Selection of drug-resistant HIV

Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness

HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.

Time to Viremia for Patients Taking their First Antiretroviral Regimen and the Subsequent Resistance Profiles

BACKGROUND

The resistance profiles for patients on first-line antiretroviral therapy (ART) regimens after viremia have not been well studied in community clinic settings in the modern treatment era.

OBJECTIVE

To determine time to viremia and the ART resistance profiles of viremic patients.

METHODS

HIV-positive patients aged ≥16 years initiating a three-drug regimen were retrospectively identified from 01/01/06 to 12/31/12. The regimens were a backbone of two nucleoside reverse transcriptase inhibitors (NRTIs) and a third agent: a protease inhibitor (PI), non-nucleoside reverse transcriptase inhibitor (NNRTI), or an integrase inhibitor (II). Time to viremia was compared using a proportional hazards model, adjusting for demographic and clinical factors. Resistance profiles were described in those with baseline and follow-up genotypes.

RESULTS

For 653 patients, distribution of third-agent use and viremia was: 244 (37%) on PIs with 80 viremia, 364 (56%) on NNRTIs with 84 viremia, and 45 (7%) on II with 11 viremia. Only for NNRTIs, time to viremia was longer than PIs (p = 0.04) for patients with a CD4 count ≥200 cells/mm(3). Of the 175 with viremia, 143 (82%) had baseline and 37 (21%) had follow-up genotype. Upon viremia, emerging ART resistance was rare. One new NNRTI (Y181C) mutation was identified and three patients taking PI-based regimens developed NRTI mutations (M184 V, M184I, and T215Y).

CONCLUSIONS

Time to viremia for NNRTIs was longer than PIs. With viremia, ART resistance rarely developed without PI or II mutations, but with a few NRTI mutations in those taking PI-based regimens, and NNRTI mutations in those taking NNRTI-based regimens.

Analysis of histidine phosphorylation using tandem MS and ion-electron reactions

Phosphorylation of proteins is essential in intracellular signal transduction pathways in eukaryotic and prokaryotic cells. Histidine phosphorylation plays an important role in two-component signal transduction in bacteria. In this study, we describe the characterization of a synthetic histidine-phosphorylated peptide with four different mass spectrometric (MS) fragmentation techniques: Collision-induced dissociation (CID), electron capture dissociation, electron-transfer dissociation, and electron detachment dissociation. Furthermore, LC-MS methods were developed to detect histidine-phosphorylated peptides, which are acid-labile, in more complex samples. From these results, we concluded that nonacidic solvent systems or fast LC methods provide the best conditions for separation of histidine-phosphorylated peptides prior to electrospray ionization mass spectrometry analysis. Electron-based fragmentation methods should be used for determination of histidine phosphorylation sites, since CID results in very facile phosphate-related neutral losses. The developed LC-MS/MS methods were successfully applied to a tryptic digest of the cytoplasmic part of the histidine kinase EnvZ, which was in vitro autophosphorylated. Finally, a new method is described for nonretentive solid-phase extraction of histidine-phosphorylated peptides using polymeric Strata-X microcolumns.

Evolutionary potential of an RNA virus

RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, phi 6, containing a beta-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another beta-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for beta-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.

Results of the 2001 AcroMetrix HIV-1 resistance proficiency program

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) drug resistance mutation testing has become a useful tool in assessing antiretroviral treatment and managing patient care. As these complex molecular genotyping procedures move into routine use in clinical laboratories, the need arises for quality control procedures that will ensure that drug resistance associated mutations are accurately identified.

OBJECTIVES

The AcroMetrix HIV-1 Resistance Proficiency Program was designed to assess proficiency in the identification of HIV-1 drug resistance mutations using molecular genotyping methods. This study describes results obtained from a variety of laboratories participating in the 2001 proficiency program.

STUDY DESIGN

The 2001 program included three challenges, each comprised of five blind-labeled panel members containing mutations in the reverse transcriptase (RT) and/or protease (PR) genes. Challenge HIV-R01 was distributed to 19 laboratories in May 2001, challenge HIV-R02 was shipped to 25 participants in August 2001, and challenge HIV-R03 was distributed to 31 laboratories in November 2001.

RESULTS AND CONCLUSION

Participants correctly identified 74% of the total number of mutations and 82% of the panel members (i.e. all appropriate mutations detected in each panel member) in HIV-R01, 88% of the mutations and 91% of the panel members in HIV-R02, and 75% of the mutations and 52% of the panel members in HIV-R03. The AcroMetrix HIV-1 Resistance Proficiency Program, along with AcroMetrix's Internet-based reporting system (http://www.labqc.org), provides a useful tool for assessing operator proficiency within individual laboratories, and for comparing HIV-1 resistance testing proficiency among laboratories and technology platforms worldwide.

Neuroimmune and neurovirological aspects of human immunodeficiency virus infection

Like most lentiviruses, HIV-1 causes both immune suppression and neurological disease. Neurological disease may occur at any stage of HIV infection but is most apparent with severe immune suppression. Cognitive impairment, reflected strikingly by HIV-associated dementia, has attracted intense interest since the outset of the HIV epidemic, and understanding of its pathogenesis has been spurred on by the emergence of several hypotheses outlining potential pathogenic mechanisms. The release of inflammatory molecules by HIV-infected microglia and macrophages and the concurrent neuronal damage play central roles in the conceptualization of HIV neuropathogenesis. Many inflammatory molecules appear to contribute to the pathogenic cascade and their individual roles remain undefined. At the same time, the abundance of virus in the brain and the type or strain of virus found in the brain may also be important codeterminants of neurological disease, as shown for other neurotropic viruses. Coreceptor use by HIV found in the brain appears to closely mirror what has been reported in systemic macrophages. The impact of HAART on viral genotype and phenotype found in the brain, and its relationship to clinical disease, remain uncertain. Several interesting animal models have been developed, using other lentiviruses, transgenic animals, and HIV-infected SCID mice, that may prove useful in future pathogenesis and therapeutic studies. Despite the progress in the understanding of HIV neuropathogenesis, many questions remain unanswered.

Progress in clinical neurosciences: The neuropathogenesis of HIV infection: host-virus interaction and the impact of therapy

Despite the availability of highly active antiretroviral therapy (HAART), primary HIV-related neurological diseases remain major problems in HIV clinics. The present review examines the pathogenesis of HIV-related dementia and the less severe minor cognitive and motor deficit, together with distal sensory and drug-induced toxic polyneuropathies. Abnormal host immune responses within the nervous system and the role of viral expression and diversity are emphasized in relation to neurovirulence. Induction of innate immune responses within the central and peripheral nervous systems, largely mediated by cells of macrophage lineage, appear to be common to the development of primary HIV-related neurological disease. Activation of these cell types results in the release of a cascade of inflammatory molecules including cytokines, chemokines, matrix metalloproteinases, and arachidonic acid metabolites that influence neuronal survival. Individual viral proteins encoded by envelope and tat genes and discrete sequences within these genes influence the extent to which these pro-inflammatory molecules are induced. At the same time, systemic immune suppression may influence the occurrence and severity of HIV-related neurological diseases. Implementation of HAART and neuroprotective treatments improves neurological function although the evolution of drug-resistant viral strains limits the sustained benefits of HAART.