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1.
Sensors and Actuators B: Chemical ; : 131974, 2022.
Article in English | ScienceDirect | ID: covidwho-1815176

ABSTRACT

The outbreak of COVID-19 caused by SARS-CoV-2 urges the development of rapid and accurate diagnostic methods. Here, one high-sensitivity and point-of-care detection method based on magnetic SERS biosensors composed of Fe3O4-Au nanocomposite and Au nanoneedles array was developed to detect SARS-CoV-2 directly. Among, the magnetic Fe3O4-Au nanocomposite is applied to capture and separate virus from nasopharyngeal swabs and enhance the Raman signals of SARS-CoV-2. The magnetic SERS biosensor possessed high sensitivity by optimizing the Fe3O4-Au nanocomposite. More significantly, the on-site detection of inactivated SARS-CoV-2 virus was achieved based on the magnetic SERS biosensor with ultra-low limitation of detection of 100 copies/mL during 15mins. Furthermore, the contaminated throat and nasal swabs samples were identified by support vector machine, and the diagnostic accuracy of 100% was obtained. The magnetic SERS biosensor combined with support vector machine provides giant potential as the point-of-care detection tool for SARS-CoV-2.

2.
iScience ; : 104309, 2022.
Article in English | ScienceDirect | ID: covidwho-1804380

ABSTRACT

SUMMARY MicroRNAs (miRNAs) have been shown to play important roles in viral infections, but their associations with SARS-CoV-2 infection remain poorly understood. Here we detected 85 differentially expressed miRNAs (DE-miRNAs) from 2,336 known and 361 novel miRNAs that were identified in 233 plasma samples from 61 healthy controls and 116 COVID-19 patients using the high throughput sequencing and computational analysis. These DE-miRNAs were associated with SASR-CoV-2 infection, disease severity, and viral persistence in the COVID-19 patients, respectively. Gene ontology and KEGG pathway analyses of the DE-miRNAs revealed their connections to viral infections, immune responses, and lung diseases. Finally, we established a machine learning model using the DE-miRNAs between various groups for classification of COVID-19 cases with different clinical presentations. Our findings may help understand the contribution of miRNAs to the pathogenesis of COVID-19 and identify potential biomarkers and molecular targets for diagnosis and treatment of SARS-CoV-2 infection.

3.
Front Immunol ; 13: 868679, 2022.
Article in English | MEDLINE | ID: covidwho-1785351

ABSTRACT

Coronavirus disease 2019 (COVID-19), an infectious respiratory disease propagated by a new virus known as Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has resulted in global healthcare crises. Emerging evidence from patients with COVID-19 suggests that endothelial cell damage plays a central role in COVID-19 pathogenesis and could be a major contributor to the severity and mortality of COVID-19. Like other infectious diseases, the pathogenesis of COVID-19 is closely associated with metabolic processes. Lactate, a potential biomarker in COVID-19, has recently been shown to mediate endothelial barrier dysfunction. In this review, we provide an overview of cardiovascular injuries and metabolic alterations caused by SARS-CoV-2 infection. We also propose that lactate plays a potential role in COVID-19-driven endothelial cell injury.


Subject(s)
COVID-19 , Vascular Diseases , COVID-19/complications , Endothelial Cells/metabolism , Endothelium , Humans , Lactic Acid/metabolism , SARS-CoV-2 , Vascular Diseases/pathology
4.
Transbound Emerg Dis ; 2022 Mar 27.
Article in English | MEDLINE | ID: covidwho-1765050

