Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection

Abstract Background A major immune evasion mechanism of HIV-1 is the accumulation of non-synonymous mutations in and around T cell epitopes, resulting in loss of T cell recognition and virus escape. Results Here we analyze primary CD8+ T cell responses and virus escape in a HLA B*81 expressing subject who was infected with two T/F viruses from a single donor. In addition to classic escape through non-synonymous mutation/s, we also observed rapid selection of multiple recombinant viruses that conferred escape from T cells specific for two epitopes in Nef. Conclusions Our study shows that recombination between multiple T/F viruses provide greater options for acute escape from CD8+ T cell responses than seen in cases of single T/F virus infection. This process may contribute to the rapid disease progression in patients infected by multiple T/F viruses

Simultaneous Detection of Major Drug Resistance Mutations in the Protease and Reverse Transcriptase Genes for HIV-1 Subtype C by Use of a Multiplex Allele-Specific Assay

High-throughput, sensitive, and cost-effective HIV drug resistance (HIVDR) detection assays are needed for large-scale monitoring of the emergence and transmission of HIVDR in resource-limited settings. Using suspension array technology, we have developed a multiplex allele-specific (MAS) assay that can simultaneously detect major HIVDR mutations at 20 loci. Forty-five allele-specific primers tagged with unique 24-base oligonucleotides at the 5′ end were designed to detect wild-type and mutant alleles at the 20 loci of HIV-1 subtype C. The MAS assay was first established and optimized with three plasmid templates (C-wt, C-mut1, and C-mut2) and then evaluated using 148 plasma specimens from HIV-1 subtype C-infected individuals. All the wild-type and mutant alleles were unequivocally distinguished with plasmid templates, and the limits of detection were 1.56% for K219Q and K219E, 3.13% for L76V, 6.25% for K65R, K70R, L74V, L100I, K103N, K103R, Q151M, Y181C, and I47V, and 12.5% for M41L, K101P, K101E, V106A, V106M, Y115F, M184V, Y188L, G190A, V32I, I47A, I84V, and L90M. Analyses of 148 plasma specimens revealed that the MAS assay gave 100% concordance with conventional sequencing at eight loci and >95% (range, 95.21% to 99.32%) concordance at the remaining 12 loci. The differences observed were caused mainly by 24 additional low-abundance alleles detected by the MAS assay. Ultradeep sequencing analysis confirmed 15 of the 16 low-abundance alleles. This multiplex, sensitive, and straightforward result-reporting assay represents a new efficient genotyping tool for HIVDR surveillance and monitoring

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape.

HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell–mediated in vivo control of HIV-1. Primary HIV-1–specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response was associated with more rapid escape, the most significant T cell measure was its relative immunodominance measured in acute infection. This identified subject-level or “vertical” immunodominance as the primary determinant of in vivo CD8+ T cell pressure in HIV-1 infection. Conversely, escape was slowed significantly by lower population variability, or entropy, of the epitope targeted. Immunodominance and epitope entropy combined to explain half of all the variability in time to escape. These data explain how CD8+ T cells can exert significant and sustained HIV-1 pressure even when escape is very slow and that within an individual, the impacts of other T cell factors on HIV-1 escape should be considered in the context of immunodominance

Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies

Development of strategies for induction of HIV-1 broadly neutralizing antibodies (bnAbs) by vaccines is a priority. Determining the steps of bnAb induction in HIV-1-infected individuals who make bnAbs is a key strategy for immunogen design. Here we study the B cell response in a bnAb-producing individual, and report cooperation between two B cell lineages to drive bnAb development. We isolated an autologous virus-neutralizing antibody lineage that targeted an envelope region (loop D) and selected virus escape mutants that resulted in both enhanced bnAb lineage envelope binding and escape mutant neutralization—traits associated with increased B cell antigen drive. Thus, in this individual, two B cell lineages cooperated to induce the development of bnAbs. Design of vaccine immunogens that simultaneously drive both autologous and broadly neutralizing B cell lineages may be important for vaccine-induced recapitulation of events that transpire during the maturation of neutralizing antibodies in HIV-1-infected individuals

