scholarly journals Wide-scale Pooled Sample Testing for COVID-19: Application, Optimisation and Probabilistic Analysis

2021 ◽  
Author(s):  
Xiaolong Su ◽  
Man Zhou
Keyword(s):  
Nucleic Acid ◽  
Optimal Number ◽  
Nucleic Acid Testing ◽  
Infection Rates ◽  
Testing Methods ◽  
Pooled Testing ◽  
Testing Method ◽  
Epidemic Period ◽  
The World ◽  
Wide Scale

Abstract Background Currently, coronavirus disease 2019 (COVID-19) has become the most severe infectious disease affecting the world, which has spread around the world to more than 200 countries in 2020. Until COVID-19 vaccine technology completely matures, nucleic acid testing is considered as an effective way to screen virus carriers and control the spread of the virus. Considering that the medical resources and infection rates are different across various countries and regions, if all infected areas adopt the traditional individual nucleic acid testing method, the workload will be heavy and time-consuming. Therefore, this will not lead to the control of the pandemic. Methods After Wuhan completed a citywide nucleic acid testing in May 2020, China basically controlled the spread of COVID-19 and entered the post-epidemic period. Since then, although some cities in China, such as Qingdao, Xinjiang, Beijing, Dalian, have experienced a local epidemic resurgence, the pandemic was quickly suppressed through wide-scale pooled nucleic acid testing methods. Combined with the successful experience of mass nucleic acid testing in China, this study introduces two main pooled testing methods used in two cities with a population of more than ten million people, Wuhan’s “five-in-one” and Qingdao's “ten-in-one” rapid pooled testing methods. This study proposes an improved method for optimising the second round of “ten-in-one” pooled testing, known as “the pentagram mini-pooled testing method”, which speeds up the testing process (as a result of reducing the numbers of testing by 40%) and significantly reduces the cost. Findings Qingdao's optimised “ten-in-one” pooled testing method quickly screens out the infections by running fewer testing. This study also mathematically examines the probabilistic principles and applicability conditions for pooled testing of COVID-19. Herein, the study theoretically determines the optimal number of samples that could successfully be combined into a pool under different infection rates. Then, it quantitatively discusses the applicability and principles for choosing the pooled testing instead of individual testing.Interpretation Overall, this research offers a reference for other countries with different infection rates to help them in implementing the mass testing for COVID-19 to reduce the spread of coronavirus.

scholarly journals Effects of prolonged incubation period and centralized quarantine on the COVID-19 outbreak in Shijiazhuang, China: a modeling study

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Wenlong Zhu ◽  
Mengxi Zhang ◽  
Jinhua Pan ◽  
Ye Yao ◽  
Weibing Wang
Keyword(s):  
Nucleic Acid ◽  
Incubation Period ◽  
Likelihood Method ◽  
Cumulative Number ◽  
Nucleic Acid Testing ◽  
Prolonged Incubation ◽  
Serial Interval ◽  
Epidemic Period ◽  
Epidemiological Characteristics ◽  
The Impact

Abstract Background From 2 January to 14 February 2021, a local outbreak of COVID-19 occurred in Shijiazhuang, the capital city of Hebei Province, with a population of 10 million. We analyzed the characteristics of the local outbreak of COVID-19 in Shijiazhuang and evaluated the effects of serial interventions. Methods Publicly available data, which included age, sex, date of diagnosis, and other patient information, were used to analyze the epidemiological characteristics of the COVID-19 outbreak in Shijiazhuang. The maximum likelihood method and Hamiltonian Monte Carlo method were used to estimate the serial interval and incubation period, respectively. The impact of incubation period and different interventions were simulated using a well-fitted SEIR+q model. Results From 2 January to 14 February 2021, there were 869 patients with symptomatic COVID-19 in Shijiazhuang, and most cases (89.6%) were confirmed before 20 January. Overall, 40.2% of the cases were male, 16.3% were aged 0 to 19 years, and 21.9% were initially diagnosed as asymptomatic but then became symptomatic. The estimated incubation period was 11.6 days (95% CI 10.6, 12.7 days) and the estimated serial interval was 6.6 days (0.025th, 0.975th: 0.6, 20.0 days). The results of the SEIR+q model indicated that a longer incubation period led to a longer epidemic period. If the comprehensive quarantine measures were reduced by 10%, then the nucleic acid testing would need to increase by 20% or more to minimize the cumulative number of cases. Conclusions Incubation period was longer than serial interval suggested that more secondary transmission may occur before symptoms onset. The long incubation period made it necessary to extend the isolation period to control the outbreak. Timely contact tracing and implementation of a centralized quarantine quickly contained this epidemic in Shijiazhuang. Large-scale nucleic acid testing also helped to identify cases and reduce virus transmission.

