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Coronavirus disease 2019 (COVID-19) is an acute respiratory infection. Its virus called SARS-COV-2 which is an RNA virus with high homology to the bat coronavirus. In this review study, first the molecular and cellular characteristics and the proliferation and replication of SARS-COV-2 are investigated. Then, by reviewing bioinformatics studies regarding protected domain analysis, homology modeling, and molecular docking, the biological role of some specific SARS-COV-2 proteins are examined. The results showed that the open reading frame 8 (ORF8) and surface glycoprotein could bind to porphyrin. At the same time, ORF1ab, ORF10, and ORF3a can attack the heme part of hemoglobin to dissociate iron and form porphyrin. This attack reduces hemoglobin ability to carry oxygen and carbon dioxide. As a result, lung cells become severely inflamed due to their inability to exchange carbon dioxide and oxygen, which leads to large ground-glass opacities on CT scan images. Based on the bioinformatics results, chloroquine can prevent ORF1ab, ORF3a, and ORF10 from attacking hemoglobin to form porphyrin and avoid the binding of ORF8 and surface glycoprotein to porphyrin, which effectively relieves the symptoms of acute respiratory syndrome. In the current pandemic, bioinformatics studies are of great importance for preventing the spread of COVID-19, developing drugs and vaccines, and clinical practice.
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Whole-genome sequencing of upper respiratory tract specimens from patients with confirmed COVID-19 in Henan Province was performed to compare the performance of the Illumina and Oxford Nanopore sequencing platforms, thus providing a reference for whole-genome monitoring of the novel coronavirus (SARS-CoV-2). Ten samples from COVID-19 cases in Henan Province from June 2021 to January 2022 were collected and sequenced with Illumina and Nanopore high-through-put sequencing technology to obtain full genome sequences of the novel coronavirus, which were compared with the Wuhan reference sequence (Wuhan-Hu-1). Bioinformatics software (CLC) was used for sequence alignment analysis. Three of the ten samples were Omicron (BA.1) variants with 55,61 nucleotide variation sites. One sample was an Alpha (B.1.1.7) variant with 41 nucleotide variation sites. Six samples were Delta (8.1.617.2) variants with 35,42,47 nucleotide variation sites. The sequence identity of mutation sites in six samples was 100%, and the mutation sites in the S genome segment of seven samples were consistent. For samples with a Ct value < 33, both next-generation and third-generation sequencing achieved high genome coverage and sequencing depth. A significant difference in coverage was observed between second-generation sequencing and third-generation sequencing (t=-2.037, P < 0.06). However, the coverage at different time points of the third-generation sequencing did not significantly differ (F=2.498, P > 0.05). The needs for SARS-CoV-2 mutant detection could be met through use of either high-throughput sequencing platform. The identification of mutations in the novel coronavirus through Illumina high-throughput sequencing was more accurate, whereas Nanopore high-throughput sequencing technology could be used for rapid detection and typing of different novel coronaviruses.
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The devastating COVID-19 outbreak posed serious challenges for the diagnostics laboratories, facing global shortage of reagents and equipment. This study aimed at evaluating an additional RNA extraction method respect to those already recommended by WHO and CDC. A new protocol for RNA extraction from nasopharyngeal swab was set up, adapting a Qiagen kit, and validated on a set of 96 clinical samples. The analysis showed a sensitivity of 94% and a specificity of 97%, but considering samples with Ct< 36.5, the sensitivity and the specificity increased to 100%. The adapted method was also able to detect samples with very low viral load (Ct> 38), indicating that the two approaches can be considered equivalent for the SARS-CoV-2 diagnostics. This extraction method can help in increasing the throughput for SARS-CoV-2 molecular test, even in a low automation setting.
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Horses may act as incidental host and experience silent infection following spillover from humans with COVID-19. SARS-CoV-2-infected humans should avoid close contact with equids during the time of their illness.
