Biology subjects

Rahman, S. A.

Publications and source records attributed to Rahman, S. A..

17 recordsLinked to original sources

bioRxiv2026

Experimental Assessment of Iris Water Content and Sex Differences in Mature Rabbits

Iris biomechanics plays a key role in primary angle-closure glaucoma (PACG). Soft tissue biomechanics is heavily influenced by tissue water content; therefore, accurately assessing water content is needed to describe iris biomechanics in a physiologically relevant manner. Yet, accurate experimental measurements of iris water content are rare in the literature. Therefore, our objective was to experimentally assess iris water content and potential sex differences in New Zealand White rabbit iris--a suitable model for studying iris biomechanics. We also examined the effect of exposure to phosphate-buffered saline (PBS) on iris water content, given its common use to maintain hydration during soft-tissue biomechanical testing. Our results showed slightly higher water content in males (89.2% {+/-} 2.3%) than in females (87.7% {+/-} 2.2%) (p = 0.022), while we found no significant differences in gross iris morphology between the sexes, indicating subtle compositional differences. Furthermore, PBS incubation had a minimal effect on water content only in female irides. Overall, our results indicated high iris water content in both sexes compared with anatomically adjacent ocular tissues and other soft connective tissues. These results improve our understanding of iris composition and physiology and can serve as a baseline for constructing biomechanical models to assess its role in PACG.

bioengineering↗

bioRxiv2026

Microenvironment-informed inference of transcriptional progression geometry

We present BIOCURRENT, a causal inference framework that reconstructs donor-specific pseudotime geometry in transcriptomic data. By modeling gene expression as a function of baseline characteristics, microenvironmental context, and latent pseudotime, BIOCURRENT enables comparison of compressed or expanded progression intervals across transcriptional state transitions. We introduce $\Delta\Delta T$, a geometry-based estimator that quantifies differences in pseudotime intervals across conditions, enabling evaluation of changes in pseudotime intervals under hypothetical modulation of microenvironmental programs. Applications to thymic T-cell developmental lineages and to COVID-19 immune dysregulation reveal condition- and donor-specific distortions of progression intervals. Counterfactual simulation links microenvironmental context to changes in specific intracellular state transition intervals. By localizing deviations in pseudotime geometry, BIOCURRENT identifies whether shifts in transcriptomic programs emerge early or later along transcriptomic coordinates and reveals upstream programs associated with these distortions. Such localization supports transcriptional stage-aware mechanistic hypotheses and suggests candidate intervention checkpoints in complex biological systems.

bioinformatics↗

bioRxiv2026

Preexisting chronic infection skews the epigenetic landscape of subsequent memory CD8 T cell responses

Previous studies suggest that preexisting chronic disease impairs immune responses to subsequent infection and vaccination. However, the underlying epigenetic mechanisms are understudied. Here, we show that preexisting chronic infection with LCMV clone 13 (CL13) compromised the formation of central memory CD8 T cells (TCM) to subsequent Listeria monocytogenes infection, despite not profoundly impacting effector responses. This correlated with a skewed cytokine milieu. Our chromatin-accessibility profiling of Listeria-specific CD8 T cells showed significant epigenetic skewing of both TCM and effector memory (TEM) in mice with preexisting LCMV-CL13, a skewing that started in memory-precursor effector cells (MPECs) during the effector phase. Transcription-factor binding sites (TFBS) analyses highlighted the interferon regulatory factor (IRF) family as major TFs implicated in this skewing. Thus, our results suggest that preexisting persistent inflammation skews the phenotypic and epigenetic landscape of subsequent memory responses, arguing for interventions to optimize vaccine-induced memory in hosts with preexisting chronic disease.

immunology↗

bioRxiv2026

Nav1.8 mediates peripheral-to-central nociceptive transmission independently of central presynaptic mechanisms in human DRG-spinal cord circuits

