A novel strategy for community screening of SARS-CoV-2 (COVID-19): Sample pooling method

ADSP: An adaptive sample pooling strategy for diagnostic testing

BACKGROUND

We often must conduct diagnostic tests on a massive volume of samples within a limited time during outbreaks of infectious diseases (e.g., COVID-19,screening) or repeat many times routinely (e.g., regular and massive screening for plant virus infections in farms). These tests aim to obtain the diagnostic result of all samples within a limited time. In such scenarios, the limitation of testing resources and human labor drives the need to pool individual samples and test them together to improve testing efficiency. When a pool is positive, further testing is required to identify the affected individuals; whereas when a pool is negative, we conclude all individuals in the pool are negative. How one splits the samples into pools is a critical factor affecting testing efficiency.

OBJECTIVE

We aim to find the optimal strategy that adaptively guides users on optimally splitting the sample cohort into test-pools.

METHODS

We developed an algorithm that minimizes the expected number of tests needed to obtain the diagnostic results of all samples. Our algorithm dynamically updates the critical information according to the result of the most recent test and calculates the optimal pool size for the next test. We implemented our novel adaptive sample pooling strategy into a web-based application, ADSP (https://ADSP.uvic.ca). ADSP interactively guides users on how many samples to be pooled for the current test, asks users to report the test result back and uses it to update the best strategy on how many samples to be pooled for the next test.

RESULTS

We compared ADSP with other popular pooling methods in simulation studies, and found that ADSP requires fewer tests to diagnose a cohort and is more robust to the inaccurate initial estimate of the test cohort's disease prevalence.

CONCLUSION

Our web-based application can help researchers decide how to pool their samples for grouped diagnostic tests. It improves test efficiency when grouped tests are conducted.

Evaluation of Rapid Multiplex Reverse Transcription-Quantitative Polymerase Chain Reaction Assays for SARS-CoV-2 Detection in Individual and Pooled Samples

Although coronavirus disease 2019 (COVID-19) is no longer a Public Health Emergency of International Concern (PHEIC), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has had a vast impact to date. Hence, continuous management is required, given the uncertainty caused by the potential evolution of SARS-CoV-2. Reverse transcription-quantitative PCR (RT-qPCR) diagnosis has been fundamental in overcoming this issue. In this study, the performances of two rapid RT-qPCR assays (Real-Q Direct SARS-CoV-2 Detection Kit and Allplex™ SARS-CoV-2 fast PCR Assay) with short PCR times were comparatively evaluated using a STANDARD M nCoV Real-Time Detection Kit (STANDARD M, conventional RT-qPCR assay). All kits showed a limit of detection values (102-103 copies/reaction). The evaluation showed that the two rapid assay tests had ≥97.89% sensitivity and ≥99.51% specificity (κ = 0.98) for individual samples and ≥97.32% sensitivity and ≥97.67% specificity for pooled samples compared to STANDARD M. These results indicate that the two rapid RT-qPCR kits, which showed significant time reduction in performance, are as effective as a conventional RT-qPCR assay. They are likely to increase not only the number of tests that can be performed but also the efficiency of sustainable management of COVID-19 in the long term.

Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting

For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.

Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2

WHO declared the outbreak of COVID-19, caused by SARS-CoV-2, a pandemic in March 2020. More than 223 million cases and approximately 4.6 million deaths have been confirmed. Early diagnosis and immediate treatment became a priority during this pandemic. However, COVID-19 diagnostic testing resources are limited, especially early in the pandemic. Apart from being limited, the COVID-19 diagnostic tests using reverse transcription polymerase chain reaction (RT-PCR) have encountered storage, transportation, and safety issues. These problems are mainly experienced by developing poor countries, countries in the equatorial region, and archipelagic countries. VITPAD® is a guanidine-based inactivation transport medium (ITM) formulated to maintain the RNA quality of SARS-CoV-2 during transportation without cold chains. This study, conducted from September 2020 to March 2021, performed clinical validation of VITPAD® by comparing its performance with a globally commercially available ITM from the NEST brand. Its stability at room temperature, safety, and resistance at high temperatures was also tested using RT-PCR analysis. VITPAD® can reduce the infectious nature of the specimen, preserve the SARS-CoV-2 for 18 days at an ambient temperature, and resist high temperatures (40°C for 3 hours). A guanidine-based transport medium, such as VITPAD®, is compatible and recommended for RT-PCR-based molecular diagnosis of COVID-19.

