Biology subjects

Sowpati, D. T.

Publications and source records attributed to Sowpati, D. T..

At least 19 recordsLinked to original sources

bioRxiv2026

Population-Scale Landscape of Mobile Element Insertions Across 82 Diverse Indian Populations

Mobile element insertions (MEIs) are a major source of structural variation in human DNA that can affect gene regulation and disrupt coding sequences. Population-scale MEI catalogs remain disproportionately skewed toward European-ancestry cohorts, with limited representation from India despite comprising nearly one-sixth of the global population and encompassing thousands of genetically distinct, largely endogamous communities. We characterized non-reference Alu and LINE1 insertions in 7,478 whole genomes from the GenomeIndia project, representing 82 populations selected to capture Indias geographic, linguistic, and social diversity. We cataloged 26,977 Alu and 7,075 LINE1 insertions, identifying 18,982 previously unreported insertions absent from existing publicly available MEI databases. Insertions bore signatures of purifying selection, depleted in exons and active chromatin and enriched in quiescent regions. MEI variants recapitulated the population structure seen in SNP data. Regulatory variation associated with MEIs was strongly population-structured, with a substantial fraction of European-defined MEI-eQTLs absent in the GenomeIndia cohort or carried at sharply different frequencies across communities, and MEIs in high linkage disequilibrium with GWAS variants. Sixty-nine insertions fell within exons, including a truncating LINE1 in CYP2J2 carried across five populations and a community-specific Alu in CABYR with a founder-effect signature. Collectively, these results reveal a layer of population-specific mobile element variation in Indian populations that is not captured by existing European-anchored reference resources. These variants represent potentially novel sources of genetic variation contributing to lack of transferability of disease associations across populations.

genomics↗

bioRxiv2025

ATaRVa: Analysis of Tandem Repeat Variation from Long Read Sequencing data

Tandem Repeats (TRs) are contiguous repetitions of DNA motifs whose variations modulate key cellular processes and traits. Their expansions are causally linked to over 70 neurological disorders in humans. Historically, genotyping TRs has been challenging due to their low sequence complexity and allele lengths exceeding typical short-read sequencing capabilities. While long-read sequencing improves TR genotyping by spanning large expansions and sequencing native DNA molecules, existing long-read genotypers often are inaccurate, computationally inefficient, and show platform-specific biases. Here, we present ATaRVa, a genotyper that achieves superior accuracy across both PacBio and Oxford Nanopore platforms, while running [~]15x faster than existing tools. Beyond genotyping, ATaRVa features sequence-level motif decomposition and methylation profiling. Evaluated across diverse datasets and genome-wide catalogs, ATaRVa especially excels in low coverage datasets, and accurately identifies known pathogenic expansions in clinical samples. Importantly, by quantifying uninterrupted target motifs in a population scale analysis, the tool systematically resolves false positives caused by benign, interrupted alleles. In addition, we present VisuaMiTRa, an auxiliary interface that enables interactive visualization of motif-level decomposition and base-level methylation of the TR alleles. By combining high computational efficiency with sequence-level structural awareness, ATaRVa provides a highly scalable framework for TR analysis in both population cohorts and clinical settings.

genomics↗

bioRxiv2025

Ribbit: Accurate identification and annotation of complex tandem repeat sequences in genomes

DNA tandem repeats (TRs) are crucial for genomic functions like protein binding, chromatin modulation, splicing, and gene regulation. Abnormal length variations in TRs, especially expansions, are associated with over 60 neurodegenerative diseases. The function and stability of a TR locus is dependent on its sequencing composition and purity. Recent studies report the disease-causing propensity of non-canonical motif expansions in TR loci, and highlight the intricate polymorphism dynamics in complex loci encompassing adjacent, overlapping, and nested TRs. These reports emphasize the need for precise definition and motif decomposition of TR loci. To address this, we present Ribbit, a tool that accurately and efficiently identifies and annotates TR loci in a genome. Ribbit uses 2-bit representation of DNA sequences for rapid identification of TRs of 2-100 bp motif size and resolves complex TR structures. Ribbit efficiently handles imperfections such as indels and substitutions, providing insights into nested and compound TR relationships through detailed motif decomposition. Comparative analyses using simulated data show Ribbit outperforms existing tools like Dot2dot and TRF in terms of runtime and accuracy. Ribbit reports TR loci in the human genome with lower redundancy than TRF and provides resolved TR regions comparable to variation clusters reported in recent catalogues. Therefore, Ribbit can be leveraged to understand the evolution and biology of complex TR regions in large genomes.

