A VRC13-like bNAb response is associated with complex escape pathways in HIV-1 envelope

The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous env sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential N-linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 env evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (env). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.

Functional impairment of HIV-specific CD8+ T cells precedes aborted spontaneous control of viremia

Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters longitudinally among 34 HIV-infected subjects with differential outcomes. Despite sustained recognition of autologous virus, HIV-specific proliferative and cytolytic T cell effector functions became selectively and intrinsically impaired prior to aborted control. Longitudinal transcriptomic profiling of functionally impaired HIV-specific CD8+ T cells revealed altered expression of genes related to activation, cytokine-mediated signaling, and cell cycle regulation, including increased expression of the antiproliferative transcription factor KLF2 but not of genes associated with canonical exhaustion. Lymphoid HIV-specific CD8+ T cells also exhibited poor functionality during aborted control relative to durable control. Our results identify selective functional impairment of HIV-specific CD8+ T cells as prognostic of impending aborted HIV control, with implications for clinical monitoring and immunotherapeutic strategies.

Gp41-targeted antibodies restore infectivity of a fusion-deficient HIV-1 envelope glycoprotein

The HIV-1 envelope glycoprotein (Env) mediates viral entry via conformational changes associated with binding the cell surface receptor (CD4) and coreceptor (CCR5/CXCR4), resulting in subsequent fusion of the viral and cellular membranes. While the gp120 Env surface subunit has been extensively studied for its role in viral entry and evasion of the host immune response, the gp41 transmembrane glycoprotein and its role in natural infection are less well characterized. Here, we identified a primary HIV-1 Env variant that consistently supports >300% increased viral infectivity in the presence of autologous or heterologous HIV-positive plasma. However, in the absence of HIV-positive plasma, viruses with this Env exhibited reduced infectivity that was not due to decreased CD4 binding. Using Env chimeras and sequence analysis, we mapped this phenotype to a change Q563R, in the gp41 heptad repeat 1 (HR1) region. We demonstrate that Q563R reduces viral infection by disrupting formation of the gp41 six-helix bundle required for virus-cell membrane fusion. Intriguingly, antibodies that bind cluster I epitopes on gp41 overcome this inhibitory effect, restoring infectivity to wild-type levels. We further demonstrate that the Q563R change increases HIV-1 sensitivity to broadly neutralizing antibodies (bNAbs) targeting the gp41 membrane-proximal external region (MPER). In summary, we identify an HIV-1 Env variant with impaired infectivity whose Env functionality is restored through the binding of host antibodies. These data contribute to our understanding of gp41 residues involved in membrane fusion and identify a mechanism by which host factors can alleviate a viral defect.

Structural topology defines protective CD8+ T cell epitopes in the HIV proteome

Mutationally constrained epitopes of variable pathogens represent promising targets for vaccine design but are not reliably identified by sequence conservation. In this study, we employed structure-based network analysis, which applies network theory to HIV protein structure data to quantitate the topological importance of individual amino acid residues. Mutation of residues at important network positions disproportionately impaired viral replication and occurred with high frequency in epitopes presented by protective human leukocyte antigen (HLA) class I alleles. Moreover, CD8⁺ T cell targeting of highly networked epitopes distinguished individuals who naturally control HIV, even in the absence of protective HLA alleles. This approach thereby provides a mechanistic basis for immune control and a means to identify CD8⁺ T cell epitopes of topological importance for rational immunogen design, including a T cell-based HIV vaccine.

Dengue Virus Evades AAV-Mediated Neutralizing Antibody Prophylaxis in Rhesus Monkeys

Development of vaccines against mosquito-borne Flaviviruses is complicated by the occurrence of antibody-dependent enhancement (ADE), which can increase disease severity. Long-term delivery of neutralizing antibodies (nAbs) has the potential to effectively block infection and represents an alternative to vaccination. The risk of ADE may be avoided by using prophylactic nAbs harboring amino acid mutations L234A and L235A (LALA) in the immunoglobulin G (IgG) constant region. Here, we used recombinant adeno-associated viruses (rAAVs) to deliver the anti-dengue virus 3 (DENV3) nAb P3D05. While the administration of rAAV-P3D05-rhesus immunoglobulin G1 (rhIgG1)-LALA to rhesus macaques engendered DENV3-neutralizing activity in serum, it did not prevent infection. The emergence of viremia following DENV3 challenge was delayed by 3-6 days in the rAAV-treated group, and replicating virus contained the envelope mutation K64R. This neutralization-resistant variant was also confirmed by virus outgrowth experiments in vitro. By delivering P3D05 with unmutated Fc sequences, we further demonstrated that DENV3 also evaded wild-type nAb prophylaxis, and serum viral loads appeared to be higher in the presence of low levels of unmutated P3D05-rhIgG1. Our study shows that a vectored approach for long-term delivery of nAbs with the LALA mutations is promising, but prophylaxis using a single nAb is likely insufficient at preventing DENV infection and replication.

