Introduction
Crimean-Congo haemorrhagic fever virus (CCHFV) has tripartite RNA genome and is endemic in various countries of Asia, Africa and Europe.
Method
The present study is focused on mutation ...profiling of CCHFV L segment and phylogenetic clustering of protein dataset into six CCHFV genotypes.
Results
Phylogenetic tree rooted with NCBI reference sequence (YP_325663.1) indicated less divergence from genotype III and the sequences belonging to same genotypes have shown less divergence among each other. Mutation frequency at 729 mutated positions was calculated and 563, 49, 33, 46 and 38 amino acid positions were found to be mutated at mutation frequency intervals of 0–0.2, 0.21–0.4, 0.41–0.6, 0.61–0.8 and 0.81–1.0 respectively. Thirty-eight highly frequent mutations (0.81–1.0 interval) were found in all genotypes and mapping in L segment (encoded for RdRp) revealed four mutations (V2074I, I2134T/A, V2148A and Q2695H/R) in catalytic site domain and no mutation in OTU domain. Molecular dynamic simulation and in silico analysis showed that catalytic site domain displayed large deviation and fluctuation upon introduction of these point mutations.
Conclusion
Overall study provides strong evidence that OTU domain is highly conserved and less prone to mutation whereas point mutations recorded in catalytic domain have affected the stability of protein and were found to be persistent in the large population.
The present work focusses on development of a safe, inexpensive, and more accessible source for biosynthesis of silver nanoparticles. Four different in-house probiotic isolates, i.e.,
Lactobacillus ...pentosus
S6,
Lactobacillus plantarum
F22,
Lactobacillus crustorum
F11, and
Lactobacillus paraplantarum
KM1 isolated from different food sources, were used in the current study to check their ability to synthesize silver nanoparticles. All the probiotic-synthesized silver nanoparticles show maximum surface plasmon resonance (SPR) at a peak of 450 nm, which confirms the formation of silver nanoparticles. Scanning electron microscopy (SEM) analysis identified the shape and distribution of silver nanoparticles. Transmission electron microscopy (TEM) revealed the average size of synthesized nanoparticles in the range of 10–50 nm, with the smallest size of 5 nm for silver nanoparticles synthesized by
L. crustorum
F11. Further, Fourier-transform infrared spectroscopy (FTIR) detected the presence of different functional groups responsible for reduction of silver ion to form silver nanoparticles. The antimicrobial activity of these AgNPs was also found to be effective against different bacterial and fungal pathogens, viz., antibiotic-resistant
Staphylococcus aureus
,
Bacillus cereus
,
Listeria monocytogenes
,
Pythium aphanidermatum
,
Fusarium oxysporum
, and
Phytopthora parasitica.
However,
L. crustorum
F11–synthesized AgNP showed maximum inhibition against all the bacterial and fungal pathogens, with highest against
S. aureus
(20 ± 0.61 mm) and
F. oxysporum
(23 ± 0.37). Findings from this study provide a durable and eco-friendly method for the biosynthesis of silver nanoparticles, having strong antimicrobial activity against different multidrug-resistant microorganisms.
Graphical abstract
Introduction
The current need of the food industry is to develop a safe packaging system that maintains the quality of food and prevents its spoilage. Food safety techniques improvised using ...functional nanoparticles minimize the chances of spoilage by maintaining moisture stability, mechanical strength, and durability and ensuring product safety. In the present study, we synthesized silver nanoparticles using purified bacteriocins obtained from probiotics. Bacteriocin-synthesized AgNPs are eco-friendly and secure packaging solutions that can be utilized in the packaging industry for the storage of food products.
Methods
Crude, partially purified and purified bacteriocin was obtained from three potential probiotic isolates, i.e.,
Lactobacillus pentosus
S6 (KU92122),
Lactobacillus crustorum
F11 (KT865221) and
Lactobacillus spicheri
G2 (JX481912). The antimicrobial efficacy of bacteriocin was tested against two food-borne spoilage-causing pathogens, i.e.,
Bacillus cereus
and
Staphylococcus aureus
. The purified bacteriocin obtained was used for the synthesis of AgNPs. The synthesized AgNPs were characterized using UV-vis spectroscopy, TEM, and SEM techniques. The AgNPs were used for coating cellulose paper. The coated paper was characterized using SEM and was used for the storage of tomato fruit.
Results and discussion
The purified bacteriocin obtained was used for the synthesis of AgNPs. The formation of AgNPs was confirmed by using UV-vis spectroscopy, which showed maximum absorption at 450 nm. Furthermore, we confirm shape and morphology by using Scanning Electron Microscopy (SEM). Transmission Electron Microscopy (TEM) analysis showed the mean size of synthesized AgNPs in the range of 5–20 nm. Bacteriocin-synthesized AgNPs were then used for the coating of cellulose paper with the main motive to avoid spoilage and enhance the shelf stability of tomato fruit during storage. SEM analysis confirmed the coating of AgNPs in the cellulose paper. The enhanced antimicrobial efficacy of different treatments coated paper was observed against
B. cereus
and
S. aureus
. Out of all, F11 AgNPs coated paper showed maximum inhibition of 24 mm for
S. aureus
and 22 mm for
B. cereus
. The coated paper from three different bacteriocin-synthesized AgNPs, along with silver nitrate (AgNO
3
) coated and uncoated paper, was used for the storage of tomato fruit for a period of 10 days at room temperature. Changes during storage were determined by analyzing morphological and color changes. Compared to AgNO
3
coated and uncoated paper, tomato fruit preserved in F11 AgNPs coated paper maintained and held its appearance and firmness, thereby confirming their effectiveness in the preservation of tomatoes.
