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Imran, M.

Publications and source records attributed to Imran, M..

18 recordsLinked to original sources
bioRxiv2025

The study of differential expressions of MCPH and Seckel syndrome genes and their paralogues

Seckel syndrome and MCPH are single-gene neurodevelopmental disorders, with or without dwarfism. These genes are parts of essential cellular pathways but are regulated differently in both forms of microcephaly. These genes have diverged from single ancestral genes in to related but different gene paralogues during evolution. It is suggested that the paralogues might be redundant in other body organs and might rescue any abnormality in cases of MCPH, but not in Seckel syndrome. This study uncovers the spatio-temporal dynamics of these genes together with their paralogues at the mRNA level where the different tissues of embryos might exhibit different transcript variants or different levels of the various transcript variants to find the complementation in case of the MCPH but divergence in case of the Seckel syndrome. Here, we studied Cdk5Rap2-Pde4dip, Phc1-Phc3 (for MCPH) and Cep63-Ccdc67 (for Seckel) in the embryonic mouse tissues using RT-PCR throughout the peak of neurogenesis from E12.5 to E18.5. We found already known and novel spatio-temporal differential expression suggesting different regulation at the mRNA level. The results of PCR were analyzed on the agarose gel and were quantified by assigning relative intensity percentage scores to each band and plotting the cumulative expression of each gene in to the graphs for spatio-temporal dynamics and plotted each gene separately for temporal dynamics. For MCPH, Cdk5Rap2-Pde4dip had similar profiles and seemed to be redundant whereas Phc1-Phc3 seem to have complementary roles in brain development. The expression profiles of Cep63-Ccdc67 were very different indicating of their divergent and essential roles in development.

genetics↗
bioRxiv2025

In vitro and in vivo synergy of Vancomycin and β-lactams against drug-resistant Mycobacterium tuberculosis and Non-tuberculous mycobacteria

The unabated increase in antimicrobial resistance has underlined the importance of identifying novel drug combinations which eliminate infections more potently and likely reduce the emergence of resistance. In this context, we have identified Vancomycin and many {beta}-lactams as being potently active against drug-resistant Mycobacterium tuberculosis and non-tuberculous mycobacteria including M. abscessus, emerging as pathogens of concern owing to their inherent drug resistance profile. In this study, we have identified combinations of Vancomycin, a glycopeptide and {beta}-lactams, especially Ceftriaxone, Ceftazidime and Meropenem, in the presence or absence of Sulbactam, a {beta}- lactamase inhibitor, as possessing potent antimicrobial activity against several drug-resistant mycobacterial strains. The combination of Vancomycin and {beta}-lactams exhibited potent bactericidal activity and reduced the bacterial load better than either drug alone. The molecular basis of synergy was mediated by increase in permeability of mycobacterial cell as demonstrated by ethidium bromide assay. In the murine model of mycobacterial infection, synergistic combination of Vancomycin and {beta}-lactams outperformed clinically utilized drugs including Isoniazid, Rifampicin and Ethambutol against M. tuberculosis and Amikacin, Clarithromycin against M. abscessus. The combinations caused a significant reduction in bacterial load in various organs in M. tuberculosis and M. abscessus infected mice. Thus, the synergistic combination of Vancomycin and {beta}-lactams could potentially be utilized for treatment of recalcitrant mycobacterial infection especially those caused due to drug-resistant pathogens.

microbiology↗
bioRxiv2024

Phytochemical Analysis and Nematicidal Activity of Medicinal Plants Against Meloidogyne javanica