bioinformatics↗

bioRxiv2024

Developmental functions of rapgef1b in neural crest specification and presomitic mesoderm patterning

RAPGEF1, a guanine nucleotide exchange factor, regulates signaling and cytoskeletal dynamics in mammalian cells, yet its role in development remains unclear as Rapgef1 null mouse embryos do not survive beyond implantation. We demonstrate that zebrafish rapgef1 is maternally expressed, and its paralogs, rapgef1a and rapgef1b, exhibit tissue and developmental stage-specific splicing. Disruption of rapgef1b caused brain and somite defects, impaired cranial neural crest specification, and microcephaly-like phenotypes, uncovering its previously uncharacterized functions in morphogenesis and tissue patterning. Transcriptomic analyses and differential gene expression provide fresh insights into the developmental functions of rapgef1b in presomitic mesoderm and somitogenesis by modulating the Wnt/{beta} catenin signaling. Rapgef1b deficient embryos also showed spindle pole disorganization and chromosome mis-congression, linking Rapgef1 to centrosome-mediated mitotic fidelity. Together, our findings identify Rapgef1b as a key regulator of neural crest development, mesodermal morphogenesis, and early mitoses, highlighting its tissue-specific functions during vertebrate embryogenesis. TeaserIn this study, we show that rapgef1b is essential for shaping the embryonic brain, somites, and body axis by regulating gene expression, cell division, survival, and differentiation. Our findings reveal a new dimension of signaling-mediated cell fate specification during early vertebrate development.

developmental biology↗

bioRxiv2024

Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation

Long read sequencing technologies such as Oxford Nanopore (ONT) offer direct, simultaneous detection of DNA base modifications. The recent migration of ONT to the upgraded R10 chemistry has spurred the development of diverse methylation detection models. However, their performance and accuracy remain unclear. Here, leveraging diverse bacterial, plant, and mammalian datasets, we systematically evaluate the current landscape of tools and models for studying DNA methylation using nanopore sequencing. Our results demonstrate that the older models remain the best choice for studying CpG methylation. We note substantial improvement of newer tools in identifying 5-methylcytosine in non-CG contexts, 6-methyladenine, and 4-methylcytosine. We highlight the sensitivity of various tools to confounding methylation nearby. We also assess the computational performance of various tools, and effects of sequencing depth, methylation abundance, read quality, and basecalling mode. Our reusable pipelines and fully open access datasets provide a framework of resources to empower future benchmarking efforts. Our work thus details the strengths and limitations of the state-of-the-art methylation models and outlines practical guidelines for researchers using nanopore sequencing to study DNA modifications.

genomics↗

bioRxiv2024

Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation

Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. We show that stiffness-dependent spreading of mouse ESCs (mESCs) induces DNA damage through nuclear compression, with DNA damage causing differentiation through early induction of Lamin A/C expression. Interestingly, differentiation is associated with rescue of DNA damage and activation of the DDR factor ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression upon ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.

cell biology↗

bioRxiv2024

NEMO: Improved and accurate models for identification of 6mA using Nanopore sequencing

DNA methylation plays a key role in epigenetic regulation across lifeforms. Nanopore sequencing enables direct detection of base modifications. While multiple tools are currently available for studying 5-methylcytosine (5mC), there is a paucity of models that can detect 6-methyladenine (6mA) from raw nanopore data. Leveraging the motif-driven nature of bacterial methylation systems, we generated 6mA identification models that vastly surpass the accuracy of the current best model. Our work enables the study of 6mA at a single-base resolution in new as well as existing nanopore datasets.

genomics↗

bioRxiv2023

Divergent downstream biosynthetic pathways are supported by L-cysteine synthases of Mycobacterium tuberculosis