ABSTRACT

A novel swine enteric alphacoronavirus, swine acute diarrhoea syndrome coronavirus (SADS-CoV), related to Rhinolophus bat CoV HKU2 in the subgenus Rhinacovirus emerged in southern China in 2017, causing diarrhoea in newborn piglets, and critical questions remain about the pathogenicity, cross-species transmission and potential animal reservoirs. Our laboratory's previous research has shown that SADS-CoV can replicate in various cell types from different species, including chickens. Here, we systematically explore the susceptibility of chickens to a cell-adapted SADS-CoV strain both in vitro and in vivo. First, evidence of SADS-CoV replication in primary chicken cells, including cytopathic effects, immunofluorescence staining, growth curves and structural protein expression, was proven. Furthermore, we observed that SADS-CoV replicated in chicken embryos without causing gross lesions and that experimental infection of chicks resulted in mild respiratory symptoms. More importantly, SADS-CoV shedding and viral distribution in the lungs, spleens, small intestines and large intestines of infected chickens were confirmed by quantitative reverse transcription polymerase chain reaction and immunohistochemistry. The genomic sequence of the original SADS-CoV from the pig source sample in 2017 was determined to have nine nucleotide differences compared to the cell-adapted strain used; among these were three nonsynonymous mutations in the spike gene. These results collectively demonstrate that chickens are susceptible to SADS-CoV infection, suggesting that they are a potential animal reservoir. To our knowledge, this study provides the first experimental evidence of cross-species infection in which a mammalian alphacoronavirus is able to infect an avian species.

5.
Signal Transduct Target Ther ; 7(1): 83, 2022 03 11.
Article in English | MEDLINE | ID: covidwho-1740428

ABSTRACT

SARS-CoV-2 induced marked lymphopenia in severe patients with COVID-19. However, whether lymphocytes are targets of viral infection is yet to be determined, although SARS-CoV-2 RNA or antigen has been identified in T cells from patients. Here, we confirmed that SARS-CoV-2 viral antigen could be detected in patient peripheral blood cells (PBCs) or postmortem lung T cells, and the infectious virus could also be detected from viral antigen-positive PBCs. We next prove that SARS-CoV-2 infects T lymphocytes, preferably activated CD4 + T cells in vitro. Upon infection, viral RNA, subgenomic RNA, viral protein or viral particle can be detected in the T cells. Furthermore, we show that the infection is spike-ACE2/TMPRSS2-independent through using ACE2 knockdown or receptor blocking experiments. Next, we demonstrate that viral antigen-positive T cells from patient undergone pronounced apoptosis. In vitro infection of T cells induced cell death that is likely in mitochondria ROS-HIF-1a-dependent pathways. Finally, we demonstrated that LFA-1, the protein exclusively expresses in multiple leukocytes, is more likely the entry molecule that mediated SARS-CoV-2 infection in T cells, compared to a list of other known receptors. Collectively, this work confirmed a SARS-CoV-2 infection of T cells, in a spike-ACE2-independent manner, which shed novel insights into the underlying mechanisms of SARS-CoV-2-induced lymphopenia in COVID-19 patients.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , SARS-CoV-2/metabolism , T-Lymphocytes/metabolism , Animals , Caco-2 Cells , Chlorocebus aethiops , Humans , Vero Cells
6.
Arch Virol ; 167(2): 493-499, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1712247

ABSTRACT

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating infectious diseases in the global swine industry. A rapid and sensitive on-site detection method for PRRS virus (PRRSV) is critically important for diagnosing PRRS. In this study, we established a method that combines reverse transcription recombinase polymerase amplification (RT-RPA) with a lateral flow dipstick (LFD) for detecting North American PRRSV (PRRSV-2). The primers and probe were designed based on the conserved region of all complete PRRSV-2 genomic sequences available in China (n = 512) from 1996 to 2020. The detection limit of the assay was 5.6 × 10-1 median tissue culture infection dose (TCID50) per reaction within 30 min at 42 °C, which was more sensitive than that of reverse transcription polymerase chain reaction (RT-PCR) (5.6 TCID50 per reaction). The assay was highly specific for the epidemic lineages of PRRSV-2 in China and did not cross-react with pseudorabies virus, porcine circovirus 2, classical swine fever virus, or porcine epidemic diarrhea virus. The assay performance was evaluated by testing 179 samples and comparing the results with those of quantitative RT-PCR (RT-qPCR). The results showed that the detection coincidence rate of RT-RPA and RT-qPCR was 100% when the cycle threshold values of RT-qPCR were < 32. The assay provides a new alternative for simple and reliable detection of PRRSV-2 and has great potential for application in the field.