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Children are usually affected by pneumonia, which is a common ailment caused by Pathogenic Streptococcus pneumoniae. This study's objective was to isolate and identify S. pneumoniae, which was recovered from blood samples of suspected paediatric pneumonia patients using conventional techniques, such as antibiotic sensitivity profiles and molecular approaches. In this study, forty (40) samples from three major hospitals in the Dinajpur region of Bangladesh were collected and assessed using various bacteriological, biochemical, antibiotic susceptibility test, and molecular techniques. 37.5% of the 40 samples tested positive for pneumonia, and 15 isolates were discovered. In terms of age, pneumonia was more common in children aged 3-5 years (50%) than in those aged 6 to 8 (33.33%), 9 to 11 (25%) and 12 to 15 (20%). According to the results of the current study, the study area had no statistically significant impact (P > 0.05), while age and socioeconomic status had a significant impact on the prevalence of pneumonia in patients with pneumonia (P 0.05). The age group for which pneumonia was most prevalent (at 50%) was that for children between the ages of 3-5. Poor socioeconomic status was associated with the highest prevalence of pneumonia (54.54%). By sequencing the 16S rRNA gene, S. pneumoniae was identified as S. pneumoniae NBRC102642. In the antibiotic investigation, S. pneumoniae was found to be extremely resistant to ciprofloxacin, amikacin, vancomycin, and cefexime, but responsive to erythromycin and azithromycin, as well as neomycin, kanamycin, streptomycin, and bacitracin. S. pneumoniae causes serious complications in paediatric patients, and this scenario requires prevention through vaccination and the development of new, efficient antibiotic therapies for pneumonia. If specific laboratory features of paediatric patients with pneumonia are understood, sepsis will be easier to detect early, treat, and reduce mortality.
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AIM: The New South Wales (NSW) biochemical genetics (BG) service in Australia developed business continuity plans (BCPs) in response to the COVID-19 pandemic to ensure the essential service remained operational. This article aims to discuss the effects of the COVID-19 BCPs on the NSW BG service and patient care. METHODS: BCPs were developed that included charting of NSW BG service workflow and services against staff resources and clinical impact on patients. The effect of the BCPs was analysed quantitatively by reviewing key performance indicators (result turnaround time, frequency and severity of clinical incidents and laboratory nonconformities) and qualitatively from staff feedback generated by a BG laboratory-wide survey. RESULTS: Alternative BCPs were implemented during the pre-defined period March 2020 to November 2021 (inclusive), to reflect changes in COVID-19 community transmission, vaccination rates; and health orders. Operation of our essential pathology service was maintained, with no significant difference observed in key performance indicators when compared to pre-COVID. During the pre-defined period of the COVID-19 pandemic, staff reported increased levels of both work- and out-of-work-related stress. CONCLUSION: The successful continuation of the BG service, with no statistically significant impact on patient care and delivery of essential services, can be attributed to strategic planning and timely implementation of these BCPs. In conjunction with the resilient and robust attitude of the staff during this ever-changing situation, this experience has served as an invaluable tool for future disaster management planning.
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Since the Corona Virus Disease 2019 (COVID-19) caused by the infection of SARS-CoV-2 was first reported in 2019, COVID-19 has spread rapidly around the world, causing serious negative impacts on the daily life and work of people around the world. Recently, several studies on SARS-CoV-2 detection approaches based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology have been reported, showing that CRISPR technology can be used to detect SARS-CoV-2 rapidly, sensitively, specifically, visually and on-site. There are already detection kits based on CRISPR technology in clinical application at home and abroad, and good clinical feedback has been obtained. Therefore, the SARS-CoV-2 detection method based on CRISPR technology is expected to overcome the shortcomings of the existing RT-PCR approach in clinical practice, and replace RT-PCR as the gold standard for the next generation of SARS-CoV-2 nucleic acid detection. In this article, the research and progress of SARS-CoV-2 nucleic acid detection methods based on CRISPR technology are introduced, the principle and clinical application of CRISPR technology are reviewed, and the future development of the technology is prospected in order to promote its clinical transformation speed.