Mycobacterium tuberculosiss (Mtb) autarkic lifestyle within the host involves rewiring its transcriptional networks to combat host-induced stresses. With the help of RNA-seq performed under various stress conditions, we identified that genes belonging to Mtb sulfur metabolism pathways are significantly upregulated during oxidative stress. Using an integrated approach of microbial genetics, transcriptomics, metabolomics, animal experiments, chemical inhibition, and rescue studies, we investigated the biological role of non-canonical L-cysteine synthases, CysM and CysK2. While transcriptome signatures of Rv{Delta}cysM and Rv{Delta}cysK2 appear similar under regular growth conditions, we observed unique transcriptional signatures when subjected to oxidative stress. We followed pool size and labelling (34S) of key downstream metabolites, viz. mycothiol and ergothioneine, to monitor L-cysteine biosynthesis and utilization. This revealed the significant role of distinct L-cysteine biosynthetic routes on redox stress and homeostasis. CysM and CysK2 independently facilitate Mtb survival by alleviating host-induced redox stress, suggesting they are not fully redundant during infection. With the help of genetic mutants and chemical inhibitors, we show that CysM and CysK2 serve as unique, attractive targets for adjunct therapy to combat mycobacterial infection.

microbiology↗

bioRxiv2023

De novo genome assembly of the saw-scaled viper Echis carinatus, a medically important venomous snake in the Indian Subcontinent

Echis carinatus is a widely distributed venomous snake in the Indian subcontinent. It is one of the "Big Four" snake species responsible for mortality and severe health complications caused by envenomations. Given the significance of the species for human health, we assembled and annotated the whole genome of E. carinatus. Using long reads for assembly and short reads for correction, we achieved a highly contiguous 1.57Gb assembly, with a contig N50 of 17.1 Mb and scaffold N50 of 23.5 Mb. We could map 96.58% of our reads back to the assembled genome, and Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 97.4%, indicates near completeness. 48.59% of the genome had repeat elements. The predominant types of repeats include retrotransposons (LINEs, SINEs and LTR elements), DNA transposons and satellite DNA (SSRs). Additionally, we conducted a gene prediction analysis, identifying a total of 26,711 protein-coding genes. These genes included alternatively spliced products, leading to the prediction of 31,106 proteins, 77.6% of which were successfully annotated using Blastp and InterProScan. Out of the total predicted gene set, we identified 119 toxin-coding genes, crucial for venom toxin production in the species. The acquisition of toxin sequence-based information resulted in a valuable dataset of genes that are involved in venom production in E. carinatus. This dataset advances our understanding of the biological processes underlying venom production and lays the foundation for the development of new antivenom formulations.

genomics↗

bioRxiv2023

Derivation of trophoblast stem cells unveils unrestrained potential of mouse ESCs and epiblast

mESCs and epiblast are considered to follow strict lineage adherence and lack the potential to contribute to trophoectoderm. Here, we report the derivation of trophoblast stem cells (ESTS) from the mESCs. The single-cell transcriptome and molecular characterization of ESTS show similarity with TSCs. They efficiently integrate into the TE compartment of the blastocyst and contribute to the placenta during development. We discovered GSK3{beta} as a critical regulator of the TE fate of ESCs. It plays a vital stage-specific role during ESTS derivation. We further show {beta}-CATENIN and an intron-I regulatory element of Cdx2 are essential for the TE fate of ESCs. We further show that the mouse epiblast can readily differentiate into TE lineage. In contrast to the paradigm of the restricted potential of pluripotent ESCs and epiblast, our data shows that murine ESCs and epiblast have the unrestrained developmental potential for extraembryonic lineages.

developmental biology↗

bioRxiv2023

Efficient self-organization of blastoids solely from mouse ESCs is facilitated by transient reactivation of 2C gene network

Human pluripotent stem cells (hPSCs) can self-organize into a blastocyst-like structure (blastoid) by virtue of their full developmental potential. The pluripotent mouse embryonic stem cells (mESC) are considered to lack this potential and hence can form blastoids only when combined with trophoblast stem cells. We performed a small molecule and cytokine screen to demonstrate that mESC have full potential to efficiently self-organize themselves into E-blastoids (ESC-blastoids). The morphology, cell lineages and the transcriptome of these blastoids resemble the mouse blastocyst. The E-blastoids undergo implantation and in utero development in mice. The transient reactivation of the 2C-gene network by retinoid signaling is essential for E-blastoid generation. GSK3{beta} activity is critical for retinoid signaling and consequent 2C gene network activation. Collectively, the mESC possess full developmental potential to generate blastoids similar to hPSCs and other mammals. The plasticity of PSCs to self-organize into blastoids is not exclusive to humans or larger mammals; rather, it could be a general feature shared by most mammals, including rodents.