Subject(s)
Porcine Reproductive and Respiratory Syndrome , Porcine respiratory and reproductive syndrome virus , Animals , Porcine Reproductive and Respiratory Syndrome/diagnosis , Porcine respiratory and reproductive syndrome virus/genetics , Porcine respiratory and reproductive syndrome virus/metabolism , Recombinases , Reverse Transcription , Sensitivity and Specificity , Swine
7.
Arch Toxicol ; 2022 Feb 28.
Article in English | MEDLINE | ID: covidwho-1712224

ABSTRACT

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 has rapidly expanded into a serious global pandemic. Due to the high morbidity and mortality of COVID-19, there is an urgent need to develop safe and effective vaccines. AdC68-19S is an investigational chimpanzee adenovirus serotype 68 (AdC68) vector-based vaccine which encodes the full-length spike protein of SARS-CoV-2. Here, we evaluated the immunogenicity, biodistribution and safety profiles of the candidate vaccine AdC68-19S in Sprague Dawley (SD) rat and rhesus macaque under GLP conditions. To characterize the biodistribution profile of AdC68-19S, SD rats were given a single intramuscular injection of AdC68-19S 2 × 1011 VP/dose. Designated organs were collected on day 1, day 2, day 4, day 8 and day 15. Genomic DNA was extracted from all samples and was further quantified by real-time quantitative polymerase chain reaction (qPCR). To characterize the toxicology and immunogenicity profiles of AdC68-19S, the rats and rhesus macaques were injected intramuscularly with AdC68-19S up to 2 × 1011vp/dose or 4 × 1011vp/dose (2 and fourfold the proposed clinical dose of 1 × 1011vp/dose) on two or three occasions with a 14-day interval period, respectively. In addition to the conventional toxicological evaluation indexes, the antigen-specific cellular and humoral responses were evaluated. We proved that multiple intramuscular injections could elicit effective and long-lasting neutralizing antibody responses and Th1 T cell responses. AdC68-19S was mainly distributed in injection sites and no AdC68-19S related toxicological reaction was observed. In conclusion, these results have shown that AdC68-19S could induce an effective immune response with a good safety profile, and is a promising candidate vaccine against COVID-19.

8.
Nat Commun ; 13(1): 871, 2022 02 15.
Article in English | MEDLINE | ID: covidwho-1692611

ABSTRACT

The SARS-CoV-2 Delta variant is currently the dominant circulating strain in the world. Uncovering the structural basis of the enhanced transmission and altered immune sensitivity of Delta is particularly important. Here we present cryo-EM structures revealing two conformational states of Delta spike and S/ACE2 complex in four states. Our cryo-EM analysis suggests that RBD destabilizations lead to population shift towards the more RBD-up and S1 destabilized fusion-prone state, beneficial for engagement with ACE2 and shedding of S1. Noteworthy, we find the Delta T478K substitution plays a vital role in stabilizing and reshaping the RBM loop473-490, enhancing interaction with ACE2. Collectively, increased propensity for more RBD-up states and the affinity-enhancing T478K substitution together contribute to increased ACE2 binding, providing structural basis of rapid spread of Delta. Moreover, we identify a previously generated MAb 8D3 as a cross-variant broadly neutralizing antibody and reveal that 8D3 binding induces a large K478 side-chain orientation change, suggesting 8D3 may use an "induced-fit" mechanism to tolerate Delta T478K mutation. We also find that all five RBD-targeting MAbs tested remain effective on Delta, suggesting that Delta well preserves the neutralizing antigenic landscape in RBD. Our findings shed new lights on the pathogenicity and antibody neutralization of Delta.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Antibodies, Monoclonal/immunology , COVID-19/transmission , Protein Domains/genetics , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/genetics , Amino Acid Substitution/genetics , Antibodies, Viral/immunology , Binding Sites , Broadly Neutralizing Antibodies/immunology , Cryoelectron Microscopy , Humans , Immunoglobulin Fab Fragments/immunology , Protein Binding/genetics , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism
9.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324340