History and genomic sequence analysis of the herpes simplex virus 1 KOS and KOS1.1 sub-strains

A collection of genomic DNA sequences of herpes simplex virus (HSV) strains has been defined and analyzed, and some information is available about genomic stability upon limited passage of viruses in culture. The nature of genomic change upon extensive laboratory passage remains to be determined. In this report we review the history of the HSV-1 KOS laboratory strain and the related KOS1.1 laboratory sub-strain, also called KOS (M), and determine the complete genomic sequence of an early passage stock of the KOS laboratory sub-strain and a laboratory stock of the KOS1.1 sub-strain. The genomes of the two sub-strains are highly similar with only five coding changes, 20 non-coding changes, and about twenty non-ORF sequence changes. The coding changes could potentially explain the KOS1.1 phenotypic properties of increased replication at high temperature and reduced neuroinvasiveness. The study also provides sequence markers to define the provenance of specific laboratory KOS virus stocks.

Genotype-specific variation in West Nile virus dispersal in California

West Nile virus (WNV) is an arbovirus that was first reported in North America in New York in 1999 and, by 2003, had spread more than 4000 km to California. However, variation in viral genetics associated with spread is not well understood. Herein, we report sequences for more than 100 WNV isolates made from mosquito pools that were collected from 2003 to 2011 as part of routine surveillance by the California Mosquito-borne Virus Surveillance System. We performed phylogeographic analyses and demonstrated that 5 independent introductions of WNV (1 WN02 genotype strain and 4 SW03 genotype strains) occurred in California. The SW03 genotype of WNV was constrained to the southwestern U.S. and had a more rapid rate of spread. In addition, geographic constraint of WNV strains within a single region for up to 6 years suggest viral maintenance has been driven by resident, rather than migratory, birds and overwintering in mosquitoes.

Standardized metadata for human pathogen/vector genomic sequences

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants

BACKGROUND

 Infection with hepatitis C virus (HCV) is a burgeoning worldwide public health problem, with 170 million infected individuals and an estimated 20 million deaths in the coming decades. While 6 main genotypes generally distinguish the global geographic diversity of HCV, a multitude of closely related subtypes within these genotypes are poorly defined and may influence clinical outcome and treatment options. Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes.

METHODS

 Here we combined long-range polymerase chain reaction amplification with pyrosequencing for a rapid approach to generate the complete viral coding region of 31 samples representing poorly defined HCV subtypes.

RESULTS

 Phylogenetic classification based on full genome sequences validated previously identified HCV subtypes, identified a recombinant sequence, and identified a new distinct subtype of genotype 4. Unlike conventional sequencing methods, use of deep sequencing also facilitated characterization of minor drug resistance variants within these uncommon or, in some cases, previously uncharacterized HCV subtypes.

CONCLUSIONS

 These data aid in the classification of uncommon HCV subtypes while also providing a high-resolution view of viral diversity within infected patients, which may be relevant to the development of therapeutic regimens to minimize drug resistance.

Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity

Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5α^Q, Trim5α^TFP and Trim5^CypA. Despite the high degree of amino acid identity between Trim5α^Q and Trim5α^TFP alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5α^Q and Trim5α^TFP alleles. While both alleles recognize the capsid surface, Trim5α^Q and Trim5α^TFP alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5α^Q alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5α^TFP (without affecting Trim5α^Q) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

