Multiple V1/V2 env Variants Are Frequently Present during Primary Infection with Human Immunodeficiency Virus Type 1

Human immunodeficiency virus type 1 (HIV-1) exists as a complex population of multiple genotypic variants in persons with chronic infection. However, acute HIV-1 infection via sexual transmission is a low-probability event in which there is thought to be low genetic complexity in the initial inoculum. In order to assess the viral complexity present during primary HIV-1 infection, the V1/V2 and V3 variable regions of the env gene were examined by using a heteroduplex tracking assay (HTA) capable of resolving these genotypic variants. Blood plasma samples from 26 primary HIV-1-infected subjects were analyzed for their level of diversity. Half of the subjects had more than one V1/V2 viral variant during primary infection, indicating the frequent transmission of multiple variants. This observation is inconsistent with the idea of infrequent transmission based on a small transmitting inoculum of cell-free virus. In chronically infected subjects, the complexity of the viral populations was even greater in both the V1/V2 and the V3 regions than in acutely infected subjects, indicating that in spite of the presence of multiple variants in acute infection, the virus does pass through a genetic bottleneck during transmission. We also examined how well the infecting virus penetrated different anatomical compartments by using the HTA. Viral variants detected in blood plasma were compared to those detected in seminal plasma and/or cerebral spinal fluid of six individuals. The virus in each of these compartments was to a large extent identical to virus in blood plasma, a finding consistent with rapid penetration of the infecting variant(s). The low-probability transmission of multiple variants could be the result of transient periods of hyperinfectiousness or hypersusceptibility. Alternatively, the inefficient transfer of a multiply infected cell could account for both the low probability of transmission and the transfer of multiple variants

Seven-year efficacy and safety of treatment with tenofovir disoproxil fumarate for chronic hepatitis b virus ınfection

Background Long-term tenofovir disoproxil fumarate (TDF) treatment for chronic hepatitis B (CHB) is associated with sustained viral suppression and regression of fibrosis and cirrhosis at year 5 (240 weeks) and no TDF resistance through 6 years (288 weeks). Aim We assessed the efficacy, safety, and resistance of TDF for up to 7 years (336 weeks) in HBeAg-positive and HBeAg-negative CHB patients. Methods Patients who completed 1 year (48 weeks) of randomized treatment with TDF or adefovir dipivoxil were eligible to receive open-label TDF for a total duration of 8 years (384 weeks). Results Of 641 patients initially randomized, 585 (91.3 %) entered the open-label phase; 437/585 (74.7 %) remained on study at year 7. For patients on treatment at year 7, 99.3 % maintained viral suppression (HBV DNA = 0.5 mg/dL above baseline. No significant change in bone mineral density was observed from year 4 to year 7 (week 192 to week 336). Conclusions Long-term TDF treatment was associated with sustained virologic, biochemical, and serologic responses, without resistance. TDF treatment was well tolerated, with a low incidence of renal and bone events. These data confirm the safety and efficacy of long-term TDF for CHB.Gilead Science

Non-random pre-transcriptional evolution in HIV-1. A refutation of the foundational conditions for neutral evolution

The complete base sequence of HIV-1 virus and GP120 ENV gene were analyzed to establish their distance to the expected neutral random sequence. An especial methodology was devised to achieve this aim. Analyses included: a) proportion of dinucleotides (signatures); b) homogeneity in the distribution of dinucleotides and bases (isochores) by dividing both segments in ten and three sub-segments, respectively; c) probability of runs of bases and No-bases according to the Bose-Einstein distribution. The analyses showed a huge deviation from the random distribution expected from neutral evolution and neutral-neighbor influence of nucleotide sites. The most significant result is the tremendous lack of CG dinucleotides (p < 10-50 ), a selective trait of eukaryote and not of single stranded RNA virus genomes. Results not only refute neutral evolution and neutral neighbor influence, but also strongly indicate that any base at any nucleotide site correlates with all the viral genome or sub-segments. These results suggest that evolution of HIV-1 is pan-selective rather than neutral or nearly neutral

Characterization of a thymus-tropic HIV-1 isolate from a rapid progressor: role of the envelope