Mathematical Model and Optimization Methods of Wide-Scale Pooled Sample Testing for COVID-19

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 the number of COVID-19 vaccines is insufficient, 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. 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, and 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. Qingdao’s optimised “ten-in-one” pooled testing method quickly screens out the infections by running fewer testing samples. 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. 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.

Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

The COVID-19 pandemic requires sensitive detection of the SARS-CoV-2 virus from samples to ensure accurate detection of infected patients, an essential component of effective national track and trace programs. Due to the scaling challenges of large sample numbers, sample pooling is an attractive solution to reduce both extraction and amplification reagent costs, if high sensitivity can be maintained. We demonstrate that the Erba Molecular ErbaMDx SARS-CoV-2 RT-PCR Kit (EM kit) delivers high sensitivity, achieving analytical detection of 5 copies/reaction SARS-CoV-2 genomic RNA, and 200 copies/mL SARS-CoV-2 inactivated virus spiked into nasopharyngeal swab (NP) samples and extracted through workflow. Furthermore, the EM Kit demonstrates high sensitivity in both pooled (1 in 5) and non-pooled NP samples when compared to an FDA Emergency Use Authorization approved assay, following published FDA guidelines. These findings demonstrate that the EM Kit is suitable for sample pooling, with minimal impact on assay performance. As the COVID-19 pandemic progresses, high sensitivity assays such as the EM Kit will have an important role in ensuring high throughput and sensitive testing using pooled samples can be maintained, delivering the most cost-effective sample extraction and amplification option for national test and trace programs.

Homebrew: An economical and sensitive glassmilk-based nucleic-acid extraction method for SARS-CoV-2 diagnostics

Management of COVID-19 and other epidemics requires large-scale diagnostic testing. The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains reverse transcription quantitative PCR (qRT-PCR) analysis, which detects viral RNA more sensitively than any other method. However, the resource use and supply-chain requirements of RT-PCR have continued to challenge diagnostic laboratories worldwide. Here, we establish and characterize a low-cost method to detect SARS-CoV-2 in clinical combined nose and throat swabs, allowing for automation in high-throughput settings. This method inactivates virus material with sodium dodecylsulfate (SDS) and uses silicon dioxide as the RNA-binding matrix in combination with sodium chloride (NaCl) and isopropanol. With similar sensitivity for SARS-CoV-2 viral targets but a fraction of time and reagent expenditure compared with commercial kits, our method also enables sample pooling without loss of sensitivity. We suggest that this method will facilitate more economical widespread testing, particularly in resource-limited settings.

Cost-effectiveness of anti-SARS-CoV-2 antibody diagnostic tests in Brazil

Background

Although serologic tests for COVID-19 diagnosis are rarely indicated nowadays, they remain commercially available and widely used in Brazil. The objective of this study was to evaluate the cost-effectiveness of anti-SARS-CoV-2antibody diagnostic tests for COVID-19 in Brazil.

Methods

Eleven commercially available diagnostic tests, comprising five lateral-flow immunochromatographic assays (LFAs) and six immunoenzymatic assays (ELISA) were analyzed from the perspective of the Brazilian Unified Health System.

Results

The direct costs of LFAs ranged from US$ 11.42 to US$ 17.41and of ELISAs, from US$ 6.59 to US$ 10.31. Considering an estimated disease prevalence between 5% and 10%, the anti-SARS-CoV-2 ELISA (IgG) was the most cost-effective test, followed by the rapid One Step COVID-19 Test, at an incremental cost-effectiveness ratio of US$ 2.52 and US$ 1.26 per properly diagnosed case, respectively. Considering only the LFAs, at the same prevalence estimates, two tests, the COVID-19 IgG/IgM and the One Step COVID-19 Test, showed high effectiveness at similar costs. For situations where the estimated probability of disease is 50%, the LFAs are more costly and less effective alternatives.

Conclusions

Nowadays there are few indications for the use of serologic tests in the diagnosis of COVID-19 and numerous commercially available tests, with marked differences are observed among them. In general, LFA tests are more cost-effective for estimated low-COVID-19-prevalences, while ELISAs are more cost-effective for high-pretest-probability scenarios.