This study examined the nematicidal potential of ethanol extracts derived from four plants, namely Actinidia deliciosa (Chev.), Carica papaya, Citrus paradise, and Raphanus sativus, against the root-knot nematode Meloidogyne javanica. Experimental results indicated a significant reduction in the survival of second-stage juveniles of M. javanica when exposed to these plant extracts. Notably, concentrations of 2% and 1% were found to be more effective in comparison to 0.5% and 0.25%, yielding statistically significant outcomes. Furthermore, the mortality rate of the nematodes exhibited a direct correlation with the duration of exposure for most plant extracts. The fruit extracts obtained from A. deliciosa, C. papaya, C. paradise, and R. sativus demonstrated a substantial decrease in nematode infestation compared to the control group. The nematicidal activity of KI3a (BuOH) significant from 0.1356 to 1.9076 over 72 hours, while P-KI-2a (EtOAc) showed rose from 0.1206 to 0.6456. In compare, GF-3 (EtOAc) and Carbofuran to 0.0179 and 0.0098, respectively. PA-1 (MeOH) and RS-3 (EtOAc) showed modest nematicidal potential. This research emphasizes the efficacy of plant extract in mitigating root-knot nematode infestation, offering a promising alternative to chemical managements. Additionally, comprehensive phytochemical analysis should be achieved to recognize the active chemical constituents responsible for their effects. Exploring synergistic effects between these compounds and other natural or synthetic agents could further improve their potential applications in sustainable agriculture, improving crop protection and promoting eco-friendly practices.

plant biology↗
bioRxiv2024

Elucidating Molecular Mechanism and Chemical Space of Chalcones through Knowledge Graph and Machine Learning: A Combined Bio-Cheminformatic Pipeline

We developed a bio-cheminformatics method, exploring disease inhibition mechanisms using machine learning-enhanced quantitative structure-activity relationship (ML-QSAR) models and knowledge-driven neural networks. ML-QSAR models were developed using molecular fingerprint descriptors and the Random Forest algorithm to explore the chemical spaces of Chalcones inhibitors against diverse disease properties, including antifungal, anti-inflammatory, anticancer, antimicrobial, and antiviral effects. We generated and validated robust machine learning-based bioactivity prediction models ((https://ashspred.streamlit.app/) for the top genes. These models underwent ROC and applicability domain analysis, followed by molecular docking studies to elucidate the molecular mechanisms of the molecules. Through comprehensive neural network analysis, crucial genes such as AKT1, HSP90A1, SRC, and STAT3 were identified. The PubChem fingerprint-based model revealed key descriptors: PubchemFP521 for AKT1, PubchemFP180 for SRC, PubchemFP633 for HSP90, and PubchemFP145 and PubchemFP338 for STAT3, consistently contributing to bioactivity across targets. Notably, chalcone derivatives demonstrated significant bioactivity against target genes, with compound RA1 displaying a predictive pIC50 value of 5.76 against HSP90A and strong binding affinities across other targets. Compounds RA5 to RA7 also exhibited high binding affinity scores comparable to or exceeding existing drugs. These findings emphasize the importance of knowledge-based neural network-based research for developing effective drugs against diverse disease properties. These interactions warrant further in vitro and in vivo investigations to elucidate their potential in rational drug design. The presented models provide valuable insights for inhibitor design and hold promise for drug development. Future research will prioritize investigating these molecules for mycobacterium tuberculosis, enhancing the comprehension of effectiveness in addressing infectious diseases.

