RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

Chen, Liangjun; Liu, Weiyong; Zhang, Qi; Xu, Ke; Ye, Guangming; Wu, Wei-Chen; Sun, Ziyong; Liu, Fang; Wu, Kailang; Zhong, Bo; Man, Yi; Zhang, Wenxia; Chen, Yu; Li, Yirong; Shī, Mǎng; Lan, Ke; Liu, Yingle

doi:10.1080/22221751.2020.1725399

Cited by 550 publications

(524 citation statements)

References 14 publications

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“…Then the full genome sequence of SARS-CoV-2 (29870-bp, excluding the poly (A) tail) in GenBank (accession number MN908947) was released quickly on January 10, 2020, which is more than 82% identical to those of SARS-CoV and bat SARS-like coronavirus (SL-CoV) 12 . On the basis of analysis of this complete genomes obtained in this study, several laboratories developed molecular detection tools based on targeting ORF1ab, RNA-dependent RNA polymerase (RdRp) gene N, and E regions of viral spike genes [13][14][15] . And then the rapid identification of this novel coronavirus is attributed to recent advances in the detection of SARS-CoV-2, including RT-PCR, real-time reverse transcription PCR (rRT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and microarray-based assays.…”

Section: Identification Of Pathogens Mainly Includes Virus Isolationmentioning

confidence: 99%

“…And the patients confirmed with the COVID-19 pneumonia had 2 or 3 continuous negative RT-PCR results for nasopharyngeal and throat swab specimens can discharge from hospital. However, the scholar around china indicated that cases of COVID-19 that had 2 or 3 continuous negative RT-PCR results for nasopharyngeal and throat swab specimens before finally laboratory-confirmed [13]. And currently, several reports has reported the positive RT-PCR results for stool of COVID-19 patients 16,17 .…”

Section: Identification Of Pathogens Mainly Includes Virus Isolationmentioning

confidence: 99%

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Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

Jiang

Ren

Liu

et al. 2020

Preprint

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syndrome coronavirus 2 (SARS-CoV-2) has become a global threat to public health. Aiming to construct an efficient screening pattern, we comprehensively evaluated the performances of RT-PCR and chest CT in diagnosing COVID-19. Methods:The records including demographics, RT-PCR, and CT from 87 confirmed cases and 481 exclusion cases were collected. The diagnostic accuracy of the pharyngeal swab RT-PCR, CT, combination with the second pharyngeal swab RT-PCR or with CT were evaluated individually.Besides, all the stool RT-PCR results were plotted by time to explore the value of stool RT-PCR. Findings: Combination of RT-PCR and CT has the higher sensitivity (91.9%,79/86) than RT-PCR alone (78.2% ， 68/87) or CT alone (66.7%, 54 of 81) or combination of two RT-PCR tests (86.2%,75/87). There was good agreement between RT-PCR and CT (kappa-value, 0.430). In 34 COVID-19 cases with inconsistent results, 94.1% (n=32) are mild infection, 62.5% of which (20/32) showed positive RT-PCR. 46.7% (35/75) COVID-19 patients had at least one positive stool during the course. Two cases had positive stool earlier than the pharyngeal swabs. Importantly, one patient had consecutive positive stool but negative pharyngeal swabs.Interpretation: Combination of RT-PCR and CT with the highest sensitivity is an optimal pattern to screen COVID-19. RT-PCR is superior to CT in diagnosing mild infections. Stool RT-PCR should be considered as an item for improving discovery rate and hospital discharge. This study shed light for optimizing scheme of screening and monitoring of SARS-CoV-2 infection. : medRxiv preprint person-to-person transmission of SARS-CoV-2 in hospital and family settings 2,6,7 . As of February 17, 2020, more than 71,000 laboratory-confirmed and 1,770 death cases have been documented in China and in other countries worldwide (including the USA, German, japan and South Korea) 8,9 . The mortality rate of SARS-CoV-2 was around 2%. The WHO has recently declared the SARS-CoV-2 a public health emergency of international concern 10 . Thus, diagnostic tests specific for this infection are urgently needed for confirming suspected cases, screening patients and conducting virus surveillance.Identification of pathogens mainly includes virus isolation and viral nucleic acid detection.According to the traditional Koch's postulates, virus isolation is the gold standard for virus diagnosis in the laboratory. Thus, based on SARS-CoV-2 possesses a strong capability to infect humans, CDC recommends that clinical virology laboratories should not attempt viral isolation from specimens collected from COVID-19 patients under investigation. Because SARS-CoV-2 is a newly discovered virus, the spectrum of the available diagnostic tools is tight. In the early stage, SARS-CoV-2 has been detected in human clinical specimens by next-generation sequencing, cell culture, and electron microscopy 11 . Further development of accurate and rapid methods to identify this emergency . CC-BY-ND 4.0 International license It is made available under a author/funder, who has...