Loss of T cell homeostasis usually precedes the onset of AIDS. We hypothesized that rapid progressors may be transmitted with HIV-1 that is particularly able to perturb T cell homeostasis. To this end, we have tested two transmitted, syncytium-inducing (SI) viral isolates from a rapid progressor in two thymus models. One of the isolates (R3A) exhibited markedly rapid kinetics of replication and thymocyte depletion. These phenotypes mapped to the envelope, as a recombinant NL4-3 virus encoding the R3A envelope had similar phenotypes, even in the absence of nef. Notably, the viruses with high pathogenic activity in the thymus (R3A and NL4-R3A) did not show enhanced replication or cytopathicity in PHA-stimulated PBMCs. Furthermore, NL4-R3A did not enhance replication of the coinfected NL4-3 virus in the thymus, suggesting an intrinsic advantage of the R3 A envelope. The R3 A envelope showed higher entry activity in infecting human T cells and in depleting CD4+ thymocytes when expressed in trans. These data suggest that SI viruses with unique envelope functions which can overcome barriers to transmission may hasten disease progression by perturbing T cell homeostasis

Turnover of env Variable Region 1 and 2 Genotypes in Subjects with Late-Stage Human Immunodeficiency Virus Type 1 Infection

The env gene of human immunodeficiency virus type 1 (HIV-1) includes some of the most genetically diverse regions of the viral genome, which are called variable regions 1 through 5 (V1 through V5). We have developed a heteroduplex tracking assay to detect changes in variable regions 1 and 2 of env (V1/V2-HTA). Using sequences from two molecular clones as probes, we have studied the nature of longitudinal virus population changes in a cohort of HIV-1-infected subjects. Viral sequences present in 21 subjects with late-stage HIV-1 infection were initially screened for stability of the virus population by V1/V2-HTA. The virus populations at entry comprised an average of five coexisting V1/V2 genotypic variants (as identified by HTA). Eight of the 21 subjects were examined in detail because of the dynamic behavior of their env variants over an approximately 9-month period. In each of these cases we detected a single discrete transition of V1/V2 genotypes based on monthly sampling. The major V1/V2 genotypes (those present at >10% abundance) from the eight subjects were cloned and sequenced to define the nature of V1/V2 variability associated with a discrete transition. Based on a comparison of V1/V2 genotypic variants present at entry with the newly emerged variants we categorized the newly emerged variants into two groups: variants without length differences and variants with length differences. Variants without length differences had fewer nucleotide substitutions, with the changes biased to either V1 or V2, suggestive of recent evolutionary events. Variants with length differences included ones with larger numbers of changes that were distributed, suggestive of recall of older genotypes. Most length differences were located in domains where the codon motif AVT (V = A, G, C) had become enriched and fixed. Finally, recombination events were detected in two subjects, one of which resulted in the reassortment of V1 and V2 regions. We suggest that turnover in V1/V2 populations was largely driven by selection on either V1 or V2 and that escape was accomplished either through changes focused in the region under selection or by the appearance of a highly divergent variant

Chemistry and Materials Science Directorate 2005 Annual Report

In 1952, we began laboratory operations in the barracks building of the Naval Air Station with approximately 50 employees. Today, the Chemistry and Materials Science (CMS) Directorate is a major organization at the Lawrence Livermore National Laboratory with more than 500 employees who continue to contribute to our evolving national security mission. For more than half a century, the mission of the Laboratory revolved primarily around nuclear deterrence and associated defense technologies. Today, Livermore supports a broad-based national security mission, and our specialized capabilities increasingly support emerging missions in human health and energy security. In the future, CMS will play a significantly expanded role in science and technology at the intersection of national security, energy and environment, and health. Our world-class workforce will provide the science and technology base for radically innovative materials to our programs and sponsors. Our 2005 Annual Report describes how our successes and breakthroughs follow a path set forward by our strategic plan and four organizing research themes, each with key scientific accomplishments by our staff and collaborators. Organized into two major sections-research themes and dynamic teams, this report focuses on achievements arising from earlier investments that address future challenges. The research presented in this annual report gives substantive examples of how we are proceeding in each of these four theme areas and how they are aligned with our national security mission. Research Themes: (1) Materials Properties and Performance under Extreme Conditions--We are developing ultrahard nanocrystalline metals, exploring the properties of nanotubes when exposed to very high temperatures, and engineering stronger materials to meet future needs for materials that can withstand extreme conditions. (2) Chemistry under Extreme Conditions and Chemical Engineering to Support National-Security Programs--Our recent discovery of a new source of coherent light adds a new tool to an array of methods we use to more fully understand the properties of materials. Insights into the early stages of polymer crystallization may lead to new materials for our national-security mission and private industry. (3) Science Supporting National Objectives at the Intersection of Chemistry, Materials Science, and Biology--We are improving drug binding for cancer treatment through the use of new tools that are helping us characterize protein-antibody interactions. By probing proteins and nucleic acids, we may gain an understanding of Alzheimer's, Mad Cow, and other neurodegenerative diseases. (4) Applied Nuclear Science for Human Health and National Security--Our work with cyanobacteria is leading to a fuller understanding of how these microorganisms affect the global carbon cycle. We are also developing new ways to reduce nuclear threats with better radiation detectors. Dynamic Teams: The dynamic teams section illustrates the directorate's organizational structure that supports a team environment across disciplinary and institutional boundaries. Our three divisions maintain a close relationship with Laboratory programs, working with directorate and program leaders to ensure an effective response to programmatic needs. CMS's divisions are responsible for line management and leadership, and together, provide us with the flexibility and agility to respond to change and meet program milestones. The three divisions are: Materials Science and Technology Division; Chemistry and Chemical Engineering Division; and Chemical Biology and Nuclear Science Division. By maintaining an organizational structure that offers an environment of collaborative problem-solving opportunities, we are able to nurture the discoveries and breakthroughs required for future successes. The dynamic teams section also presents the work of CMS's postdoctoral fellows, who bring to the Laboratory many of the most recent advances taking place in academic departments and provide a research stimulus to established research teams. Postdoctoral fellows are selected for their scientific expertise, capability, and enthusiasm for working in a highly productive environment that places a premium on scientific innovation

