato feathery mottle virus (SPFMV) may be able to revert to virus-free status. In this study, we analysed reversion from SPFMV, Sweet potato virus C, Sweet potato mild mottle virus, Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato leaf curl Uganda virus using the indicator plant I. setosa and PCR/reverse-transcriptase PCR. We also investigated environmental factors (temperature and soil nutrients) that may influence reversion from virus infection. We tested reversion in the East African cultivars New Kawogo, NASPOT 1 and NASPOT 11, and the United States cultivars Resisto and Beauregard. Reverted plants were asymptomatic and virus was undetectable in assayed parts of the plant. After graft inoculation, only the East African cultivars mostly reverted at a high rate and from most viruses though cultivar Beauregard fully reverted following sap inoculation with Sweet potato virus C. None of the tested cultivars fully reverted from single or double infections involving SPCSV, and reversion was only observed in co-infections involving potyviruses. Root sprouts derived from SPFMV-reverted plants were also virus free. Reversion generally increased with increasing temperature and by improved soil nutrition. Overall, these results indicate variation in reversion by cultivar and that the natural ability of sweetpotato plants to revert from viruses is malleable, which has implications for both breeding and virus control.

Biocuration of functional annotation at the European nucleotide archive.

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed.

'Meet and greet' intake appointments in primary care: a new pattern of patient intakes?

Background: Family physicians (FPs) are expected to take on new patients fairly and equitably and to not discriminate based on medical or social history. 'Meet and greet' appointments are initial meetings between physicians and prospective patients to establish fit between patient needs and provider scope of practice. The public often views these appointments as discriminatory; however, there is no empirical evidence regarding their prevalence or outcomes. Objectives: To determine the proportion of FPs conducting 'meet and greets' and their outcomes. Methods: Study design and setting: Census telephone survey of all FP practices in Nova Scotia (NS). Participants: Person who answers the FP office telephone. Main Outcomes: Proportion of FPs holding 'meet and greets'; proportion of FPs conducting 'meet and greets' who have ever decided not to continue seeing a patient after the meeting. Results: 9.2% of FPs accept new patients unconditionally; 51.1% accept new patients under certain conditions. Of those accepting patients unconditionally or with conditions, 46.9% require a 'meet and greet'; 41.8% have a first-come, first-serve policy. Among FPs who require a 'meet and greet', 44.0% decided, at least once, not to continue seeing a patient after the first meeting. Conclusion: 'Meet and greets' are common among FPs in NS and result in some patients not being accepted into practice. More research is needed to understand the intentions, processes, and outcomes of 'meet and greets'. We recommend that practice scope be made clear to prospective patients before their first visit, which may eliminate the need for 'meet and greets'.

Impaired human immunodeficiency virus type 1 replicative fitness in atypical viremic non-progressor individuals.

BACKGROUND: Progression rates from initial HIV-1 infection to advanced AIDS vary significantly among infected individuals. A distinct subgroup of HIV-1-infected individuals-termed viremic non-progressors (VNP) or controllers-do not seem to progress to AIDS, maintaining high CD4+ T cell counts despite high levels of viremia for many years. Several studies have evaluated multiple host factors, including immune activation, trying to elucidate the atypical HIV-1 disease progression in these patients; however, limited work has been done to characterize viral factors in viremic controllers. METHODS: We analyzed HIV-1 isolates from three VNP individuals and compared the replicative fitness, near full-length HIV-1 genomes and intra-patient HIV-1 genetic diversity with viruses from three typical (TP) and one rapid (RP) progressor individuals. RESULTS: Viremic non-progressors and typical patients were infected for >10 years (range 10-17 years), with a mean CD4+ T-cell count of 472 cells/mm3 (442-529) and 400 cells/mm3 (126-789), respectively. VNP individuals had a less marked decline in CD4+ cells (mean -0.56, range -0.4 to -0.7 CD4+/month) than TP patients (mean -10.3, -8.2 to -13.1 CD4+/month). Interestingly, VNP individuals carried viruses with impaired replicative fitness, compared to HIV-1 isolates from the TP and RP patients (p < 0.05, 95% CI). Although analyses of the near full-length HIV-1 genomes showed no clear patterns of single-nucleotide polymorphisms (SNP) that could explain the decrease in replicative fitness, both the number of SNPs and HIV-1 population diversity correlated inversely with the replication capacity of the viruses (r = -0.956 and r = -0.878, p < 0.01, respectively). CONCLUSION: It is likely that complex multifactorial parameters govern HIV-1 disease progression in each individual, starting with the infecting virus (phenotype, load, and quasispecies diversity) and the intrinsic ability of the host to respond to the infection. Here we analyzed a subset of viremic controller patients and demonstrated that similar to the phenomenon observed in patients with a discordant response to antiretroviral therapy (i.e., high CD4+ cell counts with detectable plasma HIV-1 RNA load), reduced viral replicative fitness seems to be linked to slow disease progression in these antiretroviral-naïve individuals.

Content discovery and retrieval services at the European Nucleotide Archive.

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its discoverability and usability. In response to this, ENA has been introducing and improving checklists for use during submission and expanding its search facilities to provide targeted search results. Here, we give a brief update on ENA content and some major developments undertaken in data submission services during 2014. We then describe in more detail the services we offer for data discovery and retrieval.

RNAcentral: an international database of ncRNA sequences.

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure.

Most patients failing antiretroviral treatment in Uganda continue to fail their treatment regimen even if a dominant drug-resistant HIV-1 genotype is not detected. In a recent retrospective study, we observed that approximately 30% of HIV-infected individuals in the Joint Clinical Research Centre (Kampala, Uganda) experienced virologic failure with a susceptible HIV-1 genotype based on standard Sanger sequencing. Selection of minority drug-resistant HIV-1 variants (not detectable by Sanger sequencing) under antiretroviral therapy pressure can lead to a shift in the viral quasispecies distribution, becoming dominant members of the virus population and eventually causing treatment failure. Here, we used a novel HIV-1 genotyping assay based on deep sequencing (DeepGen) to quantify low-level drug-resistant HIV-1 variants in 33 patients failing a first-line antiretroviral treatment regimen in the absence of drug-resistant mutations, as screened by standard population-based Sanger sequencing. Using this sensitive assay, we observed that 64% (21/33) of these individuals had low-frequency (or minority) drug-resistant variants in the intrapatient HIV-1 population, which correlated with treatment failure. Moreover, the presence of these minority HIV-1 variants was associated with higher intrapatient HIV-1 diversity, suggesting a dynamic selection or fading of drug-resistant HIV-1 variants from the viral quasispecies in the presence or absence of drug pressure, respectively. This study identified low-frequency HIV drug resistance mutations by deep sequencing in Ugandan patients failing antiretroviral treatment but lacking dominant drug resistance mutations as determined by Sanger sequencing methods. We showed that these low-abundance drug-resistant viruses could have significant consequences for clinical outcomes, especially if treatment is not modified based on a susceptible HIV-1 genotype by Sanger sequencing. Therefore, we propose to make clinical decisions using more sensitive methods to detect minority HIV-1 variants.