Envelope Region Research Articles

Nuclear basket proteins regulate the distribution and mobility of nuclear pore complexes in budding yeast.

Nuclear pore complexes (NPCs) mediate all traffic between the nucleus and the cytoplasm and are among the most stable protein assemblies in cells. Budding yeast cells carry two variants of NPCs which differ in the presence or absence of the nuclear basket proteins Mlp1, Mlp2, and Pml39. The binding of these basket proteins occurs very late in NPC assembly and Mlp-positive NPCs are excluded from the region of the nuclear envelope that borders the nucleolus. Here, we use recombination-induced tag exchange to investigate the stability of all the NPC subcomplexes within individual NPCs. We show that the nuclear basket proteins Mlp1, Mlp2, and Pml39 remain stably associated with NPCs through multiple cell-division cycles, and that Mlp1/2 are responsible for the exclusion of NPCs from the nucleolar territory. In addition, we demonstrate that binding of the FG-nucleoporins Nup1 and Nup2 depletes also Mlp-negative NPCs from this region by an independent pathway. We develop a method for single NPC tracking in budding yeast and observe that NPCs exhibit increased mobility in the absence of nuclear basket components. Our data suggest that the distribution of NPCs on the nucleus is governed by multiple interaction of nuclear basket proteins with the nuclear interior.

Single-molecule sequencing of the whole HCV genome revealed envelope deletions in decompensated cirrhosis associated with NS2 and NS5A mutations.

Defective hepatitis C virus (HCV) genomes with deletion of the envelope region have been occasionally reported by short-read sequencing analyses. However, the clinical and virological details of such deletion HCV have not been fully elucidated. We developed a highly accurate single-molecule sequencing system for full-length HCV genes by combining the third-generation nanopore sequencing with rolling circle amplification (RCA) and investigated the characteristics of deletion HCV through the analysis of 21 patients chronically infected with genotype-1b HCV. In 5 of the 21 patients, a defective HCV genome with approximately 2000bp deletion from the E1 to NS2 region was detected, with the read frequencies of 34-77%, suggesting the trans-complementation of the co-infecting complete HCV. Deletion HCV was found exclusively in decompensated cirrhosis (5/12 patients), and no deletion HCV was observed in nine compensated patients. Comparing the amino acid substitutions between the deletion and complete HCV (DAS, deletion-associated substitutions), the deletion HCV showed higher amino acid mutations in the ISDR (interferon sensitivity-determining region) in NS5A, and also in the TMS (transmembrane segment) 3 to H (helix) 2 region of NS2. Defective HCV genome with deletion of envelope genes is associated with decompensated cirrhosis. The deletion HCV seems susceptible to innate immunity, such as endogenous interferon with NS5A mutations, escaping from acquired immunity with deletion of envelope proteins with potential modulation of replication capabilities with NS2 mutations. The relationship between these mutations and liver damage caused by HCV deletion is worth investigating.

Comparative genomics and evolutionary analysis of dengue virus strains circulating in Pakistan.

Dengue fever virus (DENV) poses a significant public health risk in tropical and subtropical regions across the world. Although the dengue fever virus (DENV) exhibits significant genetic diversity and has the potential to evolve, there is a lack of comprehensive research on the comparative genomics and evolutionary dynamics of the virus in Pakistan. Phylogenetic analysis demonstrated the circulation of all four dengue virus serotypes (DENV-1, -2, -3, and -4) with prevalent genotypes III and V within DENV-1, cosmopolitan genotype within DENV-2, genotype III within DENV-3, and genotype I within DENV-4 during 2006-2014. Based on the complete envelope region, genome-wide residue signature and genetic diversity indicate that there is a high level of genetic diversity among DENV-1 strains, while DENV-3 strains exhibit the least genetic diversity. Comparative analysis of all four DENV serotypes revealed that certain codons in DENV-2 and -4 were subject to strong purifying selection, while a few codon sites in the envelope region showed evidence of positive selection. These findings provided valuable insights into the comparative genomics and evolutionary pattern of DENV strains reported from Pakistan. Whether those characteristics conferred a fitness advantage to DENV-1 genotypes within a specific geography and time interval warrants further investigations. The findings of the current study will contribute to tracking disease dynamics, understanding virus transmission and evolution, and formulating effective disease control strategies.

