Biology subjects

Bansal, K.

Publications and source records attributed to Bansal, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Mutation in Ralstonia pseudosolanacearum F1C1 cytochrome p450 homologue impairs virulence through root but not through shoot of tomato plants

Ralstonia pseudosolanacearum causes a lethal bacterial wilt disease in many plants. The pathogen enters through roots and systemically colonizes the xylem tissue, resulting in wilting and eventual death of the host. Using transposon mutagenesis followed by screening in tomato seedlings, we identified a mutant exhibiting virulence deficiency by root inoculation, but not by leaf inoculation. The mutation was recreated in the wild-type genome via natural transformation to prove the linkage of virulence deficiency with the transposon insertion. Whole genome sequencing revealed that the transposon insertion was in a cyp450 homologue, encoding cytochrome P450 monooxygenase. Two independent targeted mutations were generated in the cyp450 gene, and both the mutants recapitulated the root-specific virulence deficiency. The mutants rarely cause disease in mature plants following soil drenching but remained fully virulent upon petiole pricking inoculation. Complementation with the full length cyp450 gene amplified from the wild-type strain F1C1 restored virulence in the mutant. Compared to the wild-type F1C1, the cyp450 mutants exhibited greater sensitivity to tomato root extracts. HR-LCMS of tomato root extracts revealed the occurrence of several antimicrobial compounds. Cytochrome P450 enzymes are known to mediate the degradation or biosynthesis of diverse metabolites in bacteria. Considering the virulence difference due to the mode of inoculation, our findings indicate that cyp450 contributes to tissue-specific adaptation of the pathogen during infection has opened an avenue for integrating tissue metabolomics with bacterial wilt susceptibility research.

pathology↗

bioRxiv2026

Diversified Portfolios of Bacterial Communities in Peri-urban Miyawaki Forests and Grassland Shaping Ecosystem Functions and Services

Soil microflora is fundamental to ecosystem functioning, yet their contribution in Miyawaki afforestation, a globally implemented ecological engineering approach, remains poorly characterized. In the present study, we examined the bacterial taxonomic diversity and their functional potential in a peri-urban Miyawaki mini-forest and compared with a nearby grassland the pre-existing ecosystem across dry and wet seasons. The Miyawaki plantation comprised of highly diverse native trees, sub-trees and shrubs spanning evergreen and deciduous varieties, potentiating nitrogen-fixation, diverse litter generation and rooting strategies resulting in pronounced functional heterogeneity. Notably relative to grassland, the Miyawaki forest was intensively managed and supplemented with organic amendments, and supportive irrigation, buffering the seasonal moisture stress. Using 16S rRNA amplicon sequencing of soil eDNA, we characterized seasonal variation in soil bacterial communities in both the systems. The observed soil bacterial community organization in forest as compared to the unmanaged grassland indicates combined influence of vegetation structure, dense canopy cover, continuous litter generation and root exudates. Microbial assemblages in the forest specialised in heterotrophic complex carbon degradation, biofilm formation, exopolysaccharide production and sporulation pathways which suggests adaptive abilities to anoxic microsites and other stressful conditions. In contrast, grassland soils harboured less diversified bacterial communities dominated by phototrophic and oxidative stress adaptation pathways consistent with sun lit, non-irrigated and moisture-variable conditions. Nonetheless, functional divergence in dry season reflects temporal reorganization of microbial communities marking a gradual trend towards soil ecosystem development. Together, these findings establish microbial baseline for Miyawaki forests revealing how tree-dense mini-forests restructure soil bacterial communities relative to grasslands highlighting the value of identifying soil microbial indicators for critically evaluating urban afforestation outcomes over extended time scales to inform sustainable design and policy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/704982v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@15e1bb1org.highwire.dtl.DTLVardef@16c1dddorg.highwire.dtl.DTLVardef@11c99ecorg.highwire.dtl.DTLVardef@bd6d1d_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic representation of the study depicting the Miyawaki forest and nearby grassland.

