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1.
Front Immunol ; 13: 936106, 2022.
Article in English | MEDLINE | ID: covidwho-2109761

ABSTRACT

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection triggers inflammatory clinical stages that affect the outcome of patients with coronavirus disease 2019 (COVID-19). Disease severity may be associated with a metabolic imbalance related to amino acids, lipids, and energy-generating pathways. The aim of this study was to characterize the profile of amino acids and acylcarnitines in COVID-19 patients. A multicenter, cross-sectional study was carried out. A total of 453 individuals were classified by disease severity. Levels of 11 amino acids, 31 acylcarnitines, and succinylacetone in serum samples were analyzed by electrospray ionization-triple quadrupole tandem mass spectrometry. Different clusters were observed in partial least squares discriminant analysis, with phenylalanine, alanine, citrulline, proline, and succinylacetone providing the major contribution to the variability in each cluster (variable importance in the projection >1.5). In logistic models adjusted by age, sex, type 2 diabetes mellitus, hypertension, and nutritional status, phenylalanine was associated with critical outcomes (odds ratio=5.3 (95% CI 3.16-9.2) in the severe vs. critical model, with an area under the curve of 0.84 (95% CI 0.77-0.90). In conclusion the metabolic imbalance in COVID-19 patients might affect disease progression. This work shows an association of phenylalanine with critical outcomes in COVID-19 patients, highlighting phenylalanine as a potential metabolic biomarker of disease severity.


Subject(s)
COVID-19 , Diabetes Mellitus, Type 2 , Humans , SARS-CoV-2 , Cross-Sectional Studies , Amino Acids , Phenylalanine
2.
Ann Med ; 54(1): 3189-3200, 2022 12.
Article in English | MEDLINE | ID: covidwho-2106905

ABSTRACT

INTRODUCTION: In order to identify therapeutic targets in Coronavirus disease 2019 (COVID-19), it is important to identify molecules involved in the biological responses that are modulated in COVID-19. Lysophosphatidic acids (LPAs) are involved in the pulmonary inflammation and fibrosis are one of the candidate molecules. The aim of this study was to evaluate the association between the serum levels of autotaxin (ATX), which are enzymes involved in the synthesis of lysophosphatidic acids. MATERIAL AND METHODS: We enrolled 134 subjects with COVID-19 and 58 normal healthy subjects for the study. We measured serum ATX levels longitudinally in COVID-19 patients and investigated the time course and the association with severity and clinical parameters. RESULTS: The serum ATX levels were reduced in all patients with COVID-19, irrespective of the disease severity, and were negatively associated with the serum CRP, D-dimer, and anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody levels. DISCUSSION: Considering the biological properties of LPAs in the pulmonary inflammation and fibrosis, modulation of ATX might be compensatory biological responses to suppress immunological overreaction especially in the lung, which is an important underlying mechanism for the mortality of the disease. CONCLUSIONS: COVID-19 patients showed a decrease in the serum levels of ATX, irrespective of the disease severity. Key MessagesAutotaxin (ATX) is an enzyme involved in the synthesis of lysophosphatidic acid (LPA), which has been reported to be involved in pulmonary inflammation and fibrosis. Patients with COVID-19 show decrease in the serum levels of ATX. Modulation of ATX might be compensatory biological responses to suppress immunological overreaction.


Subject(s)
COVID-19 , Phosphoric Diester Hydrolases , Humans , COVID-19/blood , Fibrosis , Lung , Lysophospholipids , Phosphoric Diester Hydrolases/blood , SARS-CoV-2
3.
Chembiochem ; : e202200561, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2103500

ABSTRACT

Peptidic motifs folded in a defined conformation are able to inhibit protein-protein interactions (PPIs) covering large interfaces and as such they are biomedical molecules of interest. Mimicry of such natural structures with synthetically tractable constructs often requires complex scaffolding and extensive optimization to preserve the fidelity of binding to the target. Here, we present a novel proteomimetic strategy based on a 2-helix binding motif that is brought together by hybridization of peptide nucleic acids (PNA) and stabilized by a rationally positioned intermolecular disulfide crosslink. Using a solid phase synthesis approach (SPPS), the building blocks are easily accessible and such supramolecular peptide-PNA helical hybrids could be further coiled using precise templated chemistry. The elaboration of the structural design afforded high affinity SARS CoV-2 RBD (receptor binding domain) binders without interference with the underlying peptide sequence, creating a basis for a new architecture of supramolecular proteomimetics.

