Rajesh Pandey

Rajesh Pandey
Institute of Genomics and Integrative Biology | IGIB · Genomics and Molecular Medicine Research Area (IGIB)

About

142
Publications
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Publications

Publications (142)
Article
Infectious diseases are the leading cause of morbidity and mortality worldwide. Causative pathogenic microbes readily mutate their genome and lead to outbreaks, challenging the healthcare and the medical support. Understanding how certain symptoms manifest clinically is integral for therapeutic decisions and vaccination efficacy/protection. Notably...
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Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based therapeutics. The present study is aimed to isolate and evaluate the probiotic potential of a hu...
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Many adults in India have received at least one dose of COVID-19 vaccine with or without a prior history SARS-CoV-2 infection. However, there is limited information on the effect of prior immunity on antibody response upon vaccination in India. As immunization of individuals continues, we aimed to assess whether pre-existing antibodies are further...
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Background: Emergence of SARS-CoV-2 VOCs at different time points through COVID-19 pandemic raised concern for increased transmissibility, infectivity and vaccination breakthroughs. Methods: 1567 international travellers plus community transmission COVID-19 cases were analysed for mutational profile of VOCS, that led to notable waves in India, n...
Preprint
Mapping of somatic variations has enabled understanding the progression of clonal variations from healthy skin to cutaneous malignancies. Highlighting, the adaptive nature of pigmentation, germline mutations in albinism amplify skin cancer susceptibility. However, lower incidence of non-melanoma skin cancer among subjects with acquired depigmenting...
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COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients.
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The variability of clinical course and prognosis of COVID-19 highlights the necessity of patient sub-group risk stratification based on clinical data. In this study, clinical data from a cohort of Indian COVID-19 hospitalized patients is used to develop risk stratification and mortality prediction models. We analyzed a set of 70 clinical parameters...
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Vaccine development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been of primary importance to contain the ongoing global pandemic. However, studies have demonstrated that vaccine effectiveness is reduced and the immune response is evaded by variants of concern (VOCs), which include Alpha, Beta, Delta, and, the most rece...
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an enormous burden on the healthcare system worldwide as a consequence of its new emerging variants of concern (VOCs) since late 2019. Elucidating viral genome characteristics and its influence on disease severity and clinical outcome has been one of the crucial aspects toward pan...
Preprint
Most adults in India have received at least one dose of COVID-19 vaccine and also been infected naturally during the pandemic. As immunization of individuals continues under this situation where the virus has attained endemicity, we assessed whether this hybrid immunity is further boosted by a single dose of BBV152, an inactivated SARS-CoV-2 vaccin...
Preprint
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SARS-CoV-2 variants are emerging at frequent intervals with an ability to transmit faster and evade the immune responses. Most of Indian adults have received one or two doses of vaccination and, have also been infected naturally during the first and second waves. However, whether or not this hybrid immunity is protective against the emerging varian...
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This study elucidated the clinical, humoral immune response and genomic analysis of vaccine breakthrough (VBT) infections after ChAdOx1 nCoV-19/Covishield vaccine in healthcare workers (HCWs). Amongst 1858 HCWs, 1639 had received either two doses (1346) or a single dose (293) of ChAdOx1 nCoV-19 vaccine. SARS-CoV-2 IgG antibodies and neutralizing an...
Preprint
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Background: Various inflammatory markers are commonly assessed in many patients to help in the management of COVID-19 patients. It is not clear, though, how much risk of mortality their different levels of elevations entail, and which marker signifies more risk than others and how much. This study was undertaken to describe their levels and to answ...
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The global coronavirus disease 2019 (COVID-19) pandemic has demonstrated the range of disease severity and pathogen genomic diversity emanating from a singular virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). This diversity in disease manifestations and genomic mutations has challenged healthcare management and resource allocati...
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Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcar...
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Saturation suppressor mutagenesis was used to generate thermostable mutants of the SARS-CoV-2 spike receptor-binding domain (RBD). A triple mutant with an increase in thermal melting temperature of ~7°C with respect to the wild-type B.1 RBD and was expressed in high yield in both mammalian cells and the microbial host, Pichia pastoris , was downsel...
Article
Over 90% of the COVID-19 patients manifest mild/moderate symptoms or are asymptomatic. Although comorbidities and dysregulation of immune response have been implicated in severe COVID-19, the host factors that associate with asymptomatic or mild infections have not been characterized. We have collected serial samples from 23 hospitalized COVID-19 p...
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Since the time when detection of gene expression in single cells by microarrays to the Next Generation Sequencing (NGS) enabled Single Cell Genomics (SCG), it has played a pivotal role to understand and elucidate the functional role of cellular heterogeneity. Along this journey to becoming a key player in the capture of the individuality of cells,...