bioinformatics↗
bioRxiv2023

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods

The seed serves as the primary source of microbial inoculum for plant microbiota, playing a crucial role in establishing microbial populations in plants across subsequent generations, ultimately impacting plant growth and its overall health. Cropping conditions, especially farming practices, can influence the composition and functionality of the seed microbiome. Very little is known about the differences in seed microbiome between organic and conventional production systems. In this study, we characterized the endophytic microbial populations in seeds of rice grown under organic and conventional management practices through culture-dependent and independent analyses. The V4 region of 16S rRNA was used for bacterial taxa identification, and the ITS1 region was used in the identification of fungal taxa. Our results revealed significantly higher Shannon and Simpson indices for bacterial diversity in the conventional farming system whereas the fungal diversity was higher for observed, Shannon, and Simpson indices in the organic farming system. The cultivable endophytic bacteria were isolated and identified by the full-length 16S rRNA gene. There was no difference in culturable endophytic bacterial isolates in rice seeds grown under both conventional and organic farming systems. Among 33 unique isolates tested in vitro, three bacteria Bacillus sp. ST24, Burkholderia sp. OR5, and Pantoea sp. ST25, showed antagonistic activities against Marasmius graminum, Rhizoctonia solani AG4, and R. solani AG11, the fungal pathogens causing rice seedling blight. IMPORTANCEIn this paper, we studied the differences in the endophytic microbial composition of rice seeds grown in conventional and organic farming systems. Our results demonstrate a greater bacterial diversity in conventional farming, while organic farming showcases a higher fungal diversity. Additionally, our research reveals the ability of seed bacterial endophytes to inhibit the growth of three fungal pathogens responsible for causing seedling blight in rice. This study provides valuable insights into the potential use of beneficial seed microbial endophytes for developing a novel microbiome-based strategy in the management rice diseases. Such an approach has the potential to enhance overall plant health and improve crop productivity.

microbiology↗
bioRxiv2023

Indigenous probiotics Lactobacillus reuteri and Enterococcus faecium exhibit positive growth performance and disease prevention against extended-spectrum cephalosporin and fluoroquinolones resistant Salmonella enterica in broiler chicks.

ABSTRACTThe rapid increase in antibiotic resistance poses a global threat to public health, necessitating the development of effective antimicrobial alternatives. This study compared an indigenous probiotic mix containing Lactobacillus reuteri and two strains of Enterococcus faecium to a commercial probiotic blend ProtexinR on the growth performance, mortality rate, histomorphology, serum immunoglobulins, and intestinal microflora of broiler chickens challenged with two multi drug resistant Salmonella serovars, Typhimurium and Enteritidis. Two hundred and forty day-old broiler chicks were randomly assigned to six treatment groups for 4 weeks: the treatment groups were; birds continuously supplemented with only indigenous probiotic strains (108 CFU/mL) (IPRO-); birds challenged with Salmonella serovars 106 (CFU/mL) (PC+); birds continuously supplemented with indigenous probiotic strains and challenged with Salmonella serovars (IPRO+); birds supplemented with ProtexinR and challenged with Salmonella serovars (CM+); birds supplemented with only ProtexinR (CM-); and birds with no Salmonella challenge or probiotics (negative control; PC-). The results revealed that IPRO- diets significantly improved feed conversion ratio (FCR) and increased body weight (BW) (P [≤] 0.05). No effect of probiotic treatments was observed on IPRO- and CM- on relative organ weights as compared to the negative control (PC-). The Salmonella- challenged group PC+ had the highest (20%) mortality rate and lowest BW. The IPRO- had significantly lower FCR (1.55) compared to PC- (1.86) and PC+ (1.95). The broilers in the IPRO- group showed significantly increased serum concentrations of IgA and IgG relative to both control groups (P [≤] 0.05). Morphological analysis of the ileum revealed significant increases (P [≤] 0.05) in the villus height and villus height/crypt depth in birds fed IPRO- compared with the PC+. Cecal Lactobacillus and Enterococcus counts were the highest (P [≤] 0.05) and Salmonella counts were the lowest (P [≤] 0.05) in the IPRO- group compared to the Salmonella infected group PC+. These results indicated that indigenous probiotic strains Lactobacillus reuteri and Enterococcus faecium can be an effective and low-cost alternative compared to commercial probiotics in the Pakistan poultry industry.

microbiology↗
bioRxiv2023

Indigenous Reduction of Multi-drug Resistant Bacterial Pathogens in a Natural Uncontrolled Fermented Milk Ecosystem