In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies

SARS-CoV-2 neutralizing antibodies (NAbs) protect against COVID-19. A concern regarding SARS-CoV-2 antibodies is whether they mediate disease enhancement. Here, we isolated NAbs against the receptor-binding domain (RBD) and the N-terminal domain (NTD) of SARS-CoV-2 spike from individuals with acute or convalescent SARS-CoV-2 or a history of SARS-CoV infection. Cryo-electron microscopy of RBD and NTD antibodies demonstrated function-specific modes of binding. Select RBD NAbs also demonstrated Fc receptor-g (FcgR)-mediated enhancement of virus infection in vitro, while five non-neutralizing NTD antibodies mediated FcgR-independent in vitro infection enhancement. However, both types of infection-enhancing antibodies protected from SARS-CoV-2 replication in monkeys and mice. Three of 46 monkeys infused with enhancing antibodies had higher lung inflammation scores compared to controls. One monkey had alveolar edema and elevated bronchoalveolar lavage inflammatory cytokines. Thus, while in vitro antibody-enhanced infection does not necessarily herald enhanced infection in vivo, increased lung inflammation can rarely occur in SARS-CoV-2 antibody-infused macaques

Analysis of Energy Loss Characteristics of Vertical Axial Flow Pump Based on Entropy Production Method under Partial Conditions

The energy loss of the vertical axial flow pump device increases due to the unstable internal flow, which reduces the efficiency of the pump device and increases its energy consumption of the pump device. The research results of the flow loss characteristics of the total internal conduit are still unclear. Therefore, to show the internal energy loss mechanism of the axial flow pump, this paper used the entropy production method to calculate the energy loss of the total conduit of the pump device to clarify the internal energy loss mechanism of the pump device. The results show that the energy loss of the impeller is the largest under various flow conditions, accounting for more than 40% of the total energy loss of the pump device. The variation trend of the volume average entropy production and the energy loss is similar under various flow coefficients (KQ). The volume average entropy production rate (EPR) and the energy loss decrease first and then increase with the increase of flow, the minimum volume average entropy production is 378,000 W/m3 at KQ = 0.52, and the area average EPR of the impeller increases gradually with the increase of flow. Under various flow coefficient KQ, the energy loss of campaniform inlet conduit is the smallest, accounting for less than 1% of the total energy loss. Its maximum value is 63.58 W. The energy loss of the guide vane and elbow increases with the increase of flow coefficient KQ, and the maximum ratio of energy loss to the total energy loss of the pump device is 29% and 21%, respectively, at small flow condition KQ = 0.38. The energy loss of straight outlet conduit reduces first and then increases with the increase of flow coefficient KQ. When flow coefficient KQ = 0.62, it accounts for 27% of the total energy loss of the pump device, but its area average entropy production rate (EPR) and volume average entropy production rate (EPR) are small. The main entropy production loss in the pump device is dominated by entropy production by turbulent dissipation (EPTD), and the proportion of entropy production by direct dissipation (EPDD) is the smallest

Numerical Study for Flow Loss Characteristic of an Axial-Flow Pump as Turbine via Entropy Production Analysis

Low-head vertical axial-flow pump as turbine (PAT) devices play a vital part in the development of clean energy for hydropower in plain areas. The traditional method of evaluating the flow loss in hydraulic machinery is calculated by the pressure drop method, the limitation of which is that the location of the occurrence of large losses cannot be accurately determined. In this paper, entropy production theory is introduced to evaluate the irreversible losses in the axial-flow PAT from the perspective of the second law of thermodynamics. A three-dimensional model of the axial-flow PAT is established and solved numerically using the Reynolds time-averaged equation, and the turbulence model is adopted as Shear Stress Transport–Curvature Correction (SST-CC) model. The validity of the entropy production theory to evaluate the energy loss distribution of the axial-flow PAT is illustrated by comparing the flow loss calculated by the pressure drop and the entropy production theory, respectively. The entropy production by turbulent dissipative dominates the total entropy production in the whole flow conduit, and the turbulent dissipative entropy accounts for the smallest percentage of the whole conduit entropy production at the optimal working condition Qbep, which is 51%. The impeller and the dustpan-shaped conduit are the essential sources of hydraulic loss in the entire flow conduit of the axial-flow PAT, and most of the energy loss of the impeller occurs at the blade leading edge, the trailing edge, and the flow separation zone near the suction surface. The energy loss of the dustpan-shaped conduit results from the high-speed flow from the impeller outlet to dustpan-shaped conduit to form a vortex, backflow and other chaotic flow patterns. Flow impact, flow separation, vortex and backflow are the main causes of high entropy production and energy loss