The Positive Rate of Nucleic Acid Testing and the Epidemiological Characteristics of COVID-19 in Chongqing

Objective

The purpose of this study is to analyze the positive rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid testing (NAT), cases of and deaths due to SARS-CoV-2, and the epidemiological characteristics of SARS-CoV-2 to identify high-risk populations.

Methods

A retrospective study in Jiulongpo district of Chongqing was conducted by performing continuous observations of the frequency of SARS-CoV-2 NAT, analyzing the data of close contacts of patients and asymptomatic carriers, and collecting epidemiological data. Data were collected from January 20, 2020, when the first case of SARS-CoV-2 infection was reported, to March 26, 2020. Descriptive statistical analysis and Cochrane–Mantel–Haenszel analysis were used to compare the positive detection rates and positive diagnostic rates of different exposure groups.

Results

A total of 7,118 people received 10,377 SARS-CoV-2 nucleic acid tests in one district, and the SARS-CoV-2 positive rates were 0.40% (18/4446) and 0.15% (4/2672) in people receiving one and ≥ two nucleic acid tests (p = 0.06), respectively. Those with suspected cases (12.35%) and close contacts (8%) had higher positive rates than people tested at fever clinics (0.39%) (p < 0.001). The median latency (range) of cases was 5 (2, 9) days, and the median time from diagnosis to recovery was 22 (14, 25) days. One recovered patient received a positive test result at 28 days after recovery when she attempted to donate blood. Six clustered cases, including one patient who died, indicated persistent human-to-human transmission. One patient who was diagnosed after death was found to have infected 13 close contacts. People working in catering and other public service departments (36.36%) and people who are unemployed and retirees (45.45%) have an increased risk of infection compared with technical staff (9.09%) and farmers (9.09%).

Conclusion

The total positive rate was low in the tested population, and more effective detection ranges should be defined to improve precise and differentiated epidemic control strategies. Moreover, in asymptomatic carriers, SARS-CoV-2 tests were positive after recovery, and patients with suspected SARS-CoV-2 infection who die may pose serious potential transmission threats.

Natural language processing enabling COVID-19 predictive analytics to support data-driven patient advising and pooled testing

OBJECTIVE

The COVID-19 (coronavirus disease 2019) pandemic response at the Medical University of South Carolina included virtual care visits for patients with suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The telehealth system used for these visits only exports a text note to integrate with the electronic health record, but structured and coded information about COVID-19 (eg, exposure, risk factors, symptoms) was needed to support clinical care and early research as well as predictive analytics for data-driven patient advising and pooled testing.

MATERIALS AND METHODS

To capture COVID-19 information from multiple sources, a new data mart and a new natural language processing (NLP) application prototype were developed. The NLP application combined reused components with dictionaries and rules crafted by domain experts. It was deployed as a Web service for hourly processing of new data from patients assessed or treated for COVID-19. The extracted information was then used to develop algorithms predicting SARS-CoV-2 diagnostic test results based on symptoms and exposure information.

RESULTS

The dedicated data mart and NLP application were developed and deployed in a mere 10-day sprint in March 2020. The NLP application was evaluated with good accuracy (85.8% recall and 81.5% precision). The SARS-CoV-2 testing predictive analytics algorithms were configured to provide patients with data-driven COVID-19 testing advices with a sensitivity of 81% to 92% and to enable pooled testing with a negative predictive value of 90% to 91%, reducing the required tests to about 63%.

CONCLUSIONS

SARS-CoV-2 testing predictive analytics and NLP successfully enabled data-driven patient advising and pooled testing.

An Expectation Maximization based Adaptive Group Testing Method for Improving Efficiency and Sensitivity of Large-Scale Screening of COVID-19

The pathogen of the ongoing coronavirus disease 2019 (COVID-19) pandemic is a newly discovered virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Testing individuals for SARS-CoV-2 plays a critical role in containing COVID-19. For saving medical personnel and consumables, many countries are implementing group testing against SARS-CoV-2. However, existing group testing methods have the following limitations: (1) The group size is determined without theoretical analysis, and hence is usually not optimal. This adversely impacts the screening efficiency. (2) These methods neglect the fact that mixing samples together usually leads to substantial dilution of the SARS-CoV-2 virus, which seriously impacts the sensitivity of tests. In this paper, we aim to screen individuals infected with COVID-19 with as few tests as possible, under the premise that the sensitivity of tests is high enough. We propose an eXpectation Maximization based Adaptive Group Testing (XMAGT) method. The basic idea is to adaptively adjust its testing strategy between a group testing strategy and an individual testing strategy such that the expected number of samples identified by a single test is larger. During the screening process, the XMAGT method can estimate the ratio of positive samples. With this ratio, the XMAGT method can determine a group size under which the group testing strategy can achieve a maximal expected number of negative samples and the sensitivity of tests is higher than a user-specified threshold. Experimental results show that the XMAGT method outperforms existing methods in terms of both efficiency and sensitivity.

