Biology subjects

Selvaraj, P.

Publications and source records attributed to Selvaraj, P..

18 recordsLinked to original sources

bioRxiv2025

Characterization of a new laboratory colony of Anopheles funestus mosquitoes established in Ifakara, Tanzania

BackgroundAnopheles funestus, a major vector of malaria in Africa, has proven difficult to colonize in laboratory settings, impeding research on its biology and control. After several attempts, our team recently succeeded in colonizing a strain of An. funestus from Tanzania (FUTAZ). The objective of this study was to analyse the key fitness and genotypic characteristics of these mosquitoes during multiple filial generations of laboratory adaptation and compare them to wild An. funestus from Tanzania and a pre-existing colony of An. funestus from Mozambique (FUMOZ). MethodsMeasures of mating success (percentage of female mosquitoes inseminated), body size (wing length), fecundity (number of eggs laid per female), and insecticide susceptibility (percentage of 24-hour mortality after exposure to insecticides) were compared between the newly established colonies of Tanzanian An. funestus (FUTAZ colonies), the long-established FUMOZ colonies, and a colony of Anopheles arabiensis maintained in the same laboratory. The maternal lineages of the An. funestus mosquitoes were investigated through a hydrolysis probe analysis of their mitochondrial DNA to identify distinct clades, I and II. Additionally, other intragenomic variations were examined through a PCR analysis of restriction fragment length polymorphisms (RFLP) on the third domain of 28S ribosomal DNA. These molecular markers were used to compare the FUTAZ colonies, FUMOZ colonies in Tanzania and South Africa, and the wild-collected An. funestus from Tanzania. ResultThe mating success and body size of FUTAZ females declined significantly from filial generations F1 to F6 relative to the founder population (F0), but then increased from F7 onwards eventually matching FUMOZ by F9. Fecundity was similar across all colonies tested. However, it took significantly longer for 50% of the females in the FUTAZ and FUMOZ colonies (over 10 days) to mate compared to females in the An. arabiensis colony (approximately 5 days). Insecticide resistance appeared to be lost during colonization, but this varied with insecticide classes. Majority of mosquitoes in the FUTAZ colony, as well as the wild-caught Tanzanian An. funestus belonged to Clade I (80.4-89.4%) and RFLP type "Y" (90.5-91.4%), while the FUMOZ colonies were mostly Clade II (65.5-88.5%) and RFLP type "MW" (90.5-91.5%). ConclusionThis study suggests that the mating success and body size of An. funestus decreases significantly during the early stages of colonization, then increase as the mosquitoes adapt to laboratory conditions. It is therefore crucial to have a large enough founder population to persist through these early generations in order to achieve stable colonization of An. funestus. The Clade and RFLP genotyping demonstrated the genetic similarities between the FUTAZ mosquitoes and wild-caught Tanzanian An. funestus, but also showed that the new colony can be distinguished from the FUMOZ colony.

ecology↗

bioRxiv2025

Multitask deep learning for the emulation and calibration of an agent-based malaria transmission model

Agent-based models of malaria transmission are useful tools for understanding disease dynamics and planning interventions, but they can be computationally intensive to calibrate. We present a multitask deep learning approach for emulating and calibrating a complex agent-based model of malaria transmission. Our neural network emulator was trained on a large suite of simulations from the EMOD malaria model, an agent-based model of malaria transmission dynamics, capturing relationships between immunological parameters and epidemiological outcomes such as age-stratified incidence and prevalence across eight sub-Saharan African study sites. We then use the trained emulator in conjunction with parameter estimation techniques to calibrate the underlying model to reference data. Taken together, this analysis shows the potential of machine learning-guided emulator design for complex scientific processes and their comparison to field data. Author summaryMathematical models can help understand and design interventions for infectious diseases such as malaria, but they can be complex and time-consuming to work with. In this study, we developed a machine learning approach to create a fast and accurate emulator for a detailed malaria transmission model. Our emulator can quickly predict various disease outcomes based on different immune system parameters. We trained it using a large set of simulations created using the EMOD malaria model and tested it against real-world data from multiple African countries. The emulator not only matches the original models predictions closely, but can also be used to efficiently find the best parameter values to match field observations. We hope that this work can serve as a demonstration of machine learning tools to link complex models of disease transmission to field data.