ecology↗

bioRxiv2024

The neuroreceptors and transporters underlying spontaneous brain activity

Determining the neuromodulators driving brain activity is critical for understanding cognition and neuropathology. Neuromodulators act through neuroreceptors in a coordinated manner, yet their interconnected dynamics are often overlooked. We show that a neuroreceptor-based modeling framework using cortical density maps of 19 neuroreceptors and transporters from Positron Emission Tomography (PET) can model BOLD-derived brain activity. This framework reconstructs activity across four datasets (N = 314) identifying two neuroreceptor modules linked to higher-order associative or somatomotor and visual networks. Applying the framework to independent datasets, we recover the binding profiles of LSD and Modafinil, demonstrating consistency with known pharmacological and neurobiological associations. Additionally, it uncovered associations between neuroreceptors, transporters, and altered brain activity in neuropsychiatric disorders. These findings demonstrate the frameworks potential to elucidate neuromodulatory mechanisms and advance our understanding of brain function across diverse states and conditions.

neuroscience↗

bioRxiv2024

Quantifying the influence of biophysical factors in shaping brain communication through remnant functional networks

Functional connectivity (FC) reflects brain-wide communication essential for cognition, yet the role of underlying biophysical factors in shaping FC remains unclear. We quantify the influence of physical factors--structural connectivity (SC) and Euclidean distance (DC), which capture anatomical wiring and regional distance--and molecular factors--gene expression similarity (GC) and neuroreceptor congruence (RC), representing neurobiological similarity--on resting- state FC. We assess how these factors impact graph-theoretic and gradient features, capturing pairwise and higher-order interactions. By generating remnant functional networks after selectively removing connections tied to specific factors, we show that molecular factors, particularly RC, dominate graph-theoretic features, while gradient features are shaped by a mix of molecular and physical factors, especially GC and DC. SC has a surprisingly minor role. We also link FC alterations to biophysical factors in schizophrenia, bipolar disorder, and ADHD, with physical factors differentiating these groups. These insights are key for understanding FC across various applications, including task performance, development, and clinical conditions.

neuroscience↗

bioRxiv2024

A modulator of cognitive function: Cerebellum modifies human cortical network dynamics via integration

The cerebellum, with distinctive architecture and extensive cortical connections, has long been associated with motor control; however, evidence suggests its role extends beyond motor functions, playing a crucial role in cognitive processes. Despite these insights, how cerebellar computations modulate cortical networks remains elusive. Here, we evaluate dynamic network reconfigurations in the cerebral cortex connectivity following noninvasive inhibitory repetitive transcranial magnetic stimulation (rTMS) targeting the right cerebellum. Using dynamic community detection, we uncover the dynamic network properties by which cerebellar stimulation spreads through the cortex, inspecting the evolution of modular network structures prior to and after cerebellar stimulation. Our results indicate that: (1) flexibility, or the likelihood of network nodes to change module allegiances, increases post stimulation; (2) dynamic patterns in which module allegiances emerge and evolve are individualistic and do not follow a single functional prototype; and (3) cerebellar nodes play the role of integrators for distinct network modules. These results suggest that the cerebellum plays a pivotal role in modulating distributed cortical activity, seamlessly integrating and segregating information beyond motor control. This integrative capacity may underlie the cerebellums contributions to high-level cognitive functions and, more broadly, to the foundation of human intelligence.

neuroscience↗

bioRxiv2023

Phase variation in LPS O-antigen biosynthetic gene cluster of the rice pathogen Xanthomonas oryzaepv. oryzae