Suzetrigine, a selective Nav1.8 blocker, despite its significant role as a non-opioid analgesic, exhibits modest efficacy. The potential enhancement of Nav1.8 blocker efficacy through engagement of Nav1.8 at central terminals remains uncertain. We established a donor-derived human organotypic nociceptive circuit to determine where and how clinically relevant analgesics suppress pain signaling. Using ELISA and immunohistochemistry, we quantified calcitonin gene-related peptide (CGRP) release from acute explants of adult human spinal cord, dorsal root ganglia (DRG), and an intact DRG-spinal cord preparation preserving primary afferent anatomy and directional signaling. In isolated spinal cords, capsaicin evoked concentration-dependent spinal CGRP release without compromising viability, and clinically used analgesics inhibited it, validating the assay. In the intact circuit, the application of capsaicin to the DRG cell bodies triggered CGRP release exclusively in the spinal cord, consistent with compartmentalized neuropeptide release at central terminals. Selective Nav1.8 inhibition with suzetrigine reduced spinal CGRP release only when applied to the DRG or nerve root, not the spinal cord, indicating that Nav1.8 regulates peripheral action potential propagation rather than presynaptic transmitter release. These findings establish the first intact human pain circuit-based assay to study analgesics and demonstrate that the analgesic efficacy of Nav1.8 inhibitors is unlikely to increase with improved CNS penetration.

neuroscience↗

bioRxiv2026

Interleukin-6 restricts pre-thymic T cell lineage commitment of progenitors driving loss of SIV control

Effective T cell reconstitution in people living with HIV is central to durable immune control and cure strategies. Sustained thymic output underpins T cell recovery and requires continuous seeding by T cell-committed progenitors originating in the bone marrow (BM). Using the SIV/rhesus macaque model, we identified a thymus-seeding progenitor (TSP; CD4-CD8-CD34CD38-CD7) in BM declining rapidly following SIV infection. This loss closely associated with reduction in T cell lineage committed differentiation of BM-derived hematopoietic stem and progenitor cells (HSPCs). Importantly, both the decline in TSPs and the impairment of pre-thymic T cell potential were strongly associated with early loss of viral control, independent of peripheral T cell dynamics. Plasma interleukin-6 (IL-6) levels robustly predicted the magnitude of TSP loss and the restriction of T cell-biased HSPC differentiation. Integrated transcriptomic and proteomic analyses revealed inflammatory imprinting of HSPCs characterized by activation of the IL-6-JAK-STAT axis, inflammasome engagement, and coordinated suppression of key T cell specification factors, including RUNX1, FYN, and ZAP70. In a nonanimal model of thymopoiesis, IL-6 exposure of rhesus macaque and human HSPCs inhibited their transition from DN1 (CD38-) to DN2 (CD38) TSP states, indicating an early block in T cell lineage commitment. Conversely, ex vivo IL-6 receptor blockade restored thymocyte differentiation to levels comparable to untreated controls. Collectively, these findings demonstrate that pathogenic inflammation restricts pre-thymic T cell development early after infection, directly contributing to loss of viral control. These findings have important implications for understanding the mediators of anti-viral T cell immunity and HIV cure.

immunology↗

bioRxiv2025

A thymus-independent artificial organoid system supports complete thymopoiesis from Rhesus macaque-derived hematopoietic stem and progenitor cells

Thymic output has been extensively studied. While advanced ex-vivo T cell generative approaches exist for mouse and human models, such advancements for nonhuman primate model are lacking. We report the establishment of a rhesus macaque-specific artificial thymic organoid (Rh-ATO) system enabling robust ex vivo T cell generation from CD34 hematopoietic stem and progenitor cells (HSPCs). A continuum of distinct thymopoietic stages were recorded - robust T cell specification of HSPCs resembling thymus seeding progenitors, emergence of CD4+CD3-immature single positive, CD4+CD8+ double positive thymocytes, and finally, generation of CD4 and CD8 single-positive T cell subsets expressing CD38, consistent with recent thymic emigrant phenotype. These events closely mirrored Bonafide thymopoietic stages observed in the thymus. T cells expressed TCRs and exhibited polyfunctional cytokine expression. Thus, we report first demonstration of an off the shelf NHP-specific 3D system recapitulating thymopoiesis, providing a translational platform for modeling T cell development, therapeutic strategies, and immunopathogenesis.

immunology↗

bioRxiv2025

A unified network systems approach uncovers a core novel program underlying T follicular helper cell differentiation