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Section: Identification Of Pathogens Mainly Includes Virus Isolationmentioning

confidence: 99%

Section: Identification Of Pathogens Mainly Includes Virus Isolationmentioning

confidence: 99%

Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

Jiang

Ren

Liu

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The causative pathogen of the COVID-19 outbreak has been identified as a highly infectious novel coronavirus which is referred to as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). [1][2][3] The transmission of SARS-CoV-2 in humans is thought to be via at least 3 sources: 1) inhalation of liquid droplets produced by and/or 2) close contact with infected persons and 3) contact with surfaces contaminated with SARS-CoV-2. 4 Moreover, aerosol transmission of pathogens has been shown in confined spaces.…”

Section: Introductionmentioning

confidence: 99%

Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak

Liu

Ning

Chen

et al. 2020

Preprint

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223

284

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Background:The ongoing outbreak of COVID-19 has spread rapidly and sparked global concern. While the transmission of SARS-CoV-2 through human respiratory droplets and contact with infected persons is clear, the aerosol transmission of SARS-CoV-2 has been little studied.Methods: Thirty-five aerosol samples of three different types (total suspended particle, size segregated and deposition aerosol) were collected in Patient Areas (PAA) and Medical Staff Areas (MSA) of Renmin Hospital of Wuhan University (Renmin) and Wuchang Fangcang Field Hospital (Fangcang), and Public Areas (PUA) in Wuhan, China during COVID-19 outbreak. A robust droplet digital polymerase chain reaction (ddPCR) method was employed to quantitate the viral SARS-CoV-2 RNA genome and determine aerosol RNA concentration. Results:The ICU, CCU and general patient rooms inside Renmin, patient hall inside Fangcang had undetectable or low airborne SARS-CoV-2 concentration but deposition samples inside ICU and air sample in Fangcang patient toilet tested positive. The airborne SARS-CoV-2 in Fangcang MSA had bimodal distribution with higher concentration than those in Renmin during the outbreak but turned negative after patients number reduced and rigorous sanitization implemented. PUA had undetectable airborne SARS-CoV-2 concentration but obviously increased with accumulating crowd flow. Conclusions:Room ventilation, open space, proper use and disinfection of toilet can effectively limit aerosol transmission of SARS-CoV-2. Gathering of crowds with asymptomatic carriers is a potential source of airborne SARS-CoV-2. The virus aerosol deposition on protective apparel or floor surface and their subsequent resuspension is a potential transmission pathway and effective sanitization is critical in minimizing aerosol transmission of SARS-CoV-2.

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“…SARS-CoV-2 detection from COVID-19 patient samples in Wuhan, China. Samples testing positive(1)(2)(3)(4)(5)(6) or negative(7) with commercial RT-qPCR tests were assayed using colorimetric LAMP assay with primer set targeting ORF1a (A) and GeneN (B). Yellow indicates a positive detection after 30 min incubation, and pink a negative reaction with results compared to the negative control (N).…”

mentioning

confidence: 99%

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

Zhang

Odiwuor

Xiong

et al. 2020

Preprint

359

477

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The ability to detect an infectious agent in a widespread epidemic is crucial to the success of quarantine efforts in addition to sensitive and accurate screening of potential cases of infection from patients in a clinical setting. Enabling testing outside of sophisticated laboratories broadens the scope of control and surveillance efforts, but also requires robust and simple methods that can be used without expensive instrumentation. Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This simple and sensitive method provides an opportunity to facilitate virus detection in the field without a requirement for complex diagnostic infrastructure.. CC-BY 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) The copyright holder for this preprint .

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RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

Cited by 550 publications

References 14 publications

Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

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