SARS-CoV-2 has spread very quickly from its first reported case on 19 January 2020 in the United Stated of America, leading WHO to declare pandemic by 11 March 2020. RNA viruses accumulate mutations ...following replication and passage in human population, which prompted us to determine the rate and the regions (hotspots) of the viral genome with high rates of mutation. We analyzed the rate of mutation accumulation over a period of 11 weeks (submitted between 19th January to 15 April 2020) in USA SARS-CoV-2 genome. Our analysis identified that majority of the viral genes accumulated mutations, although with varying rates and these included NSP2, NSP3, RdRp, helicase, Spike, ORF3a, ORF8, and Nucleocapsid protein. Sixteen mutations accumulated in Spike protein in which four mutations are located in the receptor binding domain. Intriguingly, we identified a fair number of viral proteins (NSP7, NSP9, NSP10, NSP11, Envelop, ORF6, and ORF7b proteins), which did not accumulate any mutation. Limited changes in these proteins may suggest that they have conserved functions, which are essential for virus propagation. This provides a basis for a better understanding of the genetic variation in SARS-CoV-2 circulating in the US, which could help in identifying potential therapeutic targets for controlling COVID-19.
SputnikV is a vaccine against SARS-CoV-2 developed by the Gamaleya National Research Centre for Epidemiology and Microbiology. The vaccine has been shown to induce both humoral and cellular immune ...responses, yet the mechanisms remain largely unknown. Forty SputnikV vaccinated individuals were included in this study which aimed to demonstrate the location of immunogenic domains of the SARS-CoV-2 S protein using an overlapping peptide library. Additionally, cytokines in the serum of vaccinated and convalescent COVID-19 patients were analyzed. We have found antibodies from both vaccinated and convalescent sera bind to immunogenic regions located in multiple domains of SARS-CoV-2 S protein, including Receptor Binding Domain (RBD), N-terminal Domain (NTD), Fusion Protein (FP) and Heptad Repeats (HRs). Interestingly, many peptides were recognized by immunized and convalescent serum antibodies and correspond to conserved regions in circulating variants of SARS-CoV-2. This breadth of reactivity was still evident 90 days after the first dose of the vaccine, showing that the vaccine has induced a prolonged response. As evidenced by the activation of T cells, cellular immunity strongly suggests the high potency of the SputnikV vaccine against SARS-CoV-2 infection.
Early indications of the likelihood of severe coronavirus disease 2019 COVID-19 can influence treatments and could improve clinical outcomes. However, knowledge on the prediction markers of COVID-19 ...fatality risks remains limited. Here, we analyzed and quantified the reactivity of serum samples from acute (non-fatal and fatal) and convalescent COVID-19 patients with the spike surface glycoprotein (S protein) and nucleocapsid phosphoprotein (N protein) SARS-CoV-2 peptide libraries. Cytokine activation was also analyzed. We demonstrated that IgM from fatal COVID-19 serum reacted with several N protein peptides. In contrast, IgM from non-fatal serum reacted more with S protein peptides. Further, higher levels of pro-inflammatory cytokines were found in fatal COVID-19 serum compared to non-fatal. Many of these cytokines were pro-inflammatory and chemokines. Differences in IgG reactivity from fatal and non-fatal COVID-19 sera were also demonstrated. Additionally, the longitudinal analysis of IgG reactivity with SARS-CoV-2 S and N protein identified peptides with the highest longevity in humoral immune response. Finally, using IgM antibody reactivity with S and N SARS-CoV-2 peptides and selected cytokines, we have identified a panel of biomarkers specific to patients with a higher risk of fatal COVID-19 compared with that of patients who survive. This panel could be used for the early prediction of COVID-19 fatality risk.
Identifying immunogenic targets of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to advance diagnostic and disease control strategies. We analyzed humoral (ELISA) and ...T-cell (ELISpot) immune responses to spike (S) and nucleocapsid (N) SARS-CoV-2 proteins as well as to human endemic coronavirus (eCoV) peptides in serum from convalescent coronavirus disease 2019 (COVID-19) patients from Tatarstan, Russia. We identified multiple SARS-CoV-2 peptides that were reactive with serum antibodies and T cells from convalescent COVID-19. In addition, age and gender associated differences in the reactivity to S and N protein peptides were identified. Moreover, several SARS-CoV-2 peptides tested negatively correlated with disease severity and lung damage. Cross-reactivity to eCoV peptides was analyzed and found to be lower in COVID-19 compared to controls. In this study, we demonstrate the changing pattern of immunogenic peptide reactivity in COVID-19 serum based on age, gender and previous exposure to eCoVs. These data highlight how humoral immune responses and cytotoxic T cell responses to some of these peptides could contribute to SARS-CoV-2 pathogenesis.