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The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is 6-fold less sensitive to serum neutralising antibodies from recovered individuals, and 8-fold less sensitive t...
Article
Background SARS-CoV-2 variants of concern (VOCs) have threatened COVID-19 vaccine effectiveness. We aimed to assess the effectiveness of the ChAdOx1 nCoV-19 vaccine, predominantly against the delta (B.1.617.2) variant, in addition to the cellular immune response to vaccination. Methods We did a test-negative, case-control study at two medical rese...
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Sambhar Salt Lake, situated in the state of Rajasthan, India is a unique temperate hypersaline ecosystem. Exploration of the salt lake microbiome will enable us to understand microbiome functioning in nutrient-deprived extreme conditions, as well as enrich our understanding of the environment-specific microbiome evolution. The current study has bee...
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Delhi, the national capital of India, has experienced multiple SARS-CoV-2 outbreaks in 2020 and reached population seropositivity of over 50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant B.1.617.2 (Delta) replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta t...
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Disease caused by SARS-CoV-2 coronavirus (COVID-19) led to significant morbidity and mortality worldwide. A systemic hyper-inflammation characterizes severe COVID-19 disease, often associated with acute respiratory distress syndrome (ARDS). Blood biomarkers capable of risk stratification are of great importance in effective triage and critical care...
Article
The SARS-CoV-2 B.1.617.2 (Delta) variant was frst identifed in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1 . In vitro, B.1.617.2 is 6-fold less sensitive to serum neutralising antibodies from recovered individuals, and 8-fold less sensitive to...
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Full-text available
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) manifests a broad spectrum of clinical presentations, varying in severity from asymptomatic to mortality. As the viral infection spread, it evolved and developed into many variants of concern. Understanding the impact of mutations in the SARS-CoV-2 genome on the clinical phenotype and ass...
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Background: Post infection immunity and post vaccination immunity both confer protection against COVID-19. However, there have been many whole genome sequencing proven reinfections and breakthrough infections. Both are most often mild and caused by Variants of Concern (VOC). Methods: The patient in our study underwent serial COVID-19 RT-PCR, blood...
Article
Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response...
Preprint
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Background: India saw a massive surge and emergence of SARS CoV2 variants. We elucidated clinical and humoral immune response and genomic analysis of vaccine breakthrough (VBT) infections after ChAdOx1 nCoV-19 vaccine in healthcare workers (HCWs). Methods: The study was conducted on 1858 HCWs receiving two doses of ChAdOx1 nCoV- 19 vaccine. Serial...
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Human host and pathogen interaction is dynamic in nature and often modulated by co-pathogens with a functional role in delineating the physiological outcome of infection. Co-infection may present either as a pre-existing pathogen which is accentuated by the introduction of a new pathogen or may appear in the form of new infection acquired secondari...
Preprint
Full-text available
Disease caused by SARS-CoV-2 coronavirus (COVID-19) has resulted in significant morbidity and mortality world-wide. A systemic hyper-inflammation characterizes the severe COVID-19 disease often associated with acute respiratory distress syndrome (ARDS). Blood biomarkers capable of risk stratification are of great importance in effective triage and...
Preprint
Full-text available
The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and has spread throughout India, displacing the B.1.1.7 (Alpha) variant and other pre-existing lineages. Mathematical modelling indicates that the growth advantage is most likely explained by a combination of increased transmissibility and immune...
Article
Full-text available
The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations, some of which have recently been linked with increased viral...
Preprint
Full-text available
After multiple SARS-CoV2 outbreaks in 2020 and a population seropositivity of about 50%, Delhi was overwhelmed by the fourth wave. Multi-modal data, including genomic surveillance, shows that a controlled phase characterized by Alpha variant (B.1.1.7) dominance, became uncontrollable during its displacement by the new Delta variant (B.1.617.2). Bay...
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Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-inf...
Preprint
The B.1.617 variant emerged in the Indian state of Maharashtra in late 2020 and has spread throughout India and to at least 40 countries. There have been fears that two key mutations seen in the receptor binding domain L452R and E484Q would have additive effects on evasion of neutralising antibodies. Here we delineate the phylogenetics of B.1.617 a...
Article
Mealybugs are aggressive pests with world-wide distribution and are suitable for study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome and compared it with four mealybug...
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This communication highlights a case report from Delhi, India of a 52‐year‐old male, with two instances of SARS‐CoV2 infection. Next‐generation sequencing has shown two distinct SNP profile of SARS‐CoV2 genomes from both the episodes, thus highlighting a possible scenario of re‐infection against relapse. Additionally, this study highlights the pres...