Bacteria respond to environmental cues in different ways. Phase variation is one such adaptation where heritable and reversible changes in DNA aid bacteria to alter the expression of specific genes. The bacterial plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) causes the serious bacterial blight disease of rice. The mucoid phenotype of Xoo colonies is attributed to the secreted exopolysaccharide (EPS), xanthan gum. Spontaneous non-mucoid variants of Xoo which are deficient in EPS production and virulence were observed to accumulate in long-term stationary phase cultures. This phenomenon was termed stationary phase variation and variant colonies as stationary phase variants (SPV). Several but not all of these SPVs have been earlier described to carry spontaneous insertions of endogenous insertion sequence elements in the gum operon which encodes genes involved in EPS biosynthesis. In this study, we show that a number of SPVs harbour variations in the lipopolysaccharide (LPS) outer antigen (O-antigen) biosynthetic gene cluster. The data revealed that the vast majority of variations are due to either insertion of endogenous insertion sequence (IS) elements or slipped strand mispairing (SSM). Also, it was observed that many of these SPVs exhibited reversion to wild type mucoid phenotype via restoration of the wild type genotype. The results indicate that the phenomenon of phase variation is occurring in the LPS O-antigen biosynthetic gene cluster of Xoo.

microbiology↗

bioRxiv2022

Deep phylotaxonogenomic revision of the genus Xanthomonas within family Xanthomonadaceae and proposal of novel family Frateuriaceae within order Xanthomonadales

Genus Xanthomonas is primarily comprise phytopathogenic species. In a recent study by carrying out deep phyto-taxonogenomics, we reported that even the genera Xylella, Stenotrophomonas and Pseudoxanthomonas are miss-classified and belong to genus Xanthomonas. Hence to understand the breadth of the genus, we carried out deep phylo-taxonogenomics of the order Xanthomonadales. Such investigation revealed that at least four more genera belong to genus Xanthomonas with prominent being Lysobacter. Further order level deep phylo-taxonogenomics revealed two major families. One being the original family Xanthomonadaceae and other is proposed as Frateuriaceae fam. nov. as synonym of family Rhodanobacteraceae with novel genus Frateuria gen. nov.

microbiology↗

bioRxiv2022

UVC-based air disinfection system for rapid inactivation of SARS-CoV-2 present in the air

The novel coronavirus disease 2019 (COVID-19) infections have rapidly spread throughout the world, and the virus has acquired an ability to spread via aerosols even at long distances. Hand washing, face-masking, and social distancing are the primary preventive measures against infections. With mounting scientific evidence, World Health Organisation (WHO) declared COVID-19 an air-borne disease. This ensued the need to disinfect air to reduce the transmission. Ultraviolet C (UVC) comprising the light radiation of 200-280 nm range is a commonly used method for inactivation of pathogens. The heating, ventilation, and air conditioning (HVAC) systems are not beneficial in closed spaces due to poor or no ability to damage circulating viruses. Therefore, standard infection-prevention practices coupled with a strategy to reduce infectious viral load in air substantially might be helpful in reducing virus transmissibility. In this study, we implemented UV light-based strategies to combat COVID-19 and future pandemics. We tested various disinfection protocols by using UVC-based air purification systems and currently installed such a system in workspaces, rushed out places, hospitals and healthcare facilities for surface, air, and water disinfection. In this study, we designed a prototype device to test the dose of UVC required to inactivate SARS-CoV-2 in aerosols and demonstrate that the radiation rapidly destroys the virus in aerosols. The UVC treatment renders the virus non-infectious due to chemical modification of nucleic acid. We also demonstrate that UVC treatment alters the Spike protein conformation that may further affect the infectivity of the virus. We show by using a mathematical model based on the experimental data that UVC-based air disinfection strategy can substantially reduce the risk of virus transmission. The systematic treatment by UVC of air in the closed spaces via ventilation systems could be helpful in reducing the active viral load in the air.

microbiology↗

bioRxiv2022

Within- and between-subject reproducibility and variability in multi-modal, longitudinal brain networks