developmental biology↗

bioRxiv2023

Composition of nasopharyngeal microbiota in individuals with SARS-COV-2 infection across three COVID-19 waves in India

Multiple variants of the SARS-CoV-2 virus have been plaguing the world through successive waves of infection over the past three years. Studies by independent research groups across geographies have shown that the microbiome composition in COVID-19 patients (CP) differ from that of healthy individuals (CN). However, such observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern. We also present the variations in microbiota of symptomatic vs asymptomatic COVID-19 patients. The nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection. To our knowledge, this is the first longitudinal study which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Such studies not only pave way for better understanding of the disease pathophysiology but also help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery.

microbiology↗

bioRxiv2022

SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses

Delta variant of SARS-CoV-2 has caused more severe infections than its previous variants. We studied the host innate immune response to Delta, Alpha and two earlier variants to map the evolution of the recent ones. Our biochemical and transcriptomic studies reveal that Alpha and Delta have progressively evolved over the ancestral variants by silencing innate immune response, thereby limiting cytokine and chemokine production. Though Alpha silenced RLR pathway just as Delta, it failed to persistently silence the innate immune response unlike Delta. Both Alpha and Delta have evolved to resist IFN treatment while they are still susceptible to RLR activation, further highlighting the importance of RLR-mediated, IFN-independent mechanisms in restricting SARS-CoV-2. Our studies reveal that SARS-CoV-2 Delta has integrated multiple mechanisms to silence host innate immune response and evade IFN response. Deltas silent replication and sustained suppression of host innate immune response, possibly resulting in delayed or reduced intervention by the adaptive immune response, could potentially contribute to the severe symptoms and poor recovery index associated with it.

immunology↗

bioRxiv2021

DiviSSR: Simple arithmetic for efficient identification of tandem repeats

Numerical or vector representations of DNA sequences have been applied for identification of specific sequence characteristics and patterns which are not evident in their character (A, C, G, T) representations. These transformations often reveal a mathematical structure to the sequences which can be captured efficiently using established mathematical methods. One such transformation, the 2-bit format, represents each nucleotide using only two bits instead of eight for efficient storage of genomic data. Here we describe a mathematical property that exists in the 2-bit representation of tandemly repeated DNA sequences. Our tool, DiviSSR (pronounced divisor), leverages this property and subsequent arithmetic to achieve ultrafast and accurate identification of tandem repeats. DiviSSR can process the entire human genome in [~]30s, and short sequence reads at a rate of >1 million reads/s on a single CPU thread. Our work also highlights the implications of using simple mathematical properties of DNA sequences for faster algorithms in genomics. AvailabilityDiviSSR can be installed directly using python pip. The source code and documentation of DiviSSR are available at https://github.com/avvaruakshay/divissr.git.

bioinformatics↗

bioRxiv2021

Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients

BackgroundOne of the most perplexing aspects of infection with the SARS-CoV-2 virus has been the variable response elicited in its human hosts. Investigating the transcriptional changes in individuals affected by COVID-19 can help understand and predict the degree of illness and guide clinical outcomes in diverse backgrounds. MethodsAnalysis of host transcriptome variations via RNA sequencing from naso/oropharyngeal swabs of COVID-19 patients. ResultsWe report strong upregulation of the innate immune response, especially type I interferon pathway, upon SARS-CoV-2 infection. Upregulated genes were subjected to a comparative meta-analysis using global datasets to identify a common network of interferon stimulated and viral response genes that mediate the host response and resolution of infection. A large proportion of mis-regulated genes showed a reduction in expression level, suggesting an overall decrease in host mRNA production. Significantly downregulated genes included those encoding olfactory, taste and neuro-sensory receptors. Many pro-inflammatory markers and cytokines were also downregulated or remained unchanged in the COVID-19 patients. Finally, a large number of non-coding RNAs were identified as down-regulated, with a few of the lncRNAs associated with functional roles in directing the response to viral infection. ConclusionsSARS-CoV-2 infection results in the robust activation of the bodys innate immunity. Reduction of gene expression is well correlated with the clinical manifestations and symptoms of COVID-19 such as the loss of smell and taste, and myocardial and neurological complications. This study provides a critical dataset of genes that will enhance our understanding of the nature and prognosis of COVID-19.

bioinformatics↗

bioRxiv2020

Intra-host variability in global SARS-CoV-2 genomes as signatures of RNA editing: implications in viral and host response outcomes