ABSTRACT

Background: Shenzhen implement classification management to prevent and control coronavirus disease 2019 (COVID-19) outbreak. Individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms were instructed to take home quarantine for 14 days and nucleic acid testing (NAT) for SARS-CoV-2. We described the infection status of the home-quarantined individuals, and effects of community control strategies in the three incubations after Wuhan closure in Shenzhen. Methods: : This was a descriptive research, the sample size was 2,004 individuals based on multistage sampling during the pre-investigation. And the formal investigation expanded the sample size to 57,012 individuals based on pre-investigation. A single throat swab was collected from each individual for nucleic acid testing (NAT) by reverse transcription-polymerase chain reaction (RT-PCR). NAT was performed by a third-party institution. We collected information related to demographics, disease history, travel history, and personal protective measures before home quarantine, and monitored close-contact histories using the We Chat questionnaire. Results: : The total infection rate of home-quarantined individuals was 0.12‰ (95% CI: 0.05‰–0.24‰) out of the total sample size of 59,016. The detection period for seven confirmed cases was primarily concentrated between February 8 and 18, 2020, which was during the second incubation period after Wuhan's closure. The home quarantined individuals with epidemic histories (came from Hubei and any other affected regions) were considered the high risk population during the first two incubations after Wuhan’s closure. No positive cases were detected from February 25 to March 5(the third incubation after Wuhan’s closure). The number of newly-confirmed cases per day was 0 for eight consecutive days from February 22 to 29 in Shenzhen. Conclusions: : The community control strategies for home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms to take the NAT in the first two incubations is effective to control COVID-19. But it is not advocating for home-quarantined person to take the NAT since the third incubation.

10.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324149

ABSTRACT

Objective: To investigate the epidemiological characteristics, clinical features, treatment and short-term prognosis of SARS-CoV-2 infection in children. Methods: A retrospective analysis was conducted in children with SARS-CoV-2 admitted to twelve hospitals in eight cities in Hunan province, China, from January 26, 2020 to June 30, 2020. Results: A total of 48 children were enrolled in this study. 11 cases (23%) were asymptomatic, 15 cases (31%) were mild, 20 cases (42%) were moderate, and 2 cases (4%) were severe. No children were critical requiring intensive care. The most common symptom was fever (42%), cough (40%), fatigue (17%) and diarrhea (10%). The total peripheral blood leukocytes count decreased in two case (4%), Lymphocytopenia was present in 5 cases (10%). There were abnormal chest CT changes in 22 children (46%), including 15 (68%) with patchy ground glass opacity. In addition to supportive treatment, 41 children (85%) received antiviral therapy, 11 patients and (23%) were treated with antibiotics, 2 children (4%) were treated with methylprednisolone and IVIG. There was no death occurred. Conclusions: Most children with SARS CoV-2 infection in Hunan province were asymptomatic, mild or moderate. Severe cases are rare. Close family contact was the main route of infection. The younger the age, the less obvious symptoms for children might be. Epidemiological history, nucleic acid test and chest imaging were important tools for the diagnosis in children.

11.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323548

ABSTRACT

Background: The clinical characteristics and outcomes of the 2019 novel coronavirus (COVID-19) pneumonia are different in Hubei compared to other regions in China. But there are few comparative studies on the differences between imported and local patients which may provide information of the different courses of the virus after transmission. Methods: : We investigated 169 cases of COVID-19 pneumonia in two centers in Hunan Province, and divided them into two groups according to epidemiological history, "imported patients" refers to patient with a clear history of travel in Wuhan within 14 days before onset, and " local patients” refers to local resident without a recent history of travel in Wuhan, aiming to analyze the difference in clinical characteristics and outcomes between the two groups. All the epidemiological, clinical, imaging, and laboratory data were analyzed and contrasted. Results: : The incidence of fever on admission in imported patients was significantly higher than local patients. There was a significantly higher proportion of abnormal pulmonary signs, hypokalemia, hyponatremia, prolonged PT, elevated D-dimer and elevated blood glucose in imported patients. Compared with local patients, the proportion using antibiotics, glucocorticoids and gamma globulin were significantly higher in imported patients. The moderate type was more common in local patients, and the severe type were more frequent in imported patients. In addition, the median duration of viral clearance was longer in imported patients. Conclusions: : In summary, we found that imported cases were more likely to develop into severe cases, compared with local patients and required more powerful treatments. Trial registration: Registered 21 st March 2020, and this study has been approved by the Medical Ethics Committee (Approved Number. 2020017).