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Objective: To investigate the molecular mechanism of the action by which the MERS-CoV E proxein induces autophagy in 293T cells.
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A new type of coronavirus (SARS-CoV-2) infection caused acute or fatal pneumonia. The virus is another coronavirus that is transmitted from animal to human and capable of transmitted from human to human, following the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS CoV). In order to control the epidemic as soon as possible, there is an urgent need, for rapid detection and confirmation of infected patients. In this study, according to the SARS CoV-2 whole genome published in GenBank as target gene, LAMP Desiner 2.0 software was used to screen efficient and highly specific combinatorial loop primers. The amplification characteristics of Bst 4.0 DNA polymerase relys RNA as template for DNA synthesis. Viral RNA-positive test results showed that 5 to 20 copies of virus nucleic acid could be detected. The inactivated virus was directly used as amplification template for clinical detection. The amplified nucleic acid molecules are combined with OG (Orange-Green) dye. Positive samples are green and negative samples are orange yellow.. The established SARS-CoV-2 one-step visual constant temperature rapid detection method realizes rapid detection of nucleic acids with high sensitivity. This study provides a new method for SARS-CoV-2 detection.
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Avian infectious bronchitis (IB) is one of the acute and highly contagious upper respiratory tract infectious diseases in poultry caused by the Infectious bronchitis virus (IBV), which significantly affects the health and development of world poultry farming industry. IBV RNA polymerase lacks a complete correctional function and is prone to gene mutation and RNA-RNA recombination during the replication process, resulting in the emergence of new serotypes, genotypes and mutant strains. The continuous generation of recombinant strains through homologous recombination between strains also complicates the prevention and control of IB. Therefore, monitoring the genetic evolutionary characteristics of circulating strains and evaluating the protective effect of commonly used vaccines against local circulating strains of IBV are the keys to preventing and controlling this disease.
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"Novel coronavirus 2019" (which was renamed subsequently "severe acute respiratory syndrome coronavirus-2" (SARS-CoV-2) on 11 February 2020) caused a pneumonia outbreak in Wuhan (Hubei Province, China) in December 2019. In our previous studies, two important findings regarding SARS-CoV-2 were reported, for the first time, on 21 January 2020: (1) multiple alternative translations of a coding sequence in genomes of betacoronavirus subgroup B;(2) a novel mutation in the spike (S) proteins of betacoronavirus. By this mutation, SARS-CoV-2 acquired a cleavage site for the furin enzyme in its S protein, which is not present in the S proteins of most other betacoronaviruses (e.g. SARS-CoV). In the present study, we performed analyses of 5' untranslated regions (UTRs) in betacoronavirus. Using 5' UTR barcodes, 1,265 betacoronaviruses were clustered into four classes, and viruses in each class had similar virulence. The class 1, 2, 3 and 4 match the subgroup C, B, A and D of betacoronavirus, respectively. In particular, SARS-CoV-2 and SARS-CoV have the same 5' UTR barcode. As the main contribution of the present study, we developed 5' UTR barcoding to be used in the detection, identification, classification and phylogenetic analysis of, but not limited to coronavirus. Our method is very useful for early-warning, prevention and control of coronavirus. We found that Internal Ribosome Entry Sites (IRESs) may have important roles in the virulence of betacoronavirus. This important finding is reported, for the first time, to understand the virulence of SARS-CoV-2 at the molecular level. This finding can be used directly for vaccine development and design of drugs against SARS-CoV-2, but such development is not limited to coronavirus only. In addition, we propose that the upstream hairpin structures neighboring the start codons in mRNAs have important roles in protein translation in eukaryotes.