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying Variants Of Concern (VOC). Besides, viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host Single Nucleotide Variations (iSNVs). Analysing 1, 347 samples collected till June 2020, we recorded 18, 146 iSNV sites throughout the SARS-CoV-2 genome. Both, mutations in RdRp as well as APOBEC and ADAR mediated RNA editing seem to contribute to the differential prevalence of iSNVs in hosts. Noteworthy, 41% of all unique iSNVs were reported as SNVs by 30th September 2020 in samples submitted to GISAID, which increased to [~]80% by 30th June 2021. Following this, analysis of another set of 1, 798 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) variations appeared as iSNVs before getting fixed in the population. We also observe hyper-editing events at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/417519v3_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@12b6ac2org.highwire.dtl.DTLVardef@16df897org.highwire.dtl.DTLVardef@dbbec2org.highwire.dtl.DTLVardef@c8de14_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2020

Docosahexaenoic acid (DHA), a nutritional supplement, modulates steroid insensitivity in asthma

Asthmatics with poor steroid responsiveness are now found to use health services at higher frequency and contribute to socio-economic burden disproportionately. We have previously shown that a ω-6 fatty acid metabolite leads to a severe and steroid insensitive asthma-like condition in mice. Here, we investigated the role of retinoid-x-receptor gamma (RXRγ) and Docosahexaenoic acid (DHA), a ω3 fatty acid rexinoid ligand of RXR, on the features of steroid insensitivity in asthmatic condition. RXRγ was found to be reduced in the lungs of human asthmatics and mice with steroid insensitive allergic airway inflammation. RXRγ knockdown in naïve mice led to spontaneous asthma like features whereas RXRγ knockdown in allergic mice led to steroid insensitive asthma features. We observed while RXRγ binds to the glucocorticoid receptor (GR) gene and regulates its transcription, DHA increases the GRα expression in human bronchial epithelial cells and reverses the steroid insensitive features in mice with allergic airway inflammation. Docosahexaenoic acid (DHA), a ligand of RXR, was reduced in the sera of steroid-insensitive asthmatics. We conclude that DHA may prove to be a promising steroid sensitizing agent for the treatment of steroid insensitive asthmatics.Summary The molecular regulation of glucocorticoid receptor by retinoid-x-receptor gamma (RXRgama) has an implication in steroid insensitive asthma as we found that Docosahexaenoic acid (DHA), a nutritional supplement and natural ligand of RXRgamma, improves steroid sensitivity in steroid insensitive mice model of asthma and DHA levels are found to be low in steroid insensitive asthmatic patients.Competing Interest StatementThe authors have declared no competing interest.Abbreviations usedAAIAllergic airway inflammationAHRAirway hyper-responsivenessATRAAll-trans retinoic acidAUArbitrary unitsBALBronchoalveolar lavageBEAS-2BHuman bronchial epithelial cellsCECockroach allergen extractChIPChromatin Immunoprecipitation9CRA9-cis retinoic acidDEXDexamethasoneDHADocosahexaenoic acidDMSODimethyl sulfoxideELISAEnzyme-linked immunosorbent assayGAPDHGlyceraldehyde 3-phosphate dehydrogenaseGLucGaussia luciferaseGRαGlucocorticoid receptor alphaGREGlucocorticoid receptor elementH & EHaematoxylin and eosinIFNγInterferon gammaIgEImmunoglobulinE ILInterleukinKCKeratinocyte chemoattractant15-LOX15-lipoxygenaseMCF-7Human breast adenocarcinoma cell lineMCP1-αMonocyte chemoattractant protein1-αNF-κBNuclear Factor kappa-light-chain-enhancer of activated B cellsO.EOverexpressionOVAOvalbuminp38-MAPKp38 mitogen-activated protein kinasePBSPhosphate buffered salineRARRetinoic acid receptorPDTCPyrrolidinedithiocarbamateRXRERexinoid receptor elementRXRγRetinoid-x-receptor gamma13-S-HODE13-hydroxyoctadecadienoic acidSEMStandard error meansiRNASmall interfering RNASTAT-6Signal transducer and activator of transcription 6ThT helperVEHVehicleView Full Text

immunology↗

bioRxiv2020

A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates

From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants - C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 x 10-3 variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India.

genomics↗