scholarly journals Illiteracy Classification Using K Means-Naïve Bayes Algorithm

2018 ◽  
Vol 2 (3) ◽  
pp. 153 ◽  
Author(s):  
Muhammad Firman Aji Saputra ◽  
Triyanna Widiyaningtyas ◽  
Aji Prasetya Wibawa
Keyword(s):  
Error Rate ◽  
Naive Bayes ◽  
Research Result ◽  
Naïve Bayes ◽  
Optimal Number ◽  
Testing Method ◽  
The World ◽  
Bayes Algorithm ◽  
Number Of Classes

Illiteracy is an inability to recognize characters, both in order to read and write. It is a significant problem for countries all around the world including Indonesia. In Indonesia, illiteracy rate is generally set as an indicator to see whether or not education in Indonesia is successful. If this problem is not going to be overcome, it will affect people’s prosperity. One system that has been used to overcome this problem is prioritizing the treatment from areas with the highest illiteracy rate and followed by areas with lower illiteracy rate. The method is going to be a way easier to be applied if it is supported by classification process. Since the classification process needs a class, and there has not been any fine classification of illiteracy rate, there is needed a clustering process before classification process. This research is aimed to get optimal number of classes through clustering process and know the result of illiteracy classification process. The clustering process is conducted by using k means algorithm, and for the classification process is conducted by using Naïve Bayes algorithm. The testing method used to assess the success of classification process is 10-fold method. Based on the research result, it can be concluded that the optimal illiteracy classes are three classes with the classification accuracy value of 96.4912% and error rate value of 3.5088%. Whereas the classification with two classes get the accuracy value of 93.8596% and error rate value of 6.1404%. And for the classification with five classes get the accuracy value of 90.3509% and error rate value of 9.6491%.

scholarly journals Efficacy of the Confidential Unit Exclusion Option in Blood Donors in Tehran, Iran, Determined by Using the Nucleic Acid Testing Method in 2008–2009

2011 ◽  
Vol 11 (11) ◽  
pp. 907-912 ◽  
Author(s):  
Elham Farhadi ◽  
Ahmad Gharehbaghian ◽  
Gharib Karimi ◽  
Shahram Samiee ◽  
Farzaneh Tavasolli ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Blood Donors ◽  
Nucleic Acid Testing ◽  
Testing Method

scholarly journals Complete Genome Sequences of Dengue Virus Type 1 to 4 Strains Used for the Development of CBER/FDA RNA Reference Reagents and WHO International Standard Candidates for Nucleic Acid Testing

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Germán Añez ◽  
Daniel A. Heisey ◽  
Evgeniya Volkova ◽  
Maria Rios
Keyword(s):  
Nucleic Acid ◽  
Dengue Virus ◽  
Nucleic Acid Testing ◽  
Genome Sequences ◽  
International Standard ◽  
Denv Serotypes ◽  
The World ◽  
Complete Sequences ◽  
Clinically Significant

Dengue virus (DENV), a member of the Flaviviridae family, is the most common and clinically significant arbovirus in the world and is endemic in more than 100 countries. Here, we report the complete sequences of four DENV serotypes used in the development of the CBER/FDA RNA reference reagents and WHO International Standard candidates for nucleic acid testing.