Detection of SARS-CoV-2 through pool testing for COVID-19: an integrative review

INTRODUCTION

The pool testing technique optimizes the number of tests performed and reduces the delivery time of results, which is an interesting strategy for the health crisis caused by the COVID-19 pandemic. This integrative review investigated studies in which pool testing was carried out for epidemiological or screening purposes to analyze its clinical or cost effectiveness and assessed the applicability of this method in high-, middle-, and low-income countries.

METHODS

This integrative review used primary studies published in the MEDLINE, EMBASE, Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS), and Cochrane Library databases.

RESULTS

A total of 435 studies were identified: 35.3% were carried out in Asia, 29.4% in Europe, 29.4% in North America, and 5.9% in Oceania.

CONCLUSIONS

This review suggests that pool testing in the general population may be a useful surveillance strategy to detect new variants of SARS-CoV-2 and to evaluate the period of immunogenicity and global immunity from vaccines.

Clinical Impact, Costs, and Cost-effectiveness of Expanded Severe Acute Respiratory Syndrome Coronavirus 2 Testing in Massachusetts

BACKGROUND

We projected the clinical and economic impact of alternative testing strategies on coronavirus disease 2019 (COVID-19) incidence and mortality in Massachusetts using a microsimulation model.

METHODS

We compared 4 testing strategies: (1) hospitalized: polymerase chain reaction (PCR) testing only for patients with severe/critical symptoms warranting hospitalization; (2) symptomatic: PCR for any COVID-19-consistent symptoms, with self-isolation if positive; (3) symptomatic + asymptomatic once: symptomatic and 1-time PCR for the entire population; and (4) symptomatic + asymptomatic monthly: symptomatic with monthly retesting for the entire population. We examined effective reproduction numbers (Re = 0.9-2.0) at which policy conclusions would change. We assumed homogeneous mixing among the Massachusetts population (excluding those residing in long-term care facilities). We used published data on disease progression and mortality, transmission, PCR sensitivity/specificity (70%/100%), and costs. Model-projected outcomes included infections, deaths, tests performed, hospital-days, and costs over 180 days, as well as incremental cost-effectiveness ratios (ICERs, $/quality-adjusted life-year [QALY]).

RESULTS

At Re = 0.9, symptomatic + asymptomatic monthly vs hospitalized resulted in a 64% reduction in infections and a 46% reduction in deaths, but required >66-fold more tests/day with 5-fold higher costs. Symptomatic + asymptomatic monthly had an ICER <$100 000/QALY only when Re ≥1.6; when test cost was ≤$3, every 14-day testing was cost-effective at all Re examined.

CONCLUSIONS

Testing people with any COVID-19-consistent symptoms would be cost-saving compared to testing only those whose symptoms warrant hospital care. Expanding PCR testing to asymptomatic people would decrease infections, deaths, and hospitalizations. Despite modest sensitivity, low-cost, repeat screening of the entire population could be cost-effective in all epidemic settings.

Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda

Real-time polymerase chain reaction (RT-PCR) remains the gold standard for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study tested the performance of a pooled testing strategy for RT-PCR and its cost-effectiveness. In total, 1280 leftover respiratory samples collected between 19 April and 6 May 2021 were tested in 128 pools of 10 samples each, out of which 16 pools were positive. The positivity rate of the unpooled samples was 1.9% (24/1280). After parallel testing using the individual and pooled testing strategies, positive agreement was 100% and negative agreement was 99.8%. The overall median cycle threshold (Ct) value of the unpooled samples was 29.8 (interquartile range 22.3-34.3). Pools that remained positive when compared with the results of individual samples had lower median Ct values compared with those that turned out to be negative (28.8 versus 34.8; P=0.0.035). Pooled testing reduced the cost >4-fold. Pooled testing may be a more cost-effective approach to diagnose SARS-CoV-2 in resource-limited settings without compromising diagnostic performance.