4.
Metabolites ; 12(11)2022 Nov 02.
Article in English | MEDLINE | ID: covidwho-2099658

ABSTRACT

The COVID-19 pandemic boosted the development of diagnostic tests to meet patient needs and provide accurate, sensitive, and fast disease detection. Despite rapid advancements, limitations related to turnaround time, varying performance metrics due to different sampling sites, illness duration, co-infections, and the need for particular reagents still exist. As an alternative diagnostic test, we present urine analysis through flow-injection-tandem mass spectrometry (FIA-MS/MS) as a powerful approach for COVID-19 diagnosis, targeting the detection of amino acids and acylcarnitines. We adapted a method that is widely used for newborn screening tests on dried blood for urine samples in order to detect metabolites related to COVID-19 infection. We analyzed samples from 246 volunteers with diagnostic confirmation via PCR. Urine samples were self-collected, diluted, and analyzed with a run time of 4 min. A Lasso statistical classifier was built using 75/25% data for training/validation sets and achieved high diagnostic performances: 97/90% sensitivity, 95/100% specificity, and 95/97.2% accuracy. Additionally, we predicted on two withheld sets composed of suspected hospitalized/symptomatic COVID-19-PCR negative patients and patients out of the optimal time-frame collection for PCR diagnosis, with promising results. Altogether, we show that the benchmarked FIA-MS/MS method is promising for COVID-19 screening and diagnosis, and is also potentially useful after the peak viral load has passed.

5.
Curr Dev Nutr ; 6(10): nzac107, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2097323

ABSTRACT

Background: Comanagement of glycemia and adiposity is the cornerstone of cardiometabolic risk reduction in type 1 diabetes (T1D), but targets are often not met. The intestinal microbiota and microbiota-derived short-chain fatty acids (SCFAs) influence glycemia and adiposity but have not been sufficiently investigated in longstanding T1D. Objectives: We evaluated the hypothesis that an increased abundance of SCFA-producing gut microbes, fecal SCFAs, and intestinal microbial diversity were associated with improved glycemia but increased adiposity in young adults with longstanding T1D. Methods: Participants provided stool samples at ≤4 time points (NCT03651622: https://clinicaltrials.gov/ct2/show/NCT03651622). Sequencing of the 16S ribosomal RNA gene measured abundances of SCFA-producing intestinal microbes. GC-MS measured total and specific SCFAs (acetate, butyrate, propionate). DXA (body fat percentage and percentage lean mass) and anthropometrics (BMI) measured adiposity. Continuous glucose monitoring [percentage of time in range (70-180 mg/dL), above range (>180 mg/dL), and below range (54-69 mg/dL)] and glycated hemoglobin (i.e., HbA1c) assessed glycemia. Adjusted and Bonferroni-corrected generalized estimating equations modeled the associations of SCFA-producing gut microbes, fecal SCFAs, and intestinal microbial diversity with glycemia and adiposity. COVID-19 interrupted data collection, so models were repeated restricted to pre-COVID-19 visits. Results: Data were available for ≤45 participants at 101 visits (including 40 participants at 54 visits pre-COVID-19). Abundance of Eubacterium hallii was associated inversely with BMI (all data). Pre-COVID-19, increased fecal propionate was associated with increased percentage of time above range and reduced percentage of time in target and below range; and abundances of 3 SCFA-producing taxa (Ruminococcus gnavus, Eubacterium ventriosum, and Lachnospira) were associated inversely with body fat percentage, of which two microbes were positively associated with percentage lean mass. Abundance of Anaerostipes was associated with reduced percentage of time in range (all data) and with increased body fat percentage and reduced percentage lean mass (pre-COVID-19). Conclusions: Unexpectedly, fecal propionate was associated with detriment to glycemia, whereas most SCFA-producing intestinal microbes were associated with benefit to adiposity. Future studies should confirm these associations and determine their potential causal linkages in T1D.This study is registered at clinical.trials.gov (NCT03651622; https://clinicaltrials.gov/ct2/show/NCT03651622).