bioinformatics↗

bioRxiv2024

Phospholipid signaling and multivesicular endolysosomes modulate membrane dynamics at the biotrophic interface in Rice Blast

Magnaporthe oryzae, the rice blast pathogen, secretes an arsenal of apoplastic and cytoplasmic effector proteins to suppress host immunity during the biotrophy phase. The proposed non-conventional secretion of cytoplasmic effectors into the Biotrophic Interfacial Complex (BIC), remains uncharted except for the involvement of the exocyst complex therein. Recently, the plant endocytic machinery has been implicated in translocation of cytoplasmic effectors to the host. Here, we used live cell imaging and mutant analyses to provide new insight into late endolysosomal mediators as conduits for establishment of the BIC and/or unconventional secretion across the host interface. Rerouting of the late endocytic GTPase Rab7 occurs at the BIC; and the dominant negative Rab7T22N led to significant defects in focal interface formation. FYVE biosensor and pharmacological interventions revealed that Rab7 membrane trafficking and establishment/integrity of the biotrophy interface requires the PI3 kinase Vps34 and phosphoinositide PI3(P) function. Additional pharmacological evidence supports endolysosomal trafficking to the host interface follows a distinct non-conventional secretion route too. Finally, we show that the Multi-Vesicular Bodies and lysosomal membranes act as downstream modules of the Rab7 function in precise sorting and specialised traffic of cytoplasmic effectors across the Magnaporthe-Rice interface during blast disease.

cell 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↗

bioRxiv2024

Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera

Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.

microbiology↗

bioRxiv2024

Differential Patterns of Cross-Protection against Antigenically Distinct Variants in Small Animal Models of SARS-CoV-2 Infection

Continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will likely force more future updates of vaccine composition. Based on a series of studies carried out in human ACE2 transgenic mice (K18-hACE2) and Syrian hamsters, we show that immunity at the respiratory tract, acquired through either previous infection or vaccination with an in-house live attenuate virus, offers protection against antigenically distinct variants in the absence of variant spike-specific neutralizing antibodies. Interestingly, immunity acquired through infection of a modern variant (XBB.1.5) was insufficient in preventing brain infection by the ancestral virus (WA1/2020) in K18-hACE2 mice. Similarly, previous infection with WA1/2020 did not protect against brain infection by XBB.1.5. Our results highlight the importance of immune components other than neutralizing antibodies in maintaining protection against new variants in the respiratory tract, but also paint scenarios where a monovalent vaccine based on a contemporary variant may be less effective against the ancestral strain. ImportanceMany studies have assessed the cross neutralization of various SARS-CoV-2 variants induced by breakthrough infections or vaccine boosters. Few studies, however, have modeled a more severe type of breakthrough infection. Here, we show that immunity acquired through a previous infection by either a historical virus (WA1/2020) or a contemporary variant (XBB.1.5) failed to protect against brain infection of K18-hACE2 mice by an antigenically distinct virus, although it largely protected the respiratory tract. Our results provided a potential model to investigate the role of different immune components in curbing SARS-CoV-2 infection.

microbiology↗

bioRxiv2023

Condensate formation of the human RNA-binding protein SMAUG1 is controlled by its intrinsically disordered regions and interactions with 14-3-3 proteins