Network analysis provides new and important insights into the function of complex systems such as the brain by examining structural and functional networks constructed from diffusion Magnetic Resonance Imaging (dMRI), functional MRI (fMRI) and Electro/Magnetoencephalography (E/MEG) data. Although network models can shed light on cognition and pathology, questions remain regarding the importance of these findings, due in part to the reproducibility of the core measurements and subsequent modeling strategies. In order to ensure that results are reproducible, we need a better understanding of within- and between-subject variability over long periods of time. Here, we analyze a longitudinal, 8 session, multi-modal (dMRI, and simultaneous EEG-fMRI), and multiple task imaging data set. We first investigate the reproducibility of individual brain connections and network measures and find that across all modalities, within-subject reproducibility is higher than between-subject reproducibility, reaffirming the ability to detect individual differences in network structure in both structural and functional human brain networks. We see high variability in the reproducibility of pairwise connections between brain regions, but observe that in EEG-derived networks, during both rest and task, alpha-band connectivity is consistently more reproducible than networks derived from other frequency bands. Further, reproducible connections correspond to strong connections. Structural networks show a higher reliability in network statistics than functional networks, and certain measures such as synchronizability and eigenvector centrality are consistently less reliable than other network measures across all modalities. Finally, we find that structural dMRI networks outperform functional networks in their ability to identify individuals using a fingerprinting analysis. Our results highlight that functional networks likely reflect state-dependent variability not present in structural networks, and that the analysis of either structural or functional networks to study individual differences should depend on whether or not one wants to take into account state dependencies of the observed networks.

neuroscience↗

bioRxiv2022

Xanthomonas indica sp. nov., a non-pathogenic bacterium isolated from healthy rice (Oryza sativa) seeds from India

Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560T and PPL568 were identified as members of genus Xanthomonas based on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage with X. sontii and X. sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of genus Xanthomonas with PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.

evolutionary biology↗

bioRxiv2022

Systematic hyper-variation and evolution at a lipopolysaccharide locus in the population of Xanthomonas species that infect rice and sugarcane

Advent of high throughput sequencing and population genomics is enabling researchers to investigate selection pressure at hyper-variable genomic loci encoding pathogen-associated molecular patter (PAMP) molecules like lipopolysaccharide (LPS) in an unprecedented manner. Xanthomonas is a model group of phytopathogenic bacteria that infects host in tissue-specific manner. Our in-depth investigation revealed that the successful emergence of lineages infecting major cereals and grasses like rice, sugarcane, and wheat was mediated by acquisition and later replacement of an ancestral type (BXO8) of LPS cassette by distinct one. In the population of the rice xylem pathogen, X. oryzae pv. oryzae (Xoo), the BXO8 is replaced by a distinct BXO1 type of cassette. Alternatively, in diverse Xanthomonas species that infect sugarcane, the BXO8 ancestral cassette has been replaced by yet another kind of Xvv type of LPS cassette, suggesting convergent evolution at an LPS locus mediated by horizontal gene transfer (HGT) events. Aside from xylem, two closely related lineages of X. oryzae that infect parenchyma tissue of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect citrus, walnut, and strawberry parenchyma, indicating yet another instance of parallel evolution facilitated by HGT. Our targeted and mega-population-based genome dynamic studies revealed potential role of acquisition of specific types of LPS cassettes in the emergence and evolution of tissue specificity in Xanthomonas. Additional cellular, molecular, genetic, and plant studies will help us figure out how a distinct type of LPS help Xanthomonas pathovars and lineages adapt to parenchyma and xylem tissues.

genomics↗

bioRxiv2021

Intermittent brain network reconfigurations and the resistance to social media influence

Since their development, social media has grown as a source of information and has a significant impact on opinion formation. Individuals interact with others and content via social media platforms in a variety of ways but it remains unclear how decision making and associated neural processes are impacted by the online sharing of informational content, from factual to fabricated. Here, we use EEG to estimate dynamic reconfigurations of brain networks and probe the neural changes underlying opinion change (or formation) within individuals interacting with a simulated social media platform. Our findings indicate that the individuals who changed their opinions are characterized by less frequent network reconfigurations while those who did not change their opinions tend to have more flexible brain networks with frequent reconfigurations. The nature of these frequent network configurations suggests a fundamentally different thought process between intervals in which individuals are easily influenced by social media and those in which they are not. We also show that these reconfigurations are distinct to the brain dynamics during an in-person discussion with strangers on the same content. Together, these findings suggest that brain network reconfigurations may not only be diagnostic to the informational context but also the underlying opinion formation. Author SummaryDistinctive neural underpinnings of opinion formation and change during in-person and online social interactions are not well understood. Here, we analyze EEG recordings of the participants interacting with a simulated social media platform and during an in-person discussion using a network-based analysis approach. We show that the structure of network reconfigurations during these interactions is diagnostic of the opinion change and the context in which information was received.

