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1.
Biosaf Health ; 2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2085979

ABSTRACT

We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3-31 days later. All 47 nasopharyngeal swabs were deep sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n=31), Beta (n=1), and C.1.2 (n=1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95%CI]: 2.77-10.22) than did the first samples (T1; median: 2; 95%CI: 1.63-3.74; Wilcoxon test, P=0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.

2.
Biosens Bioelectron ; 219: 114816, 2022 Oct 17.
Article in English | MEDLINE | ID: covidwho-2068733

ABSTRACT

Airborne transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the urgent need for aerosol monitoring of SARS-CoV-2 to prevent sporadic outbreaks of COVID-19. The inadequate sensitivity of conventional methods and the lack of an on-site detection system limited the practical SARS-CoV-2 monitoring of aerosols in public spaces. We have developed a novel SARS-CoV-2-in-aerosol monitoring system (SIAMs) which consists of multiple portable cyclone samplers for collecting aerosols from several venues and a sensitive "sample-to-answer" microsystem employing an integrated cartridge for the analysis of SARS-CoV-2 in aerosols (iCASA) near the sampling site. By seamlessly combining viral RNA extraction based on a chitosan-modified quartz filter and "in situ" tetra-primer recombinase polymerase amplification (tpRPA) into an integrated microfluidic cartridge, iCASA can provide an ultra-high sensitivity of 20 copies/mL, which is nearly one order of magnitude greater than that of the commercial kit, and a short turnaround time of 25 min. By testing various clinical samples of nasopharyngeal swabs, saliva, and exhaled breath condensates obtained from 23 COVID-19 patients, we demonstrate that the positive rate of our system was 3.3 times higher than those of the conventional method. Combining with multiple portable cyclone samplers, we detected 52.2% (12/23) of the aerosol samples, six times higher than that of the commercial kit, collected from the isolation wards of COVID-19 patients, demonstrating the excellent performance of our system for SARS-CoV-2-in-aerosol monitoring. We envision the broad application of our microsystem in aerosol monitoring for fighting the COVID-19 pandemic.

3.
Sci Adv ; 8(38): eabm6668, 2022 09 23.
Article in English | MEDLINE | ID: covidwho-2053083

ABSTRACT

Viruses exploit host cell machinery to support their replication. Defining the cellular proteins and processes required for a virus during infection is crucial to understanding the mechanisms of virally induced disease and designing host-directed therapeutics. Here, we perform a genome-wide CRISPR-Cas9-based screening in lung epithelial cells infected with the PR/8/NS1-GFP virus and use GFPhi cell as a unique screening marker to identify host factors that inhibit influenza A virus (IAV) infection. We discovered that APOE affects influenza virus infection both in vitro and in vivo. Cell deficiency in APOE conferred substantially increased susceptibility to IAV; mice deficient in APOE manifested more severe lung pathology, increased virus load, and decreased survival rate. Mechanistically, lack of cell-produced APOE results in impaired cell cholesterol homeostasis, enhancing influenza virus attachment. Thus, we identified a previously unrecognized role of APOE in restraining IAV infection.


Subject(s)
Communicable Diseases , Influenza A virus , Influenza, Human , Orthomyxoviridae Infections , Animals , Apolipoproteins , Apolipoproteins E/genetics , Cholesterol , Host-Pathogen Interactions , Humans , Influenza, Human/genetics , Mice , Orthomyxoviridae Infections/genetics , Virus Replication
5.
Lancet Microbe ; 3(5): e348-e356, 2022 05.
Article in English | MEDLINE | ID: covidwho-1984300