12.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-312713

ABSTRACT

Background: An ideal animal model to study SARS-coronavirus 2 (SARS-CoV-2) pathogenesis and evaluate therapies and vaccines should reproduce SARS-CoV-2 infection and recapitulate lung disease like those seen in humans. The angiotensin-converting enzyme 2 (ACE2) is a functional receptor for SARS-CoV-2, but mice are resistant to the infection because their ACE2 is incompatible with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Methods: We generated a mouse-adapted strain SARS-CoV-2 by serial passages in the lung of BALB/c mice. Complete genome deep sequencing of different generations of viruses was performed to characterize the dynamics of the adaptive mutations in SARS-CoV-2. Indirect immunofluorescence analysis and Biolayer interferometry experiments demonstrated that two mutations in RBD significantly increased its binding affinity towards mouse ACE2. Significantly, TLR7/8 agonist Resiquimod block SARS-CoV-2 in vitro and in vivo. Findings: We adapted a wild-type SARS-CoV-2 by serial passages in the lung of BALB/c mice. The mouse-adapted strain WBP-1 showed increased infectivity in BALB/c mice and led to severe interstitial pneumonia. We characterized the dynamics of the adaptive mutations in SARS-CoV-2 and demonstrated that Q493K and Q498H in RBD significantly increased its binding affinity towards mouse ACE2. Additionally, The TLR7/8 agonist Resiquimod was able to protect mice against WBP-1 challenge, demonstrating this mouse-adapted strain is a useful tool to investigate COVID-19 and develop new therapies. Interpretation: We found for the first time that the Q493K and Q498H mutations in the RBD of WBP-1 enhanced its interactive affinities with mACE2. The mouse-adapted SARS-CoV-2 provides a valuable tool for the evaluation of novel antiviral and vaccine strategies, especially in determining the immunopathological consequences of any intervention. This study also verified the antiviral activity of TLR7/8 agonist Resiquimod against SARS-CoV-2 in vitro and in vivo.Funding Statement: This research was funded by Emergency Science and Technology Project of Hubei Province(2020FCA046)and Independent Science and Technology Innovation Fund of Huazhong Agricultural University in 2020 (2662020PY002).Declaration of Interests: The authors declare no competing interests.Ethics Approval Statement: The animal experiments were approved by the Research Ethics Committee, Huazhong Agricultural University, Hubei, China (HZAUMO-2020-0007). All the animal experiments were conducted in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals from the Research Ethics Committee, Huazhong Agricultural University, Hubei, China.