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Sodium benzoate is one of the widely used food preservatives and its metabolism in the human body has been studied only with the host perspective. Despite the human gut microbiome being considered as a virtual human organ, its role in benzoate metabolism is yet to be elucidated. The current study uses a multi-omic approach to rationalize the role o...
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Background: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection. Methods: Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (W...
Preprint
Full-text available
The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions. During the passage of the virus through affected populations, it has undergone mutations- some of which have recently been linked with increased viral...
Article
Full-text available
The human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncoding RNAs (ncRNAs) are significa...
Preprint
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The Receptor Binding Domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein was expressed at a yield of ∼80-100 mg/liter in...
Article
Novel coronavirus SARS-CoV2, causing coronavirus disease 2019 or COVID-19, led to significant morbidity and mortality. While most suffer from mild symptoms, some patients progress to a severe disease with acute respiratory distress syndrome (ARDS) and an associated systemic hyper-inflammation. First to characterize key cytokines and their dynamics...
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Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has led to significant morbidity and mortality. While most suffer from mild symptoms, some patients progress to severe disease with acute respiratory distress syndrome (ARDS) and associated systemic hyperinflammation. Methods First...
Chapter
The human gut hosts 10–100 trillion of microbes, including bacteria, virus, fungi and archaea, many of them are directly or indirectly involved with host homeostasis. The liver is constantly exposed to the microbial endotoxins, metabolites, and microbes through hepatic circulation. Dysbiosis in the gut microbiota leading to activation of immune and...
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Findings Of 2379 cases of confirmed SARS-CoV-2 infection, 85 (3 6%) were fully vaccinated compared with 168 (8 5%) of 1981 controls (adjusted OR [aOR] 0 37 [95% CI 0 28–0 48]), giving a vaccine effectiveness against SARS-CoV-2 infection of 63 1% (95% CI 51 5–72 1). 157 (6 4%) of 2451 of cases and 181 (9 1%) of 1994) controls had received a single d...
Preprint
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The clinical course of coronavirus disease 2019 (COVID-19) infection is highly variable with the vast majority recovering uneventfully but a small fraction progressing to severe disease and death. Appropriate and timely supportive care can reduce mortality and it is critical to evolve better patient risk stratification based on simple clinical data...
Chapter
Human gut harbors diverse microorganisms influencing host metabolism and homeostasis. But evidence about the epigenetic mechanisms influencing gut microbiome as well as host is also known. Factors like diet, exercise, and age influence the gut microbiota. Microbial-derived metabolites decide the species richness of microbiome and induce specific ep...
Preprint
Introduction A single center open label phase II randomised control trial was done to assess the pathogen and host-intrinsic factors influencing clinical and immunological benefits of passive immunization using convalescent plasma therapy (CPT), in addition to standard of care (SOC) therapy in severe COVID-19 patients, as compared to patients only...
Article
Pandemic have affected us before and possibly will be challenging us in future with COVID-19 being an eye opener. One of the ways to understand our challenger is to know their genome sequence which helps identify the pathogen, vis-a-vis new strain or novel mutations in the pre-existing pathogen. The strength of Next Generation Sequencing (NGS) base...
Preprint
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Over 95% of the COVID-19 cases are mild-to-asymptomatic who contribute to disease transmission whereas most of the severe manifestations of the disease are observed in elderly and in patients with comorbidities and dysregulation of immune response has been implicated in severe clinical outcomes. However, it is unclear whether asymptomatic or mild i...
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Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Our study highlights how exonized Alus could nucleate large-scale mRNA-miRNA interactions. Using a functional genomics approach, we characterize a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that has exonization of 23 Alus in its 3’UTR....
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has challenged the research community globally to innovate, interact, and integrate findings across hierarchies. Research on SARS-CoV-2 has produced an abundance of data spanning multiple parallels, including clinical data, SARS-CoV-2 genome architecture, host response captur...
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Vanillin is a phenolic food additive commonly used for flavor, antimicrobial, and antioxidant properties. Though it is one of the widely used food additives, strategies of the human gut microbes to evade its antimicrobial activity await extensive elucidation. The current study explores the human gut microbiome with a multi-omics approach to elucida...
Preprint
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To characterize key components and dynamics of the cytokine storm associated with severe COVID-19 disease, we assessed abundance and correlative expression of a panel of forty eight cytokines in patients suffering from acute respiratory distress syndrome (ARDS), as compared to patients with mild disease. Then in a randomized control trial on conval...
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Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequen...
Preprint
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Background: Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Exaptation of Alus in transcript isoforms could nucleate large-scale mRNA-miRNA interactions and modulate cellular outcomes. Result: Using a functional genomics approach, we report a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-L...