ABSTRACT

Background: The memory immune response is crucial for preventing reinfection or reducing disease severity. However, the robustness and functionality of the humoral and T-cell response to SARS-CoV-2 remains unknown 12 months after initial infection. The aim of this study is to investigate the durability and functionality of the humoral and T-cell response to the original SARS-CoV-2 strain and variants in recovered patients 12 months after infection. Methods: In this longitudinal cohort study, we recruited participants who had recovered from COVID-19 and who were discharged from the Wuhan Research Center for Communicable Disease Diagnosis and Treatment at the Chinese Academy of Medical Sciences, Wuhan, China, between Jan 7 and May 29, 2020. Patients received a follow-up visit between Dec 16, 2020, and Jan 27, 2021. We evaluated the presence of IgM, IgA, and IgG antibodies against the SARS-CoV-2 nucleoprotein, Spike protein, and the receptor-binding domain 12 months after initial infection, using ELISA. Neutralising antibodies against the original SARS-CoV-2 strain, and the D614G, beta (B.1.351), and delta (B.1.617.2) variants were analysed using a microneutralisation assay in a subset of plasma samples. We analysed the magnitude and breadth of the SARS-CoV-2-specific memory T-cell responses using the interferon γ (IFNγ) enzyme-linked immune absorbent spot (ELISpot) assay and intracellular cytokine staining (ICS) assay. The antibody response and T-cell response (ie, IFN-γ, interleukin-2 [IL-2], and tumour necrosis factor α [TNFα]) were analysed by age and disease severity. Antibody titres were also analysed according to sequelae symptoms. Findings: We enrolled 1096 patients, including 289 (26·4%) patients with moderate initial disease, 734 (67·0%) with severe initial disease, and 73 (6·7%) with critical initial disease. Paired plasma samples were collected from 141 patients during the follow-up visits for the microneutralisation assay. PBMCs were collected from 92 of 141 individuals at the 12-month follow-up visit, of which 80 were analysed by ELISpot and 92 by ICS assay to detect the SARS-CoV-2-specific memory T-cell responses. N-IgG (899 [82·0%]), S-IgG (1043 [95·2%]), RBD-IgG (1032 [94·2%]), and neutralising (115 [81·6%] of 141) antibodies were detectable 12 months after initial infection in most individuals. Neutralising antibodies remained stable 6 and 12 months after initial infection in most individuals younger than 60 years. Multifunctional T-cell responses were detected for all SARS-CoV-2 viral proteins tested. There was no difference in the magnitude of T-cell responses or cytokine profiles in individuals with different symptom severity. Moreover, we evaluated both antibody and T-cell responses to the D614G, beta, and delta viral strains. The degree of reduced in-vitro neutralising antibody responses to the D614G and delta variants, but not to the beta variant, was associated with the neutralising antibody titres after SARS-CoV-2 infection. We also found poor neutralising antibody responses to the beta variant; 83 (72·2%) of 115 patients showed no response at all. Moreover, the neutralising antibody titre reduction of the recovered patient plasma against the delta variant was similar to that of the D614G variant and lower than that of the beta variant. By contrast, T-cell responses were cross-reactive to the beta variant in most individuals. Importantly, T-cell responses could be detected in all individuals who had lost the neutralising antibody response to SARS-CoV-2 12 months after the initial infection. Interpretation: SARS-CoV-2-specific neutralising antibody and T-cell responses were retained 12 months after initial infection. Neutralising antibodies to the D614G, beta, and delta viral strains were reduced compared with those for the original strain, and were diminished in general. Memory T-cell responses to the original strain were not disrupted by new variants. This study suggests that cross-reactive SARS-CoV-2-specific T-cell responses could be particularly important in the protection against severe disease caused by variants of concern whereas neutralising antibody responses seem to reduce over time. Funding: Chinese Academy of Medical Sciences, National Natural Science Foundation, and UK Medical Research Council.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/epidemiology , Cohort Studies , Cytokines , Humans , Immunoglobulin G , Longitudinal Studies , T-Lymphocytes
6.
Geophysical research letters ; 2022.
Article in English | EuropePMC | ID: covidwho-1981038

ABSTRACT

Widespread wildfires struck the western United States in 2020, damaging properties and threating human lives. Meanwhile, the COVID‐19 pandemic spread across the globe, which disrupted human activities. Here, we investigate the effects of the emissions reductions during the pandemic on fire weather in 2020 over the western United States by using an earth system model together with observations. We show that reductions in aerosols dominate the increases in wildfire risks, whereas greenhouse gas decrease counteracts this influence. The aerosol emissions reductions increased surface air temperature and decreased precipitation and relative humidity due to a weakened moisture transport, which explains one‐third of the observed increase in wildfire risks during August–November over the western United States in 2020. This study suggests that COVID‐19‐related emissions reductions have an unexpected influence on wildfires, highlighting a different but important role of human activities in affecting wildfire risks. Key Points The impacts of COVID‐19 emissions reductions on weather conditions for wildfire over the western United States in 2020 were investigated The COVID‐19 emissions reductions increased surface air temperature and decreased precipitation and relative humidity Reductions in aerosols explain one‐third of the observed wildfire risk increase, whereas greenhouse gas decrease counteracts this influence