TRIM5α is an intrinsic immunity protein that blocks retrovirus infection through a specific interaction with the viral capsid. Uniquely among primates, rhesus macaques harbor three functionally distinct kinds of Trim5 alleles: rhTrim5α^TFP, rhTrim5α^Q and rhTrim5^CypA. SIVmac239, a simian immunodeficiency virus that causes AIDS in rhesus macaques, is resistant to all three, whereas its relative, the human AIDS virus HIV-1, is inhibited by rhTrim5α^TFP and rhTrim5α^Q alleles. We exploited this difference between these two retroviruses to figure out how Trim5α proteins recognize viral capsids. By combining mutagenesis, structural biology and evolutionary data we determined that both rhTrim5α^TFP and rhTrim5α^Q recognize a conserved structure common to all retroviral capsids. However, we also found evidence suggesting that rhTrim5α^TFP evolved to recognize an additional target that is specifically conserved among primate immunodeficiency viruses. Molecular evolutionary analysis indicates that this expanded function appeared in a common ancestor of modern African monkeys sometime between 9–12 million years ago, and that it thereafter continued to be modified by strong evolutionary pressure. Our results provide insight into the evolutionary flexibility of Trim5α-capsid interactions, and support the notion that viruses related to modern HIV and SIV have been present in Africa for millions of years.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data

Viruses diversify over time within hosts, often undercutting the effectiveness of host defenses and therapeutic interventions. To design successful vaccines and therapeutics, it is critical to better understand viral diversification, including comprehensively characterizing the genetic variants in viral intra-host populations and modeling changes from transmission through the course of infection. Massively parallel sequencing technologies can overcome the cost constraints of older sequencing methods and obtain the high sequence coverage needed to detect rare genetic variants (<1%) within an infected host, and to assay variants without prior knowledge. Critical to interpreting deep sequence data sets is the ability to distinguish biological variants from process errors with high sensitivity and specificity. To address this challenge, we describe V-Phaser, an algorithm able to recognize rare biological variants in mixed populations. V-Phaser uses covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. Overall, V-Phaser achieved >97% sensitivity and >97% specificity on control read sets. On data derived from a patient after four years of HIV-1 infection, V-Phaser detected 2,015 variants across the ∼10 kb genome, including 603 rare variants (<1% frequency) detected only using phase information. V-Phaser identified variants at frequencies down to 0.2%, comparable to the detection threshold of allele-specific PCR, a method that requires prior knowledge of the variants. The high sensitivity and specificity of V-Phaser enables identifying and tracking changes in low frequency variants in mixed populations such as RNA viruses.

New sequencing technologies provide unprecedented resolution to study pathogen populations, such as the single stranded RNA viruses HIV, dengue (DENV), and West Nile (WNV), and how they evolve within infected individuals in response to immune, therapeutic, and vaccine pressures. While these new technologies provide high volumes of data, these data contain process errors. To detect biological variants, especially those occurring at low frequencies in the population, these technologies require a method to differentiate biological variants from process errors with high sensitivity and specificity. To address this challenge, we introduce the V-Phaser algorithm, which distinguished the covariation of biological variants from that of process errors. We validate the method by measuring how frequently it correctly identifies variants and errors on actual read sets with known variation. Further, using data derived from a patient following four years of HIV-1 infection, we show that V-Phaser can detect biological variants at frequencies comparable to approaches that require prior knowledge. V-Phaser is available for download at: http://www.broadinstitute.org/scientific-community/software.

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice

Most RNA viruses exist in their hosts as a heterogeneous population of related variants. Due to error prone replication, mutants are constantly generated which may differ in individual fitness from the population as a whole. Here we characterize three WNV isolates that contain, along with full-length genomes, mutants with large internal deletions to structural and nonstructural protein-coding regions. The isolates were all obtained from lorikeets that died from WNV at the Rio Grande Zoo in Albuquerque, NM between 2005 and 2007. The deletions are approximately 2kb, in frame, and result in the elimination of the complete envelope, and portions of the prM and NS-1 proteins. In Vero cell culture, these internally deleted WNV genomes function as defective interfering particles, reducing the production of full-length virus when introduced at high multiplicities of infection. In mosquitoes, the shortened WNV genomes reduced infection and dissemination rates, and virus titers overall, and were not detected in legs or salivary secretions at 14 or 21 days post-infection. In mice, inoculation with internally deleted genomes did not attenuate pathogenesis relative to full-length or infectious clone derived virus, and shortened genomes were not detected in mice at the time of death. These observations provide evidence that large deletions may occur within flavivirus populations more frequently than has generally been appreciated and suggest that they impact population phenotype minimally. Additionally, our findings suggest that highly similar mutants may frequently occur in particular vertebrate hosts.

Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008

West Nile virus (WNV) has become firmly established in northeastern US, reemerging every summer since its introduction into North America in 1999. To determine whether WNV overwinters locally or is reseeded annually, we examined the patterns of viral lineage persistence and replacement in Connecticut over 10 consecutive transmission seasons by phylogenetic analysis. In addition, we compared the full protein coding sequence among WNV isolates to search for evidence of convergent and adaptive evolution. Viruses sampled from Connecticut segregated into a number of well-supported subclades by year of isolation with few clades persisting ≥2 years. Similar viral strains were dispersed in different locations across the state and divergent strains appeared within a single location during a single transmission season, implying widespread movement and rapid colonization of virus. Numerous amino acid substitutions arose in the population but only one change, V→A at position 159 of the envelope protein, became permanently fixed. Several instances of parallel evolution were identified in independent lineages, including one amino acid change in the NS4A protein that appears to be positively selected. Our results suggest that annual reemergence of WNV is driven by both reintroduction and local-overwintering of virus. Despite ongoing evolution of WNV, most amino acid variants occurred at low frequencies and were transient in the virus population.

TRIM5 suppresses cross-species transmission of a primate immunodeficiency virus and selects for emergence of resistant variants in the new species

Cross-species transmission of simian immunodeficiency virus from sooty mangabeys (SIVsm) into rhesus macaques, and subsequent emergence of pathogenic SIVmac, required adaptation to overcome restriction encoded by the macaque TRIM5 gene.

Simian immunodeficiency viruses of sooty mangabeys (SIVsm) are the source of multiple, successful cross-species transmissions, having given rise to HIV-2 in humans, SIVmac in rhesus macaques, and SIVstm in stump-tailed macaques. Cellular assays and phylogenetic comparisons indirectly support a role for TRIM5α, the product of the TRIM5 gene, in suppressing interspecies transmission and emergence of retroviruses in nature. Here, we investigate the in vivo role of TRIM5 directly, focusing on transmission of primate immunodeficiency viruses between outbred primate hosts. Specifically, we retrospectively analyzed experimental cross-species transmission of SIVsm in two cohorts of rhesus macaques and found a significant effect of TRIM5 genotype on viral replication levels. The effect was especially pronounced in a cohort of animals infected with SIVsmE543-3, where TRIM5 genotype correlated with approximately 100-fold to 1,000-fold differences in viral replication levels. Surprisingly, transmission occurred even in individuals bearing restrictive TRIM5 genotypes, resulting in attenuation of replication rather than an outright block to infection. In cell-culture assays, the same TRIM5 alleles associated with viral suppression in vivo blocked infectivity of two SIVsm strains, but not the macaque-adapted strain SIVmac239. Adaptations appeared in the viral capsid in animals with restrictive TRIM5 genotypes, and similar adaptations coincide with emergence of SIVmac in captive macaques in the 1970s. Thus, host TRIM5 can suppress viral replication in vivo, exerting selective pressure during the initial stages of cross-species transmission.

The human immunodeficiency viruses HIV-1 and HIV-2 originated from cross-species transmission of simian immunodeficiency viruses (SIVs) from chimpanzees (SIVcpz) and sooty mangabeys (SIVsm), respectively. A related virus, SIVmac, causes AIDS-like pathogenesis in rhesus macaques; like HIV-2, SIVmac is the product of a cross-species jump of SIVsm from sooty mangabeys. The primate TRIM5 gene encodes a factor with potent antiviral activity when tested in the laboratory, and TRIM5 proteins are thought to play a role in restricting the movement of viruses between species in nature. In this study, we show that genetic variation in the TRIM5 gene of rhesus macaques heavily influences the outcome of cross-species transmission of SIVsm and that emergence of SIVmac in rhesus macaques in the 1970s required adaptations to circumvent the genetic barrier imposed by the rhesus macaque TRIM5 gene. Our results confirm the hypothesis that TRIM5 can influence the process of cross-species transmission and emergence of viruses related to HIV-1 and HIV-2 and serve as a striking illustration of how host genes can influence virus evolution.

