Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.

Mixed Nanocomposite Fertilizers Influencing Endophytic Symbiosis and Nutritional and Antioxidant Properties of Oryza sativa as a Sustainable Alternative for Commercial Fertilizers.

This study investigated the comparative effects of mixed nanocomposite (MNC) fertilizers as an alternative to commercial fertilizers (CFs) on endophytic symbiosis and nutritional properties of rice grains. We synthesized MNC fertilizers with different concentrations and characterized them by using scanning electron microscopy and Fourier transform infrared spectroscopy. The CF was applied as per the method followed by local farmers; however, for MNC fertilizers both foliar and soil applications were done. Comparative analysis of growth and development, rice-endophyte symbiosis, and nutritional properties of rice grains was conducted. The panicles per hill, length of panicles, grain per panicles, 1000-grain weight, and dry matter of rice plants treated with MNC fertilizers were found to be not statistically (p > 0.05) different compared to those of CF. However, growth parameters were significantly (p < 0.05) higher in MNC fertilizer-treated crops than in CF-treated crops. Several predominant endophytes such as Penicillium spp., Aspergillus fumigatus, Rhizopus spp., and Fusarium spp. that could have significant effects on the enhancement of growth and nutritional properties of rice grains were identified in rice plants treated with MNC fertilizers at different concentrations. Contrarily, stem-associated Cercospora spp. was found in the CF-treated field and fission yeast was observed in the blank-treated field. In addition, the contents of proteins, fibers, carbohydrates, energy-yielding components, vitamin A, and minerals were significantly increased in rice plants treated with MNC fertilizers. Thus, we would like to conclude that MNC fertilizers could be one of the most potential alternatives to CFs for achieving better rice-endophyte symbiosis as well as nutritional improvements in rice grains for sustainable production.

Relative expression of proinflammatory molecules in COVID-19 patients who manifested disease severities.

Aggressive immune response, due to overexpressed proinflammatory molecules, has been characterized in coronavirus disease 2019 (COVID-19) patients. Some of those mediators have a dual and opposite role on immune systems at play behind differential disease severities. We investigated the expression of some cytokines and chemokines in COVID-19 patients in Bangladesh. We diagnosed the patients by detecting severe acute respiratory syndrome coronavirus 2 RNA in nasal swab samples by the real-time RT-PCR method. Thirty adult patients were preselected based on their disease severities and grouped into mild, moderate, and severe cases. Nine healthy volunteers participated in this study as a control. Relative expression of nine cytokines/chemokine in total leukocytes was semi-quantified in SYBRgreen-based real-time quantitative reverse-transcriptase polymerase chain reaction. We performed statistical tests on transformed log data using SPSS 24.0. At the onset of symptoms (Day 1), angiotensin-converting enzyme 2 (ACE2) (p < 0.05) and interleukin (IL)-6 (p > 0.05) were upregulated in all COVID-19 groups, although the expression levels did not significantly correlate with disease severities. However, expressions of IL-6, monocyte chemotactic protein-1, macrophage inflammatory protein-1α, tumor necrosis factor-α (TNF-α), RANTES (regulated upon activation, normal T cell expressed and secreted), and ACE2, on Day 14, were positively correlated with disease severities. Relative viral load at Day 1 showed no significant correlation with cytokine expression but had a significant positive correlation with RANTES and ACE2 expression on Day 14 (p < 0.05). Male patients had a higher level of IL-6 than female patients on Day 1 (p < 0.05). All COVID-19 patients showed upregulated cytokines and chemokines on Day 14 compared to Day 1 except TNF-α. Female patients had a higher expression of ACE2 and IL-12 on Day 14. Upregulated cytokines/chemokines at the convalescent stage, especially IL-6, may help in targeting anticytokine therapy in post-COVID-19 patients' management.

Novel multi-strain probiotics reduces Pasteurella multocida induced fowl cholera mortality in broilers.

Pasteurella multocida causes fowl cholera, a highly contagious poultry disease of global concern, causing significant ecological and economic challenges to the poultry industry each year. This study evaluated the effects of novel multi-strain probiotics consisting of Lactobacillus plantarum, L. fermentum, Pediococcus acidilactici, Enterococcus faecium and Saccharomyces cerevisiae on growth performance, intestinal microbiota, haemato-biochemical parameters and anti-inflammatory properties on broilers experimentally challenged with P. multocida. A total of 120 birds were fed with a basal diet supplemented with probiotics (108 CFU/kg) and then orally challenged with 108 CFU/mL of P. multocida. Probiotics supplementation significantly (P < 0.05) improved growth performance and feed efficiency as well as reducing (P < 0.05) the population of intestinal P. multocida, enterobacteria, and mortality. Haemato-biochemical parameters including total cholesterol, white blood cells (WBC), proteins, glucose, packed cell volume (PCV) and lymphocytes improved (P < 0.05) among probiotic fed birds when compared with the controls. Transcriptional profiles of anti-inflammatory genes including hypoxia inducible factor 1 alpha (HIF1A), tumor necrosis factor- (TNF) stimulated gene-6 (TSG-6) and prostaglandin E receptor 2 (PTGER2) in the intestinal mucosa were upregulated (P < 0.05) in probiotics fed birds. The dietary inclusion of the novel multi-strain probiotics improves growth performance, feed efficiency and intestinal health while attenuating inflammatory reaction, clinical signs and mortality associated with P. multocida infection in broilers.