Effect of testing methods on incidence of Clostridioides difficile infection rates in Veterans’ Affairs medical centers

2020 ◽  
pp. 1-3
Author(s):  
Brian P. McCauley ◽  
Martin E. Evans ◽  
Loretta A. Simbartl ◽  
Shantini D. Gamage ◽  
Stephen M. Kralovic ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Veterans Affairs ◽  
Nucleic Acid Amplification ◽  
Infection Rates ◽  
Testing Methods ◽  
Clostridioides Difficile ◽  
Medical Centers ◽  
Significant Difference ◽  
Clostridioides Difficile Infection ◽  
Veterans Affairs Medical Centers

Abstract Clostridioidesdifficile infection rates from 7 facilities that used nucleic acid amplification testing (NAAT) alone for 12 months then switched to NAAT plus toxin enzyme immunoassay (EIA) and reported the latter result for 12 months were compared to 70 facilities that used NAAT alone for all 24 months. There was no significant difference in rates between facility groups over the first 12 months (P = .21, linear regression), but we detected a decrease in rates for the facilities that changed to NAAT+EIA (P < .0001).

Efficacy of the Confidential Unit Exclusion Option in Blood Donors in Tehran, Iran, Determined by Using the Nucleic Acid Testing Method in 2008 and 2009

2011 ◽  
Vol 11 (11) ◽  
pp. 907-12
Author(s):  
Elham Farhadi ◽  
Ahmad Gharehbaghian ◽  
Gharib Karimi ◽  
Shahram Samiee ◽  
Farzaneh Tavasolli ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Blood Donors ◽  
Nucleic Acid Testing ◽  
Testing Method

scholarly journals Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jan-Hendrik Trösemeier ◽  
Didier Musso ◽  
Johannes Blümel ◽  
Julien Thézé ◽  
Oliver G. Pybus ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
World Health Organization ◽  
Zika Virus ◽  
Reference Strain ◽  
Nucleic Acid Amplification ◽  
World Health ◽  
Nucleic Acid Testing ◽  
The World ◽  
Health Organization ◽  
Detection And Quantification

We report here the sequence of a candidate reference strain of Zika virus (ZIKV) developed on behalf of the World Health Organization (WHO). The ZIKV reference strain is intended for use in nucleic acid amplification (NAT)-based assays for the detection and quantification of ZIKV RNA.

Genotypic Methods for HIV Drug Resistance Monitoring: The Opportunities and Challenges Faced by China

2019 ◽  
Vol 17 (4) ◽  
pp. 225-239 ◽  
Author(s):  
Lulu Zuo ◽  
Ke Peng ◽  
Yihong Hu ◽  
Qinggang Xu
Keyword(s):  
Drug Resistance ◽  
Virological Suppression ◽  
Testing Methods ◽  
Hiv Drug Resistance ◽  
Advantages And Disadvantages ◽  
Hiv Epidemic ◽  
Routine Surveillance ◽  
The World ◽  
Global Project ◽  
Hiv 1

AIDS is a globalized infectious disease. In 2014, UNAIDS launched a global project of “90-90-90” to end the HIV epidemic by 2030. The second and third 90 require 90% of HIV-1 infected individuals receiving antiretroviral therapy (ART) and durable virological suppression. However, wide use of ART will greatly increase the emergence and spreading of HIV drug resistance and current HIV drug resistance test (DRT) assays in China are seriously lagging behind, hindering to achieve virological suppression. Therefore, recommending an appropriate HIV DRT method is critical for HIV routine surveillance and prevention in China. In this review, we summarized the current existing HIV drug resistance genotypic testing methods around the world and discussed the advantages and disadvantages of these methods.

scholarly journals Prediction‐driven pooled testing methods: Application to HIV treatment monitoring in Rakai, Uganda

2021 ◽  
Author(s):  
Adam Brand ◽  
Susanne May ◽  
James P. Hughes ◽  
Gertrude Nakigozi ◽  
Steven J. Reynolds ◽  
...  
Keyword(s):  
Treatment Monitoring ◽  
Hiv Treatment ◽  
Testing Methods ◽  
Pooled Testing
Sign in / Sign up

Export Citation Format

Share Document