Dengue virus type 3 infection in a traveler returning from Costa Rica to Japan in 2023

The number of dengue cases has increased dramatically in recent years. In Latin America, the number of cases and deaths in 2023 was the highest ever recorded. We report on a patient who had been infected with dengue virus during his stay in Costa Rica in September 2023, and developed the disease after returning to Japan. Plasma obtained from the patient was used for diagnosis and dengue virus serotyping by real-time PCR. The nucleotide sequence of the envelope region of dengue virus was then determined by the direct sequencing method, and this sequence was used for phylogenetic analyses. The patient was found to be infected with dengue virus type 3 genotype III. The sequence from the present case was more homologous with sequences registered in Florida, USA, associated with travel to Cuba in 2022 than with sequences registered in Costa Rica 10 years ago. The Pan American Health Organization reported that only dengue virus type 1 and 2 cases were reported in Costa Rica in 2019–2021, whereas dengue virus type 3 and 4 cases started being reported in 2022. In 2023, the reported numbers of cases with dengue virus types 3 and 4 exceeded those of dengue virus types 1 and 2. In addition, regional differences in endemic strains have been observed in Costa Rica. Our findings suggest that the dengue virus type 3 that infected the patient was more likely an influx of a strain that had been circulating in Caribbean countries such as Cuba in recent years, rather than a re-emergence of an indigenous virus in Costa Rica. The serotypes of dengue virus prevalent in Costa Rica have been changing since 2022. All four serotypes were prevalent in 2023, with a particularly sharp increase in the number of cases of dengue virus types 3 and 4. Future monitoring and surveillance are essential because changes in endemic serotypes can cause antibody-dependent enhancement, which can lead to severe dengue disease presentations.

Using a Drug Repurposing Strategy to Virtually Screen Potential HIV-1 Entry Inhibitors That Block the NHR Domain of the Viral Envelope Protein gp41

Using a drug repurposing strategy, virtual screening of potential inhibitors of the NHR domain of the HIV-1 gp41 protein, a conserved region critical for the virus-cell membrane fusion and viral infectivity, was carried out. The used computational approach included: (1) molecular docking of this functionally significant region of the HIV-1 envelope with compounds from a library of bioactive molecules containing clinically approved drugs, experimental drugs, and investigational drug candidates; (2) assessing the binding affinity of these compounds to the therapeutic target; (3) molecular dynamics simulations of ligand/NHR-gp41 complexes; (4) calculations of the binding free energy followed by the analysis of molecular dynamics trajectories and selection of compounds promising to test for anti-HIV-1 activity. As a result, six compounds that exhibited the high binding affinity to the NHR domain of the HIV-1 gp41 protein and showed acceptable pharmacological properties were identified. The predicted compounds are assumed to form a promising basis for the development of new, effective and safe broad-spectrum antiviral agents able to inhibit the HIV-1 entry into the host cell.

The contribution of the Gaza envelope region to Israel's food security.

Abstract Armed conflicts can have severe implications on food security by displacing farmers, destroying farms and agricultural infrastructure, disrupting supply chains, and limiting the ability of governance to control the highly volatile food markets. Here, we aim to understand the impact of the current Israel-Hamas War on local food production in Israel. Our analysis focused on challenges in food production in the Gaza Envelope region, the region in Israel that borders the Gaza Strip that has been significantly affected by the conflict. Our goals were to understand the agricultural significance of the region- both regarding crop diversity and the risks posed to individual crops due to the conflict, and to assess the nutritional contribution of the region's agricultural output. We found that the Gaza Envelope region is crucial for the propagation of several key crops, notably cherry tomatoes, radishes, and sweet potatoes. Furthermore, we identified 16 crops whose local production is particularly vulnerable due to their proximity to conflict, including radishes and potatoes. The nutritional output of the edible crops of the Gaza Envelope region is extensive and produces over 50% of the annual energetic requirements of the Israeli population. Beyond the caloric contribution, the produce of the region is nutrient-dense, exceeding 100% of the annual Dietary Reference Intakes for the Israeli population of 12 vital nutrients. These 12 nutrients include dietary fiber, six vitamins such as Vitamin A, Vitamin C, and Vitamin K, and five minerals including Potassium and Iron. Based on these findings, we suggest that the Israel-Hamas War also has detrimental ramifications on local food production in Israel.