A brief history of TRIM5alpha

In spite of the fact that the first isolates of HIV-1 became available more than 20 years ago, there is still no robust animal model for HIV-1 replication and pathogenesis. This is largely due to the existence of multiple genetic barriers to HIV-1 replication in most nonhuman primates, including a severe block targeting the early, post-entry phase of the viral replication cycle. It is now known that a protein called TRIM5alpha mediates this early restriction in nonhuman primate cells. Tissue culture experiments, together with genetic association studies involving multiple HIV/AIDS cohorts, indicate that the human orthologue of TRIM5alpha does not have a significant impact on HIV-1 replication. However, most human alleles encode a functional protein that can restrict at least one retrovirus unrelated to HIV-1 (N-tropic murine leukemia virus), although one deleterious mutation (H43Y) is present at high frequency in human populations. Phylogenetic analyses of the TRIM5 locus reveal that prehistoric retroviral epidemics, not unlike the current HIV/AIDS pandemic, played a significant role in the evolutionary history of humans and their primate relatives. The discovery of TRIM5alpha's antiretroviral activity sparked the imaginations of many laboratories, and considerable effort has now been channeled into characterizing the protein and determining its possible mechanism(s) of action. It is hoped that research on TRIM5alpha will contribute to the establishment of new and improved models for HIV replication and AIDS pathogenesis, point the way towards novel therapeutic targets to stem the tide of the human AIDS epidemic, provide an experimental window onto the early, post-entry stages of the retroviral replication cycle, and even inspire the search for other cellular factors that modulate retroviral infection.

Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5alpha

Retroviral restriction factor TRIM5alpha exhibits a high degree of sequence variation among primate species. It has been proposed that this diversity is the cumulative result of ancient, lineage-specific episodes of positive selection. Here, we describe the contribution of within-species variation to the evolution of TRIM5alpha. Sampling within two geographically distinct Old World monkey species revealed extensive polymorphism, including individual polymorphisms that predate speciation (shared polymorphism). In some instances, alleles were more closely related to orthologues of other species than to one another. Both silent and nonsynonymous changes clustered in two domains. Functional assays revealed consequences of polymorphism, including differential restriction of a small panel of retroviruses by very similar alleles. Together, these features indicate that the primate TRIM5alpha locus has evolved under balancing selection. Except for the MHC there are few, if any, examples of long-term balancing selection in primates. Our results suggest a complex evolutionary scenario, in which fixation of lineage-specific adaptations is superimposed on a subset of critical polymorphisms that predate speciation events and have been maintained by balancing selection for millions of years.

Identification and characterization of a novel bacterial virulence factor that shares homology with mammalian Toll/interleukin-1 receptor family proteins

Many important bacterial virulence factors act as mimics of mammalian proteins to subvert normal host cell processes. To identify bacterial protein mimics of components of the innate immune signaling pathway, we searched the bacterial genome database for proteins with homology to the Toll/interleukin-1 receptor (TIR) domain of the mammalian Toll-like receptors (TLRs) and their adaptor proteins. A previously uncharacterized gene, which we have named tlpA (for TIR-like protein A), was identified in the Salmonella enterica serovar Enteritidis genome that is predicted to encode a protein resembling mammalian TIR domains, We show that overexpression of TlpA in mammalian cells suppresses the ability of mammalian TIR-containing proteins TLR4, IL-1 receptor, and MyD88 to induce the transactivation and DNA-binding activities of NF-kappaB, a downstream target of the TIR signaling pathway. In addition, TlpA mimics the previously characterized Salmonella virulence factor SipB in its ability to induce activation of caspase-1 in a mammalian cell transfection model. Disruption of the chromosomal tlpA gene rendered a virulent serovar Enteritidis strain defective in intracellular survival and IL-1beta secretion in a cell culture infection model using human THP1 macrophages. Bacteria with disrupted tlpA also displayed reduced lethality in mice, further confirming an important role for this factor in pathogenesis. Taken together, our findings demonstrate that the bacterial TIR-like protein TlpA is a novel prokaryotic modulator of NF-kappaB activity and IL-1beta secretion that contributes to serovar Enteritidis virulence.

Multiple Roles of CLAN (Caspase-Associated Recruitment Domain, Leucine-Rich Repeat, and NAIP CIIA HET-E, and TP1-Containing Protein) in the Mammalian Innate Immune Response

NAIP CIIA HET-E and TP1 (NACHT) family proteins are involved in sensing intracellular pathogens or pathogen-derived molecules, triggering host defense responses resulting in caspase-mediated processing of proinflammatory cytokines and NF-kappaB activation. Caspase-associated recruitment domain, leucine-rich repeat, and NACHT-containing protein (CLAN), also known as ICE protease-activating factor, belongs to a branch of the NACHT family that contains proteins carrying caspase-associated recruitment domains (CARDs) and leucine-rich repeats (LRRs). By using gene transfer and RNA-interference approaches, we demonstrate in this study that CLAN modulates endogenous caspase-1 activation and subsequent IL-1beta secretion from human macrophages after exposure to LPS, peptidoglycan, and pathogenic bacteria. CLAN was also found to mediate a direct antibacterial effect within macrophages after Salmonella infection and to sensitize host cells to Salmonella-induced cell death through a caspase-1-independent mechanism. These results indicate that CLAN contributes to several biological processes central to host defense, suggesting a prominent role for this NACHT family member in innate immunity.