Pooled Testing Strategies for SARS-CoV-2 diagnosis: A comprehensive review

SARS-CoV-2 has surged across the globe causing the ongoing COVID-19 pandemic. Systematic testing to facilitate index case isolation and contact tracing is needed for efficient containment of viral spread. The major bottleneck in leveraging testing capacity has been the lack of diagnostic resources. Pooled testing is a potential approach that could reduce cost and usage of test kits. This method involves pooling individual samples and testing them 'en bloc'. Only if the pool tests positive, retesting of individual samples is performed. Upon reviewing recent articles on this strategy employed in various SARS-CoV-2 testing scenarios, we found substantial diversity emphasizing the requirement of a common protocol. In this article, we review various theoretically simulated and clinically validated pooled testing models and propose practical guidelines on applying this strategy for large scale screening. If implemented properly, the proposed approach could contribute to proper utilization of testing resources and flattening of infection curve.

Prospective evaluation of specimen pooling strategy for detection of SARS-CoV-2 using pools of five and six specimens

The increased demand for SARS-CoV-2 molecular testing during the COVID-19 pandemic resulted in shortage of reagents and consumables. Pooling of specimens could be an alternative strategy to overcome these problems. Initial evaluation of the pooling strategy was performed using known positive specimens, previously tested individually, and their respective pools of plus four (5X), five (6X) and nine (10X) known negative specimens. Subsequently, 35 positive 5X and 35 positive 6X pools containing only one positive specimen per pool were analyzed prospectively regarding the difference in Ct values in pooled versus individual specimens. When the number of samples in the pool were five or six, the average deviation of Ct differences was < 1; therefore, this strategy was followed in the prospective study. Significant difference in Ct values was observed in positive specimens when tested individually and in 5X pools (p = 0.006), while the difference was not significant when positive specimens were tested individually and in 6X pools (p = 0.07). The difference in Ct values was not significant between the 5X and 6X pools. Testing in pools of five or six specimens is a reliable option for SARS-CoV-2 RNA detection when mass testing is needed.

A Longitudinal Survey for Genome-based Identification of SARS-CoV-2 in Sewage Water in Selected Lockdown Areas of Lahore City, Pakistan: A Potential Approach for Future Smart Lockdown Strategy

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has affected more than 15 million people and, as of 22 July 2019, caused deaths of more than 0.6 million individuals globally. With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number of positive cases in a population. This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown. Sewage samples, from 28 pre-selected sites, were collected on alternate days from 13-25 July, 2020 from two selected areas [Johar Town (n = 05) and Township (n = 23)], where smart lockdown were implemented by the government authorities on 9th July, 2020. Genomic RNA was extracted and the SARS-CoV-2 was detected and quantified using commercially available kit through Real-Time PCR. Out of 28, sixteen samples were positive on day one while 19, 17, 23, 17, 05 and 09 samples were positive on day 3, 5, 7, 9, 11, and 13, respectively. Results revealed a decreased positivity rate and SARS CoV-2 genome copies in sewage towards the end of lockdown however few sampling sites did not follow a clear pattern indicating the complexities in sewage water based surveillance i.e time of sampling etc. Hourly sampling from two sites for 24 hours also revealed the impact of sampling time on detection of SARS-CoV-2 genome in sewage. Results of current study insinuate a possible role of sewage-based COVID-19 surveillance in monitoring and execution of smart lockdowns.

Molecular diagnostics in the era of COVID-19

As the COVID-19 pandemic continues to escalate globally and acquires new mutations, accurate diagnostic technologies continue to play a vital role in controlling and understanding the epidemiology of this disease. A plethora of technologies have enabled the diagnosis of individuals, informed clinical management, aided population-wide screening to determine transmission rates and identified cases within the wider community and high-risk settings. This review explores the application of molecular diagnostics technologies in controlling the spread of COVID-19, and the key factors that affect the sensitivity and specificity of the tests used.

Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings

Alternatives to nasopharyngeal sampling are needed to increase capacity for SARS-CoV-2 testing. Among 275 participants, we piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including polyester flocked swabs as well as 3D-printed plastic lattice swabs, placed into viral transport media or an RNA stabilization agent. Flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), missing those with low viral load (<10⁶ viral copies/mL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into RNA preservative, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. We also evaluated pooling strategies that involved pooling specimens in the lab versus pooling swabs at the point of collection, finding both successfully detected samples with >10⁵ viral copies/mL.

