Papers by Kayzad Nilgiriwala
Social Science Research Network, 2024
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Nature Communications, Jan 11, 2024
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Journal of Medical Virology, May 25, 2022
The present study was initiated to understand the proportion of predominant variants of severe ac... more The present study was initiated to understand the proportion of predominant variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in postvaccination infections during the Delta dominated second wave of coronavirus disease 2019 (COVID‐19) in the Mumbai Metropolitan Region (MMR) in India and to understand any mutations selected in the postvaccination infections or showing association with any patient demographics. Samples were collected (n = 166) from severe/moderate/mild COVID‐19 patients who were either vaccinated (COVISHIELD/COVAXIN—partial/fully vaccinated) or unvaccinated, from a city hospital and from home isolation patients in MMR. A total of 150 viral genomes were sequenced by Oxford Nanopore sequencing and the data of 136 viral genomes were analyzed for clade/lineage and for identifying mutations. The sequences belonged to three clades (21A, 21I, and 21J) and their lineage was identified as either Delta (B.1.617.2) or Delta+ (B.1.617.2 + K417N) or sub‐lineages of Delta variant (AY.120/AY.38/AY.99). A total of 620 mutations were identified of which 10 mutations showed an increase in trend with time (May–October 2021). Associations of six mutations (two in spike, three in orf1a, and one in nucleocapsid) were shown with milder forms of the disease and one mutation (in orf1a) with partial vaccination status. The results indicate a trend toward reduction in disease severity as the wave progressed.
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Journal of Nanoparticle Research, Sep 1, 2019
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Current Microbiology, Nov 16, 2017
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PLOS ONE, Oct 29, 2018
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Journal of Biotechnology, Nov 1, 2010
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Canadian journal of biotechnology, Dec 11, 2017
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ACS Synthetic Biology, Mar 7, 2013
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medRxiv (Cold Spring Harbor Laboratory), Mar 2, 2022
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Microbiology resource announcements, Apr 15, 2021
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Applied and Environmental Microbiology, Sep 1, 2008
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The Lancet Microbe
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ACS Synthetic Biology, Oct 21, 2014
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BackgroundUniversal access to drug susceptibility testing for newly diagnosed tuberculosis patien... more BackgroundUniversal access to drug susceptibility testing for newly diagnosed tuberculosis patients is recommended. Access to culture-based diagnostics remains limited and targeted molecular assays are vulnerable to emerging resistance conferring mutations. Improved sample preparation protocols for direct-from-sputum sequencing ofMycobacterium tuberculosiswould accelerate access to comprehensive drug susceptibility testing and molecular typing.MethodsWe assessed a thermo-protection buffer-based direct-from-sampleM. tuberculosiswhole-genome sequencing protocol. We prospectively processed and analyzed 60 acid-fast bacilli smear-positive sputum samples from tuberculosis patients in India and Madagascar. A diversity of semi-quantitative smear positivity level samples were included. Sequencing was performed using Illumina and MinION (monoplex and multiplex) technologies. We measured the impact of bacterial inoculum and sequencing platforms onM. tuberculosisgenomic mean read depth, drug s...
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Journal of Medical Virology
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Bioinformatics, 2019
MotivationResistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phe... more MotivationResistance co-occurrence within first-line anti-tuberculosis (TB) drugs is a common phenomenon. Existing methods based on genetic data analysis of Mycobacterium tuberculosis (MTB) have been able to predict resistance of MTB to individual drugs, but have not considered the resistance co-occurrence and cannot capture latent structure of genomic data that corresponds to lineages.ResultsWe used a large cohort of TB patients from 16 countries across six continents where whole-genome sequences for each isolate and associated phenotype to anti-TB drugs were obtained using drug susceptibility testing recommended by the World Health Organization. We then proposed an end-to-end multi-task model with deep denoising auto-encoder (DeepAMR) for multiple drug classification and developed DeepAMR_cluster, a clustering variant based on DeepAMR, for learning clusters in latent space of the data. The results showed that DeepAMR outperformed baseline model and four machine learning models wit...
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Genome Medicine
Background Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a seri... more Background Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined. Methods In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively. Result...
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Papers by Kayzad Nilgiriwala