7.
J Med Virol ; 94(12): 5746-5757, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1976742

ABSTRACT

We evaluated and compared humoral immune responses after inactivated coronavirus disease 2019 (COVID-19) vaccination among naïve individuals, asymptomatically infected individuals, and recovered patients with varying severity. In this multicenter, prospective cohort study, blood samples from 666 participants were collected before and after 2 doses of inactivated COVID-19 vaccination. Among 392 severe acute respiratory syndrome coronavirus 2-naïve individuals, the seroconversion rate increased significantly from 51.8% (median antispike protein pan-immunoglobulins [S-Igs] titer: 0.8 U/ml) after the first dose to 96% (median S-Igs titer: 79.5 U/ml) after the second dose. Thirty-two percent of naïve individuals had detectable neutralizing antibodies (NAbs) against the original strain but all of them lost neutralizing activity against the Omicron variant. In 274 individuals with natural infection, humoral immunity was significantly improved after a single vaccine dose, with median S-Igs titers of 596.7, 1176, 1086.5, and 1828 U/ml for asymptomatic infections, mild cases, moderate cases, and severe/critical cases, respectively. NAb titers also improved significantly. However, the second dose did not substantially increase antibody levels. Although a booster dose is needed for those without infection, our findings indicate that recovered patients should receive only a single dose of the vaccine, regardless of the clinical severity, until there is sufficient evidence to confirm the benefits of a second dose.


Subject(s)
COVID-19 , Viral Vaccines , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/prevention & control , COVID-19 Vaccines , Humans , Prospective Studies , SARS-CoV-2 , Vaccination , Vaccines, Inactivated
8.
Hum Vaccin Immunother ; : 2099166, 2022 Jul 29.
Article in English | MEDLINE | ID: covidwho-1967805

ABSTRACT

Vaccination for the novel coronavirus disease 2019 (COVID-19) provides an effective approach for the general improvement of social safety and individual health. To date, few studies have analyzed the adoption of COVID-19 vaccines from an entire impact process perspective. Using the health belief model (HBM) and the valence theory, this research evaluates the impact process of vaccine adoption for COVID-19. The respondents in this study were individuals who have been vaccinated in China. The effective sample included 595 individuals. Four valuable and novel findings are identified through this research. First, neither perceived susceptibility nor perceived severity has a statistically significant impact on the benefits from vaccination, threats from vaccination and self-efficacy. Second, benefits from vaccination produce a significant positive effect on self-efficacy and vaccine adoption. Third, threats from vaccination produce a significant negative effect on self-efficacy and vaccine adoption. Fourth, both self-efficacy and cues to adoption produce a significantly positive impact on vaccine adoption. Our theoretical model, which is the main contribution of this research, indicates that individual vaccine adoption is simply a process that leads from behavioral cognition to behavioral intention, rather than from psychological perception to behavioral cognition and then from behavioral cognition to behavioral intention.

10.
Respir Res ; 23(1): 188, 2022 Jul 15.
Article in English | MEDLINE | ID: covidwho-1938326

ABSTRACT

BACKGROUND: Assessing the humoral immunity of patients with underlying diseases after being infected with SARS-CoV-2 is essential for adopting effective prevention and control strategies. The purpose of this study is to analyze the seroprevalence of people with underlying diseases and the dynamic change features of anti-SARS-CoV-2 antibodies. METHODS: We selected 100 communities in Wuhan using the probability-proportional-to-size sampling method. From these 100 communities, we randomly selected households according to a list provided by the local government. Individuals who have lived in Wuhan for at least 14 days since December 2019 and were ≥ 40 years old were included. From April 9-13, 2020, community staff invited all selected individuals to the community healthcare center in batches by going door-to-door or telephone. All participants completed a standardized electronic questionnaire simultaneously. Finally, 5 ml of venous blood was collected from all participants. Blood samples were tested for the presence of pan-immunoglobulins, IgM, IgA, and IgG antibodies against SARS-CoV-2 nucleocapsid protein and neutralising antibodies were assessed. During the period June 11-13, 2020 and October 9-December 5, 2020, all family members of a positive family and matched negative families were followed up twice. RESULTS: The seroprevalence of anti-SARS-CoV-2 antibodies in people with underlying diseases was 6.30% (95% CI [5.09-7.52]), and that of people without underlying diseases was 6.12% (95% CI [5.33-6.91]). A total of 313 people were positive for total antibodies at baseline, of which 97 had underlying disease. At the first follow-up, a total of 212 people were positive for total antibodies, of which 66 had underlying disease. At the second follow-up, a total of 238 people were positive for total antibodies, of which 68 had underlying disease. A total of 219 participants had three consecutive serum samples with positive total antibodies at baseline. The IgG titers decreased significantly with or without underlying diseases (P < 0.05) within the 9 months at least, while the neutralizing antibody titer remained stable. The titer of asymptomatic patients was lower than that of symptomatic patients (baseline, P = 0.032, second follow-up, P = 0.018) in the underlying diseases group. CONCLUSION: Our research focused on the serological changes of people with and without underlying diseases in a state of single natural infection. Regardless of the underlying diseases, the IgG titer decreased significantly over time, while there was no significant difference in the decline rate of IgG between with and without underlying diseases. Moreover, the neutralizing antibody titer remained relatively stable within the 9 months at least.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/diagnosis , COVID-19/epidemiology , Humans , Immunoglobulin G , Longitudinal Studies , Seroepidemiologic Studies
11.
Chin Med J (Engl) ; 135(10): 1213-1222, 2022 May 20.
Article in English | MEDLINE | ID: covidwho-1922353