SMAUG1 is a human RNA-binding protein that is known to be dysregulated in a wide range of diseases. It is evolutionarily conserved and has been shown to form condensates containing translationally repressed RNAs. This indicates that condensation is central to proper SMAUG1 function; however, the factors governing condensation are largely unknown. In this work, we show that SMAUG1 drives the formation of liquid-like condensates in cells through its non-conventional C-terminal prion-like disordered region. We use biochemical assays to show that this liquid-liquid phase separation is independent of RNA binding and does not depend on other large, disordered regions that potentially harbor several binding sites for partner proteins. Using a combination of computational predictions, structural modeling, in vitro and in cell measurements, we also show that SMAUG1-driven condensation is negatively regulated by direct interactions with members of the 14-3-3 protein family. These interactions are mediated by four distinct phospho-regulated short linear motifs embedded in the disordered regions of SMAUG1, working synergistically. Interactions between SMAUG1 and 14-3-3 proteins drive the dissolution of condensates, alter the dynamics of the condensed state, and are likely to be intertwined with currently unknown regulatory mechanisms. Our results provide information on how SMAUG1 phase separation is regulated and the first known instance of 14-3-3 proteins being able to completely dissolve condensates by directly interacting with a phase separation driver, which might be a general mechanism in cells to regulate biological condensation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/527857v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@868746org.highwire.dtl.DTLVardef@1b3318org.highwire.dtl.DTLVardef@1b78868org.highwire.dtl.DTLVardef@5c7e5e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISMAUG1 is a human RNA-binding protein capable of condensation with unknown regulation C_LIO_LIA prion-like domain of SMAUG1 drives condensation via liquid-liquid phase separation C_LIO_LISMAUG1 interacts with 14-3-3 proteins via four phospho-regulated short linear motifs C_LIO_LI14-3-3 interactions change the dynamics of SMAUG1 condensates, promoting their dissolution C_LIO_LIThis is the first described regulatory mechanism for SMAUG1-driven condensation C_LI

molecular biology↗

bioRxiv2022

Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra

Accurate prediction of mosquito population age structures can improve the evaluation of mosquito-targeted interventions since old mosquitoes are more likely to transmit malaria than young ones. Mid-infrared spectroscopy (MIRS) reveals age-associated variation in the biochemical composition of the mosquito cuticle, which can then be used to train machine learning (ML) models to predict mosquito ages. However, these MIRS-ML models are not always generalisable across different mosquito populations. Here, we investigated whether dimensionality reduction applied to the MIRS input data and transfer learning could improve the generalisability of MIRS-ML predictions for mosquito ages. We reared adults of the malaria vector, Anopheles arabiensis, in two insectaries (Ifakara, Tanzania and Glasgow, UK). The heads and thoraces of female mosquitoes of two age classes (1-9 day-olds and 10-17 day-olds) were scanned using an attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectrometer (4000 cm-1 to 400 cm-1). The dimensionality of the spectra data was reduced using unsupervised principal component analysis (PCA) or t-distributed stochastic neighbour embedding (t-SNE), and then the spectra were used to train deep learning (DL) and standard machine learning (ML) classifiers. Transfer learning was also evaluated for improving the computational cost of the models when predicting mosquito age classes from new populations. Model accuracies for predicting the age of test mosquitoes from the same insectary as the training samples reached 99% for DL and 92% for ML, but did not generalise to a different insectary, achieving only 46% and 48% for ML for DL, respectively. Dimensionality reduction did not improve the model generalisability between locations but reduced computational time up to 5-fold. However, transfer learning by updating pre-trained models with 2% of mosquitoes from the alternate location brought both DL and standard ML model performance to ~98% accuracy for predicting mosquito age classes in the alternative insectary. Combining dimensionality reduction and transfer learning can reduce computational costs and improve the transferability of both deep learning and standard machine learning models for predicting the age of mosquitoes. Future studies could investigate the optimal quantities and diversity of training data necessary for transfer learning, and implications for broader generalisability to unseen datasets.

bioinformatics↗

bioRxiv2022

Rab7/Retromer-based endolysosomal trafficking facilitates effector secretion and host invasion in rice blast