Antizyme targets cyclin D1 for degradation. A novel mechanism for cell growth repression

Overproduction of the ornithine decarboxylase (ODC) regulatory protein ODC-antizyme has been shown to correlate with cell growth inhibition in a variety of different cell types. Although the exact mechanism of this growth inhibition is not known, it has been attributed to the effect of antizyme on polyamine metabolism. Antizyme binds directly to ODC, targeting ODC for ubiquitin-independent degradation by the 26 S proteasome. We now show that antizyme induction also leads to degradation of the cell cycle regulatory protein cyclin D1. We demonstrate that antizyme is capable of specific, noncovalent association with cyclin D1 and that this interaction accelerates cyclin D1 degradation in vitro in the presence of only antizyme, cyclin D1, purified 26 S proteasomes, and ATP. In vivo, antizyme up-regulation induced either by the polyamine spermine or by antizyme overexpression causes reduction of intracellular cyclin D1 levels. The antizyme-mediated pathway for cyclin D1 degradation is independent of the previously characterized phosphorylation- and ubiquitination-dependent pathway, because antizyme up-regulation induces the degradation of a cyclin D1 mutant (T286A) that abrogates its ubiquitination. We propose that antizyme-mediated degradation of cyclin D1 by the proteasome may provide an explanation for the repression of cell growth following antizyme up-regulation.

Preoperative abdominal ultrasound may be misleading in risk stratification for presence of common bile duct abnormalities

BACKGROUND

Following the advent of laparoscopic cholecystectomy (LC), the preoperative predictors of common bile duct (CBD) abnormalities became more important in perioperative decision making. Preoperative transabdominal ultrasound (US) is used to assess the preoperative risks associated with CBD abnormalities. This study attempts to determine the sensitivity and specificity of US in determining CBD abnormalities in patients prior to LC.

METHODS

US measurements of the CBD diameter and presence of stones were ascertained from radiology reports in 100 patients who had LC with a routine intraoperative cholangiogram (IOC). The same information was obtained from the patients' IOC. A supraduodenal CBD diameter of >8 mm was considered dilated.

RESULTS

US demonstrated a sensitivity of 25% and a specificity of 70% for the detection of CBD dilatation compared to IOC. The sensitivity of US for predicting CBD dilatation was 55% when the IOC-derived diameter was >10 mm and 100% when it was >15 mm. The overall sensitivity of US for detection of stones was 10%; it improved to 17% in patients with a dilated CBD on US.

CONCLUSIONS

Preoperative ultrasound is neither sensitive nor specific for detecting CBD dilatation or presence of stones. A negative preoperative US report may be misleading in risk stratification for the presence of these CBD abnormalities. In order to avoid missing any CBD pathology, we recommend the routine use of intraoperative cholangiography.

Nortriptyline versus fluoxetine in the treatment of depression and in short-term recovery after stroke: a placebo-controlled, double-blind study

OBJECTIVE

This study compared nortriptyline and fluoxetine with placebo in the treatment of depression and in recovery from physical and cognitive impairments after stroke.

METHOD

A total of 104 patients with acute stroke enrolled between 1991 and 1997 entered a double-blind randomized study comparing nortriptyline, fluoxetine, and placebo over 12 weeks of treatment. The majority of patients were recruited from a rehabilitation hospital in Des Moines, Iowa, but other enrollment sites were also used. Both depressed and nondepressed patients were enrolled to determine whether improved recovery could be mediated by mechanisms unrelated to depression. Nortriptyline in doses of 25 mg/day gradually increased to 100 mg/day or fluoxetine in doses of 10 mg/day gradually increased to 40 mg/day or identical placebo were given over 12 weeks. Response to treatment of depression for individual patients was defined as a greater-than-50% reduction in scores on the Hamilton Rating Scale for Depression and no longer fulfilling diagnostic criteria for major or minor depression. Improved recovery for a treatment group was defined as a significantly higher mean score from baseline to end of the treatment trial, compared with patients treated with placebo, on measures of impairment in activities of daily living and levels of cognitive and social functioning.