T follicular helper (Tfh) cells are central to the adaptive immune response and exhibit remarkable functional diversity and plasticity. The complex nature of Tfh cell populations, inconsistent findings across experimental systems and potential differences across species have fueled ongoing debate regarding core regulatory pathways that govern Tfh differentiation. Many studies have experimentally investigated individual proteins and circuits involved in Tfh differentiation in limited contexts, each providing only a partial understanding of the process. To address this, we adopted a novel multi-scale network systems approach that incorporates both regulatory and protein-protein interactions. Our approach integrates diverse data types, captures regulation across multiple levels of immune system organization, and recapitulates known drivers. Further, we discover a core Tfh gene set that is conserved across tissue types and disease contexts, and is consistent across data modalities - bulk, single-cell and spatial. While components of this set have been individually reported, a novel aspect of our work lies in the discovery, characterization, and connectivity of this core signature using a single unbiased approach. Using this method, we also uncover a novel function of IL-12, a molecule with reported conflicting functions, in the regulation of Tfh differentiation. Notably, we find that, in both humans and mice, IL-12 is permissive for the differentiation of Tfh precursors, but blocks subsequent differentiation into GC Tfh cells. Overall, this work elucidates novel networks with unexplored roles in governing Tfh cell differentiation across species and tissues, paving the way for novel -therapeutic interventions.

immunology↗

bioRxiv2025

Novel regional specific voltage-gated sodium channel (vgsc) mutations underlying pyrethroid resistance in Aedes albopictus (Skuse) from Northern Peninsular Malaysia

BackgroundControlling Aedes mosquitoes remains as a primary means through the application of synthetic insecticides in Malaysia, but its efficacy is undermined by the evolution of resistance. Aedes albopictus as one of the dominant and competent arboviral vectors has an elusive insecticide resistance status in different geographical regions of Northern Peninsular Malaysia. This underscores the importance of assessing the diverse types of insecticides used and their association with target-site resistance mechanism in this species, which forms the basis of the present study. MethodsWHO-bioassays were performed on Ae. albopictus larvae and adults from four localities (Penang and Perlis), towards 0.034 ppm temephos, 0.25% permethrin, 0.03% deltamethrin, 0.25% primiphos methyl and 0.1% propoxur. The partial voltage-gated sodium channel (vgsc) gene domain (DIIS6, DIIIS6, and DIVS6) of pyrethroid-exposed samples were subsequently genotyped through direct sequencing for any diagnostic single-nucleotide mutations, together with genetic variations and haplotype networks analysis. The predicted protein structures for the mutated regions and their binding affinities to pyrethroids were also evaluated using in-silico docking. Results and discussionsVarying degrees of resistance were observed in all Penang and Perlis strains to all tested insecticides. Moreover, the detection of the F1534L mutation and newly discovered non-synonymous mutations (A1022S/P, E1041K, P1585R, and F1695L) suggest the progression of resistance alleles dissemination in other strains. The analysis of genetic variations, resistance allele distribution patterns, and haplotype networks showed evidence for multiple origins of these mutations. Data also revealed the discovered mutations affect the affinity of vgsc-binding proteins to pyrethroids. ConclusionThis study highlights the genotype-phenotype associations in Ae. albopictus and their genetic links to pyrethroid resistance, offering insights to strengthen vector control strategies in Malaysia. Author summaryIn Malaysia, as in many other countries, dengue epidemic control primarily relies on managing the main vector, Ae. albopictus through commercially available insecticide applications. Vector control strategies have been extensively implemented by local health authorities, often without comprehensive information on insecticide resistance mechanisms in vector populations that could pose a major drawback of insecticide used. In an effort to assess the susceptibility status of Ae. albopictus populations, and determine the most effective insecticide for reducing Malaysian vector populations from different geographical settings, we conducted bioassays towards pyrethroid, organophosphate, and carbamate insecticide classes. Altogether, molecular-based assays were incorporated with phenotypic assay to elucidate the mechanisms modulating insecticide resistance and to unravel their genetic dynamics. Such screening offers detailed insights into specific mechanisms involved in conferring resistance for distinct adopted insecticides. This evidence aims to guide local health authorities in developing vector control strategies and exploring alternative solutions.

evolutionary biology↗

bioRxiv2024

Immunogenicity and protective efficacy of an influenza virus-like particle-based SARS-CoV-2 hybrid vaccine candidate in rhesus macaques