ABSTRACT

ABSTRACT: The pandemic of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to major public health challenges globally. The increasing viral lineages identified indicate that the SARS-CoV-2 genome is evolving at a rapid rate. Viral genomic mutations may cause antigenic drift or shift, which are important ways by which SARS-CoV-2 escapes the human immune system and changes its transmissibility and virulence. Herein, we summarize the functional mutations in SARS-CoV-2 genomes to characterize its adaptive evolution to inform the development of vaccination, treatment as well as control and intervention measures.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mutation/genetics , Pandemics , SARS-CoV-2/genetics , Virulence
12.
Emerg Microbes Infect ; 11(1): 1819-1827, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1915486

ABSTRACT

The emergence of SARS-CoV-2 Omicron and other variants of concern (VOCs) has brought huge challenges to control the COVID-19 pandemic, calling for urgent development of effective vaccines and therapeutic drugs. In this study, we focused on characterizing the impacts of divergent VOCs on the antiviral activity of lipopeptide-based fusion inhibitors that we previously developed. First, we found that pseudoviruses bearing the S proteins of five VOCs (Alpha, Beta, Gamma, Delta, and Omicron) and one variant of interest (Lambda) exhibited greatly decreased infectivity relative to the wild-type (WT) strain or single D614G mutant, especially the Omicron pseudovirus. Differently, the most of variants exhibited an S protein with significantly enhanced cell fusion activity, whereas the S protein of Omicron still mediated decreased cell-cell fusion. Next, we verified that two lipopeptide-based fusion inhibitors, IPB02V3 and IPB24, maintained the highly potent activities in inhibiting various S proteins-driven cell fusion and pseudovirus infection. Surprisingly, both IPB02V3 and IPB24 lipopeptides displayed greatly increased potencies against the infection of authentic Omicron strain relative to the WT virus. The results suggest that Omicron variant evolves with a reduced cell fusion capacity and is more sensitive to the inhibition of fusion-inhibitory lipopeptides; thus, IPB02V3 and IPB24 can be further developed as potent, broad-spectrum antivirals for combating Omicron and the potential future outbreak of other emerging variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Anti-Retroviral Agents/therapeutic use , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Humans , Lipopeptides/pharmacology , Pandemics/prevention & control , SARS-CoV-2/genetics , Virus Internalization
13.
Am J Transl Res ; 14(5): 3132-3142, 2022.
Article in English | MEDLINE | ID: covidwho-1887956

ABSTRACT

OBJECTIVE: To explore the application value of mobile cabin hospitals in combating COVID-19 outbreak. METHODS: The basic clinical data, the number of admission, CT scan, novel coronavirus nucleic acid testing results were collected and calculated. The operational elements of running this temporary hospital were reviewed from its construction to closing. RESULTS: Wuhan Hanyang Mobile Cabin Hospital was transformed from Hall B1 of Wuhan International Expo Center. With a total of 930 beds in this temporary hospital, 1,028 patients were admitted, among them, 598 patients were cured, and 430 patients were transferred to designated hospitals in the special period. Totally, 1,206 mobile CT scan were conducted. 2,295 novel coronavirus nucleic acid tests were performed, among which, 1,032 tests showed two continuous negative results, 924 tests with one negative, while 302 tests with positive result (13.16%). No nosocomial infection of working staff was found due to the conduction of multiple measures. The patients' livelihoods were well safeguarded in mobile cabin hospitals. CONCLUSION: The mobile cabin hospital compulsory quarantine for mild patients can serve as an alternative method to combat COVID-19.

14.
Clin Infect Dis ; 74(8): 1485-1488, 2022 04 28.
Article in English | MEDLINE | ID: covidwho-1816023

ABSTRACT

A false-positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction result can lead to unnecessary public health measures. We report 2 individuals whose respiratory specimens were contaminated by an inactivated SARS-CoV-2 vaccine strain (CoronaVac), likely at vaccination premises. Incidentally, whole genome sequencing of CoronaVac showed adaptive deletions on the spike protein, which do not result in observable changes of antigenicity.