13.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-305955

ABSTRACT

Abstract Background: To study the prevention and control strategies of coronavirus disease 2019 (COVID-19), and to analyze the infection of the home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms in the three incubations after Wuhan closure in Shenzhen. Methods: : The sample size was 2,004 individuals based on multistage sampling during the pre-investigation. Based on the results of the pre-investigation, the formal investigation expanded the sample size to 57,012 individuals. A single throat swab was collected from each individual for nucleic acid testing (NAT) by reverse transcription-polymerase chain reaction (RT-PCR). NAT was performed by a third-party institution, BGI. We collected information related to demographics, disease history, travel history, and personal protective measures before home quarantine, and monitored close-contact histories using the We Chat questionnaire. Results: : The total infection rate of home-quarantined individuals was 0.11% (95% CI: 0.05%–0.24%) out of the total sample size of 59,016. The detection period for seven confirmed cases was primarily concentrated between February 8 and 18, 2020, which was during the second incubation period after Wuhan's closure. The home quarantined individuals with epidemic histories (came from Hubei and any other affected regions) were considered the high risk population during the first two incubations after Wuhan’s closure. No positive cases were detected from February 25 to present (the third incubation after Wuhan’s closure). The number of newly-confirmed cases per day was 0 for 8 days from February 22 to 29 in Shenzhen. Thus, the strategies of prevention and control were effective. Conclusions: : The strategies and policies were effective for the prevention and control of COVID-19. Additionally, the strategy of implementing NAT during the first two incubations for home-quarantined individuals with epidemic histories (came from Hubei and any other affected regions), but without symptoms, facilitated early detection, early reporting, early diagnosis, early quarantining, and early treatment. However, our findings do not support NAT for home quarantined persons during the third incubation after Wuhan’s closure to present.

14.
Matter ; 5(2): 694-709, 2022 Feb 02.
Article in English | MEDLINE | ID: covidwho-1670871

ABSTRACT

The current COVID-19 pandemic urges us to develop ultra-sensitive surface-enhanced Raman scattering (SERS) substrates to identify the infectiousness of SARS-CoV-2 virions in actual environments. Here, a micrometer-sized spherical SnS2 structure with the hierarchical nanostructure of "nano-canyon" morphology was developed as semiconductor-based SERS substrate, and it exhibited an extremely low limit of detection of 10-13 M for methylene blue, which is one of the highest sensitivities among the reported pure semiconductor-based SERS substrates. Such ultra-high SERS sensitivity originated from the synergistic enhancements of the molecular enrichment caused by capillary effect and the charge transfer chemical enhancement boosted by the lattice strain and sulfur vacancies. The novel two-step SERS diagnostic route based on the ultra-sensitive SnS2 substrate was presented to diagnose the infectiousness of SARS-CoV-2 through the identification standard of SERS signals for SARS-CoV-2 S protein and RNA, which could accurately identify non-infectious lysed SARS-CoV-2 virions in actual environments, whereas the current PCR methods cannot.

15.
Virol Sin ; 2022 Jan 25.
Article in English | MEDLINE | ID: covidwho-1648554

ABSTRACT

The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of 2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-CoV-2 epidemics in several large cities or provinces of China. However, information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-CoV-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-CoV-2 transmission profiles. Genomic epidemiology revealed multiple SARS-CoV-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size. Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-CoV-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-CoV-2 strains during the early COVID-19 epidemic in China.

16.
Life (Basel) ; 12(1)2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1613886

ABSTRACT

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly contagious and causes coronavirus disease 2019 (COVID-19). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most accurate and reliable molecular assay to detect active SARS-CoV-2 infection. However, a rapid increase in test subjects has created a global bottleneck in testing capacity. Given that efficient nucleic acid extraction greatly affects reliable and accurate testing results, we compared three extraction platforms: MagNA Pure 96 DNA and Viral NA Small Volume kit on MagNA Pure 96 (Roche, Basel, Switzerland), careGENETM Viral/Pathogen HiFi Nucleic Acid Isolation kit (WELLS BIO Inc., Seoul, Korea) on KingFisher Flex (Thermo Fisher Scientific, Rocklin, CA, USA), and SGRespiTM Pure kit (Seegene Inc., Seoul, Korea) on Maelstrom 9600 (Taiwan Advanced Nanotech Inc., Taoyuan, Taiwan). RNA was extracted from 245 residual respiratory specimens from the different types of samples (i.e., NPS, sputum, and saliva) using three different kits. The 95% limits of detection of median tissue culture infectious dose per milliliter (TCID50/mL) for the MagNA Pure 96, KingFisher Flex, and Maelstrom 9600 were 0.37-3.15 × 101, 0.41-3.62 × 101, and 0.33-1.98 × 101, respectively. The KingFisher Flex platform exhibited 99.2% sensitivity and 100% specificity, whereas Maelstrom 9600 exhibited 98.3-100% sensitivity and 100% specificity. Bland-Altman analysis revealed a 95.2% concordance between MagNA Pure 96 and KingFisher Flex and 95.4% concordance between MagNA Pure 96 and Maelstrom 9600, indicating that all three platforms provided statistically reliable results. This suggests that two modifying platforms, KingFisher Flex and Maelstrom 9600, are accurate and scalable extraction platforms for large-scale SARS-CoV-2 clinical detection and could help the management of COVID-19 patients.