Probing the magnetic field and dust grain properties of two dark clouds L1495 and L1498 through photopolarimetry

ABSTRACT We present the R-band polarimetry of two low-latitude Lynd’s clouds L1495 and L1498 acquired with AIMPOL at Aryabhatta Research Institute of Observational Sciences, Nainital, India. The estimated polarization across the regions of L1495 and L1498 is typically in the range of ∼1–5 per cent and the position angle is typically in the range of ∼100°–137° from which we infer the morphologies of the corresponding magnetic field in the envelope region ($\theta_{\rm B}^{\rm env}$). In both clouds, the magnetic fields are found to be aligned with the galactic field (θGP). Due to their close proximity to the galactic plane, we incorporate the values of offset ($\theta _{\rm off} = |\theta _{\rm B}^{\rm env} - \theta _{\rm GP}|$) from this study into our previously established geometrical correlation between the variation in relative orientation with the galactic longitude. We find that the offsets estimated for two clouds L1495 and L1498 in this investigation are consistent with the offsets predicted by our previous study. We also generate the extinction map for the two clouds using the NICE technique, and the extinction structure is found to be analogous to the dust structure at the denser region of the cloud as obtained from the 500 µm dust continuum emission maps of Herschel1 SPIRE. Three distinct cores with high extinction are detected in L1495, and two such cores are also detected in L1498. We also estimate the mean particle density ($\lt n_{\rm H_2}\gt $) at the peripheral region as well as the high extinction cores of the clouds.

Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn?

Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.

Decoding the role of mycobacterial lipid remodelling and membrane dynamics in antibiotic tolerance.

Current treatments for tuberculosis primarily target Mycobacterium tuberculosis (Mtb) infections, often neglecting the emerging issue of latent tuberculosis infection (LTBI) which are characterized by reduced susceptibility to antibiotics. The bacterium undergoes multiple adaptations during dormancy within host granulomas, leading to the development of antibiotic-tolerant strains. The mycobacterial membrane plays a crucial role in drug permeability, and this study aims to characterize membrane lipid deviations during dormancy through extensive lipidomic analysis of bacteria cultivated in distinct media and growth stages. The results revealed that specific lipids localize in different regions of the membrane envelope, allowing the bacterium to adapt to granuloma conditions. These lipid modifications were then correlated with the biophysical properties of the mycomembrane, which may affect interactions with antibiotics. Overall, our findings offer a deeper understanding of the bacterial adaptations during dormancy, highlighting the role of lipids in modulating membrane behaviour and drug permeability, ultimately providing the groundwork for the development of more effective treatments tailored to combat latent infections.

An Effective Spinning Reserve Allocation Method Considering Operational Reliability With Multi-Uncertainties

Spinning reserve (SR) is a crucial resource for ensuring power system reliability by lowering operational risk. The operational risk is contingent on the unpredictability of renewable energy as well as the replacement rate of electrical devices in relation to operating conditions. Previous research on SR allocation ignoring the condition-dependent outage replacement rate (CDORR) of electrical equipment may have allocated insufficient SR capacity that cannot adjust for unanticipated power imbalances. In addition, the introduction of CDORR and various multi-uncertainty scenarios into existing SR allocation models may incur a significant computational cost. This work presents an efficient SR allocation model that takes operational reliability under multi-uncertainties into account (e.g., wind output randomness, load fluctuations, generator and transmission contingencies with CDORR). Analytical expected energy not served (EENS) formulations based on the sensitivity method are derived to estimate the operational risk under multi-uncertainties, thereby obviating the need for iterations in large uncertainty scenarios. We present an improved relaxation method based on the McCormick envelope to further enhance the model's tractability. The proposed tangent plane cut collection strategy improves the computational efficiency by reducing the redundant envelope region. Results demonstrate that the proposed method benefits the economy by considering operational reliability and accelerates computational speed with reasonable accuracy.

Vimentin regulates nuclear segmentation in neutrophils.

Granulocytes are indispensable for various immune responses. Unlike other cell types in the body, the nuclei of granulocytes, particularly neutrophils, are heavily segmented into multiple lobes. Although this distinct morphological feature has long been observed, the underlying mechanism remains incompletely characterized. In this study, we utilize cryo-electron tomography to examine the nuclei of mouse neutrophils, revealing the cytoplasmic enrichment of intermediate filaments on the concave regions of the nuclear envelope. Aided by expression profiling and immuno-electron microscopy, we then elucidate that the intermediate-filament protein vimentin is responsible for such perinuclear structures. Of importance, exogenously expressed vimentin in nonimmune cells is sufficient to form cytoplasmic filaments wrapping on the concave nuclear surface. Moreover, genetic deletion of the protein causes a significant reduction of the number of nuclear lobes in neutrophils and eosinophils, mimicking the hematological condition of the Pelger-Huët anomaly. These results have uncovered a new component establishing the nuclear segmentation of granulocytes.