Subject(s)
COVID-19 Vaccines , COVID-19 , COVID-19/prevention & control , Humans , SARS-CoV-2/genetics , Vaccination
17.
Sci Signal ; 15(715): eabh0068, 2022 01 04.
Article in English | MEDLINE | ID: covidwho-1741564

ABSTRACT

The transcription regulator ID2 plays an essential role in the development and differentiation of immune cells. Here, we report that ID2 also negatively regulates antiviral innate immune responses. During viral infection of human epithelial cells, ID2 bound to TANK-binding kinase 1 (TBK1) and to inhibitor of nuclear factor κB kinase ε (IKKε). These interactions inhibited the recruitment and activation of interferon (IFN) regulatory factor 3 (IRF3) by TBK1 or IKKε, leading to a reduction in the expression of IFN-ß1 (IFNB1). IFN-ß induced the nuclear export of ID2 to form a negative feedback loop. Knocking out ID2 in human cells enhanced innate immune responses and suppressed infection by different viruses, including SARS-CoV-2. Mice with a myeloid-specific deficiency of ID2 produced more IFN-α in response to viral infection and were more resistant to viral infection than wild-type mice. Our findings not only establish ID2 as a modulator of IRF3 activation induced by TBK1 and/or IKKε but also introduce a mechanism for cross-talk between innate immunity and cell development and differentiation.


Subject(s)
COVID-19 , I-kappa B Kinase , Animals , Antiviral Agents , Humans , I-kappa B Kinase/genetics , I-kappa B Kinase/metabolism , Immunity, Innate , Inhibitor of Differentiation Protein 2 , Interferon Regulatory Factor-3/genetics , Interferon Regulatory Factor-3/metabolism , Mice , Phosphorylation , SARS-CoV-2
18.
Biosaf Health ; 4(2): 66-69, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1734223

ABSTRACT

Upper respiratory tract samples are the most commonly used samples for coronavirus disease 2019 (COVID-19) diagnosis. The samples collected from the nasopharynx are preferred for viral nucleic acids detection. Commercial nasopharyngeal swabs (NPSs) are the major factor that influences the sampling quality. We here evaluated the acceptability and efficiency of NPSs from five manufacturers by examining the concentration of glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) retrieved from the swabs using the RT-PCR method. Significant different concentrations of GAPDH were detected, ranged from 4.36 × 108 copies/mL to 6.98 × 1010 copies/mL among the five swabs (p < 0.05). The designation of the swab head, with or without tip expansion, had limited influence on the collection efficiency. The discrepancy among the NPSs emphasized the improvement of the swab head material.

19.
Chin Med J (Engl) ; 133(9): 1015-1024, 2020 May 05.
Article in English | MEDLINE | ID: covidwho-1722617

ABSTRACT

BACKGROUND: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel bat-origin CoV causing severe and fatal pneumonia in humans. METHODS: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Wuhan Jinyintan Hospital, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. RESULTS: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown ß-CoV strain in all five patients, with 99.8% to 99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6% to 87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. CONCLUSION: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.


Subject(s)
Betacoronavirus , Coronavirus Infections/virology , Pneumonia, Viral/virology , Adult , Aged , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/therapy , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/therapy , SARS-CoV-2 , Tomography, X-Ray , Treatment Outcome
20.
Microb Biotechnol ; 15(6): 1883-1894, 2022 06.
Article in English | MEDLINE | ID: covidwho-1714095

ABSTRACT

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently posed a significant threat to global public health. The objective of this study was to develop and evaluate a rapid, expandable and sequencing-free high-resolution melting (HRM) approach for the direct detection and classification of SARS-CoV-2. Thirty-one common pathogens that can cause respiratory tract infections were used to evaluate the specificity of the method. Synthetic RNA with serial dilutions was utilized to determine the sensitivity of the method. Finally, the clinical performance of the method was assessed using 290 clinical samples. The one-step multiplex HRM could accurately identify SARS-CoV-2 and differentiate mutations in each marker site within approximately 2 h. For each target, the limit of detection was lower than 10 copies/reaction, and no cross-reactivity was observed among organisms within the specificity testing panel. The method showed good uniformity for SARS-CoV-2 detection with a consistency of 100%. Regarding the clade classification performance, the results showed good concordance compared with sequencing, with the rate of agreement being 95.1% (78/82). The one-step multiplex HRM method is a rapid method for SARS-CoV-2 detection and classification.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
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