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus co-infections present a heightened COVID-19 disease and hospitalization cases. Here, we studied the immunogenicity and efficacy of an influenza-A/PR8 virus-like particle (FluVLP)-based hybrid vaccine candidate displaying GPI-anchored SARS-CoV-2 receptor binding domain fused to GM-CSF and GPI-anchored interleukin-12 (FluVLP-RBD) in rhesus macaques. Animals (n=4/group) received two doses of either FluVLP or FluVLP-RBD vaccine four weeks apart and were challenged with SARS-CoV-2 (WA1/2020) infection via intranasal and intratracheal routes. We determined vaccine-induced IgG and neutralizing antibody titers in serum and their association with viral replication in the lower and upper airways (lung, throat, and nose) and lung-associated pathologies. FluVLP-RBD vaccine induced a strong binding IgG in serum against multiple SARS-CoV-2 variants (WA1/2020, Delta and Omicron; BA.1). Both vaccines induced strong influenza A/PR8-specific IgG. Following the SARS-CoV-2 challenge, all four animals in the FluVLP-RBD group showed a profound control of virus replication in all three airway compartments as early as day 2 through day 10 (day of euthanasia). This level of viral control was not observed in the FluVLP group as 2-3 animals exhibited high virus replication in all three airway compartments. The protection in the FluVLP-RBD vaccinated group correlated positively with post challenge neutralizing antibody titer. These results demonstrated that a FluVLP-based hybrid SARS-CoV-2 vaccine induces strong antibody responses against influenza-A/PR8 and multiple SARS-CoV-2 RBD variants and protects from SARS-CoV-2 replication in multiple compartments in macaques. These findings provide important insights for developing multivalent vaccine strategies for respiratory viruses. ImportanceCo-infection with multiple respiratory viruses poses a greater risk than individual infections, especially for individuals with underlying health conditions. Studies in humans consistently demonstrated that simultaneous infection with SARS-CoV-2 and influenza leads to more severe respiratory illness and an increased rate of hospitalization. Therefore, developing hybrid vaccines targeting multiple respiratory viruses is of high importance. The hybrid vaccines also help to reduce the economic and logistic burden associated with vaccine coverage, distribution and storage. Here, we evaluate the immunogenicity and effectiveness of a novel hybrid flu-SARS-CoV-2 vaccine candidate using a nonhuman primate pre-clinical model. Our findings reveal that this vaccine elicits a strong immune response against influenza and SARS-CoV-2 viruses. Importantly, it provides strong protection against SARS-CoV-2 infection and associated pathological conditions.

immunology↗

bioRxiv2023

Spermidine facilitates the adhesion and subsequent invasion of Salmonella Typhimurium into epithelial cells via the regulation of surface adhesive structures and the SPI-1

Polyamines are poly-cationic molecules ubiquitously present in all organisms. Salmonella synthesizes and also harbors specialized ABC transporters to uptake polyamines. Polyamines assist in pathogenesis and stress resistance in Salmonella; however, the mechanism remains elusive. The virulence trait of Salmonella depends on the injection of effector proteins into the host cell and modulation of host machinery and employs an array of arsenals to colonize in the host niche successfully. However, prior to this, Salmonella utilizes multiple surface structures to attach and adhere to the surface of the target cells. Our study solves the enigma of how polyamine spermidine assists in the pathogenesis of Salmonella. We show that spermidine mediates the initial attachment and adhesion of Salmonella Typhimurium to Caco-2 cells, facilitating its invasion. In-vivo studies showed that polyamines are required for invasion into the murine Peyers patches. Polyamines have previously been shown to regulate the transcription of multiple genes in both eukaryotes and prokaryotes. We show that spermidine controls the RNA expression of the two-component system, BarA/SirA, that further regulates multiple fimbrial and non-fimbrial adhesins in Salmonella. Flagella is also a vital surface structure aiding in motility and attachment to surfaces of host cells and gall stones. Spermidine regulated the expression of flagellin genes by enhancing the translation of s28, which features an unusual start codon and a poor Shine-Dalgarno sequence. Besides regulating the formation of the adhesive structures, spermidine tunes the expression of the Salmonella pathogenicity island-1 encoded genes. Thus, our study unravels a novel mechanism by which spermidine aids in the adhesion and the subsequent invasion of Salmonella into host cells.

