Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model

BackgroundChina adopted an unprecedented province-scale quarantine since January 23rd 2020, after the novel coronavirus (COVID-19) broke out in Wuhan in December 2019. Responding to the challenge of limited testing capacity, large-scale standardized and fully-automated laboratory (Huo-Yan) was built as an ad-hoc measure. There was so far no empirical data or mathematical model to reveal the impact of the testing capacity improvement since the quarantine. MethodsWe integrated public data released by the Health Commission of Hubei Province and Huo-Yan Laboratory testing data into a novel differential model with non-linear transfer coefficients and competitive compartments, to evaluate the trends of suspected cases under different nucleic acid testing capacities. ResultsWithout the establishment of Huo-Yan, the suspected cases would increased by 47% to 33,700, the corresponding cost of the quarantine would be doubled, and the turning point of the increment of suspected cases and the achievement of "daily settlement" (all daily new discovered suspected cases were diagnosed according to the nucleic acid testing results) would be delayed for a whole week and 11 days. If the Huo-Yan Laboratory ran at its full capacity, the number of suspected cases would decrease at least a week earlier, the peak of suspected cases would be reduced by at least 44% and the quarantine cost could be reduced by more than 72%. Ideally, if a daily testing capacity of 10,500 could achieved immediately after the Hubei lockdown, "daily settlement" for all suspected cases would be achieved immediately. ConclusionsLarge-scale and standardized clinical testing platform with nucleic acid testing, high-throughput sequencing and immunoprotein assessment capabilities need to be implemented simultaneously in order to maximize the effect of quarantine and minimize the duration and cost. Such infrastructure like Huo-Yan, is of great significance for the early prevention and control of infectious diseases for both common times and emergencies.

Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.

Clinical data and next-generation sequencing results analysis of central nervous system infection with listeria / 中华神经科杂志

Objective To evaluate the potential value of next-generation sequencing ( NGS) as a diagnostic method for listeria infection in central nervous system ( CNS ) . Methods To identify the potentially pathogenic microorganisms ( PPMs) of the five patients with CNS infection in the Department of Neurology, People's Hospital of Zhengzhou University from June 2017 to November 2017, blood or cerebrospinal fluid ( CSF ) was detected not only using common laboratory tests , including routine , biochemical, cytologic, culture and Gram-staining methods, etc, but also using the BGISEQ-100 sequencing platform to identify the PPMs of CSF .Concomitantly , we collected concurrent clinical data , then performed a comprehensive analysis of their clinical , laboratory , and auxiliary examination data .Results Of the five cases (male :female: 1:4, age ranges: 26 -61 years), the disease mainly occurred in summer.Three patients received immunosuppressants treatment before infection , and three patients had gastrointestinal syndrome in the prodromal period .Infection of CNS led to fever , headache and meningeal irritation sign in all the patients.The medical imaging examinations showed the invasion of meninges , brainstem, and the periventricular gray matter.The cell count of CSF was more than 500 ×106/L.NGS techniques showed listeria genome sequence ranged from 57 to 2611, and the coverage of listeria varied from 0.23％ to 14.00％, and PCR results supported the existence of listeria .Conclusion NGS is beneficial to make the diagnosis of listeria infection in CNS , and can help guide early treatment .

The hydride generation atomic fluorescence spectrophotometry method for determination of urinary arsenic / 中华地方病学杂志

Objective To apply hydride generation atomic fluorescence spectrophotometry (HG-AFS method) in urinary arsenic detection,and to provide a better,newer and more convenient detection method for quantitative analysis of urinary arsenic.Methods According to the Guide to Develop Biological Sample Inspection Method(WS/T 68-1996) and Guide for Establishing Occupational Health Standards-part 5:Determination Methods in Biological Materials (GB/T 210.5-2008),HG-AFS method was established to detect arsenic content in urine after modification of the method for sample pretreatment,and to verify the linear range of standard curve and linearity,detection limit,precision,accuracy,stability of the sample,and to compare the experimental results of HG-AFS method with those of standard methods of WS/T 28-1996 and Determination of Arsenic in Urine by Cyanide Generation Atomic Fluorescence Method (WS/T 474-2015).Results The HG-AFS method linear range was from 0-100 μg/L,the correlation coefficient r =0.999 9,the detection limit was 0.07 μg/L,the precision was 1.96％-3.97％,and the recovery rate was 95.1％-105.0％.There was no statistical significance between HG-AFS method,the standard of WS/T 28-1996 or WS/T 474-2015 methods (t =1.539,0.353,all P ＞ 0.05).Conclusion The new method is superior to the current detection method owing to its low detection limit,high precision,good accuracy,and wide linear range.

Detection of Listeria monocytogenes in CSF from Three Patients with Meningoencephalitis by Next-Generation Sequencing

BACKGROUND AND PURPOSE: Encephalitis caused by Listeria monocytogenes (L. monocytogenes) is rare but sometimes fatal. Early diagnosis is difficult using routine cerebrospinal fluid (CSF) tests, while next-generation sequencing (NGS) is increasingly being used for the detection and characterization of pathogens. METHODS: This study set up and applied unbiased NGS to detect L. monocytogenes in CSF collected from three cases of clinically suspected listeria meningoencephalitis. RESULTS: Three cases of patients with acute/subacute meningoencephalitis are reported. Magnetic resonance imaging and blood cultures led to a suspected diagnosis of L. monocytogenes, while the CSF cultures were negative. Unbiased NGS of CSF identified and sequenced reads corresponding to L. monocytogenes in all three cases. CONCLUSIONS: This is the first report highlighting the feasibility of applying NGS of CSF as a diagnostic method for central nervous system (CNS) L. monocytogenes infection. Routine application of this technology in clinical microbiology will significantly improve diagnostic methods for CNS infectious diseases.