Evaluation of automated molecular tests for the detection of SARS-CoV-2 in pooled nasopharyngeal and saliva specimens

Background

Pooling of samples for SARS‐CoV‐2 testing in low‐prevalence settings has been used as an effective strategy to expand testing capacity and mitigate challenges with the shortage of supplies. We evaluated two automated molecular test systems for the detection of SARS‐CoV‐2 RNA in pooled specimens.

Methods

Pooled nasopharyngeal and saliva specimens were tested by Qiagen QIAstat‐Dx Respiratory SARS‐CoV‐2 Panel (QIAstat) or Cepheid Xpert Xpress SARS‐CoV‐2 (Xpert), and the results were compared to that of standard RT‐qPCR tests without pooling.

Results

In nasopharyngeal specimens, the sensitivity/specificity of the pool testing approach, with 5 and 10 specimens per pool, were 77%/100% (n = 105) and 74.1%/100% (n = 260) by QIAstat, and 97.1%/100% (n = 250) and 100%/99.5% (n = 200) by Xpert, respectively. Pool testing of saliva (10 specimens per pool; n = 150) by Xpert resulted in 87.5% sensitivity and 99.3% specificity compared to individual tests. Pool size of 5 or 10 specimens did not significantly affect the difference of RT‐qPCR cycle threshold (C_T) from standard testing. RT‐qPCR C_T values obtained with pool testing by both QIAstat and Xpert were positively correlated with that of individual testing (Pearson's correlation coefficient r = 0.85 to 0.99, p < 0.05). However, the C_T values from Xpert were significantly stronger (p < 0.01, paired t test) than that of QIAstat in a subset of SARS‐CoV‐2 positive specimens, with mean differences of −4.3 ± 2.43 and −4.6 ± 2 for individual and pooled tests, respectively.

Conclusion

Our results suggest that Xpert SARS‐CoV‐2 can be utilized for pooled sample testing for COVID‐19 screening in low‐prevalence settings providing significant cost savings and improving throughput without affecting test quality.

COVID-19 Sample Pooling: From RNA Extraction to Quantitative Real-time RT-PCR

The COVID-19 pandemic requires mass screening to identify those infected for isolation and quarantine. Individually screening large populations for the novel pathogen, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is costly and requires a lot of resources. Sample pooling methods improve the efficiency of mass screening and consume less reagents by increasing the capacity of testing and reducing the number of experiments performed, and are therefore especially suitable for under-developed countries with limited resources. Here, we propose a simple, reliable pooling strategy for COVID-19 testing using clinical nasopharyngeal (NP) and/or oropharyngeal (OP) swabs. The strategy includes the pooling of 10 NP/OP swabs for extraction and subsequent testing via quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), and may also be applied to the screening of other pathogens.

Diagnostics for SARS-CoV-2 infections

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every corner of the globe, causing societal instability. The resultant coronavirus disease 2019 (COVID-19) leads to fever, sore throat, cough, chest and muscle pain, dyspnoea, confusion, anosmia, ageusia and headache. These can progress to life-threatening respiratory insufficiency, also affecting the heart, kidney, liver and nervous systems. The diagnosis of SARS-CoV-2 infection is often confused with that of influenza and seasonal upper respiratory tract viral infections. Due to available treatment strategies and required containments, rapid diagnosis is mandated. This Review brings clarity to the rapidly growing body of available and in-development diagnostic tests, including nanomaterial-based tools. It serves as a resource guide for scientists, physicians, students and the public at large.