Secretion is a fundamental process in all living organisms. Using conventional secretion pathways, many plant pathogens release effectors into the host plants to downregulate immunity and promote infection. However, this does not always constitute the only way that effectors are sorted and tracked to their final destination such as the biotrophic interfacial complex-associated effectors produced by the blast fungus Magnaporthe oryzae. Here, we uncover a novel unconventional route originating from fungal vacuolar membrane to the host interface and plasma membrane. We found that a GFP-MoRab7 labeled vacuole is closely associated with the interface structure throughout M. oryzae invasive growth. Conditional inactivation of MoRab7 impaired the establishment of the biotrophy interface and secretion of Pwl2 effector. To perform the vacuolar trafficking pathway, MoRab7 first recruits the retromer complex to the vacuole membrane, enabling it recognizes a batch of SNARE proteins, including the v-SNARE MoSnc1. Live-cell imaging supports both retromer complex component and MoSnc1 protein labeled vesicles showing the trafficking dynamics toward the interface or plasma membrane, and then fusion with target membranes. Lastly, disruption of the MoRab7/Retromer/MoSnc1-based endolysosomal cascade affects effector secretion and fungal pathogenicity. Taken together, we discovered an unconventional protein and membrane trafficking route starting from the fungal endolysosomes to the M. oryzae-rice interaction interface, and dissect the role of MoRab7/Retromer/MoSnc1 constituent sorting machinery in effector secretion during invasive growth in M. oryzae.

plant biology↗

bioRxiv2022

Gene drive mosquitoes can aid malaria elimination by retarding Plasmodium sporogonic development

Gene drives hold promise for the genetic control of malaria vectors. The development of vector population modification strategies hinges on the availability of effector mechanisms impeding parasite development in transgenic mosquitoes. We augmented a midgut gene of the malaria mosquito Anopheles gambiae to secrete two exogenous antimicrobial peptides, Magainin 2 and Melittin. This small genetic modification, capable of efficient non-autonomous gene drive, hampers oocyst development in both Plasmodium falciparum and Plasmodium berghei. It delays the release of infectious sporozoites while it simultaneously reduces the lifespan of homozygous female transgenic mosquitoes. Modeling the spread of this modification using a large-scale agent-based model of malaria epidemiology reveals that it can break the cycle of disease transmission across a range of endemic settings. One sentence summaryWe developed a gene drive effector that retards Plasmodium development in transgenic Anopheles gambiae mosquitoes via the expression of antimicrobial peptides in the midgut and which is predicted to eliminate malaria under a range of transmission scenarios.

genetics↗

bioRxiv2022

Spike Protein-independent Attenuation of SARS-CoV-2 Omicron Variant in Laboratory Mice

Despite being more transmissible, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant was found to cause milder diseases in laboratory animals, often accompanied by a lower viral load compared to previous variants of concern. This study revealed the structural basis for a robust interaction between the receptor binding domain of the Omicron spike protein and mouse ACE2. Pseudovirus bearing the Omicron spike protein efficiently utilized mouse ACE2 for entry. By comparing viral load and disease severity among laboratory mice infected by a natural Omicron variant or recombinant ancestral viruses bearing either the entire Omicron Spike or only the N501Y/Q493R mutations in its spike, we found that mutations outside the spike protein in the Omicron variant may be responsible for the observed lower viral load. Together, our results indicated that a post-entry block to the Omicron variant exists in laboratory mice.

microbiology↗

bioRxiv2022

Influenza virus-like particle-based hybrid vaccine containing RBD induces immunity against influenza and SARS-CoV-2 viruses

Several approaches have produced an effective vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the influence of immune responses induced by other vaccinations on the durability and efficacy of the immune response to SARS-CoV-2 vaccine is still unknown. We have developed a hybrid vaccine for SARS-CoV-2 and influenza viruses using influenza virus-like particles (VLP) incorporated by protein transfer with glycosylphosphatidylinositol (GPI)-anchored SARS-CoV-2 S1 RBD fused to GM-CSF as an adjuvant. GPI-RBD-GM-CSF fusion protein was expressed in CHO-S cells, purified and incorporated onto influenza VLPs to develop the hybrid vaccine. Our results show that the hybrid vaccine induced a strong antibody response and protected mice from both influenza virus and mouse-adapted SARS-CoV-2 challenges, with vaccinated mice having significantly lower lung viral titers compared to naive mice. These results suggest that the hybrid vaccine strategy is a promising approach for developing multivalent vaccines to prevent influenza A and SARS-CoV-2 infections.

