Objectives The spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has been unprecedentedly fast, spreading to more than 180 countries within 3 months with variable severity. One of the major reasons attributed to this variation is genetic mutation. Therefore, we aimed to predict the mutations in the spike protein (S) of the SARS-CoV-2 genomes available worldwide and analyze its impact on the antigenicity. Materials and Methods Several research groups have generated whole genome sequencing data which are available in the public repositories. A total of 1,604 spike proteins were extracted from 1,325 complete genome and 279 partial spike coding sequences of SARS-CoV-2 available in NCBI till May 1, 2020 and subjected to multiple sequence alignment to find the mutations corresponding to the reported single nucleotide polymorphisms (SNPs) in the genomic study. Further, the antigenicity of the predicted mutations inferred, and the epitopes were superimposed on the structure of the spike protein. Results The sequence analysis resulted in high SNPs frequency. The significant variations in the predicted epitopes showing high antigenicity were A348V, V367F and A419S in receptor binding domain (RBD). Other mutations observed within RBD exhibiting low antigenicity were T323I, A344S, R408I, G476S, V483A, H519Q, A520S, A522S and K529E. The RBD T323I, A344S, V367F, A419S, A522S and K529E are novel mutations reported first time in this study. Moreover, A930V and D936Y mutations were observed in the heptad repeat domain and one mutation D1168H was noted in heptad repeat domain 2. Conclusion S protein is the major target for vaccine development, but several mutations were predicted in the antigenic epitopes of S protein across all genomes available globally. The emergence of various mutations within a short period might result in the conformational changes of the protein structure, which suggests that developing a universal vaccine may be a challenging task.

Objective The primary objective of this study was to assess the diagnostic performance of multiplex polymerase chain reaction (mPCR) for the detection of Mycobacterium tuberculosis complex (MTBC) in presumptive pulmonary TB patients, in the setting of a tertiary level teaching hospital in central India, in comparison to liquid culture using BACTEC mycobacteria growth indicator tubes (MGIT) 960 TB system as the gold standard. The secondary objective was to assess the performance of mPCR for Ziehl Neelsen smear negative samples and ascertain the utility of this assay in smear negative samples. Materials and Methods Sputum or bronchoalveolar lavage samples were collected from patients who were adults, aged 18 years or older, presenting with presumptive pulmonary TB, and subjected to three microbiological investigations, that is, Ziehl Neelsen staining, mycobacterial culture using mycobacterial growth indicator tubes in the BD BACTEC MGIT 960 instrument, and the mPCR. Statistical Analysis For statistical analysis, 2 × 2 contingency tables were prepared and analyzed separately for all samples and for smear-negative samples using GraphPad and MedCalc tools. Sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of mPCR were calculated by taking MGIT culture as the reference standard. Results For all samples (n = 114), sensitivity of mPCR for the detection of (MTBC) was 93.48% (95% confidence interval [CI]: 82.10–98.63%), specificity was 95.59% (95% CI: 87.64–99.08%), positive predictive value (PPV) was 93.48% (95% CI: 82.54–97.75%), and NPV was 95.59% (95% CI: 87.87–98.48%). For smear negative samples (n = 80), sensitivity was 80.00% (95% CI: 51.91–95.67%), specificity was 98.46% (95% CI: 91.72–99.96%), PPV was 92.31% (95% CI: 62.80–98.84%), and NPV was 95.52% (95% CI: 88.57–98.33%). Conclusion In this study, we were able to demonstrate the good performance characteristics of the mPCR for the detection of MTBC from clinical samples of patients with presumptive pulmonary tuberculosis, with MGIT liquid culture as the reference standard. It may be concluded that mPCR can be considered equivalent to MGIT culture in terms of clinical decision making and yield of positivity, owing to the good sensitivity and specificity for the detection of MTBC.

Objective Microbiological confirmation of tuberculosis (TB) in pediatric cases is challenging due to its paucibacillary nature and difficulty in specimen collection. This study aimed to validate stool as an alternative sample for the diagnosis of pediatric pulmonary TB via Xpert MTB/RIF (Xpert) assay. Materials and Methods This cross-sectional study included 75 pediatric patients up to 10 years of age with signs and symptoms suggestive of TB. From each recruited patient, pulmonary and stool samples were collected in a sterile container. The collected samples were subjected to Ziehl-Neelsen staining, BACTEC MGIT 960 culture (MGIT), Xpert, and in-house multiplex polymerase chain reaction for TB diagnosis. Results About 13.33% (10/75) of the pulmonary samples and, of them, 50% (5/75) of the stool samples were positive by Xpert assay. The sensitivity and specificity of Xpert assay with stool and pulmonary samples were 50 (95% confidence interval [CI]: 18.71–81.29%) and 100% (95% CI: 94.48–100%), respectively. Conclusion The Xpert assay on stool samples showed limited sensitivity and good specificity in the diagnosis of pulmonary TB. Therefore, it can be proposed as an alternative screening sample to diagnose TB in pediatric cases for which getting a respiratory sample is extremely difficult. However, further studies with greater number of samples and multiple baseline variables are required to support our findings. Strategies to optimize stool Xpert assay should be performed to enhance the sensitivity of this method to detect Mycobacterium tuberculosis in children.

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