Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR (preprint)

BACKGROUND: The outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 140 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2. However, the positive rate of RT-qPCR assay of pharyngeal swab samples are reported to vary from 30~60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach. METHODSWe established a reverse transcription digital PCR (RT-dPCR) protocol to detect SARS-CoV-2 on 194 clinical pharyngeal swab samples, including 103 suspected patients, 75 close contacts and 16 supposed convalescents. RESULTS: The limit of blanks (LoBs) of the RT-dPCR assays were ~1.6, ~1.6 and ~0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients. CONCLUSION: RT-dPCR could be a confirmatory method for suspected patients diagnosed by RT-qPCR. Furthermore, RT-dPCR was more sensitive and suitable for low viral load specimens from the both patients under isolation and those under observation who may not be exhibiting clinical symptoms.

The epidemic characteristics, guidelines and policies: A compared analysis of literature between COVID-19 and SARS (preprint)

Background: COVID-19 broke out in Wuhan, and rapidly spread to other province of China and other countries. To understand epidemic characteristics, guidelines and policiesof COVID-19 compared to SARS, and further explore the gap of health system facing with major outbreaks for improvement in China. Methods: A systematic review was performed using China academic literature (CNKI), Wan Fang, PubMed, medRxiv, bioRxiv,offical website of World Health Organization, National Health Commission of the People’s Republic of China, the Hubei Province Health Commission, and Wuhan City Health Commission for literature of epidemiological and clinical characteristics, guidelines an policies of COVID-19 and SARS from 2003 to 2020. Two dataset were obtained from the National Health Commission's open data information, and daily SARS epidemic section authorized by the State Council`s Information Office.Results: The 113 related studies finally entered final analysis, among which 63 were Chinese articles. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and 2019 novel coronavirus (SARS-CoV-2) caused outbreak in 2002 and 2019 in China called SARS and 2019 coronavirus disease (COVID-19). Both belong to Beta Coronavirus (β-CoV). Their original cluster confirmed cases had contact history to wild animals, and clinical symptoms are similar. However, COVID-19 has a high human-to-human transmission capability, and more rapidly spread from Hubei province (97.9% cases) across China and over the world. R0 was estimated around 2.2 (1.4-3.8), and incubation period of COVID-19 is 1-14 days. Transmission routes predominantly have respiratory droplets, close contact and even air transmission by aerosols. A fatality rate was 2.70% (2004/74185) with the highest of 14.8% at over 80 years old, and cases mainly were males in the middle and elder ages. For prevention and control, strategies and policies consecutively were issued. Compared to those of SARS, responsiveness for COVID-19 is more prompt.  Policy priorities tend to multi-sectors of cooperation, strong action to cut off source of infection (sealed Wuhan city),strengthening community prevention and mental health. Conclusions: The major gap facing with epidemic outbreak exists in the weak health system especially public health system, although we already made a great progress and improvement in our preventive awareness. Therefore, we forcefully appeal to a strong public health system by government for continuous investment and improvement. An advanced public health system stands by us in times of peace, and while fights for us during epidemic outbreak period.