6.
Front Bioeng Biotechnol ; 10: 999358, 2022.
Article in English | MEDLINE | ID: covidwho-2089816

ABSTRACT

As the outbreak of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory disease coronavirus 2 (SARS-COV-2), fast, accurate, and economic detection of viral infection has become crucial for stopping the spread. Polymerase chain reaction (PCR) of viral nucleic acids has been the gold standard method for SARS-COV-2 detection, which, however, generally requires sophisticated facilities and laboratory space, and is time consuming. This review presents recent advances in PCR-free nucleic acid detection methods for SARS-CoV-2, including emerging methods of isothermal amplification, nucleic acid enzymes, electrochemistry and CRISPR.

7.
Diagnostics (Basel) ; 12(10)2022 Oct 11.
Article in English | MEDLINE | ID: covidwho-2071285

ABSTRACT

The CRISPR/Cas system is a protective adaptive immune system against attacks from foreign mobile genetic elements. Since the discovery of the excellent target-specific sequence recognition ability of the CRISPR/Cas system, the CRISPR/Cas system has shown excellent performance in the development of pathogen nucleic-acid-detection technology. In combination with various biosensing technologies, researchers have made many rapid, convenient, and feasible innovations in pathogen nucleic-acid-detection technology. With an in-depth understanding and development of the CRISPR/Cas system, it is no longer limited to CRISPR/Cas9, CRISPR/Cas12, and other systems that had been widely used in the past; other CRISPR/Cas families are designed for nucleic acid detection. We summarized the application of CRISPR/Cas-related technology in infectious-disease detection and its development in SARS-CoV-2 detection.

8.
International Journal of Noncommunicable Diseases ; 6(5):47-54, 2021.
Article in English | Web of Science | ID: covidwho-2071981

ABSTRACT

In recent years, the various health benefits of Cyanobacteria microalgae - such as Arthrospira platensis, commonly called Spirulina, an edible blue-green algae - have attracted scientific attention including micro-level examinations of its bioactive components. As a whole food and nutritional supplement, it serves as a plant protein source, which has shown positive effects across a wide range of human health concerns, from malnutrition to metabolic syndrome. Spirulina bioactives, such as essential amino acids, phycocyanin, polysaccharides, carotenoids, and chlorophyll, and essential vitamins and trace minerals, are responsible for its holistic actions against oxidative stress and inflammation, and its antiviral, antibacterial, and immune-modulating effects. Various in vitro, in vivo, and ex vivo experiments have established Spirulina's mechanism of action and its effect on immunity as a proof of concept. The phenolic compounds and extracellular metabolites released from Spirulina whole food after digestion are postulated to strengthen the epithelial lining with antibacterial effects against pathogenic bacteria, adding to its prebiotic effect on the gut microbiota (like Bifidobacterium and Lactobacillus) due to its fiber content. In this study, the digestibility of Spirulina was assessed by the determination of free amino acids and peptide release during the each phase of digestion in a simulated static digestive model system. The hypothesis bridging poor gut health to low-level inflammation and metabolic syndrome, and the potential to address those issues with nutritional supplementation, such as with Spirulina, could also be beneficial in the long run to reduce comorbid illnesses, such as those associated with the currently prevailing coronavirus disease 2019 pandemic.

9.
Comput Struct Biotechnol J ; 20: 5713-5728, 2022.
Article in English | MEDLINE | ID: covidwho-2068856

ABSTRACT

Since COVID-19 emerged in 2019, significant levels of suffering and disruption have been caused on a global scale. Although vaccines have become widely used, the virus has shown its potential for evading immunities or acquiring other novel characteristics. Whether current drug treatments are still effective for people infected with Omicron remains unclear. Due to the long development cycles and high expense requirements of de novo drug development, many researchers have turned to consider drug repositioning in the search to find effective treatments for COVID-19. Here, we review such drug repositioning and combination efforts towards providing better handling. For potential drugs under consideration, aspects of both structure and function require attention, with specific categories of sequence, expression, structure, and interaction, the key parameters for investigation. For different data types, we show the corresponding differing drug repositioning methods that have been exploited. As incorporating drug combinations can increase therapeutic efficacy and reduce toxicity, we also review computational strategies to reveal drug combination potential. Taken together, we found that graph theory and neural network were the most used strategy with high potential towards drug repositioning for COVID-19. Integrating different levels of data may further improve the success rate of drug repositioning.

