Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections

Yang, Yang; Yang, Minghui; Shen, Chenguang; Wang, Fuxiang; Yuan, Jing; Li, Jinxiu; Zhang, Mingxia; Wang, Zhaoqin; Li, Xing; Wei, Jinli; Peng, Ling; Wong, Gary; Zheng, Haixia; Wu, Wencan; Liao, Mingfeng; Feng, Kai; Li, Jianming; Yang, Qianting; Zhao, Juanjuan; Zhang, Zheng; Liu, Lei; Liu, Yingxia

doi:10.1101/2020.02.11.20021493

Cited by 665 publications

(768 citation statements)

References 12 publications

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“…Nasopharyngeal swabs and sputum have been suggested to be effective clinical samples for diagnosis (27,28), and we have assessed direct PCR using these matrices. It should be feasible to extend this to other common samples used for Covid- Covid-19 infection can be confirmed in less than an hour after sample collection and addition to mastermix for amplification and detection.…”

Section: Discussionmentioning

confidence: 99%

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Wee

Sivalingam

Yap

2020

Preprint

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There is an ongoing worldwide coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There is an urgent need for rapid, simplified and cost-effective detection methods. We have developed and analytically validated a protocol for direct rapid extraction-free PCR (DIRECT-PCR) detection of SARS-CoV-2 without the need for nucleic acid purification. As few as 6 RNA copies per reaction of viral nucleocapsid (N) gene from respiratory samples such as sputum and nasal exudate can be detected directly using our one-step inhibitor-resistant assay. The performance of this assay was validated on a commercially available portable PCR thermocycler. Viral lysis, reverse transcription, amplification and detection are achieved in a single-tube homogeneous reaction within 36 minutes. This minimized hands-on time, reduces turnaround-time for sample-to-result and obviates the need for RNA purification reagents. It could enable wider use of Covid-19 testing for diagnosis, screening and research in countries and regions where laboratory capabilities are limiting.

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Section: Discussionmentioning

confidence: 99%

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Wee

Sivalingam

Yap

2020

Preprint

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“…Xie et al [1] similarly considered 167 infected patients of whom 5 (3%) tested negative by RT-PCR at initial presentation. Fang et al [3] found that RT-PCR was only able to identify 36/51 (71%) of SARS-CoV-2 infected patients when using swabs taken 0-6 days after the onset of symptoms, and Luo et al [9] similarly reported that the initial sensitivity of throat swabs in secondary contacts was 71%.…”

Section: Introductionmentioning

confidence: 99%

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

Wikramaratna

Paton

Ghafari

2020

Preprint

152

167

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Reverse transcription-polymerase chain reaction (RT-PCR) assays are used to test patients and key workers for infection with the causative SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives can occur if the sample contains insufficient quantities of the virus to be successfully amplified and detected. The amount of virus in a swab is likely to vary between patients, sample location (nasal, throat or sputum) and through time as infection progresses. Here, we analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once. We identify that the probability of a positive test decreases with time after symptom onset, with throat samples less likely to yield a positive result relative to nasal samples. Empirically derived distributions of the time between symptom onset and hospitalisation allowed us to comment on the likely false negative rates in cohorts of patients who present for testing at different clinical stages. We further estimate the expected numbers of false negative tests in a group of tested individuals and show how this is affected by the timing of the tests. Finally, we assessed the robustness of these estimates of false negative rates to the probability of false positive tests. This work has implications both for the identification of infected patients and for the discharge of convalescing patients who are potentially still infectious.

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“…To fight against COVID-19 and promote the prevention and control of the epidemic, researchers have recently made efforts in various aspects; their research involves epidemiological research 5,6,7 , diagnostic methods of the novel coronavirus 8,9,10,11 , clinical characteristics of the disease 12,13,14,15,16 , characteristics of disease transmission 17,18,19 , development of candidate therapies 20,21,22 , the identification of animal hosts 23,24,25,26 , etc. However, there has been no research conducted on the public's attention to COVID-19.…”

Section: Introductionmentioning

confidence: 99%

Chinese Public Attention to COVID-19 Epidemic: Based on Social Media

Zhao

2020

Preprint

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Background:Since the new coronavirus epidemic in China in December 2019, information and discussions about COVID-19 have spread rapidly on the Internet and have quickly become the focus of worldwide attention, especially on social media. and described the trend of public attention on COVID-19 epidemic-related topics. ROST CM6.0 (ROST Content Mining System Version 6.0) was used to analyze the collected text for word segmentation, word frequency, and sentiment analysis. We further described the hot topic keywords and sentiment trends of public attention. We used VOSviewer to implement a visual cluster analysis of hot keywords and build a social network of public opinion content. Results:The study has four main findings. First, we analyzed the changing trend of the public's attention to the COVID-19 epidemic, which can be divided into three stages. Second, the hot topic keywords of public attention at each stage are : medRxiv preprint slightly different. In addition, the emotional tendency of the public toward the COVID-19 epidemic-related hot topics has changed from negative to neutral, with negative emotions weakening and positive emotions increasing as a whole. Finally, we divided the COVID-19 topics with the most public concern into five categories:(1) new COVID-19 epidemics and their impact; (2) frontline reporting of the epidemic and prevention and control measures; (3) expert interpretation and discussion on the source of infection; (4) medical services on the frontline of the epidemic; and (5) focus on the global epidemic and the search for suspected cases.Conclusions: This is the first study of public attention on the COVID-19 epidemic using a Chinese social media platform (i.e., Sina Microblog). Our study found that social media (e.g., Sina Microblog) can be used to measure public attention to public health emergencies. During the epidemic of the novel coronavirus, a large amount of information about the COVID-19 epidemic was disseminated on Sina Microblog and received widespread public attention. We have learned about the hotspots of public concern regarding the COVID-19 epidemic. These findings can help the government and health departments better communicate with the public on health and translate public health needs into practice to create targeted measures to prevent and control the spread of COVID-19.

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Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections

Abstract: 1 BackgroundThe outbreak of novel coronavirus pneumonia (NCP) caused by

Cited by 665 publications

References 12 publications

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

Chinese Public Attention to COVID-19 Epidemic: Based on Social Media

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