Crimean‐Congo hemorrhagic fever virus (CCHFV) is classified among top 10 priority pathogens by World Health Organization. CCHFV belongs to Bunyaviridae family and negative sense ssRNA genome composed ...of three RNA segments: L, M, and S. RNA viruses show higher mutation rate as compared to DNA viruses. To gain deeper understanding of impact of point mutations in CCHFV M and S segment, mutation profiling, homology modeling, and molecular dynamic (MD) simulation were performed. Structural glycoproteins (glycoprotein C Gc and glycoprotein N Gn) of CCHFV are important for host–virus interaction and genome packaging, whereas CCHFV nucleoprotein (NP) is crucial for viral replication. Hence, current study is focused on evaluation of eight mutations in structural glycoproteins (Gc: 7 and Gn: 1) of M segment and seven mutations in NP of S segment. All these mutations were highly frequent, with mutation frequency between 0.81 and 1.0 and found to be persistent in the recent strains of CCHFV. Solubility analysis predicted that selected point mutations reduce solubility of Gc protein and increase solubility of Gn and NP proteins. MD simulation study deciphered that A1046V and G1158E in Gc protein, I778T in Gn protein, and H195R in NP protein displayed large deviation and fluctuation, and affected intramolecular interactions. In conclusion, we observed that point mutations could impact structure, stability, and host–virus interaction of protein, and might lead to evolution of new strains for better survival and drug resistance.
Introduction: Burkholderia cepacia complex (BCC) is a nonfermentative Gram-negative bacillus, now increasingly recognized as an important human pathogen causing hospital-acquired infections. ...Furthermore, it is a rare cause of sepsis in pediatric age group. Objective: The study aimed to determine the pattern of BCC infection in pediatric intensive care unit (PICU), to explore the antibiotic sensitivity profile, and to identify the source of BCC if any within the PICU. Materials and Methods: The study was conducted in the Department of Microbiology and Pediatrics, JNMC, AMU, Aligarh, for a period of 8 months from January 2017 to August 2017. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) was done in the Department of Microbiology, PGI, Chandigarh. All the blood cultures received in the enteric laboratory were screened. The isolates were then identified by standard biochemical techniques, and antimicrobial sensitivity was determined by Kirby-Bauer disc diffusion method as per the Clinical and Laboratory Standards Institute guidelines. Identity was confirmed by MALDI-TOF. As the increasing number of BCC infections was being reported, additional samples were collected from the PICU to identify the source. Results: The study involved 35 cases of blood culture-proven septicemia due to BCC among patients admitted in PICU. The first clustering of cases was noted in January 2017 affecting 6 babies. Six months later in August 2017, a second cluster of cases was noted affecting 24 babies. BCC was isolated in 35 samples. Among 30 patients, 20 were infants (including 13 neonates). Ceftriaxone (100%), minocycline (95%), chloramphenicol (85%), and co-trimoxazole (84.6%) were the most effective drugs followed by levofloxacin (79.1%), meropenem (71.4%), and ceftazidime (48.3%). None of the isolates was found to be sensitive to colistin, polymyxin B, cefepime, and tobramycin. BCC was also isolated from samples of Diurese-Nierenszintigraphie (DNS) and injection fentanyl used in PICU which could have possibly served as a source for further infection. Conclusion: BCC is an important cause of bacteremia with high fatality. It possesses the intrinsic resistance to many potent antibiotics. Proper and timely identification can help reduce the mortality, and implementation of infection control measures is essential.
Dengue virus (DENV) is endemic in 100 countries with the ability to impact nearly 50% of world population. DENV envelope (E) protein is responsible for viral attachment to host cells and has been ...target of various countermeasure development efforts. The current study focuses on a consensus computational approach to identify cross‐reactive, immunogenic DENV‐2 E peptides displaying promiscuity with a wide array of human leukocyte antigen (HLA) molecules. Four conserved peptides (FP‐1, FP‐2, FP‐3 and FP‐4) containing multiple CD8+ and CD4+ T cell epitopes were identified by employment of various immunoinformatics tools. FP‐1, FP‐2, FP‐3 and FP‐4 were estimated to bind with 227, 1787, 1008 and 834 HLA alleles, respectively. Root mean square deviation (RMSD) values obtained by molecular docking (CABS‐Dock) with 20 HLA alleles (10 each of HLA classes I and II) resulted into comparable RMSD values of identified epitopes with native peptides, which represents the natural presentation of epitopes to HLA molecules. These peptides were also found to be part of previous experimentally validated immunogenic peptides. Further, a dengue immunogenic peptide construct was generated by linking the four peptides, an adjuvant and a 6× histidine tag. The construct showed strong binding and stability with Toll‐like receptor. Collectively, these results provide strong evidence in the support of the immunogenic potential of the dengue immunogenic peptide construct.
Brief schematic representation of computational study of immunogenic peptide construct of dengue virus envelope epitopes.
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