10.
Int J Mol Sci ; 23(19)2022 Oct 07.
Article in English | MEDLINE | ID: covidwho-2066142

ABSTRACT

The role of omega-3 polyunsaturated fatty acids (n-3 PUFAs) in the regulation of energy homeostasis remains poorly understood. In this study, we used a transgenic fat-1 mouse model, which can produce n-3 PUFAs endogenously, to investigate how n-3 PUFAs regulate the morphology and function of brown adipose tissue (BAT). We found that high-fat diet (HFD) induced a remarkable morphological change in BAT, characterized by "whitening" due to large lipid droplet accumulation within BAT cells, associated with obesity in wild-type (WT) mice, whereas the changes in body fat mass and BAT morphology were significantly alleviated in fat-1 mice. The expression of thermogenic markers and lypolytic enzymes was significantly higher in fat-1 mice than that in WT mice fed with HFD. In addition, fat-1 mice had significantly lower levels of inflammatory markers in BAT and lipopolysaccharide (LPS) in plasma compared with WT mice. Furthermore, fat-1 mice were resistant to LPS-induced suppression of UCP1 and PGC-1 expression and lipid deposits in BAT. Our data has demonstrated that high-fat diet-induced obesity is associated with impairments of BAT morphology (whitening) and function, which can be ameliorated by elevated tissue status of n-3 PUFAs, possibly through suppressing the effects of LPS on inflammation and thermogenesis.


Subject(s)
Adipose Tissue, Brown , Fatty Acids, Omega-3 , Adipose Tissue, Brown/metabolism , Animals , Diet, High-Fat/adverse effects , Fatty Acids, Omega-3/metabolism , Fatty Acids, Omega-3/pharmacology , Fatty Acids, Unsaturated/metabolism , Lipopolysaccharides/pharmacology , Mice , Mice, Inbred C57BL , Mice, Transgenic , Obesity/genetics , Obesity/metabolism , Thermogenesis
11.
Talanta ; 253: 123978, 2022 Oct 04.
Article in English | MEDLINE | ID: covidwho-2061902

ABSTRACT

Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.

12.
Bull Exp Biol Med ; 173(5): 606-610, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2059913

ABSTRACT

The indicators of spermatogenesis and the state of LPO and antioxidant protection in men with pathozoospermia after COVID-19 were assessed before and after treatment an antioxidant complex. Blood plasma served as the material for biochemical studies. In the examined patients, the parameters of spermatogenesis, as well as blood concentration of LPO components (diene conjugates and TBA-reactive substances) were analyzed. The total antioxidant activity of the blood was determined as an indicator characterizing the total activity of LPO inhibitors and determining its buffer capacity. In patients recovered from COVID-19, an increase in spermatogenesis disorders and shifts towards the predominance of prooxidant factors were observed. After a course (1 month) of antioxidant complex, patients showed increased sperm motility, decreased leukocyte count in the ejaculate, and restored balance in the prooxidant-antioxidant system towards antioxidant components. The effectiveness of correction of post-COVID disorders largely depends on the degree of damage to the structure and function of cell membranes caused by oxidative stress. The use of the antioxidant complex is a promising option, because it reduces the level of LPO, enhances antioxidant protection of the body, and also normalizes some parameters of spermatogenesis.


