Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction.

Universal 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 mutations. Improved protocols for direct-from-sputum Mycobacterium tuberculosis sequencing would accelerate access to comprehensive drug susceptibility testing and molecular typing. We assessed a thermo-protection buffer-based direct-from-sample M. tuberculosis whole-genome sequencing protocol. We prospectively analyzed 60 acid-fast bacilli smear-positive clinical sputum samples in India and Madagascar. A diversity of semiquantitative 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 on genomic read depth, drug susceptibility prediction performance, and typing accuracy. M. tuberculosis was identified by direct sputum sequencing in 45/51 samples using Illumina, 34/38 were identified using MinION-monoplex sequencing, and 20/24 were identified using MinION-multiplex sequencing. The fraction of M. tuberculosis reads from MinION sequencing was lower than from Illumina, but monoplexing grade 3+ samples on MinION produced higher read depth than Illumina (P < 0.05) and MinION multiplexing (P < 0.01). No significant differences in sensitivity and specificity of drug susceptibility predictions were seen across sequencing modalities or within each technology when stratified by smear grade. Illumina sequencing from sputum accurately identified 1/8 (rifampin) and 6/12 (isoniazid) resistant samples, compared to 2/3 (rifampin) and 3/6 (isoniazid) accurately identified with Nanopore monoplex. Lineage agreement levels between direct and culture-based sequencing were 85% (MinION-monoplex), 88% (Illumina), and 100% (MinION-multiplex). M. tuberculosis direct-from-sample whole-genome sequencing remains challenging. Improved and affordable sample treatment protocols are needed prior to clinical deployment.

Impact of COVID-19 vaccination on transmission risk of breakthrough infections: Lessons from adapted N95 mask sampling for emerging variants and interventions.

This study used an adapted N95 mask sampling to understand the effect of COVID-19 vaccination in the context of circulating variants on infected individuals to emit the virus into the air, a key risk factor of transmission. Mask, swab, and blood samples were collected from 92 COVID-19 patients vaccinated (Covishield/COVAXIN-partial/fully) or unvaccinated between July and September 2021 during the Delta-dominated period in Mumbai. Mask/swab samples were analyzed by reverse transcription polymerase chain reaction for viral RNA. Blood was evaluated for SARS-CoV-2 anti-spike and nucleocapsid antibody responses. At <48 h of diagnosis, 93% of the patients emitted detectable viral RNA, with 40% emitting >1000 copies in 30 min (high emitters). About 8% continued to be high emitters even after 8 days of symptom onset. No significant difference was observed in emission patterns between partial, full, and unvaccinated patients. However, when vaccinated patients were stratified based on spike protein neutralization and nucleocapsid immunoglobulin G (IgG), the group with moderate/high neutralization showed a significantly lower proportion of high emitters and viral RNA copies than the group with no/low neutralization, which further reduced in the group having antinucleocapsid IgG. In conclusion, mask sampling showed that Delta infections were associated with greater virus emission in patients, which was significantly reduced only in vaccinated patients with moderate/high SARS-CoV-2 neutralization, especially with evidence of past infection. The study demonstrated that mask sampling could be useful for understanding the transmission risk of emerging variants, screening vaccine/booster candidates, and guiding control interventions.

Genomics of postvaccination SARS-CoV-2 infections during the Delta dominated second wave of COVID-19 pandemic, from Mumbai Metropolitan Region (MMR), India.

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.

Genome Sequences of Five SARS-CoV-2 Variants from Mumbai, India, Obtained by Nanopore Sequencing.

We report here the genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from five coronavirus disease 2019 (COVID-19) patients in Mumbai, India. Viral genomic RNA was isolated from nasopharyngeal swabs and/or respiratory particles from the masks of the patients. Genomic variant analysis determined 8 to 22 mutations, and the variants belong to lineages previously associated with Indian variants.

QbD based development of proliposome of lopinavir for improved oral bioavailability.

Aim of present work was to apply quality by design (QbD) principles for the development of proliposome of poorly soluble lopinavir (LPV). The patient-centric quality target product profile (QTPP) was defined and critical quality attributes (CQAs) earmarked. Risk assessment studies were carried out to identify the probable risks affecting the CQAs of the product. On the basis of preliminary study, lipid:drug ratio and amount of carrier were selected as critical material attributes (CMAs) and were optimized by face centered central composite design. Liposome vesicle size, drug entrapment efficiency and % drug release after 60min were selected as CQAs and mathematical relationship between CQAs and CMAs was derived using multiple linear regression analysis. Optimum composition of CMAs, identified using numerical optimization and desirability function, demonstrated excellent entrapment efficiency (>90%), drug release characteristics (>95% in 60min) and had vesicle size of 659.7±23.1nm. Solid state characterization studies (Differential Scanning Calorimetry, scanning electron microscopy and X-ray diffraction) were performed for optimized proliposome, suggested transformation of crystalline to amorphous form. Oral bioavailability study in Wistar rats revealed that LPV proliposome exhibited 2.24 and 1.16 fold higher bioavailability than pure LPV and available commercial formulation of LPV/RTV (lopinavir+ritonavir), respectively. Stability study of the optimized LPV loaded proliposome was performed as per ICH guideline and was found to be stable for period of 6months. Overall results of the study indicate that the proliposome offers advantages of enhanced oral bioavailability for poorly soluble LPV.

Statistical modeling, optimization and characterization of solid self-nanoemulsifying drug delivery system of lopinavir using design of experiment.

OBJECTIVE: Lopinavir (LPV), an antiretroviral protease inhibitor shows poor bioavailability because of poor aqueous solubility and extensive hepatic first-pass metabolism. The aim of the present work was to investigate the potential of the solid self-nanoemulsifying drug delivery system (S-SNEDDS) in improving dissolution rate and oral bioavailability of LPV. MATERIALS AND METHODS: Liquid SNEDDS (L-SNEDDS) of LPV were prepared using Capmul MCM C8, Cremophor RH 40 and propylene glycol and their amounts were optimized by Scheffe's mixture design. L-SNEDDS formulations were evaluated for different physicochemical and in vitro drug release parameters. S-SNEDDS were prepared by adsorbing L-SNEDDS on Neusilin US2 and characterized for solid-state properties. In vivo bioavailability of S-SNEDDS, marketed Lopinavir + Ritonavir (LPV/RTV) formulation and pure LPV was studied in Wistar rats. Stability study of S-SNEDDS was performed as per ICH guidelines. RESULTS AND DISCUSSION: Optimized L-SNEDDS obtained by Scheffe design had drug loading 160 ± 1.15 mg, globule size 32.9 ± 1.45 nm and drug release >95% within 15 min. Solid state studies suggested the transformation of the crystalline drug to amorphous drug. The size and zeta potential of globules obtained on dilution S-SNEDDS remained similar to L-SNEEDS. In vivo bioavailability study revealed that S-SNEDDS has 2.97 and 1.54-folds higher bioavailability than pure LPV and LPV/RTV formulation, respectively. The optimized S-SNEDDS was found to be stable and had a shelf life of 2.85 years. CONCLUSION: The significant increase in drug dissolution and bioavailability by prepared SNEDDS suggest that the developed S-SNEDDS is a useful solid platform for improving oral bioavailability of poorly soluble LPV.