Operational envelope for planning cold flow production

The paper presents a method to determine an operational envelope for the cold flow technology with respect to producing gas–oil ratio (GOR) and water cut (WC). The cold flow technology is a flow assurance method that enables cold production flow in thermal equilibrium with the seabed temperature. Cold flow converts hydrate and wax into dry, non-plugging microparticles inside a subsea cold flow unit downstream the wellhead. The small particles travel along with the liquid in the form of a slurry to the receiving host. The operational envelope shows that if the production flow reaches certain combinations of GOR and Wc, the hydrate volume fraction in liquid and consequently the slurry’s effective viscosity could be too high for pipe transportation. This paper also investigates the case when the slurry is transported with remaining water, where there might be some emulsion phenomena. Results show that this could reduce the operational region of the cold flow envelope, particularly for GOR–Wc values around the inversion point volume fraction. Therefore, water–slurry emulsification should also be taken into consideration when considering the operational envelope. If the hydrate–oil mixture is found to be too viscous to transport it can be resolved by, for example, removing water from the production flow upstream the cold flow unit. GOR–WC profiles from a real field case are over-imposed on the operational envelope to see the development during the field lifetime. Tieback costs for the cold flow technology are found to be 20–30% less than conventional methods for a 100 km tieback. The relative cost reduction increases with increasing tieback distance.

Linking ice and gas in the Coronet cluster in Corona Australis

Context. During the journey from the cloud to the disc, the chemical composition of the protostellar envelope material can be either preserved or processed to varying degrees depending on the surrounding physical environment. Aims. This works aims to constrain the interplay of solid (ice) and gaseous methanol (CH3OH) in the outer regions of protostellar envelopes located in the Coronet cluster in Corona Australis (CrA), and assess the importance of irradiation by the Herbig Ae/Be star R CrA. CH3OH is a prime test case as it predominantly forms as a consequence of the solid-gas interplay (hydrogenation of condensed CO molecules onto the grain surfaces) and it plays an important role in future complex molecular processing. Methods. We present 1.3 mm Submillimeter Array (SMA) and Atacama Pathfinder Experiment (APEX) observations towards the envelopes of four low-mass protostars in the Coronet cluster. Eighteen molecular transitions of seven species were identified. We calculated CH3OH gas-to-ice ratios in this strongly irradiated cluster and compared them with ratios determined towards protostars located in less irradiated regions such as Serpens SVS 4 in Serpens Main and the Barnard 35A cloud in the λ Orionis region. Results. The CH3OH gas-to-ice ratios in the Coronet cluster vary by one order of magnitude (from 1.2 × 10−4 to 3.1 × 10−3) which is similar to less irradiated regions as found in previous studies. We find that the CH3OH gas-to-ice ratios estimated in these three regions are remarkably similar despite the different UV radiation field intensities and formation histories. Conclusions. This result suggests that the overall CH3OH chemistry in the outer regions of low-mass envelopes is relatively independent of variations in the physical conditions and hence that it is set during the prestellar stage.

Duplex One-Step RT-PCR for the detection of Dengue and Zika viruses

Dengue and Zika, arboviruses are common in Brazil and present with similar clinical symptoms making specific diagnoses difficult. Therefore, a Duplex One-step RT-PCR method for dengue and zika virus was developed and validated in vitro and in silico, based on the dengue's NS1 region and zika's Envelope region.