An efficient primary screening of COVID-19 by serum Raman spectroscopy

The outbreak of COVID-19 coronavirus disease around the end of 2019 has become a pandemic. The preferred method for COVID-19 detection is the real-time polymerase chain reaction (RT-PCR)-based technique; however, it also has certain limitations, such as sample-dependent procedures with a relatively high false negative ratio. We propose a safe and efficient method for screening COVID-19 based on Raman spectroscopy. A total of 177 serum samples are collected from 63 confirmed COVID-19 patients, 59 suspected cases, and 55 healthy individuals as a control group. Raman spectroscopy is adopted to analyze these samples, and a machine learning support-vector machine (SVM) method is applied to the spectrum dataset to build a diagnostic algorithm. Furthermore, 20 independent individuals, including 5 asymptomatic COVID-19 patients and 5 symptomatic COVID-19 patients, 5 suspected patients, and 5 healthy patients, were sampled for external validation. In these three groups-confirmed COVID-19, suspected, and healthy individuals-the distribution of statistically significant points of difference showed highly consistency for intergroups after repeated sampling processes. The classification accuracy between the COVID-19 cases and the suspected cases is 0.87 (95% confidence interval [CI]: 0.85-0.88), and the accuracy between the COVID-19 and the healthy controls is 0.90 (95% CI: 0.89-0.91), while the accuracy between the suspected cases and the healthy control group is 0.68 (95% CI: 0.67-0.73). For the independent test dataset, we apply the obtained SVM model to the classification of the independent test dataset to have all the results correctly classified. Our model showed that the serum-level classification results were all correct for independent test dataset. Our results suggest that Raman spectroscopy could be a safe and efficient technique for COVID-19 screening.

Sample pooling: burden or solution?

BACKGROUND

Pool-testing strategies combine samples from multiple people and test them as a group. A pool-testing approach may shorten the screening time and increase the test rate during times of limited test availability and inadequate reporting speed. Pool testing has been effectively used for a wide variety of infectious disease screening settings. Historically, it originated from serological testing in syphilis. During the current coronavirus disease 2019 (COVID-19) pandemic, pool testing is considered across the globe to inform opening strategies and to monitor infection rates after the implementation of interventions.

AIMS

This narrative review aims to provide a comprehensive overview of the global efforts to implement pool testing, specifically for COVID-19 screening.

SOURCES

Data were retrieved from a detailed search for peer-reviewed articles and preprint reports using Medline/PubMed, medRxiv, Web of Science, and Google up to 21st March 2021, using search terms "pool testing", "viral", "serum", "SARS-CoV-2" and "COVID-19".

CONTENT

This review summarizes the history and theory of pool testing. We identified numerous peer-reviewed articles that describe specific details and practical implementation of pool testing. Successful examples as well as limitations of pool testing, in general and specifically related to the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and antibodies, are reviewed. While promising, significant operational, pre-analytical, logistical, and economic challenges need to be overcome to advance pool testing.

IMPLICATIONS

The theory of pool testing is well understood and numerous successful examples from the past are available. Operationalization of pool testing requires sophisticated processes that can be adapted to the local medical circumstances. Special attention needs to be paid to sample collection, sample pooling, and strategies to avoid re-sampling.

Evaluation of pooling of samples for testing SARS-CoV- 2 for mass screening of COVID-19

BACKGROUND

The current pandemic of the SARS-CoV-2 virus, widely known as COVID-19, has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS-CoV-2 virus has provided the solution to mass screening of people for COVID-19. A pooled testing strategy can be very effective in testing when resources are limited, yet it comes with its own limitations. These benefits and limitations need critical consideration when it comes to testing highly infectious diseases like COVID-19.

METHODS

This study evaluated the pooled testing of nasopharyngeal swabs for SARS-COV-2 by comparing the sensitivity of individual sample testing with 4-and 8-pool sample testing. Median cycle threshold (Ct) values were compared, and the precision of pooled testing was assessed through an inter- and intra-assay of pooled samples. Coefficient of variance was calculated for inter- and intra-assay variability.

RESULTS

The sensitivity becomes considerably lower when the samples are pooled. There is a high percentage of false negative reports with larger sample pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra- and inter-assay, especially among weak positive samples and when more number of samples are pooled together.

CONCLUSION

As COVID - 19 infection numbers and need for testing remain high, we must meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to determine the optimal balance on the cost-effective strategy of resource saving and risk/ cost of missing positive patients.

Latest Effective Measures to Combat COVID-19: A Review

More and more people realize that implementation of preventive measures is the only option left to counteract the coronavirus disease 2019 (COVID-19) before specific antiviral drugs are developed. Hence, a number of behavioral, clinical and state interventions have been conducted by dozens of countries to stop or slow down the spread of the virus in the early stages of the epidemic. At present, with the evolution of COVID-19 pandemic getting worse, synthesizing and implementing all measures available are of paramount importance. However, some measures are still being controversial. We aimed to assist policymakers in decision making for better pandemic preparedness. We reviewed the literature that reported accumulated scientific experience to date and summarized the epidemic prevention and control measures in three aspects: control the source of infection, cut off the routes of transmission and protect the susceptible population. First of all, some new approaches were introduced to control the source of infection, such as implementing contact-tracing apps, nucleic acid mixed detection, repeated testing and the establishment of some specialized laboratories. Second, we need to take various measures to cut off all possible routes of transmission, especially persistently pay close attention to checking cold chain foods. Third, due to no valid vaccine has yet been developed, some measures that can cut development time of more conventional vaccines should be implemented or considered. By synthesizing the scientific experience in fighting the COVID-19 epidemic, we suggested the latest effective measures should be carried out concurrently from three aspects, so as to avoid making grim situation even worse.

