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1.
Atmospheric Chemistry and Physics ; 22(7):4355-4374, 2022.
Article in English | ProQuest Central | ID: covidwho-1776521

ABSTRACT

Nitrate aerosol plays an increasingly important role in wintertime haze pollution in China. Despite intensive research on wintertime nitrate chemistry in recent years, quantitative constraints on the formation mechanisms of nitrate aerosol in the Yangtze River Delta (YRD), one of the most developed and densely populated regions in eastern China, remain inadequate. In this study, we identify the major nitrate formation pathways and their key controlling factors during the winter haze pollution period in the eastern YRD using 2-year (2018–2019) field observations and detailed observation-constrained model simulations. We find that the high atmospheric oxidation capacity, coupled with high aerosol liquid water content (ALWC), made both the heterogeneous hydrolysis of dinitrogen pentoxide (N2O5) and the gas-phase OH oxidation of nitrogen dioxide (NO2) important pathways for wintertime nitrate formation in this region, with contribution percentages of 69 % and 29 % in urban areas and 63 % and 35 % in suburban areas during the haze pollution episodes, respectively. We further find that the gas-to-particle partitioning of nitric acid (HNO3) was very efficient so that the rate-determining step in the overall formation process of nitrate aerosol was the oxidation of NOx to HNO3 through both heterogeneous and gas-phase processes. The atmospheric oxidation capacity (i.e., the availability of O3 and OH radicals) was the key factor controlling the production rate of HNO3 from both processes. During the COVID-19 lockdown (January–February 2020), the enhanced atmospheric oxidation capacity greatly promoted the oxidation of NOx to nitrate and hence weakened the response of nitrate aerosol to the emission reductions in urban areas. Our study sheds light on the detailed formation mechanisms of wintertime nitrate aerosol in the eastern YRD and highlights the demand for the synergetic regulation of atmospheric oxidation capacity and NOx emissions to mitigate wintertime nitrate and haze pollution in eastern China.

2.
Biosaf Health ; 4(2): 70-78, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1739578

ABSTRACT

Despite multiple virus outbreaks over the past decade, including the devastating coronavirus disease 2019 (COVID-19) pandemic, the lack of accurate and timely diagnosis and treatment technologies has wreaked havoc on global biosecurity. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has the potential to address these critical needs for tackling infectious diseases to detect viral nucleic acids and inhibit viral replication. This review summarizes how the CRISPR/Cas system is being utilized for the treatment and diagnosis of infectious diseases with the help of biosafety materials and highlights the design principle and in vivo and in vitro efficacy of advanced biosafety materials used to deal with virus attacks.

3.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-309536

ABSTRACT

This protocol presents the all-in-one dual CRISPR-Cas12a (AIOD-CRISPR) assay to ultra-sensitively and visually detect SARS-CoV-2. The procedure of AIOD-CRISPR assay typically consists of three parts including sample preparation, AIOD-CRISPR reaction, and fluorescence detection. Sample preparation involves the synthetic RNA preparation and the nucleic acid extraction from SARS-CoV-2 samples. The prepared nucleic acids were then added into the AIOD-CRISPR reaction systems as templates, followed by incubation at 37°C for 20-40 min. After incubation, visual detection was immediately conducted by placing the tubes in a portable LED blue transilluminator (Maestrogen UltraSlim) or the ChemiDoc™ MP Imaging System (Bio-Rad) with its built-in UV channel. In addition to endpoint visual detection, real-time fluorescence detection was also available for AIOD-CRISPR assay. This protocol is helpful for applying AIOD-CRISPR assay to rapid, sensitive, one-pot point-of-care SARS-CoV-2 detection.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-309535

ABSTRACT

The recent outbreak of novel Coronavirus (SARS-CoV-2), the causative agent of COVID-19 disease, has spread rapidly all over the world. Human immunodeficiency virus (HIV) is another deadly virus and causes acquired immunodeficiency syndrome (AIDS). Rapid and early detection of these viruses will facilitate early intervention and prevent disease spread. Here, we present an A ll- I n- O ne D ual CRISPR -Cas12a (termed "AIOD-CRISPR") assay method for simple, rapid, ultrasensitive, specific, one-pot, and visual detection of coronavirus SARS-CoV- 2 and HIV-1 virus. In our AIOD-CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a-based detection and improve both detection sensitivity and fluorescence signals. The AIOD-CRISPR assay method was utilized to detect nucleic acids (DNA and RNA) of the SARS-CoV-2 and HIV-1 with a sensitivity of few copies. We validated our AIOD-CRISPR method by using COVID-19 swab samples and obtained consistent results with that of RT-PCR method. More importantly, we successfully demonstrated to use a low- cost hand warmer (~$ 0.3) as an incubator of our AIOD-CRISPR assay and detect COVID-19 patient samples within 20 minutes, enabling an instrument-free, visual detection of COVID-19 at the point of care. Thus, our method has significant potential for developing next-generation point-of-care molecular diagnostics.