microbiology↗

bioRxiv2022

A gut commensal protist protects against virus-mediated loss of oral tolerance

Loss of oral tolerance (LOT) to gluten, characterized by a T helper 1 (Th1) gluten-specific immune response, is a hallmark of celiac disease (CeD) and can be triggered by enteric viral infections. We hypothesized that certain gut microbes have the capacity to protect against virus-mediated LOT. By using our previously defined reovirus-mediated LOT CeD model, we discovered that the gut colonizing protist Tritrichomonas (T.) arnold promotes oral tolerance and protects against reovirus-mediated LOT by suppressing the reovirus-induced proinflammatory program of dietary-antigen-presenting CD103+ dendritic cells. Importantly, T. arnold did not affect antiviral host immunity, suggesting that T. arnold-mediated protection against T1L-induced LOT is not attributable to differences in antiviral host responses. Additionally, using gnotobiotic mice, we found that Tritrichomonas arnold colonization is sufficient to protect against reovirus-mediated LOT in the absence of the microbiota. Mechanistically, we show that Tritrichomonas arnold colonization restrains reovirus-induced inflammatory responses in dendritic cells and thus limit their ability to promote Th1 immune responses ex vivo. Finally, our studies using human stool samples support a role for Tritrichomonas sp. colonization in protecting against development of CeD. This study will motivate the design of effective therapies to prevent LOT to gluten in at-risk individuals and to reinstate tolerance to gluten in CeD patients. One Sentence SummaryTritrichomonas arnold protects against virus-mediated loss of oral tolerance to gluten and is underrepresented in celiac disease patients.

immunology↗

bioRxiv2022

Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages

Mutations in the spike glycoprotein of SARS-CoV-2 allow the virus to probe the sequence space in search of higher-fitness states. New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with such mutations. Interestingly, the sites of mutation in these sublineages vary between the VOCs. Whether such differences reflect the random nature of mutation appearance or distinct evolutionary spaces of spike in the VOCs is unclear. Here we show that each position of spike has a lineage-specific likelihood for mutations to appear and dominate descendent sublineages. This likelihood can be accurately estimated from the lineage-specific mutational profile of spike at a protein-wide level. The mutability environment of each position, including adjacent sites on the protein structure and neighboring sites on the network of comutability, accurately forecast changes in descendent sublineages. Mapping of imminent changes within the VOCs can contribute to the design of immunogens and therapeutics that address future forms of SARS-CoV-2.

bioinformatics↗

bioRxiv2022

Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19

While there have been extensive analyses characterizing cellular and humoral responses across the severity spectrum in COVID-19, predictors of outcomes within severe COVID-19 remain to be comprehensively elucidated. Recently, we identified divergent monocyte states as predictors of outcomes within severe COVID-19, but corresponding humoral profiles of risk have not been delineated. Furthermore, the nature of antibodies (Abs) directed against viral antigens beyond the spike protein or endemic coronavirus antigens and their associations with disease severity and outcomes remain poorly defined. We performed deep molecular profiling of Abs directed against a wide range of antigenic specificities in severe COVID-19 patients admitted to the ICU. The profiles consisted of canonical (S, RBD, N) and non-canonical (orf3a, orf8, nsp3, nps13 and M) antigenic specificities. Notably, multivariate machine learning (ML) models, generated using profiles of Abs directed against canonical or non-canonical antigens, were equally discriminative of recovery and mortality COVID-19 outcomes. In both ML models, survivors were associated with increased virus-specific IgA and IgG3 antibodies and with higher antigen-specific antibody galactosylation. Intriguingly, pre-pandemic healthy controls had cross-reactive Abs directed against nsp13 which is a conserved protein in other alpha and beta coronaviruses. Notably, higher levels of nsp13-specific IgA antibodies were associated with recovery in severe COVID-19. In keeping with these findings, a model built on Ab profiles for endemic coronavirus antigens was also predictive of COVID-19 outcome bifurcation, with higher levels of IgA and IgG3 antibodies against OC43 S and NL63 S being associated with survival. Our results suggest the importance of Abs targeting non-canonical SARS-CoV-2 antigens as well as those directed against endemic coronaviruses in favorable outcomes of severe COVID-19.

immunology↗

bioRxiv2021

Network-based integration of epigenetic landscapes unveils molecular programs underlying human T follicular helper cell differentiation

T follicular helper (Tfh) cells play a critical role in T-dependent humoral immune responses. While genetic programs controlling Tfh cell differentiation have been extensively studied using murine models, studies in humans have been hampered by the lack of a robust in vitro differentiation system for Tfh cells. We characterized epigenomic landscapes across stages of Tfh cell differentiation in a healthy human tonsil using ATAC-Seq and CUT&RUN for selected histone modifications. We combined these epigenomic datasets and integrated them with the reference human protein interactome using a novel network propagation approach. Our approach uncovered subnetworks integral to Tfh cell differentiation. These subnetworks captured known Tfh cell drivers to a greater extent than conventional gene-centric analyses would, and also revealed novel modules that may be required for Tfh cell differentiation. We find that human Tfh cell subnetworks are functionally associated with specific immune signaling cascades including cytokine receptor driven pathways. Analyses of transcriptomic data revealed that in addition to these immune pathways being significantly dysregulated in severe COVID-19, the corresponding Tfh cell subnetworks are also transcriptionally perturbed to a similar extent. This provides a molecular mechanistic basis for the previously observed impaired Tfh cell differentiation and loss of germinal centers in severe COVID-19.