Raw milk and its products have been questioned for microbiological safety. However, Dahi: an artisanally fermented milk product that is yet microbiologically unexplored is popularly known for therapeutic uses in public. Aiming safety and therapeutic assessment of dahi, samples of raw milk and dahi were analysed for microbiology and bacterial pathogens. The pathogens were also evaluated for antibiotic resistance. Further dahi samples were assessed for antipathogen effect. The total bacterial count of raw milk was between 3.80 x 1002 to 2.97 x 1007 and total fungal count was 2.50 x 1001 to 4.90 x 1002 whereas total bacterial and fungal count of Dahi was 3.00 x 1001 to 4.05 x 1009 and 2.00 x 1001 to 5.30 x 1007. Bacterial population of the Dahi was found dominated by lactic acid bacteria. In milk samples, E. coli was detected as 38%, S. aureus 28%, L. monocytogenes 3%, Salmonella 42% and Pseudomonas spp 31%. In Dahi samples, their percentages were 7%, 10%, 7%, 8% and 2% respectively. The detected pathogens were found resistant against different antibiotics especially to third and fourth generations of cephalosporin and other beta-lactam drugs. When assessed invitro, the low incidence of pathogens in the Dahi samples were associated to its inhibitory effect against pathogens. Dahi samples also inhibited the growth of antibiotic resistance ATCC strains. The inhibitory activity of the Dahi is due to the changes occurs during fermentation but not corelated to the pH of the Dahi.

microbiology↗
bioRxiv2022

Genetic variants of human platelet antigens in the Indian population from 1029 whole genomes

BackgroundGenetic variants in human platelet antigens (HPAs) considered as allo- or auto antigens are associated with various disorders including neonatal alloimmune thrombocytopenia, platelet transfusion refractoriness and post-transfusion purpura. While global differences in genotype frequencies were observed, the distribution of HPA variants in the Indian population are largely unknown. This study aims to explore the landscape of HPA variants in India to provide a basis for risk assessment and management of related complications. Materials and methodsPopulation specific frequencies of genetic variants associated with the 35 classes of HPAs (HPA-1 to HPA-35) were estimated by systematically analyzing genomic variations of 1029 healthy Indian individuals as well as from global population genome datasets.. ResultsAllele frequencies of the most clinically relevant HPA systems in the Indian population were found as follows, HPA-1a - 0.89, HPA-1b - 0.15, HPA-2a - 0.94, HPA-2b - 0.05, HPA-3a - 0.66, HPA-3b - 0.36, HPA-4a - 1.00, HPA-4b - 0, HPA-5a - 0.92, HPA-5b - 0.08, HPA-6a - 1.00, HPA-6b - 0, HPA-15a - 0.58 and HPA-15b - 0.42. In addition, HPA-4b allele frequencies were found to be significantly higher in India in comparison to global populations. ConclusionThis study provides the first comprehensive analysis of HPA allele and genotype frequencies using large scale representative whole genome sequencing data of the Indian population.

genomics↗
bioRxiv2022

Genetic landscape of Human neutrophil antigen variants in India from population-scale genomes

BackgroundAntibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia (NAIN). Transfusion-related acute lung injury (TRALI) and other non-hemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. MethodsGenetic variants from whole genomes of 1029 healthy Indian individuals were retrieved to accurately perform frequency estimation of HNA-1, HNA-3, HNA-4 and HNA-5 alleles using in-house computational pipeline. ResultsIn HNA class I, the genotype frequencies of FCGR3B*01 (HNA1a/a), FCGR3B*02 (HNA1b/b) and FCGR3B*03 (HNA1c/c) were 0.29%, 27.31% and 1.75% respectively. In HNA-3 the frequencies of HNA3a/a (SLC44A2*01), HNA3a/b and HNA3b/b (SLC44A2*02) were found to be 62.0%, 31.7% and 5.8% respectively. Frequency of ITGAM*01 encoding HNA4a/a was 90.1% and that of ITGAM*02 encoding HNA4b/b was 0.3%. Furthermore, HNA5a/a (ITGAL*01) and HNA5b/b (ITGAL*02) were found to have 12.9% and 48.6% genotype frequencies in the Indian population respectively. It was also found that the allele frequency HNA-5 variant, rs2230433 (ITGAL_chr16:30506720G>C) encoding 5b allele was highly prevalent (78.2%) in the Indian population which was comparable to South Asians (65.6%) but differed greatly from East Asians (14.3%), Latino Americans (25.7%), African-Americans (42.2%), European-Finnish (25.4%), European-non-Finnish (29.4%), Greater Middle Easterners (34.5%), Amish (30.2%) and Ashkenazi Jewish (31.4%). ConclusionThis study presents the first comprehensive report of HNA variant and genotype frequencies using large scale representative whole genome sequencing data of the Indian population. Significant difference was observed in the prevalence of HNA5a and HNA5b in India in comparison to other global populations.