immunology↗

bioRxiv2021

Population replacement gene drive characteristics for malaria elimination in a range of seasonal transmission settings: a modeling study

Genetically engineering mosquitoes is a promising new vector control strategy to reinvigorate the fight against malaria in Sub-Saharan Africa. Using an agent-based model of malaria transmission with vector genetics, we examine the impacts of releasing population-replacement gene drive mosquitoes on malaria transmission and quantify the gene drive system parameters required to achieve local elimination within a spatially-resolved, seasonal Sahelian setting. We evaluate the performance of two different gene drive systems: "classic" and "integral." Various transmission regimes (low, moderate, and high - corresponding to annual entomological inoculation rates of 10, 30, and 80 infectious bites per person) and other simultaneous interventions, including deployment of insecticide-treated nets (ITNs) and passive healthcare seeking, are also simulated. Local elimination probabilities decreased with pre-existing population target site resistance frequency, increased with transmission-blocking effectiveness of the introduced antiparasitic gene and drive efficiency, and were context dependent with respect to fitness costs associated with the introduced gene. Of the four parameters, transmission-blocking effectiveness may be the most important to focus on for improvements to future gene drive strains because a single release of classic gene drive mosquitoes is likely to locally eliminate malaria in low to moderate transmission settings only when transmission-blocking effectiveness is very high (above ~80-90%). However, simultaneously deploying ITNs and releasing integral rather than classic gene drive mosquitoes significantly boosts elimination probabilities, such that elimination remains highly likely in low to moderate transmission regimes down to transmission-blocking effectiveness values as low as ~50% and in high transmission regimes with transmission-blocking effectiveness values above ~80-90%. Thus, a single release of currently achievable population replacement gene drive mosquitoes, in combination with traditional forms of vector control, can likely locally eliminate malaria in low to moderate transmission regimes within the Sahel. In a high transmission regime, higher levels of transmission-blocking effectiveness than are currently available may be required. Author summaryMalaria remains a significant health burden in Sub-Saharan Africa. The mass deployment of insecticide-treated nets and antimalarial drugs have drastically reduced malaria incidence, but insecticide and drug resistance threaten to stall these efforts. The genetic engineering of mosquito populations is a promising new vector control strategy to reinvigorate the fight against malaria. Releases of engineered gene drive mosquitoes that can spread introduced antimalarial genes quickly throughout the mosquito population may be a particularly effective new method for reducing malaria transmission. Important questions arise, however, about how well these gene drive systems must work in order to deliver substantial reductions in transmission. Here we use a spatial model of individual humans and vectors to simulate the effects of releasing gene drive mosquitoes with antimalarial properties on malaria transmission in a Sahelian setting. We quantify the gene drive system parameters required to achieve local elimination and find that when deployed in combination with traditional forms of vector control, a single release of gene drive mosquitoes with realistically achievable characteristics is highly likely to locally eliminate malaria in low to moderate transmission regimes. In a high transmission regime, improved strains of gene drive mosquitoes may be required. In all settings, releasing gene drive mosquitoes with antimalarial properties helps create a window of opportunity during which malaria prevalence is suppressed and other interventions can be ramped up to achieve elimination, even when a single gene drive mosquito release by itself cannot.

genetics↗

bioRxiv2021

SARS-CoV-2 B.1.1.7 infection of Syrian hamster does not cause more severe disease and is protected by naturally acquired immunity

Epidemiological studies have revealed the emergence of multiple SARS-CoV-2 variants of concern (VOC), including the lineage B.1.1.7 that is rapidly replacing old variants. The B.1.1.7 variant has been linked to increased morbidity rates, transmissibility, and potentially mortality (1). To assess viral fitness in vivo and to address whether the B.1.1.7 variant is capable of immune escape, we conducted infection and re-infection studies in naive and convalescent Syrian hamsters (>10 months old). Hamsters infected by either a B.1.1.7 variant or a B.1 (G614) variant exhibited comparable viral loads and pathology. Convalescent hamsters that were previously infected by the original D614 variant were protected from disease following B.1.1.7 challenge with no observable clinical signs or lung pathology. Altogether, our study did not find that the B.1.1.7 variant significantly differs from the B.1 variant in pathogenicity in hamsters and that natural infection-induced immunity confers protection against a secondary challenge by the B1.1.7 variant.

