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India first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geoclimatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic. India, 2020). However, while the global focus was on China and other eastern countries like South Korea and Japan; European countries, middle-east and the USA reported a surge in cases of COVID-19, pressing the WHO to declare it as a pandemic. March 2020 onwards, India also witnessed a surge of imported cases from countries other than China which has been further assisted with local transmission. In March, imposition of nationwide lockdown checked the epidemic curve. Despite these measurements, India is at the verge of a large outbreak as the transmission is rapidly increasing with more than 100,000 cases of COVID-19 having been reported in the third week of May, 2020.We carried out WGS of SARS-CoV-2 (n=104) from Pan-India through the network of Integrated Disease Surveillance Program (IDSP) of National Centre of Disease Control (NCDC), Delhi. We report here a comprehensive and integrative genomic view of SARS-CoV-2 in the Indian subcontinent. In this study, we combine genetic and epidemiological data to understand the genetic diversity, evolution, and epidemiology of SARS-CoV-2 across India. The spectrum of variations would be an important tool towards contact tracing, effective diagnostics and backbone for drug and vaccine development. METHODS Subject recruitmentThe study was conducted jointly by the NCDC and CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB). Institutional ethical clearance was obtained at both the places prior to initiation of research. A total of 127 laboratory confirmed cases of COVID-19 from a targeted testing representing different locations (as described in Table- 1 and supplementary figure-1) were included in the study for genomic analyses. Targeted testing involved suspected cases;having symptoms (fever, cough and breathlessness) with recent travel history to high-risk countries or positive contacts of COVID-19 cases. Sample collection and Viral RNA isolationThe nasopharyngeal and oropharyngeal swabs (in ...

Over 95% of human genes undergo alternative splicing (AS) in a developmental, tissue-specific, or signal transduction-dependent manner. A number of factors including binding of cis-acting sequences by RNA-binding proteins (RBPs) are known to affect AS, but the combinatorial mechanisms leading to the distribution of spliced isoforms remain largely unstudied. Here, in 9011 samples from 532 individuals across 53 tissues from the Genotype-Tissue Expression (GTEx) resource, we identified 4,135 genes with sex-biased expression and 5,925 sex-biased AS events. We find that factors including escape from X-chromosomal inactivation, presence of Alu elements, and oestrogen receptor binding sites affect sex-biased AS. We utilize hierarchical Bayesian modelling to characterize the interactions of exon skipping, gene expression, and RBPs, and demonstrate two categories of sex-biased AS that differ with respect to splice site scores, gene expression, RBP levels, and skipping/inclusion ratio. Alternative splicing (AS), a process by which splice sites are used differentially to create protein diversity, plays an important role in development, 1 disease, 2 and aging. 3 Although some splicing isoforms are produced in the same proportions in all or most cell types, AS is often regulated by developmental or differential cues or in response to external stimuli. 4 Several mechanisms have been demonstrated to regulate AS, although their combinatorial interactions remain poorly understood. Binding of RNA-binding proteins (RBPs) to intronic or exonic cis-acting regulatory sequences may promote or suppress local AS events. 5 Additionally, chromatin-level mechanisms also play a role in AS regulation. Nucleosome density is higher within exons than in introns, suggesting the existence of RNA polymerase II (RNA Pol II)-mediated cross-talk between chromatin structure and exon-intron architecture. 6 Alternative exons with suboptimal splicing signals may require more time to be recognized by the splicing machinery, and faster transcriptional elongation by RNA Pol II may influence exon skipping. 7

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Severe asthma is chronic airway disease, exhibit poor response to conventional asthma therapies.Growing evidence suggests that elevated hypoxia increases the severity of asthmatic inflammation among patient and model systems. In this study, we elucidate the therapeutic effect and mechanistic basis of Adhatoda Vasica (AV) aqueous extract on acute allergic as well as severe asthma subtypes, at physiological, histopathological and molecular levels using mouse models.We observed, oral administration of AV extract not only attenuates the increased airway resistance and inflammation in acute allergic asthmatic mice but also alleviates the molecular signatures of steroid (dexamethasone) resistance like IL-17A, KC and HIF-1 (hypoxia inducible factor-1alpha) in severe asthmatic mice. The reversal of pathophysiological features after AV treatment is associated with inhibition of elevated HIF-1 levels by restoring the expression of its negative regulator-PHD2 (prolyl hydroxylase domain-2). This was further confirmed in acute and severe asthma model developed by augmented hypoxic response. Further, AV treatment reverses cellular hypoxia-induced mitochondrial dysfunction in human bronchial epithelial cells -evident from bioenergetic profiles and morphological analysis of mitochondria. Involvement of hypoxia and mitochondrial dysfunction in asthma severity is being increasingly realised. Extract of AV although widely used in Ayurveda practice for the treatment of diverse respiratory ailments, including asthma, its molecular basis of action and effect on severe asthma subtype is still unclear. This study, demonstrates therapeutic mechanism of Adhatoda Vasica through hypoxia-induced mitochondrial dysfunction and highlights its potential in the treatment of severe steroid-resistant asthma. Significance StatementSevere asthma is a global health concern found to be unresponsive to current treatment modalities involving corticosteroids. Recent findings suggest that elevated hypoxia has a critical role in severity of asthma. Here, we report therapeutic treatment with aqueous extract of Adhatoda Vasica (AV), an ayurvedic medicine, is effective in attenuation of severe steroid-insensitive asthmatic features in mice. The observed anti-asthmatic effects of AV was through inhibition of hypoxic response, both in vivo and in vitro. AV also reverses mitochondrial dysfunction, a key consequence associated with hypoxia, and asthma. This study not only highlights the translational potential of AV for the treatment of severe asthma but also provides opportunities for its usage in other disease conditions where hypoxia is pertinent. 250,000 annual deaths, asthma significantly contributes to the global health burden (3). Initially, it was considered to be primarily an allergic, eosinophilic Th2 biased disease with involvement of its cytokines (IL-4, IL-5 and IL-13) in the inflammatory cascade leading to allergic exacerbations (4).However, there are non-Th2 asthma patho-phenotypes, where cells like Th17, Th1 and their respective cytokines play a ...

Precision medicine aims to move from traditional reactive medicine to a system where risk groups can be identified before the disease occurs. However, phenotypic heterogeneity amongst the diseased and healthy poses a major challenge for identification markers for risk stratification and early actionable interventions. In Ayurveda, individuals are phenotypically stratified into seven constitution types based on multisystem phenotypes termed “Prakriti”. It enables the prediction of health and disease trajectories and the selection of health interventions. We hypothesize that exome sequencing in healthy individuals of phenotypically homogeneous Prakriti types might enable the identification of functional variations associated with the constitution types. Exomes of 144 healthy Prakriti stratified individuals and controls from two genetically homogeneous cohorts (north and western India) revealed differential risk for diseases/traits like metabolic disorders, liver diseases, and body and hematological measurements amongst healthy individuals. These SNPs differ significantly from the Indo-European background control as well. Amongst these we highlight novel SNPs rs304447 (IFIT5) and rs941590 (SERPINA10) that could explain differential trajectories for immune response, bleeding or thrombosis. Our method demonstrates the requirement of a relatively smaller sample size for a well powered study. This study highlights the potential of integrating a unique phenotyping approach for the identification of predictive markers and the at-risk population amongst the healthy.

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Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.