17.
PLoS One ; 16(12): e0260850, 2021.
Article in English | MEDLINE | ID: covidwho-1613341

ABSTRACT

Novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring nucleotide changes (mutations) in the spike gene have emerged and are spreading rapidly. These mutations are associated with SARS-CoV-2 transmissibility, virulence, or resistance to some neutralizing antibodies. Thus, the accurate detection of spike mutants is crucial for controlling SARS-CoV-2 transmission and identifying neutralizing antibody-resistance caused by amino acid changes in the receptor-binding domain. Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (ΔH69/V70, T95I, G142D, ΔY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay. The 5-SSG primer assay showed 100% specificity and a conservative limit of detection with a median tissue culture infective dose (TCID50) values of 1.4 × 102 TCID50/mL. The accuracy of the 5-SSG primer assay was confirmed by next generation sequencing. The results of these two approaches showed 100% consistency. Taken together, the ability of the 5-SSG primer assay to accurately detect key SARS-CoV-2 spike mutants is reliable. Thus, it is a useful tool for detecting SARS-CoV-2 spike gene mutants in a clinical setting, thereby helping to improve the management of patients with COVID-19.


Subject(s)
Mutation , SARS-CoV-2/genetics , Sequence Analysis, RNA/methods , Spike Glycoprotein, Coronavirus/genetics , DNA Primers/genetics , High-Throughput Nucleotide Sequencing , Humans , Limit of Detection , Protein Domains , Spike Glycoprotein, Coronavirus/chemistry
18.
Emerg Microbes Infect ; 11(1): 351-367, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1585238

ABSTRACT

The emergence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of currently approved vaccines and authorized therapeutic monoclonal antibodies (MAbs). It is hence important to continue searching for SARS-CoV-2 broadly neutralizing MAbs and defining their epitopes. Here, we isolate 9 neutralizing mouse MAbs raised against the spike protein of a SARS-CoV-2 prototype strain and evaluate their neutralizing potency towards a panel of variants, including B.1.1.7, B.1.351, B.1.617.1, and B.1.617.2. By using a combination of biochemical, virological, and cryo-EM structural analyses, we identify three types of cross-variant neutralizing MAbs, represented by S5D2, S5G2, and S3H3, respectively, and further define their epitopes. S5D2 binds the top lateral edge of the receptor-binding motif within the receptor-binding domain (RBD) with a binding footprint centred around the loop477-489, and efficiently neutralizes all variant pseudoviruses, but the potency against B.1.617.2 was observed to decrease significantly. S5G2 targets the highly conserved RBD core region and exhibits comparable neutralization towards the variant panel. S3H3 binds a previously unreported epitope located within the evolutionarily stable SD1 region and is able to near equally neutralize all of the variants tested. Our work thus defines three distinct cross-variant neutralizing sites on the SARS-CoV-2 spike protein, providing guidance for design and development of broadly effective vaccines and MAb-based therapies.