microbiology↗

bioRxiv2020

The PRRA insert at the S1/S2 site modulates cellular tropism of SARS-CoV-2 and ACE2 usage by the closely related Bat raTG13

Biochemical and structural analyses suggest that SARS-CoV-2 is well-adapted to infecting human and the presence of four residues (PRRA) at the S1/S2 site within the Spike protein may lead to unexpected tissue or host tropism. Here we report that SARS-CoV-2 efficiently utilized ACE2 of 9 species except mouse to infect 293T cells. Similarly, pseudoviruses bearing spike protein derived from either the bat raTG13 or pangolin GX, two closely related animal coronaviruses, utilized ACE2 of a diverse range of animal species to gain entry. Removal of PRRA from SARS-CoV-2 Spike displayed distinct effects on pseudoviral entry into different cell types. Strikingly, insertion of PRRA into the raTG13 Spike selectively abrogated the usage of horseshoe bat and pangolin ACE2 but conferred usage of mouse ACE2 by the relevant pseudovirus to enter cells. Together, our findings identified a previously unrecognized effect of the PRRA insert on SARS-CoV-2 and raTG13 spike proteins.

microbiology↗

bioRxiv2020

Vector genetics, insecticide resistance and gene drives: an agent-based modeling approach to evaluate malaria transmission and elimination

Vector control has been a key component in the fight against malaria for decades, and chemical insecticides are critical to the success of vector control programs worldwide. However, increasing resistance to insecticides threatens to undermine these efforts. Understanding the evolution and propagation of resistance is thus imperative to mitigating loss of intervention effectiveness. Additionally, accelerated research and development of new tools that can be deployed alongside existing vector control strategies is key to eradicating malaria in the near future. Methods such as gene drives that aim to genetically modify large mosquito populations in the wild to either render them refractory to malaria or impair their reproduction may prove invaluable tools. Mathematical models of gene flow in populations, which is the transfer of genetic information from one population to another through migration, can offer invaluable insight into the behavior and potential impact of gene drives as well as the spread of insecticide resistance in the wild. Here, we present the first multi-locus, agent-based model of vector genetics that accounts for mutations and a many-to-many mapping cardinality of genotypes to phenotypes to investigate gene flow, and the propagation of gene drives in Anopheline populations. This model is embedded within a large scale individual-based model of malaria transmission representative of a high burden, high transmission setting characteristic of the Sahel. Results are presented for the selection of insecticide-resistant vectors and the spread of resistance through repeated deployment of insecticide treated nets (ITNs), in addition to scenarios where gene drives act in concert with existing vector control tools such as ITNs. The roles of seasonality, spatial distribution of vector habitat and feed sites, and existing vector control in propagating alleles that confer phenotypic traits via gene drives that result in reduced transmission are explored. The ability to model a spectrum of vector species with different genotypes and phenotypes in the context of malaria transmission allows us to test deployment strategies for existing interventions that reduce the deleterious effects of resistance and allows exploration of the impact of new tools being proposed or developed. Author summaryVector control interventions are essential to the success of global malaria control and elimination efforts but increasing insecticide resistance worldwide threatens to derail these efforts. Releasing genetically modified mosquitoes that use gene drives to pass on desired genes and their associated phenotypic traits to the entire population within a few generations has been proposed to address resistance and other issues such as transmission heterogeneity that can sustain malaria transmission indefinitely. While the ethics and safety of these methods are being debated, mathematical models offer an efficient way of predicting the behavior and estimating the efficacy of these interventions if deployed to specific regions facing challenges to reaching elimination. We have developed a detailed mathematical model of vector genetics where specific genomes code for physical attributes that influence transmission and are affected by the surrounding environment. This is the first model to incorporate an individual-based multi-locus genetic model into a detailed individual-based model of malaria transmission. This model opens the door to investigate a number of subtle but important questions such as the effects of small numbers of mosquitoes in a region sustaining malaria transmission during the low transmission season, and the success of gene drives in regions where extant vector control interventions could kill off gene drive mosquitoes before establishment. Here, we investigate the reduced efficacy of current vector control measures in the presence of insecticide resistance and evaluate the likelihood of achieving local malaria elimination using gene drive mosquitoes released into a high transmission setting alongside other vector control measures.