Subject(s)
Antioxidants , COVID-19 , Antioxidants/metabolism , Antioxidants/therapeutic use , COVID-19/drug therapy , Humans , Lipid Peroxidation/physiology , Male , Oxidative Stress/physiology , Reactive Oxygen Species , Sperm Motility , Spermatogenesis
13.
Journal of Modern Laboratory Medicine ; 36(4):122-128, 2021.
Article in Chinese | GIM | ID: covidwho-2055552

ABSTRACT

The aim this meta-analaysis was to understand the current status of nucleic acid positivity rate of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in close contacts of novel coronavirus-infected patients in China. The literature related to SARS-CoV-2 nucleic acid testing in close contacts of novel coronavirus-infected patients in China was searched in PubMed, EMbase, China Journal Full-text Data Base (CNKI), Wanfang Science and Technology Journal Full-text Database, and Veep Chinese Science and Technology Journal Full-text Database (VIP) from December 2019 to December 2020. 24 December 2019-2020. The quality of the literature was evaluated with reference to the revised American Agency for Healthcare Research and Quality (AHRQ) statement. StataSE15.0 software was used for meta-analysis, combined positive rates were calculated using the Freeman-Tukey double inverse sine conversion method, subgroup analysis was performed according to sex, age, infected person relationship, mode of infection and frequency of exposure, and sensitivity analysis and Egger's method was used to test for publication bias. Results A total of 11 publications were included, with a total sample size of 24 906 cases. The SARS-CoV-2 nucleic acid positivity rate in the close contact population of novel coronavirus-infected patients was 5.42% (95% CI: 3.57%-7.64%), and subgroup analysis showed that the positivity rate was 4.35% in males and 6.36% in females;the positivity rate was 5.88% in the 0-9 years group and 4.76% in the 10-59 years group. The positive rates were 5.88% for the 0-9 years group, 4.76% for the 10-59 years group and 8.73% for the =60 years group;13.42% for family members and 2.09% for others;11.44% for people living together, 9.90% for meals and 1.95% for other modes of infection;and 1.32%, 6.12% and 9.60% for occasional, normal and frequent contacts, respectively. The differences between the subgroups were statistically significant (?2 = 37.89 to 809.90, all P < 0.05). The sensitivity analysis suggested stable results and the Egger's test for publication bias was not statistically significant (t=0.93, P=0.376). Conclusion Close contacts of novel coronavirus-infected individuals in the Chinese region have a positive rate for SARS-CoV-2 nucleic acid.

14.
4th IEEE International Conference on Power, Intelligent Computing and Systems, ICPICS 2022 ; : 906-911, 2022.
Article in English | Scopus | ID: covidwho-2052017

ABSTRACT

In the context of the emerging coronavirus pneumonia epidemic becoming a global epidemic, nucleic acid testing as a as a precise prevention and control method has been universally recognized, but because the scope of the test is too big and the production process is complicated, the kits produced by biological companies are difficult to use widely, for this reason I develop some machine learning integrated algorithms which can forecast whether a man is infected with COVID-19 based on three highly accessible features. This method can predict whether a person has been infected with COVID-19 based only on three indicators: heart rate, blood oxygen level, and body surface temperature, and we use several tree integration. We used several tree integration algorithms such as Random Forest, XGBoost, and GBM, and its accuracy, recall, and F1 score obtained 100% accuracy on the test set, which has been better than the current nucleic acid detection methods, proving that this method can be theoretically used as an accurate, convenient, and efficient self-detection method. © 2022 IEEE.

15.
Lecture Notes on Data Engineering and Communications Technologies ; 149:214-230, 2023.
Article in English | Scopus | ID: covidwho-2048147

ABSTRACT

The purpose of this study was to find the original source of envelope protein (spiked surface) of the Covid-19. It was assumed that the envelope protein was related to ordinary proteins like the human liver enzymes as possible original sources. A comparison was made on the genome sequences of the envelope protein and the human liver enzymes. The results of computational experiments showed that the longest sequence, common in both groups, was as follows: glutamine acid (e) - glutamine acid (e) - threonine (t) - glycine (g). Upon this finding further investigation was performed on the molecular structure of this sequence;and the probabilities of electron captures by the protons of the atoms were computed to determine which atoms could connect the amino acids using the approximation method taken from the quantum mechanics. The study was continued to identify which amino acid grew the genome sequence of the envelope protein differently from the human liver enzymes. And it was found that the electron capture by the proton of the atom could explain the process that formed the genome sequence of the Covid-19’s envelope protein out from the human liver enzymes. To our opinion this method could be used for identification of other candidate proteins so that to find the original source of the virus. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