Study of a sample of faint Be stars in the exofield of CoRoT

Context. The search and interpretation of non-radial pulsations from Be star light curves observed with the CoRoT satellite requires high-quality stellar astrophysical parameters. Aims. The present work is devoted to the spectroscopic study of a sample of faint Be stars observed by CoRoT in the fourth long run (LRA02). Methods. The astrophysical parameters were determined from the spectra in the λλ4000–4500 Å wavelength domain observed with the VLT/FLAMES instruments at ESO. Spectra were fitted with models of stellar atmospheres using our GIRFIT package. Spectra obtained in the λλ6400–7200 Å wavelength domain enabled the confirmation or, otherwise, a first identification of Be star candidates. Results. The apparent parameters (Teff, log g, Vsin i) for a set of 19 B and Be stars were corrected for the effects induced by the rapid rotation. These allowed us to determine: (1) stellar masses that are in agreement with those measured for detached binary systems; (2) spectroscopic distances that agree with the Gaia parallaxes; and (3) centrifugal/gravity equatorial force ratios of ~0.6–0.7, which indicate that our Be stars are subcritical rotators. A study of the Balmer Hα, Hγ and Hδ emission lines produced: (1) extents of the circumstellar disk (CD) emitting regions that agree with the interferometric inferences in other Be stars; (2) R– dependent exponents n(R) = ln[ρ(R)/ρo]/ln(Ro/R) of the CD radial density distributions; and (3) CD base densities ρo similar to those inferred in other recent works. Conclusions. The Hγ and Hδ emission lines are formed in CD layers close to the central star. These lines produced a different value of the exponent n(R) than assumed for Hα. Further detailed studies of Hγ and Hδ emission lines could reveal the physical properties of regions where the viscous transport of angular momentum to the remaining CD regions is likely to originate from. The subcritical rotation of Be stars suggests that their huge discrete mass-ejections and concomitant non-radial pulsations might have a common origin in stellar envelope regions that become unstable to convection due to rotation. If it is proven that the studied Be stars are products of binary mass transfer phases, the errors induced on the estimated Teff by the presence of stripped sub-dwarf O/B companions are not likely to exceed their present uncertainties.

Continuous speech with pauses inserted between words increases cortical tracking of speech envelope.

The decoding multivariate Temporal Response Function (decoder) or speech envelope reconstruction approach is a well-known tool for assessing the cortical tracking of speech envelope. It is used to analyse the correlation between the speech stimulus and the neural response. It is known that auditory late responses are enhanced with longer gaps between stimuli, but it is not clear if this applies to the decoder, and whether the addition of gaps/pauses in continuous speech could be used to increase the envelope reconstruction accuracy. We investigated this in normal hearing participants who listened to continuous speech with no added pauses (natural speech), and then with short (250 ms) or long (500 ms) silent pauses inserted between each word. The total duration for continuous speech stimulus with no, short, and long pauses were approximately, 10 minutes, 16 minutes, and 21 minutes, respectively. EEG and speech envelope were simultaneously acquired and then filtered into delta (1-4 Hz) and theta (4-8 Hz) frequency bands. In addition to analysing responses to the whole speech envelope, speech envelope was also segmented to focus response analysis on onset and non-onset regions of speech separately. Our results show that continuous speech with additional pauses inserted between words significantly increases the speech envelope reconstruction correlations compared to using natural speech, in both the delta and theta frequency bands. It also appears that these increase in speech envelope reconstruction are dominated by the onset regions in the speech envelope. Introducing pauses in speech stimuli has potential clinical benefit for increasing auditory evoked response detectability, though with the disadvantage of speech sounding less natural. The strong effect of pauses and onsets on the decoder should be considered when comparing results from different speech corpora. Whether the increased cortical response, when longer pauses are introduced, reflect improved intelligibility requires further investigation.

3D physico-chemical model of a pre-stellar core

Context. Pre-stellar cores represent the earliest stage of the formation process of stars and planets. By characterizing the physical and chemical structure of these cores, we can establish the initial conditions for star and planet formation and determine to what degree the chemical composition of pre-stellar cores is inherited by the later stages. Aims. We aim to determine the underlying causes of spatial chemical segregation observed in pre-stellar cores and study the effects of the core structure and external environment on the chemical structure of pre-stellar cores. Methods. A three-dimensional (3D) magnetohydrodynamic model of a pre-stellar core embedded in a dynamic star-forming cloud was post-processed with a sequentially continuum radiative transfer, a gas-grain chemical model, and a line-radiative transfer model. The results were analyzed and compared to observations of CH3OH and c-C3H2 in L1544. We compared nine different chemical models to the observations to determine which initial conditions are compatible with the observed chemical segregation in the prototypical pre-stellar core L1544. Results. The model is able to reproduce several aspects of the observed chemical differentiation in L1544. Extended methanol emission is shifted towards colder and more shielded regions of the core envelope, while c-C3H2 emission overlaps with the dust continuum, which is consistent with the observed chemical structure. Furthermore, these results are consistent across a broad spectrum of chemical models. Increasing the strength of the interstellar radiation field or the cosmic-ray ionization rate with respect to the typical values assumed in nearby star-forming regions leads to synthetic maps that are inconsistent with the observed chemical structure. Conclusions. Our model shows that the observed chemical dichotomy in L1544 can arise as a result of uneven illumination due to the asymmetrical structure of the 3D core and the environment within which the core has formed. This highlights the importance of the 3D structure at the core-cloud transition on the chemistry of pre-stellar cores. The reported effect is likely to affect later stages of the formation process of stars and planets through chemical inheritance.

Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody

Rodent-borne hantaviruses are prevalent worldwide and upon spillover to human populations, cause severe disease for which no specific treatment is available. A potent antibody response is key for recovery from hantavirus infection. Here we study a highly neutralizing human monoclonal antibody, termed SNV-42, which was derived from a memory B cell isolated from an individual with previous Sin Nombre virus (SNV) infection. Crystallographic analysis demonstrates that SNV-42 targets the Gn subcomponent of the tetrameric (Gn−Gc)4 glycoprotein assembly that is relevant for viral entry. Integration of our 1.8 Å structure with the (Gn−Gc)4 ultrastructure arrangement indicates that SNV-42 targets the membrane-distal region of the virus envelope. Comparison of the SNV-42 paratope encoding variable genes with inferred germline gene segments reveals high sequence conservation, suggesting that germline-encoded antibodies inhibit SNV. Furthermore, mechanistic assays reveal that SNV-42 interferes with both receptor recognition and fusion during host-cell entry. This work provides a molecular-level blueprint for understanding the human neutralizing antibody response to hantavirus infection.

An HIV-1/HIV-2 Chimeric Envelope Glycoprotein Generates Binding and Neutralising Antibodies against HIV-1 and HIV-2 Isolates.

The development of immunogens that elicit broadly reactive neutralising antibodies (bNAbs) is the highest priority for an HIV vaccine. We have shown that a prime-boost vaccination strategy with vaccinia virus expressing the envelope glycoprotein gp120 of HIV-2 and a polypeptide comprising the envelope regions C2, V3 and C3 elicits bNAbs against HIV-2. We hypothesised that a chimeric envelope gp120 containing the C2, V3 and C3 regions of HIV-2 and the remaining parts of HIV-1 would elicit a neutralising response against HIV-1 and HIV-2. This chimeric envelope was synthesised and expressed in vaccinia virus. Balb/c mice primed with the recombinant vaccinia virus and boosted with an HIV-2 C2V3C3 polypeptide or monomeric gp120 from a CRF01_AG HIV-1 isolate produced antibodies that neutralised >60% (serum dilution 1:40) of a primary HIV-2 isolate. Four out of nine mice also produced antibodies that neutralised at least one HIV-1 isolate. Neutralising epitope specificity was assessed using a panel of HIV-1 TRO.11 pseudoviruses with key neutralising epitopes disrupted by alanine substitution (N160A in V2; N278A in the CD4 binding site region; N332A in the high mannose patch). The neutralisation of the mutant pseudoviruses was reduced or abolished in one mouse, suggesting that neutralising antibodies target the three major neutralising epitopes in the HIV-1 envelope gp120. These results provide proof of concept for chimeric HIV-1/HIV-2 envelope glycoproteins as vaccine immunogens that can direct the antibody response against neutralising epitopes in the HIV-1 and HIV-2 surface glycoproteins.

Phenotypic analysis of HIV-1 resistance to CD4 binding site broadly-neutralizing antibodies

Abstract Broadly neutralizing antibodies (bNAbs) show strong immunotherapy potential by targeting conserved regions of the HIV-1 envelope. Single bNAb use in viremic individuals quickly results in the emergence of escape variants, likely originating from existing quasispecies. An ex vivo assay was developed to predict bNAb efficacy in viremic individuals. The development of a predictive bNAb efficacy model may assist with the planning of future clinical trials. The ex vivoassay used pre-infusion CD4 +T cells from participants enrolled in the VRC 607/ACTG A5378 phase I study of the CD4 binding site (CD4bs) bNAbs’ VRC01LS (n=7) or VRC07-523LS (n=9). From these assays, the escape variant signatures of outgrowth viruses that replicated in presence of CD4bs bNAbs, were identified. We found that these escape variants contained key changes to the ß23-V5 region of the gp120 envelope, including charge changes, glycan loss, and/or glycan shifts. Outgrowth viruses from each participant had similar escape mutation patterns. Resistance mutations of the viral env sequences were confirmed in pseudovirus-based neutralization assays. We found complementary escape profiles from 3 CD4bs bNAbs (1–18LS, N6LS, and VRC01v23) with ex vivoand neutralization assays showing suppression by 1 or 2 but not all 3 bNAbs, supporting the potential for combination bNAb therapy. Our data suggest that the simultaneous use of multiple CD4 binding site bNAbs together could aid in limiting viral escape. Supported by intramural funds from NIH.