genetics↗

bioRxiv2019

Reducing malaria burden and accelerating elimination with long-lasting systemic insecticides: a modeling study of three potential use cases

BackgroundWhile bednets and insecticide spraying have had significant impact on malaria burden in many endemic regions, outdoor vector feeding and insecticide resistance may ultimately limit their contribution to elimination and control campaigns. Complementary vector control methods such as endectocides or systemic insecticides are therefore generating much interest. Here we explore the conditions under which long-lasting systemic insecticides would have a substantial impact on transmission and burden.\n\nMethodsHypothetical long-lasting systemic insecticides with effective durations ranging from 14 days to 90 days are simulated using an individual-based mathematical model of malaria transmission. The impact of systemic insecticides when used to complement existing vector control and drug campaigns is evaluated in three settings - a highly seasonal high-transmission setting, a near-elimination setting with seasonal travel to a high-risk area, and a near-elimination setting in southern Africa.\n\nResultsAt 60% coverage, a single round of long-lasting systemic insecticide with effective duration of at least 60 days, distributed at the start of the season alongside a seasonal malaria chemoprevention campaign in a high-transmission setting, results in further burden reduction of 30-90% depending on the sub-populations targeted. In a near-elimination setting where transmission is sustained by seasonal travel to a high-risk area, targeting high-risk travelers with systemic insecticide with effective duration of at least 30 days can result in likely elimination even if intervention coverage is as low as 50%. In near-elimination settings with robust vector control, the addition of a 14-day systemic insecticide alongside an antimalarial in mass drug administration (MDA) campaigns can decrease the necessary MDA coverage from about 85% to the more easily achievable 65%.\n\nConclusionsWhile further research into the safety profile of systemic insecticides is necessary before deployment, we find that long-lasting systemic insecticides can play a critical role in reducing burden or eliminating malaria in a range of contexts with different target populations, existing malaria control methods, and transmission intensities.

epidemiology↗

bioRxiv2017

Cpk2, a catalytic subunit of cyclic AMP-PKA, regulates growth and pathogenesis in rice blast

The cAMP-Protein Kinase A signalling, anchored on CpkA, is necessary for appressorium development and host penetration, but indispensable for infectious growth in Magnaporthe oryzae. In this study, we identified and characterized the gene encoding the second catalytic subunit, CPK2, whose expression was found to be lower compared to CPKA at various stages of pathogenic growth in M. oryzae. Deletion of CPK2 caused no alterations in vegetative growth, conidiation, appressorium formation, or pathogenicity. Surprisingly, the cpkA{Delta}cpk2{Delta} double deletion strain displayed significant reduction in growth rate and conidiation compared to the single deletion mutants. Interestingly, loss of CPKA and CPK2 resulted in morphogenetic defects in germ tubes (with curled/wavy and serpentine growth pattern) on hydrophobic surfaces, and a complete failure to produce appressoria therein, thus suggesting an important role for CPK2-mediated cAMP-PKA in surface sensing and response pathway. CPKA promoter-driven CPK2 expression partially suppressed the defects in host penetration and pathogenicity in the cpkA{Delta}. Such ectopic CPK2 expressing strain successfully penetrated the rice leaves, but was unable to produce proper secondary invasive hyphae, thus underscoring the importance of CpkA in growth and differentiation in planta. The Cpk2-GFP localized to the nucleus and cytoplasmic vesicles in conidia and the germ tubes. The Cpk2-GFP colocalized with CpkA-mCherry on vesicles in the cytosol, but such overlap was not evident in the nucleus. Our studies indicate that CpkA and Cpk2 share overlapping functions, but also play distinct roles during pathogenesis-associated signalling and morphogenesis in the rice blast fungus.

cell biology↗