neuroscience↗

bioRxiv2021

Reconfigurations in brain networks upon awakening from slow wave sleep: Interventions and implications in neural communication

Sleep inertia is the brief period of impaired alertness and performance experienced immediately after waking. While the neurobehavioral symptoms of sleep inertia are well-described, less is known about the neural mechanisms underlying this phenomenon. A better understanding of the neural processes during sleep inertia may offer insight into the cognitive impairments observed and the awakening process generally. We observed brain activity following abrupt awakening from slow wave sleep during the biological night. Using electroencephalography (EEG) and a network science approach, we evaluated power, clustering coefficient, and path length across frequency bands under both a control condition and a blue-enriched light intervention condition in a within-subject design. We found that under control conditions, the awakening brain is typified by an immediate reduction in global theta, alpha, and beta power. Simultaneously, we observed a decrease in the clustering coefficient and an increase in path length within the delta band. Exposure to blue-enriched light immediately after awakening ameliorated these changes, but only for clustering. Our results suggest that long-range network communication within the brain is crucial to the waking process and that the brain may prioritize these long-range connections during this transitional state. Our study highlights a novel neurophysiological signature of the awakening brain and provides a potential mechanistic explanation for the effect of light in improving performance after waking. One sentence summaryBlue-enriched light partially accelerates the rapid prioritization of long-range communication within the human brain that characterizes sleep inertia

neuroscience↗

bioRxiv2021

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant

BackgroundEmergence of new variant of SARS-CoV-2, namely omicron, has posed a global concern because of its high rate of transmissibility and mutations in its genome. Researchers worldwide are trying to understand the evolution and emergence of such variants to understand the mutational cascade events. MethodsWe have considered all omicron genomes (n = 302 genomes) available till 2nd December 2021 in the public repository of GISAID along with representatives of variants of concern (VOC), i.e., alpha, beta, gamma, delta, and omicron; variant of interest (VOI) mu and lambda; and variant under monitoring (VUM). Whole genome-based phylogeny and mutational analysis were performed to understand the evolution of SARS CoV-2 leading to emergence of omicron variant. ResultsWhole genome-based phylogeny depicted two phylogroups (PG-I and PG-II) forming variant specific clades except for gamma and VUM GH. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). ConclusionDelta and omicron have evolutionary diverged into distinct phylogroups and do not share a common ancestry. While, omicron shares common ancestry with VOI lambda and its evolution is mainly derived by the non-synonymous mutations.

genomics↗

bioRxiv2021

Ultrasound exposure enhances cellular uptake of nanoscale cargos

DNA nanotechnology utilizes DNA as a structural molecule to design palette of nanostructures with different shapes and sizes. DNA nanocages have demonstrated significant potential for drug delivery. Therefore, enhancing the delivery of DNA nanocages into cells can improve their efficacy as drug delivery agents. Numerous studies have reported the effects of ultrasound for enhancing drug delivery across biological barriers. The mechanical bioeffects caused by cell-ultrasound interaction can cause sonoporation, leading to enhanced uptake of drugs, nanoparticles, and chemotherapeutic agents through membranes. Whether ultrasound exposure can enhance the delivery of DNA nanocages has not been explored, which is the focus of this study. Specifically, we investigated the effects of ultrasound on the cellular uptake of propidium Iodide, fluorescent dextrans, and DNA nanostructures). We provide evidence of modulation of pore formation in the cell membrane by ultrasound by studying the intracellular uptake of the impermeable dye, propidium iodide. Treatment of cells with low amplitudes of ultrasound enhanced the uptake of different sizes of dextrans and DNA based nanodevices. These findings could serve as the foundation for further development ultrasound-enabled DNA nanostructure delivery and for specific understanding of underlying biological mechanisms of interaction between ultrasound parameters and cellular components; the knowledge that can be further explored for potential biological and biomedical applications.

bioengineering↗

bioRxiv2021

"Understanding Cortical Arousals during Sleep from Leg Movements: A Pilot Study."