Subject(s)
COVID-19/virology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/immunology , Epitope Mapping , Female , Humans , Mice , Mice, Inbred BALB C , Neutralization Tests , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
19.
Mol Med Rep ; 24(6)2021 12.
Article in English | MEDLINE | ID: covidwho-1504040

ABSTRACT

The spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) emerged suddenly at the end of 2019 and the disease came to be known as coronavirus disease 2019 (COVID­19). To date, there is no specific therapy established to treat COVID­19. Identifying effective treatments is urgently required to treat patients and stop the transmission of SARS­CoV­2 in humans. For the present review, >100 publications on therapeutic agents for COVID­19, including in vitro and in vivo animal studies, case reports, retrospective analyses and meta­analyses were retrieved from PubMed and analyzed, and promising therapeutic agents that may be used to combat SARS­CoV­2 infection were highlighted. Since the outbreak of COVID­19, different drugs have been repurposed for its treatment. Existing drugs, including chloroquine (CQ), its derivative hydroxychloroquine (HCQ), remdesivir and nucleoside analogues, monoclonal antibodies, convalescent plasma, Chinese herbal medicine and natural compounds for treating COVID­19 evaluated in experimental and clinical studies were discussed. Although early clinical studies suggested that CQ/HCQ produces antiviral action, later research indicated certain controversy regarding their use for treating COVID­19. The molecular mechanisms of these therapeutic agents against SARS­CoV2 have been investigated, including inhibition of viral interactions with angiotensin­converting enzyme 2 receptors in human cells, viral RNA­dependent RNA polymerase, RNA replication and the packaging of viral particles. Potent therapeutic options were reviewed and future challenges to accelerate the development of novel therapeutic agents to treat and prevent COVID­19 were acknowledged.


Subject(s)
COVID-19/therapy , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/therapeutic use , Alanine/analogs & derivatives , Alanine/therapeutic use , Animals , Antimalarials/therapeutic use , Antiviral Agents/therapeutic use , COVID-19/diagnosis , Chloroquine/therapeutic use , Drugs, Chinese Herbal/therapeutic use , Humans , Hydroxychloroquine/therapeutic use , Immunization, Passive , SARS-CoV-2/isolation & purification
20.
Front Pediatr ; 9: 665377, 2021.
Article in English | MEDLINE | ID: covidwho-1463494

ABSTRACT

Objective: Aimed to investigate the epidemiological characteristics, clinical features, treatment, and short-term prognosis of COVID-19 in children. Methods: Retrospective analysis was conducted in 48 children with COVID-19 admitted to 12 hospitals in eight cities in Hunan province, China, from January 26, 2020 to June 30, 2020. Results: Of the 48 cases, Familial clusters were confirmed for 46 children (96%). 16 (33%) were imported from other provinces. There were 11 (23%) asymptomatic cases. only 2 cases (4%) were severe. The most common symptom was fever (n = 20, 42%). Other symptoms included cough (n = 19, 40%), fatigue (n = 8, 17%), and diarrhea (n = 5, 10%). In the early stage, the total peripheral blood leukocytes count increased in 3(6%) cases and the lymphocytes count decreased in 5 (10%) cases. C-reactive protein and procalcitonin were elevated respectively in 3 (6%) cases and 2 (4%) cases. There were abnormal chest CT changes in 22 (46%) children, including 15 (68%) with patchy ground glass opacity, 5 (22%) with consolidation, and 2 (10%) with mixed shadowing. In addition to supportive treatment, antiviral therapy was received by 41 (85%) children, 11 (23%) patients were treated with antibiotics, and 2 (4%) were treated with methylprednisolone and intravenous immunoglobulin. Compared to 2 weeks follow-up, one child developed low fever and headache during the 4 weeks follow-up, 3 (6%) children had runny noses, one of them got mild cough, and 4 (12%) children had elevated white blood cells and lymphocytes. However, LDH and CK increased at 2 weeks and 4 weeks follow-up. 2 weeks follow-up identified normal chest radiographs in 33 (69%) pediatric patients. RT-PCR detection of SARS-CoV-2 was negative in all follow-up patients at 2 and 4 weeks follow-up. All 48 pediatric patients were visited by calling after 1 year of discharge. Conclusions: Most cases of COVID-19 in children in Hunan province were asymptomatic, mild, or moderate. Close family contact was the main route of infection. It appeared that the younger the patient, the less obvious their symptoms. Epidemiological history, nucleic acid test, and chest imaging were important tools for diagnosis in children.

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