RESULTS

Nortriptyline produced a significantly higher response rate than fluoxetine or placebo in treating poststroke depression, in improving anxiety symptoms, and in improving recovery of activities of daily living as measured by the Functional Independence Measure. There was no effect of nortriptyline or fluoxetine on recovery of cognitive or social functioning among depressed or nondepressed patients. Fluoxetine in increasing doses of 10-40 mg/day led to an average weight loss of 15. 1 pounds (8% of initial body weight) over 12 weeks of treatment that was not seen with nortriptyline or placebo.

CONCLUSIONS

Given the doses of medication used in this study, nortriptyline was superior to fluoxetine in the treatment of poststroke depression. Demonstrating a benefit of antidepressant treatment in recovery from stroke may require the identification of specific subgroups of patients, alternative measurement scales, or the optimal time of treatment.

Standardization of surgeon-controlled variables: impact on outcome in patients with acute cholecystitis

OBJECTIVE

To examine the effect of standardization of surgeon-controlled variables on patient outcome after cholecystectomy for two cohorts of patients with acute cholecystitis (AC).

SUMMARY BACKGROUND DATA

Laparoscopic cholecystectomy (LC), when performed efficiently and safely, offers patients with AC a more rapid recovery and decreases the length of stay, thus reducing the health care utilization. Numerous studies have focused on the characteristics of patients with AC that may predict the conversion of LC to open cholecystectomy. However, analysis of these factors offers little insight for improving the outcome of patients with AC, because patient-controlled variables are difficult to influence. In the present study, treatment variables that were under the surgeon's control were standardized and the effects of these changes on the outcome of patients with AC were quantified.

METHODS

Beginning in August 1997, a standardized treatment protocol was initiated for patients with suspected AC. LC was initiated as early as practical from the time of admission. All operations were performed in a specially equipped and staffed laparoscopic surgery suite, and all patients were supervised by one of two attending surgeons with a special interest in laparoscopic interventions. Two cohorts of patients with AC were retrospectively analyzed: 39 patients from the 12 months before initiation of this protocol (period 1) and 49 patients from the 12 months after its inception (period 2). Medical records were reviewed for demographic, perioperative, and outcome data. Surgical reports were reviewed to ascertain the reason for conversion and whether laparoscopic technical modifications were used.

RESULTS

No significant difference was noted between the groups with regard to patient demographics, clinical presentation, or radiologic or laboratory parameters. After protocol initiation, patients received definitive treatment closer to the time of admission and had a greater percentage of laparoscopically completed cholecystectomies. Furthermore, the patients in period 2 had a significantly decreased postoperative length of stay and hospital charges than the earlier ones. Complications were infrequent and not significantly different between the groups. Two or more laparoscopic technical modifications were used in 95% of the successful LCs during period 2 versus 33.3% during period 1.

CONCLUSIONS

By controlling when, where, and by whom LC for AC was performed, the authors have significantly improved the percentage of cholecystectomies that were completed laparoscopically. This has led to improved outcomes and lower hospital charges for patients with AC at this municipal hospital.

Complete biliary avulsion from blunt compression injury

The liver is the solid organ most commonly injured as a result of blunt abdominal trauma. Complete avulsion of the common hepatic duct is a rare and devastating type of hepatobiliary trauma. Here the authors report the case of a 7-year-old child who had complete biliary disruption as a result of an abdominal crush injury that was not diagnosed correctly preoperatively. The intraoperative diagnosis and treatment of this injury is discussed.

Cost-effective minimally invasive surgery: What procedures make sense?

Because laparoscopic surgery has emerged during a time of medical cost-consciousness, emphasis has been placed on the economic implications of this emerging field. The cost of these procedures, however, is just one component in determining their overall value to most of the stakeholders in the health care system. The value of a treatment is proportional to its appropriateness and quality per unit cost. Several confounding factors affect the variables in this equation and contribute to the difficulty in this type of assessment of an emerging technology. By understanding the mechanics of value assessment and certain caveats for specific procedures, the surgeon will be better able to determine what procedures makes sense (or are of value) in their practice and for their patients.