Leg movements during sleep occur in patients with sleep pathology and healthy individuals. Some (but not all) leg movements during sleep are related to cortical arousals which occur without conscious awareness of the patient but have a significant effect of sleep fragmentation. Detecting leg movements during sleep that are associated with cortical arousals can provide unique insight into the nature and quality of sleep in both health and disease. In this study, a novel leg movement monitor is used in conjunction with polysomnography to better understand the relationship between leg movement and electroencephalogram (EEG) defined cortical arousals. In an approach that we call neuro-extremity analysis, graph theoretic, directed connectivity metrics are used to interrogate the causal links between neural activity measured by EEG and leg movements measured by the sensors within the leg movement monitor. The leg movement monitor in this study utilizes novel capacitive displacement sensors, and a 9-axis inertial measurement unit to characterize leg and foot movements. First, the capacitive displacement measures more closely related to EEG-defined cortical arousals than inertial measurements. Second, the neuro-extremity analysis reveals a temporally evolving connectivity pattern that is consistent with a model of cortical arousals in which brainstem dysfunction leads to near-instantaneous leg movements and a delayed, filtered signal to the cortex. Neuro-extremity analysis reveals causal relationships between EEG and leg movement sensor time-series data that may aid researchers to better understand the pathophysiology of cortical arousals associated with leg movements during sleep.

neuroscience↗

bioRxiv2021

Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas with Stenotrophomonas and Pseudoxanthomonas as misclassified relatives

Genus Xanthomonas is a group of phytopathogens which is phylogenetically related to Xylella, Stenotrophomonas and Pseudoxanthomonas following diverse lifestyles. Xylella is a lethal plant pathogen with highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono-genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas species. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan genome analysis identified set of unique genes associated with sub-lineages representing plant associated Xanthomonas clade and nosocomial origin Stenotrophomonas. Overall, our study reveals importance to reconcile classical phenotypic data and genomic findings in reconstituting taxonomic status of these four genera. Significance StatementXylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. The pathogen is transmitted by an insect vector to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is extremely reduced both in terms of size (2Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria along with comparative studies, we assert the need of unification of Xanthomonas with its misclassified relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.

genomics↗

bioRxiv2021

Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: a pan India study

COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India. In the present study, we aim for a cross-sectional analysis since its first incidence up to 26th July 2021. We have performed the pan Indian evolutionary study using 20,086 high-quality complete genomes of SARS-CoV-2. Based on the number of cases reported and mutation rates, we could divide the Indian epidemic into seven different phases. First, three phases constituting the pre-first wave had a very less average mutation rate (<11), which increased in the first wave to 17 and then doubled in the second wave (~34). In accordance with the mutation rate, variants of concern (alpha, beta, gamma and delta) and interest (eta and kappa) also started appearing in the first wave (1.5% of the genomes), which dominated the second (~96% of genomes) and post-second wave (100% of genomes) phases. Whole genome-based phylogeny could demarcate the post-first wave isolates from previous ones by the point of diversification leading to incidences of VOCs and VOIs in India. Nation-wide mutational analysis depicted more than 0.5 million events with four major mutations in ~97% of the total 20,086 genomes in the study. These included two mutations in coding (spike (D614G) and NSP 12b (P314L) of RNA dependent RNA polymerase), one silent mutation (NSP3 F106F) and one extragenic mutation (5 UTR 241). Large scale genome-wide mutational analysis is crucial in expanding knowledge on evolution of deadly variants of SARS-CoV-2 and timely management of the pandemic.

genomics↗