5.
Clin Infect Dis ; 73(11): e4154-e4165, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1559099

ABSTRACT

BACKGROUND: Children and older adults with coronavirus disease 2019 (COVID-19) display a distinct spectrum of disease severity yet the risk factors aren't well understood. We sought to examine the expression pattern of angiotensin-converting enzyme 2 (ACE2), the cell-entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the role of lung progenitor cells in children and older patients. METHODS: We retrospectively analyzed clinical features in a cohort of 299 patients with COVID-19. The expression and distribution of ACE2 and lung progenitor cells were systematically examined using a combination of public single-cell RNA-seq data sets, lung biopsies, and ex vivo infection of lung tissues with SARS-CoV-2 pseudovirus in children and older adults. We also followed up patients who had recovered from COVID-19. RESULTS: Compared with children, older patients (>50 years.) were more likely to develop into serious pneumonia with reduced lymphocytes and aberrant inflammatory response (P = .001). The expression level of ACE2 and lung progenitor cell markers were generally decreased in older patients. Notably, ACE2 positive cells were mainly distributed in the alveolar region, including SFTPC positive cells, but rarely in airway regions in the older adults (P < .01). The follow-up of discharged patients revealed a prolonged recovery from pneumonia in the older (P < .025). CONCLUSIONS: Compared to children, ACE2 positive cells are generally decreased in older adults and mainly presented in the lower pulmonary tract. The lung progenitor cells are also decreased. These risk factors may impact disease severity and recovery from pneumonia caused by SARS-Cov-2 infection in older patients.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , COVID-19 , Stem Cells , Aged , Child , Humans , Lung/cytology , Middle Aged , RNA-Seq , Retrospective Studies , Severity of Illness Index
6.
Biosens Bioelectron ; 199: 113865, 2022 Mar 01.
Article in English | MEDLINE | ID: covidwho-1560782

ABSTRACT

Rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for early diagnostics and timely medical treatment of coronavirus disease 2019 (COVID-19). However, current detection methods typically rely on expensive and bulky instrumentation. Here, we developed a simple, sensitive, instrument-free, CRISPR-based diagnostics of SARS-CoV-2 using a self-contained microfluidic system. The microfluidic chip integrates isothermal amplification, CRISPR cleavage, and lateral flow detection in a single, closed microfluidic platform, enabling contamination-free, visual detection. To simplify the operation and transportation of the device, we lyophilized the CRISPR reagents in the reaction chamber and pre-stored the liquid solutions in blisters. We employed a low-cost, portable hand warmer to incubate the microfluidic chip without the need for electricity. The self-contained microfluidic system can detect down to 100 copies of SARS-CoV-2 RNA. Further, we clinically validated our method by detecting 24 COVID-19 clinical nasopharyngeal swab samples, achieving excellent sensitivity (94.1%), specificity (100%), and accuracy (95.8%). This simple, sensitive, and affordable microfluidic system represents a promising tool for point-of-care diagnostics of COVID-19 and other infectious diseases.


Subject(s)
Biosensing Techniques , COVID-19 , CRISPR-Cas Systems , Humans , Microfluidics , Nucleic Acid Amplification Techniques , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity
7.
Adv Nanobiomed Res ; 2(2): 2100101, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1557774

ABSTRACT

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide. However, most SARS-CoV-2 detection methods depend on time-consuming sample preparation and large detection instruments. Herein, a method employing nonbleeding pH paper to achieve both RNA extraction and visual isothermal amplification is proposed, enabling rapid, instrument-free SARS-CoV-2 detection. By taking advantage of capillary forces, pH-paper-based RNA extraction can be accomplished within 1 min without need for any equipment. Further, the pH paper can mediate dye-free visual isothermal amplification detection. In less than a 46-min sample-to-answer time, pH-paper-based extraction and visual detection (termed pH-EVD) can consistently detect 1200 genome equivalents per microliter of SARS-CoV-2 in saliva, which is comparable to TaqMan probe-based quantitative reverse transcription PCR (RT-qPCR). Through coupling with a chemically heated incubator called a smart cup, the instrument-free, pH-EVD-based SARS-CoV-2 detection method on 30 nasopharyngeal swab samples and 33 contrived saliva samples is clinically validated. Thus, the pH-EVD method provides simple, rapid, reliable, low-cost, and instrument-free SARS-CoV-2 detection and has the potential to streamline onsite COVID-19 diagnostics.

8.
Sens Actuators B Chem ; 351: 130998, 2022 Jan 15.
Article in English | MEDLINE | ID: covidwho-1492625

ABSTRACT

Multiplexed detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rather than detection targeting a single gene is crucial to ensure more accurate coronavirus disease 2019 (COVID-19) diagnostics. Here, we develop a monolithic, 3D-printed, lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. The centrifugal lab-on-disc is fabricated in one step using simple 3D printing technology, circumventing the need for aligning and binding multiple layers. By combining isothermal amplification technology, this lab-on-disc platform is capable of simultaneously detecting the nucleoprotein and envelope genes of SARS-CoV-2 as well as an internal control of the human POP7 gene. Within a 50-minute incubation period, 100 copies SARS-CoV-2 RNA can be detected through visual observation according to color and fluorescence changes in the disc. Further, we clinically validated the lab-on-disc platform by testing 20 nasopharyngeal swab samples and demonstrated a sensitivity of 100% and an accuracy of 95%. Therefore, the monolithic, 3D-printed, lab-on-disc platform provides simple, rapid, disposable, sensitive, reliable, and multiplexed molecular detection of SARS-CoV-2, holding promise for COVID-19 diagnostics at the point of care.