Chemistry and Materials Science Directorate Annual Report 2003

Evolving challenges and solid accomplishments define the year 2003 for us. Our scientific breakthroughs validate our strategic directions and reaffirm our critical role in fulfilling the Laboratory's missions. Our growth continues in new research projects and significant new programmatic support. Our mission is clear: to enable the Laboratory to accomplish its primary mission through excellence in the chemical and materials sciences. The directorate's common theme and determination has remained constant: Deliver on our commitments, while anticipating and capitalizing on opportunities through innovation in science and technology. In this, the 2003 Annual Report, we describe how our science is built around a strategic plan with four organizing themes, each with key scientific accomplishments by our staff and collaborators. Our strategic plan is synergistic with the Laboratory's Long-Range Science and Technology Plan, which identifies six areas of institutional research and development strategy. This 2003 CMS Annual Report is organized into two major sections: research themes and dynamic teams. The research-theme section addresses challenges, achievements, and new frontiers within each of the four research themes. The dynamic-teams section illustrates the directorate's organizational structure of divisions, centers, and institutes that supports a team environment across disciplinary and institutional boundaries. The research presented gives substantive examples of how we are proceeding in each of these four theme areas and how they are aligned with the institutional strategy. Our organizational structure offers an environment of collaborative problem-solving opportunities, an environment that attracts and retains the best and the brightest from across the Laboratory and around the world

Multiple V1/V2 env Variants Are Frequently Present during Primary Infection with Human Immunodeficiency Virus Type 1

Human immunodeficiency virus type 1 (HIV-1) exists as a complex population of multiple genotypic variants in persons with chronic infection. However, acute HIV-1 infection via sexual transmission is a low-probability event in which there is thought to be low genetic complexity in the initial inoculum. In order to assess the viral complexity present during primary HIV-1 infection, the V1/V2 and V3 variable regions of the env gene were examined by using a heteroduplex tracking assay (HTA) capable of resolving these genotypic variants. Blood plasma samples from 26 primary HIV-1-infected subjects were analyzed for their level of diversity. Half of the subjects had more than one V1/V2 viral variant during primary infection, indicating the frequent transmission of multiple variants. This observation is inconsistent with the idea of infrequent transmission based on a small transmitting inoculum of cell-free virus. In chronically infected subjects, the complexity of the viral populations was even greater in both the V1/V2 and the V3 regions than in acutely infected subjects, indicating that in spite of the presence of multiple variants in acute infection, the virus does pass through a genetic bottleneck during transmission. We also examined how well the infecting virus penetrated different anatomical compartments by using the HTA. Viral variants detected in blood plasma were compared to those detected in seminal plasma and/or cerebral spinal fluid of six individuals. The virus in each of these compartments was to a large extent identical to virus in blood plasma, a finding consistent with rapid penetration of the infecting variant(s). The low-probability transmission of multiple variants could be the result of transient periods of hyperinfectiousness or hypersusceptibility. Alternatively, the inefficient transfer of a multiply infected cell could account for both the low probability of transmission and the transfer of multiple variants