16.
Uspekhi Sovremennoi Biologii ; 142(1):25-36, 2021.
Article in Russian | CAB Abstracts | ID: covidwho-2040657

ABSTRACT

The analysis of the literature of the RSCI and Web of Science on the multifunctionality of useful properties of mesophilic lactic acid bacteria Lactococcus lactis ssp. lactis, which have been used by humans for centuries in the preparation of fermented products as a way to preserve milk and food raw materials. Lactococcus lactis ssp. lactiscan become a resource for various biologically active substances - potential metabiotics, such as: bacteriocins, organic acids, short-chain fatty acids, antioxidants, adhesins, neurotransmitters. New areas of their application as suppliers of bioprotective agents for preventive therapy and the development of oral vaccines are described, which is important for the prevention and control of infections that pose an additional danger to patients during the COVID-19 pandemic.

17.
Zhongguo Bingdubing Zazhi = Chinese Journal of Viral Diseases ; - (4):284, 2022.
Article in English | ProQuest Central | ID: covidwho-2040496

ABSTRACT

Objective To understand the genomic characteristics of SARS-CoV-2 from 40 imported cases with confirmed COVID-19 in Sichuan during January and March 2022. Methods Total viral RNA was extracted from respiratory samples of 182 confirmed COVID-19 cases who entered China through Chendu International Airport from January to March 2022.Mutation nucleic acid detection kit was used to identify the mutant strains and Illumina sequencing platform was applied for whole genome sequence(WGS) of virus.SARS-CoV-2 reference sequences were downloaded from NCBI database for genetic evolution and antigen variation analysis.The Nextclade and Pangolin online virus analysis platform were used to determine the virus family and type,and to analyze the mutation loci of the virus.The phylogenetic tree was constructed,along with the epidemiological data of cases to analyze the source and correlation of viruses. Results Among 182 imported COVID-19 cases,B.1.617.2 mutations were identified in 3 cases and B.1.1.529 mutations were detected in 57 cases.A total of 40 SARS-CoV-2 whole genome sequences with coverage>95% were obtained in this study.Nextclade typing analysis showed that 3 sequences belonged to 21J(Delta),5 sequences belonged to 21K(Omicron)and the remaining 32 sequences belonged to 21L(Omicron).Pangolin typing analysis showed that the 3 sequences of 21J(Delta)belonged to AY.4,AY.109and B.1.617.2,the 5sequences of 21K(Omicron)all belonged to BA.1.1,and the remaining 32 sequences of 21L(Omicron)belonged to BA.2.Our sequence results were99.7% consistency with the Omicron variants sequences in current GISAID database.Compared with the reference sequence strain Wuhan-Hu-1(NC_045512.2),45,47and 42nucleotide variation sites and 36,25 and 36amino acid variation sites were found in the 3 sequences of 21J(Delta).There were average 59(26-64)nucleotide mutation sites and 48(10-53)amino acid mutation sites in the 5sequences of 21K(Omicron).The median number of nucleotide mutation sites of 71(66-76)and amino acid mutation sites of 53(40-56)were identified in the 32sequences of 21L(Omicron).Phylogenetic tree analysis showed that 40SARS-CoV-2WGSs were all related to the current variants of concern(VOC). Conclusions Continuous sequencing of SARS-CoV-2whole genome from imported cases with confirmed COVID-19is of great significance for the prevention and control of the outbreak and prevalence of local epidemic caused by imported viruses in Sichuan.