A combined laparoscopic and endoscopic approach to acute primary gastric volvulus

We describe the combined use of laparoscopic and endoscopic techniques in a case of acute primary gastric volvulus. Once the diagnosis is confirmed with a water-soluble upper gastrointestinal series, prompt intervention is required. With an atraumatic bowel grasper the stomach is re-oriented with the greater curvature in its normal anatomic position. Two transabdominal wall sutures are placed along the greater curvature to fix it to anterior abdominal wall. Upper endoscopy is then performed. Once confident that the gastric mucosa is viable, a 20F "pull-type" gastrostomy tube is placed endoscopically, guided by the external illumination and probing by the laparoscope. The gastrostomy tube now acts as an anterior anchor for the stomach allowing repositioning of the gastropexy sutures if necessary. Endoscopy confirms the placement of a broad, properly aligned gastropexy. Classically, gastric volvulus has been treated by laparotomy. Both endoscopic and laparoscopic techniques have been individually reported in the treatment of acute and chronic gastric volvulus, however, each has as its limitations. By combining the procedures we were able to better assess both the intra-abdominal and the intraluminal status of the stomach and its position before, during, and after fixation to the anterior abdominal wall. The postoperative stay seen with the combined technique was less than has been reported in patients treated by open surgery or by either the endoscopic or laparoscopic methods alone. The combined laparoscopic and endoscopic approach to acute gastric volvulus provides the benefit of a minimally invasive approach, to a better anterior gastropexy. This procedure should be considered when confronted with patients with acute primary, gastric volvulus.

Outcome and comorbidity in first- compared with multiple-episode mania

The aim of this study was to examine the outcome and comorbidity of patients with bipolar disorder presenting with first-episode as compared with multiple-episode mania. Based on studies from the prepharmacological era and the sensitization model of bipolar disorder, we hypothesized that compared with multiple-episode mania, first-episode mania would be associated with better outcome, milder severity, and less psychiatric comorbidity. Seventy-one hospitalized patients, age 12 years and older and meeting DSM-III-R criteria for bipolar disorder, were recruited over a 1-year period. Thirty-four (48%) first-episode and 37 (56%) multiple-episode patients were compared regarding demographics, phenomenology, comorbidity, family history, and short-term course. Compared with multiple-episode mania, first-episode mania was associated with significantly shorter hospitalization and a higher rate of comorbid impulse control disorders. These data provide indirect support for the sensitization model of bipolar disorder.

Clinically significant ureteral obstruction caused by inflammatory complications of severe pancreatitis

Clinically significant ureteral obstruction caused by the inflammatory complications of severe pancreatitis is rare with only eight previously reported cases. We present two additional cases and review the world literature. Clinically significant ureteral obstruction can affect either or both ureters and present simultaneously with an episode of pancreatitis or months later. If symptomatic ureteral obstruction is present, prompt urologic drainage is recommended. Definitive correction of the obstruction is frequently required and depends on the obstructive mechanism.

Histopathological determinants of survival in resected cases of pancreas cancer

We have examined the histopathological factors affecting the degree of local spread, regional lymph node (RLN) metastases, and overall survival (O.S.) in a group of 39 cases of resected carcinoma of the exocrine pancreas. Although the mean O.S. for the group was 14.3 months, resected patients without RLN involvement had a mean survival of 24 months. In contrast the mean O.S. rate was 8 months for patients with RLNs involved. Size, tumor location, and histological grade were compared to RLN involvement and O.S. The mean size of primary tumor did not differ significantly between patients with or without RLN's (r.1 versus 4.6 cms). However, 7 or 8 T1 tumors were < 4 cm and 35% of tumors < 4 cm were T1 lesions. In contrast, only 1 of 17 tumors (6%) > 4 cm was T1. Histological grade was correlated with nodal status and O.S. There was a significant difference between histological grade and the presence of metastatic lymph nodes (G1, 37% positive, G2-4.50% positive). Patients with well differentiated tumors had a mean survival of 21 months compared to a mean survival of 10 months for less differentiated tumors (p < 0.05). This difference was even more significant when stratified for nodal status. The patients with well differentiated tumors and no RLN involvement had a mean survival of 32.5 months compared to 8.6 months for well differentiated tumors with RLN involvement. In summary, we have shown that size, histological grade, and local spread predict for nodal status. However, specific patient subsets (G1, node negative) may exhibit an excellent survival when curative pancreas resection is successful.

Esophageal tuberculosis: a rare presentation with hematemesis

Esophageal tuberculosis is rare, with only 26 cases previously reported in the literature. Patients usually present with progressive dysphagia or odynophagia. We report a patient with hematemesis that was later attributed to the erosion of tuberculous subcarinal lymph nodes into the esophagus. This presentation has been described in only two other patients, both of whom died of exsanguinating hemorrhage. The successful outcome in the present case rested on the availability of rapid diagnostic modalities and timely surgical intervention.