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Emergence of avian infectious bronchitis virus (IBV) variants with altered tissue tropism and host range has been reported from different parts of the world. Little is known about the different IBV variants existing and emerging in India. To explore the same, an IBV isolate, namely B17 isolated from backyard chicken in Tamil Nadu was used in the present study. The complete genome of B17 was sequenced and its phylogenetic relationship with the existing vaccine strain genotypes was analysed. The phylogenetic analysis of both S1 gene and complete genome sequence grouped B17 under Mass41 genotype comprising of M41, Beaudette, H120 and H120 variant with bootstrap value of 95-100%. Further, genomic analysis of B17 revealed the possibilities of emergence of the same from H120 vaccine strain through mutations at various genes.
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In January 2020, Guangdong Province, China imported several suspected cases with SARS-CoV-2 from Wuhan City, Hubei Province. China, which were detected as SARS-CoV-2 positive in laboratory. To further understand the SARS-CoV-2 virulence, as well as drug development and epidemic prevention and control needs, we established a SARS-CoV-2 isolation procedure. Vero-E6 cells were infected with the positive bronchoalveolar-lavage sample. The cells were monitored daily for cytopathic effects using light microscopy. The presence of viral nucleic acid in the supernatant was detected by RT-PCR. RNA extracted from culture supernatants were used as a template to clone and sequence the genome. We used Illumina sequencing to characterize the virus genome and results showed that the isolated virus was SARS-CoV-2.
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Poultry enteritis is an important multifactorial disease. Avian coronavirus (ACV) is one of many viruses related to enteric diseases and infectious bronchitis. Aim of this study was to find out the occurrence of ACV in enteritis affected broiler, molecular detection, phylogenetic analysis of avian corona virus and to examine intestine and liver for gross and microscopic lesions. Dead poultry birds (N=604) affected with enteritis were examined for presence of ACV. Intestinal samples of four birds were pooled to make one biological sample enteric ACV as the causative agent of enteritis in commercial poultry sector in and around four major districts of Rajasthan by RT-PCR. Molecular characterization was carried out by partial gene sequencing. Liver and intestine were examined grossly during post-mortem and by histopathology. Out of 151 pooled samples tested 51 (35.10%) were found positive for ACV. Prevalence of enteric ACV was highest in Ajmer (45.94%) and lowest in Dungarpur (23.07%) districts. 0-1 weeks age chicken flocks were found more susceptible for enteric ACV with 33.80% prevalence. Comparison of ACV sequence of this study revealed nucleotide (nt) identities from 99.44% among themselves, 99.44% with ACV from abroad. The amino acid (aa) identities of ACV of this study among themselves and with abroad sequences was 47.06 to 100%. Further severe congestion in intestine and necrotic patches on liver were recorded. Histopathology showed severe villous atrophy, congestion and cystic glands in sub-mucosa in intestine and severe congestion and haemorrhages along with infiltration of inflammatory cells in liver parenchyma.
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It has been found in previous studies that S protein of coronavirus plays a decisive role in invading host cells. In this paper, nucleotide sequence of SARS-CoV-2 S gene and its encoding amino acid sequence were obtained from NCBI. The bioinformatics analysis of S protein was carried out by DNAMAN, DNAStar, Mega 7.0 and some online analysis and prediction websites. The S protein of SARS-CoV-2 and SARS-CoV has high homology, which suggests that the structure and function of S protein of the two strains are similar. S protein contains signal peptide sequence, and the number of potential phosphorylated amino acids is 136, and the other amino acids have high phosphorylation tendency;there are 17 N-glycosylation sites, and it is a membrane protein, containing S1 and S2 domains;in the prediction results of secondary structure, a helix accounted for 28.59%, beta turn accounted for 3.38%, extended strand accounted for 23.25%, and random coil accounted for 44.78%. The quaternary structure shows that the complete S protein is composed of three monomers. This study can provide a theoretical basis for the infection mechanism and specific treatment of SARS-CoV-2.
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Since the end of December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to global public health security. Many coronaviruses, including SARS-CoV-2, are of animal origin. Therefore, monitoring of animal coronavirus must be strengthened. Herein, the common sample types, cell types used for viral isolation and culture, viral molecular detection methods, and immunological detection of animal coronaviruses are reviewed to provide a reference for follow-up studies of animal coronaviruses.