18.
Chinese Journal of Virology ; 36(6):1020-1027, 2020.
Article in Chinese | GIM | ID: covidwho-2040438

ABSTRACT

In December 2019, a new type of pneumonia, coronavirus disease 2019 (COVID-19), caused by a novel coronavirus, SARS-CoV-2, was detected in hospitals in Wuhan, Hubei Province, China. The World Health Organization announced on 11 March 2020 that COVID-19 can be characterized as a pandemic, and since then COVID-19 has wrought havOc on public-health systems worldwide. The surface "spike" protein CS protein of SARS-CoV-2 mediates host-cell attachment and membrane fusion. The S protein is a key target for urgent development of vaccines, therapeutic antibodies, and diagnostics. To analyze the mutations and their effects on protein structure and function of the S protein, bioinformatics software has been used to analyze its nucleotide and amino-acid sequences, and Wuhan-Hu-1 (GenBank accession number: MN908947.3) was used as standard strain. As of 17 April 2020, there were 1, 002 SARS-CoV-2 strains in the GenBank database, of which 12 strains had mutations in the amino-acid sequence of the S protein. Some of these mutations could affect the physicochemical properties and secondary structures of the S protein. The R4081 mutation was located in the receptor-binding domain (RBD) and displayed on the surface, and could affect the RBD structure. The mutated amino acids 48, 74, 181, 221 and 655 were located in predicted linear epitopes of B cells, and 74, 181 and 655 mutations could greatly affect the structures and properties of linear epitopes of B cells.. The S protein of SARS-CoV-2 isolated from humans, dogs, cats and lions was highly conserved, whereas the D614G mutation was found in the isolated strain from tigers. Furthermore, the unique Flynn protease recognition site was presented in the S protein of SARS-CoV-2 compared with the coronavirus from bats. These results suggest that the S protein of SARS-CoV-2 is relatively conserved within and between species, whereas there are some mutations that can affect the physicochemical properties and structures of the S protein, which may also affect the linear epitopes of B cells. Taken together, these data provide a basis for the research and development of drugs, antibodies and vaccines against SARS-CoV-2.

19.
Chinese Journal of Virology ; 36(6):989-996, 2020.
Article in Chinese | GIM | ID: covidwho-2040437

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has become a public-health crisis worldwide. Accurate identification of the virus that causes COVID-19, SARS-CoV-2, carriers of SARS-CoV-2, and infected people is crucial for the prevention and control of this pandemic. Detection of the nucleic acids (NAs) of SARS-CoV-2 is one of the main criteria for COVID-19 diagnosis. Pharyngeal swabs (PSs) and fecal specimens (FSs) tend to be positive for SARS-CoV-2. However, there have been no reports of differences in the detection results of SARS-CoV-2 NAs in PSs and FSs of COVID-19 patients and asymptomatic SARS-CoV-2 infected persons at different exposure times. Forty-six patients diagnosed with COVID 19 in Nanyang City, China, from 2 February to 17 February 2020 and 27 asymptomatic SARS-CoV-2 infected persons screened through epidemiologic history and PSs and FSs at different exposure times were evaluated through detection of SARS-CoV-2 NAs. COVID-19 patients and asymptomatic SARS-CoV-2 infected persons had the highest positive rate of NAs in PSs at week 2 and the highest positive rate for NAs in FSs at week 3. The positive rate of NAs in PSs was significantly higher than that of FSs (P < 0.05). The difference in the positive rate of NAs in PSs between the two groups at 1, 3, and 4 weeks was significant (P < 0.05). The difference in the positive rate of NM in FSs between the two groups at 1-4 weeks was not significant (P > 0.05). The time for SARS-CoV-2 NAs to test positive in FSs lagged behind that for SARS-CoV-2 NAs to test positive in PSs (P > 0.05). The time for SARS-CoV-2 NAs to test positive in the PSs and FSs of asymptomatic SARS-CoV-2 infected persons lagged behind that for COVID-19 patients (P > 0.05). There was no significant difference in the average cycle threshold (Ct) value of the ORFlab gene and N gene of PSs and FSs between COVID-19 patients and asymptomatic SARS-Cov-2 infected persons at each exposure time tested (P > 0.05). The more severe the COVID-19, the higher was the positive rate of SARS-CoV-2 NAs in PSs and FSs, and the shorter was the time taken for SARS-CoV-2 NAs to test positive (P < 0.05). The re-positive rate of asymptomatic SARS-CoV-2 infected persons was 14.81% (4/27), higher than that of COVID-19 patients (6.52%;3/46), and the difference was significant (X2=8.193, P=0.016). Our study suggests that SARS-CoV-2 has a fecal mouth transmission route. The time taken for SARS-CoV-2 NM from FSs to turn positive lags behind that for SARS-CoV-2 NAs in PSs to turn positive, and the positive rate is lower. Test specimens should be selected according to different exposure times. Attention should he paid to younger asymptomatic SARS-CoV-2 infected persons.

20.
Chinese Journal of Virology ; 36(6):983-988, 2020.
Article in Chinese | GIM | ID: covidwho-2040436

ABSTRACT

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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