immunology↗

bioRxiv2021

Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

The SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 and nucleocapsid (N) protein of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2. SummarySince initial outbreak of COVID-19 in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N), membrane (M), and envelope (E) proteins. The S protein mediates initial contacts with human hosts while the E and M proteins function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein (Clade G), G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) were observed [2-4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness [5, 6]. As per latest WHO reports on COVID-19, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise in COVID-19 detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

bioinformatics↗

bioRxiv2020

Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome

We are in the midst of the third severe coronavirus outbreak caused by SARS-CoV-2 with unprecedented health and socio-economic consequences due to the COVID-19. Globally, the major thrust of scientific efforts has shifted to the design of potent vaccine and anti-viral candidates. Earlier genome analyses have shown global dominance of some mutations purportedly indicative of similar infectivity and transmissibility of SARS-CoV-2 worldwide. Using high-quality large dataset of 25k whole-genome sequences, we show emergence of new cluster of mutations as result of geographic evolution of SARS-CoV-2 in local population ([≥]10%) of different nations. Using statistical analysis, we observe that these mutations have either significantly co-occurred in globally dominant strains or have shown mutual exclusivity in other cases. These mutations potentially modulate structural stability of proteins, some of which forms part of SARS-CoV-2-human interactome. The high confidence druggable host proteins are also up-regulated during SARS-CoV-2 infection. Mutations occurring in potential hot-spot regions within likely T-cell and B-cell epitopes or in proteins as part of host-viral interactome, could hamper vaccine or drug efficacy in local population. Overall, our study provides comprehensive view of emerging geo-clonal mutations which would aid researchers to understand and develop effective countermeasures in the current crisis. SignificanceOur comparative analysis of globally dominant mutations and region-specific mutations in 25k SARS-CoV-2 genomes elucidates its geo-clonal evolution. We observe locally dominant mutations (co-occurring or mutually exclusive) in nations with contrasting COVID-19 mortalities per million of population) besides globally dominant ones namely, P314L (ORF1b) and D164G (S) type. We also see exclusive dominant mutations such as in Brazil (I33T in ORF6 and I292T in N protein), England (G251V in ORF3a), India (T2016K and L3606F in ORF1a) and in Spain (L84S in ORF8). The emergence of these local mutations in ORFs within SARS-CoV-2 genome could have interventional implications and also points towards their potential in modulating infectivity of SARS-CoV-2 in regional population.

bioinformatics↗

bioRxiv2020

Modified Vaccinia Ankara Based SARS-CoV-2 Vaccine Expressing Full-Length Spike Induces Strong Neutralizing Antibody Response

There is a great need for the development of vaccines for preventing SARS-CoV-2 infection and mitigating the COVID-19 pandemic. Here, we developed two modified vaccinia Ankara (MVA) based vaccines which express either a membrane anchored full-length spike protein (MVA/S) stabilized in a prefusion state or the S1 region of the spike (MVA/S1) which forms trimers and is secreted. Both immunogens contained the receptor-binding domain (RBD) which is a known target of antibody-mediated neutralization. Following immunizations with MVA/S or MVA/S1, both spike protein recombinants induced strong IgG antibodies to purified full-length SARS-CoV-2 spike protein. The MVA/S induced a robust antibody response to purified RBD, S1 and S2 whereas MVA/S1 induced an antibody response to the S1 region outside of the RBD region. Both vaccines induced an antibody response in the lung and that was associated with induction of bronchus-associated lymphoid tissue. MVA/S but not MVA/S1 vaccinated mice generated robust neutralizing antibody responses against SARS-CoV-2 that strongly correlated with RBD antibody binding titers. Mechanistically, S1 binding to ACE-2 was strong but reduced following prolonged pre-incubation at room temperature suggesting confirmation changes in RBD with time. These results demonstrate MVA/S is a potential vaccine candidate against SARS-CoV-2 infection.Competing Interest StatementThe authors have declared no competing interest.View Full Text

immunology↗