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Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) spilled over to humans via wild mammals, entering the host cell using angiotensin-converting enzyme 2 (ACE2) as receptor through Spike (S) protein binding. While SARS-CoV-2 became fully adapted to humans and globally spread, some mammal species were infected back. The present study evaluated the potential risk of mammals becoming hosts for SARS-CoV-2 through bioinformatics prediction based on ACE2 receptors.
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The new type of coronavirus (SARS-CoV-2), which is transmitted from person to person and causes Severe Acute Respiratory Distress Syndrome (SARS), emerged in Wuhan, China in December 2019. The definitive diagnosis of the coronavirus, which is transmitted from person to person through droplets, is given through PCR-based tests. The continuation of the COVID-19 pandemic has made it necessary to develop an effective vaccine against SARS-CoV-2. Vaccines developed against COVID-19 can be classified as inactivated/live virus vaccines, recombinant protein vaccines/vectored vaccines or RNA/DNA vaccines. This review aims to give information about the molecular structure and genetic features of SARSCoV- 2 virus, laboratory diagnostic methods, potential therapeutic drugs and vaccine studies.
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The present review attempts to critically examine and evaluate research findings on mushrooms as sources of vitamin D and other nutraceuticals. Recently, there is a growing concern about diseases associated with the deficiency of vitamin D in humans. As people tend to stay indoors, in present times, due to the COVID-19 pandemic, vitamin D levels are further affected. Research indicates vitamin D as a promising defensive or therapeutic agent against COVID, making this review more crucial. Mushrooms, as a rich source of vitamin D along with various bioactive compounds, perform a significant role in resolving health issues. Robust analyses of various strategies for enhancing vitamin D content in mushrooms holds significance in this study;moreover, this will help stakeholders of the mushroom industry in enriching the overall mushroom quality and human health. Mushroom-based medicinal formulations and functional foods serve to deliver vitamins and nutrients to humans, thus helping to combat malnutrition and other health problems, especially in developing countries. Evidence from pre-clinical and clinical analyses suggests that vitamin D2 bioavailability in mushrooms is comparable with vitamin D from other sources. The review also emphasises molecular findings from mushrooms related to genes responsible for morphology and metabolic production of pro-vitamin-D2.
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This study analyzed the viral genomic mutations and performed molecular source tracing on respiratory tract samples from four patients with COVID-19 in different periods in Zhuhai, China. Viral genome sequencing was performed by a nanopore high-throughput sequencing method. Viral genomes were packaged based on the Artic platform, and the consistency and phylogeny of the viral genomes with the reference sequence were assessed using bioinformatics software. A 28 298-29 819 bp genome could be obtained from four samples, with genome coverage of 94.6%-99.7%. A total of 46 single-base substitution mutations were detected, containinh 27 amino acid mutations, with the nonsynonymous mutations covering 58.7% (27/46). The percentage of nonsynonymous mutations in the ORF1ab gene was highest (44.4%, 12/27). Phylogenetic analysis showed that samples Zhuhai/ZHG9671/2020 and Zhuhai/P0717001/2020 belonged to clade B.1.1.63, sample Zhuhai/ZQ202001/2020 belonged to clade B, and sample Zhuhai/YZQ202011/2020 belonged to clade B.1.36. Zhuhai/ZQ202001/2020 showed a close connection with the early COVID-19 patients in Wuhan City. Samples Zhuhai/YZQ202011/2020, Zhuhai/P0717001/2020 and Zhuhai/ZHG9671/2020 were closest to the COVID-19 cases reported in Hong Kong in the same decade, which is consistent with the epidemiology results. The COVID-19 patients found in Zhuhai were imported cases, without local infection. Nucleotide polymorphisms were identified. Nanopore sequencing could be helpful in viral genome tracing analysis of SARS-COV-2.