genomics↗
bioRxiv2021

Comprehensive assessment of Indian variations in the druggable kinome landscape highlights distinct insights at the sequence, structure and pharmacogenomic stratum

India confines more than 17% of the worlds population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where the diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes,the second most targeted group of drug targets. The sequence level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network were investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveal critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world, and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.

genomics↗
bioRxiv2021

ESC - a comprehensive resource for SARS-CoV-2 immune escape variants

Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/ GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/431922v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@12bd86forg.highwire.dtl.DTLVardef@18e7279org.highwire.dtl.DTLVardef@fd97f8org.highwire.dtl.DTLVardef@104434b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗
bioRxiv2021

Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.

genomics↗
bioRxiv2021

From Decellurization to Imaging to 3-D Printing: low-cost plant-derived 3D-printed tissue scaffolds for tissue engineering

Natures most abundant carbohydrate, cellulose, has incredible structural properties that can be leveraged as scaffolds for tissue engineering. With plants being an inexpensive and easily accessible source, it is more feasible to experiment with these techniques and progress in the field of regenerative tissue engineering. In this study, we set out to optimize a low-cost method to obtain cellulose scaffolds that could potentially mimic a blood vessels after recellularization with endothelial cells. We chose a readily available plant specimen, i.e. cauliflower stalk, which offers anatomical similarity to blood vessels, vascular architecture and interconnected porosity. We went on to capture the cellulose scaffold digitally and created a 3-D model using a computer-aided design (CAD) software which was then used for 3-D printing the scaffold in two different sizes. We believe the decellularize-image-print cycle allows for skipping decellularization processes of new scaffolds every time a scaffold is required and therefore cutting cost and time needed, enables instant dissemination between individual researchers and communities and allows scalable printing at any size and level of detail. We hope this will catalyze even faster innovation in the space of tissue engineering and regenerative medicine.

bioengineering↗
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

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.

genomics↗
bioRxiv2020

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.

genomics↗
bioRxiv2018

Frequent variants in the Japanese population determine quasi-Mendelian inheritance of rare retinal ciliopathy

Hereditary retinal degenerations (HRDs) are Mendelian diseases characterized by progressive blindness and caused by ultra-rare mutations. In a genomic screen of 331 unrelated Japanese patients, we identify a disruptive Alu insertion and a nonsense variant (p.Arg1933*) in the ciliary gene RP1, neither of which are rare alleles in Japan. p.Arg1933* is almost polymorphic (frequency = 0.6%, amongst 12,000 individuals), does not cause disease in homozygosis or heterozygosis, and yet is significantly enriched in HRD patients (frequency = 2.1%, i.e. a 3.5-fold enrichment; p-value = 9.2x10-5). Familial co-segregation and association analyses show that p.Arg1933* can act as a Mendelian mutation, in trans with the Alu insertion, but might also cause disease in association with two alleles in the EYS gene in a non-Mendelian pattern of heredity. Our results suggest that rare conditions such as HRDs can be paradoxically determined by relatively common variants, following a quasi-Mendelian model linking monogenic and complex inheritance.

genomics↗