10.
Lab Chip ; 21(14): 2730-2737, 2021 07 13.
Article in English | MEDLINE | ID: covidwho-1260960

ABSTRACT

The COVID-19 pandemic, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), has become a public health emergency and widely spread around the world. Rapid, accurate and early diagnosis of COVID-19 infection plays a crucial role in breaking this pandemic. However, the detection accuracy is limited for current single-gene diagnosis of SARS-CoV-2. Herein, we develop an autonomous lab-on-paper platform for multiplex gene diagnosis of SARS-CoV-2 by combining reverse transcription recombinase polymerase amplification (RT-RPA) and CRISPR-Cas12a detection. The autonomous lab-on-paper is capable of simultaneously detecting nucleoprotein (N) gene and spike (S) gene of SARS-CoV-2 virus as well as human housekeeping RNAse P gene (an internal control) in a single clinical sample. With the developed platform, 102 copies viral RNA per test can be detected within one hour. Also, the lab-on-paper platform has been used to detect 21 swab clinical samples and obtains a comparable performance to the conventional RT-PCR method. Thus, the developed lab-on-paper platform holds great potential for rapid, sensitive, reliable, multiple molecular diagnostics of COVID-19 and other infectious diseases in resource-limited settings.


Subject(s)
COVID-19 , Pandemics , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats , Humans , Nucleic Acid Amplification Techniques , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity
11.
Sens Actuators B Chem ; 344: 130242, 2021 Oct 01.
Article in English | MEDLINE | ID: covidwho-1260865

ABSTRACT

Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.

12.
Biosens Bioelectron ; 184: 113218, 2021 Jul 15.
Article in English | MEDLINE | ID: covidwho-1188340

ABSTRACT

Quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is crucial for early diagnosis and timely medical treatment of coronavirus disease 2019. Here, we describe a digital warm-start CRISPR (dWS-CRISPR) assay for sensitive quantitative detection of SARS-CoV-2 in clinical samples. The dWS-CRISPR assay is initiated at above 50 °C and overcomes undesired premature target amplification at room temperature, enabling accurate and reliable digital quantification of SARS-CoV-2. By targeting SARS-CoV-2's nucleoprotein gene, the dWS-CRISPR assay is able to detect down to 5 copies/µl SARS-CoV-2 RNA in the chip. It is clinically validated by quantitatively determining 32 clinical swab samples and three clinical saliva samples. Moreover, it has been demonstrated to directly detect SARS-CoV-2 in heat-treated saliva samples without RNA extraction. Thus, the dWS-CRISPR method, as a sensitive and reliable CRISPR assay, facilitates accurate SARS-CoV-2 detection toward digitized quantification.


Subject(s)
Biosensing Techniques , COVID-19 , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats , Humans , Nucleic Acid Amplification Techniques , RNA, Viral , SARS-CoV-2
13.
Nat Commun ; 11(1): 4711, 2020 09 18.
Article in English | MEDLINE | ID: covidwho-780001

ABSTRACT

The recent outbreak of novel coronavirus (SARS-CoV-2) causing COVID-19 disease spreads rapidly in the world. Rapid and early detection of SARS-CoV-2 facilitates early intervention and prevents the disease spread. Here, we present an All-In-One Dual CRISPR-Cas12a (AIOD-CRISPR) assay for one-pot, ultrasensitive, and visual SARS-CoV-2 detection. By targeting SARS-CoV-2's nucleoprotein gene, two CRISPR RNAs without protospacer adjacent motif (PAM) site limitation are introduced to develop the AIOD-CRISPR assay and detect the nucleic acids with a sensitivity of few copies. We validate the assay by using COVID-19 clinical swab samples and obtain consistent results with RT-PCR assay. Furthermore, a low-cost hand warmer (~$0.3) is used as an incubator of the AIOD-CRISPR assay to detect clinical samples within 20 min, enabling an instrument-free, visual SARS-CoV-2 detection at the point of care. Thus, our method has the significant potential to provide a rapid, sensitive, one-pot point-of-care assay for SARS-CoV-2.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Pneumonia, Viral/virology , Betacoronavirus/genetics , COVID-19 , COVID-19 Testing , CRISPR-Cas Systems , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Genes, Viral , Humans , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pandemics , Pneumonia, Viral/diagnosis , Point-of-Care Systems , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity , Viral Proteins/analysis , Viral Proteins/genetics
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