Comprehensive large-scale nucleic acid–testing strategies support China’s sustained containment of COVID-19

A large-scale (>20,000 tests per day) standardized and fully-automated laboratory (Huo-Yan) was built as an ad-hoc measure to meet the requirement of virus detection after the novel coronavirus (COVID-19) outbreak in Wuhan, China. We integrated the brief data from Health Commission of Hubei Province and the real-world operation data of Huo-Yan laboratory, into a novel differential model with non-linear transfer coefficients and competitive compartments, to evaluate the trend of suspected cases under different nucleic acid testing capacities, including suspected cases with/without coronavirus infection, to evaluate the achievement of “daily settlement” condition of suspected cases and the control of the epidemic under different nucleic acid testing capacities.

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An Optimal Nucleic Acid Testing Strategy for COVID-19 during the Spring Festival Travel Rush in Mainland China: A Modelling Study

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18041788 ◽

2021 ◽

Vol 18 (4) ◽

pp. 1788

Author(s):

Yu-Hao Zhou ◽

Ke Ma ◽

Peng Xiao ◽

Run-Ze Ye ◽

Lin Zhao ◽

...

Keyword(s):

Nucleic Acid ◽

Public Transportation ◽

Mainland China ◽

Medical Expenditure ◽

Nucleic Acid Testing ◽

Tier 2 ◽

Testing Strategies ◽

Symptom Screening ◽

Spring Festival ◽

Local Transmission

Western countries are experiencing surges in COVID-19 cases and deaths due to increasing public transportation during holiday seasons. This study aimed to explore whether mainland China will face an epidemic rebound during the Spring Festival holiday, when millions of Chinese people travel across the country, and investigate which nucleic acid testing (NAT) strategy is optimal to contain the epidemic. A microsimulation model was used to simulate SARS-CoV-2 transmission among railway travelers and evaluated the effects of various NAT strategies. An extended susceptible-exposed-infectious-recovered (SEIR) model was built to forecast local transmission during the Spring Festival period under different scenarios of testing strategies. The total number of infections, testing burden, and medical expenditure were calculated to devise an optimal strategy during the Spring Festival travel rush. Assuming the daily incidence of 20 per 10 million persons, our model simulated that there would be 97 active infections on the day of travel among 10 million railway passengers without NAT and symptom screening. Pre-travel testing could reduce the number of active infections. Compared with no NAT, testing passengers from risk tier 2–4 regions 3 days before travelling could significantly reduce the risk of transmission, and it is more economical and efficient than testing for all passengers.

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

10.1101/2020.03.15.20036624 ◽

2020 ◽

Cited By ~ 3

Author(s):

Qing Xie ◽

Jing Wang ◽

Jianling You ◽

Shida Zhu ◽

Rui Zhou ◽

...

Keyword(s):

Nucleic Acid ◽

Prevention And Control ◽

Large Scale ◽

High Throughput Sequencing ◽

Nucleic Acid Testing ◽

Differential Model ◽

Testing Platform ◽

Public Data ◽

And Control ◽

The Impact

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.

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Elevated white blood cell count does not predict Clostridium difficile nucleic acid testing results

Clinical Infectious Diseases ◽

10.1093/cid/ciab106 ◽

2021 ◽

Author(s):

Dustin E Bosch ◽

Patrick C Mathias ◽

Niklas Krumm ◽

Andrew Bryan ◽

Ferric C Fang ◽

...

Keyword(s):

Nucleic Acid ◽

Clostridium Difficile ◽

Blood Cell ◽

Cell Count ◽

Prognostic Marker ◽

White Blood Cell Count ◽

White Blood Cell ◽

Inpatient Setting ◽

Nucleic Acid Testing ◽

Blood Cell Count

Abstract Background An elevated white blood cell count (>15 thousand/μL) is an established prognostic marker in patients with Clostridium difficile infection (CDI). Small observational studies have suggested that a markedly elevated WBC should prompt consideration of CDI. However, there is limited evidence correlating WBC elevation with the results of C. difficile nucleic acid testing (NAAT). Methods Retrospective review of laboratory testing, outcomes, and treatment of 16,568 consecutive patients presenting to 4 hospitals over four years with NAAT and WBC testing on the same day. Results No significant relationship between C. difficile NAAT results and concurrent WBC in the inpatient setting was observed. Although an elevated WBC did predict NAAT results in the outpatient and emergency department populations (p<0.001), accuracy was poor, with receiver-operator areas under the curve of 0.59 and 0.56. An elevated WBC (>15 thousand/μL) in CDI was associated with a longer median hospital length of stay (15.5 vs. 11.0 days, p<0.01), consistent with leukocytosis as a prognostic marker in CDI. NAAT-positive inpatients with elevated WBC were more likely to be treated with metronidazole and/or vancomycin (relative ratio 1.2, 95% confidence interval 1.1–1.3) and die in the hospital (relative ratio 2.9, 95% CI 2.0–4.3). Conclusions Although WBC is an important prognostic indicator in patients with CDI, an isolated WBC elevation has low sensitivity and specificity as a predictor of fecal C. difficile NAAT positivity in the inpatient setting. A high or rising WBC in isolation is not a sufficient indication for CDI testing.

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Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern

Medical Microbiology and Immunology ◽

10.1007/s00430-021-00719-0 ◽

2021 ◽

Author(s):

Andreas Osterman ◽

Maximilian Iglhaut ◽

Andreas Lehner ◽

Patricia Späth ◽

Marcel Stern ◽

...

Keyword(s):

Nucleic Acid ◽

Point Of Care ◽

Study Cohort ◽

Operating Characteristics ◽

Testing Strategies ◽

Level 3 ◽

Amino Acid Mutations ◽

Antigen Tests ◽

Roche Diagnostics ◽

Analytical Sensitivities

AbstractA versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.

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