Pooling of Nasopharyngeal Swab Samples To Overcome a Global Shortage of Real-Time Reverse Transcription-PCR COVID-19 Test Kits

The global outbreak and rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have created an urgent need for large-scale testing of populations. There is a demand for high-throughput testing protocols that can be used for efficient and rapid testing of clinical specimens. We evaluated a pooled PCR protocol for testing nasopharyngeal (NP) swabs using known positive/negative and untested clinical samples that were assigned to pools of 5 or 10. In total, 630 samples were used in this study. Individual positive samples with cycle threshold (C_T ) values as high as 33 could be consistently detected when pooled with 4 negative samples (pool of 5), and individual positive samples with C_T values up to 31 could be consistently detected when pooled with 9 negative samples (pool of 10). Pooling of up to 5 samples can be employed in laboratories for the diagnosis of COVID-19 for efficient utilization of resources, rapid screening of a greater number of people, and faster reporting of test results.

Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings

Background

Standard nasopharyngeal swab testing for SARS-CoV-2 detection by PCR is not always feasible due to limitations in trained personnel, personal protective equipment, swabs, PCR reagents, and access to cold chain and biosafety hoods.

Methods

We piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including both standard polyester flocked swabs as well as 3D printed plastic lattice swabs, placed into either viral transport media or an RNA stabilization agent. Quantitative SARS-CoV-2 viral detection by RT-qPCR was compared to that obtained by nasopharyngeal sampling as the reference standard. Pooling specimens in the lab versus pooling swabs at the point of collection was also evaluated.

Results

Among 275 participants, flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), mostly missing those with low viral load (<10^3 viral copies/uL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into an RNA stabilizer, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. Pooling sample specimens or swabs both successfully detected samples >10² viral copies/uL.

Conclusions

Nasal swabs are likely adequate for clinical diagnosis of acute infections to help expand testing capacity in resource-constrained settings. When collected into an RNA preservative that also inactivates infectious virus, nasal swabs yielded quantitative viral loads approximating those obtained by nasopharyngeal sampling.

A robust pooled testing approach to expand COVID-19 screening capacity

Limited testing capacity for COVID-19 has hampered the pandemic response. Pooling is a testing method wherein samples from specimens (e.g., swabs) from multiple subjects are combined into a pool and screened with a single test. If the pool tests positive, then new samples from the collected specimens are individually tested, while if the pool tests negative, the subjects are classified as negative for the disease. Pooling can substantially expand COVID-19 testing capacity and throughput, without requiring additional resources. We develop a mathematical model to determine the best pool size for different risk groups, based on each group's estimated COVID-19 prevalence. Our approach takes into consideration the sensitivity and specificity of the test, and a dynamic and uncertain prevalence, and provides a robust pool size for each group. For practical relevance, we also develop a companion COVID-19 pooling design tool (through a spread sheet). To demonstrate the potential value of pooling, we study COVID-19 screening using testing data from Iceland for the period, February-28-2020 to June-14-2020, for subjects stratified into high- and low-risk groups. We implement the robust pooling strategy within a sequential framework, which updates pool sizes each week, for each risk group, based on prior week's testing data. Robust pooling reduces the number of tests, over individual testing, by 88.5% to 90.2%, and 54.2% to 61.9%, respectively, for the low-risk and high-risk groups (based on test sensitivity values in the range [0.71, 0.98] as reported in the literature). This results in much shorter times, on average, to get the test results compared to individual testing (due to the higher testing throughput), and also allows for expanded screening to cover more individuals. Thus, robust pooling can potentially be a valuable strategy for COVID-19 screening.

Sample pooling as a strategy for community monitoring for SARS-CoV-2

Sample pooling strategy was intended to determine the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2 and process them without significant loss of test usability. Standard molecular diagnostic laboratory equipment, and commercially available centrifugal filters, RNA isolation kits and SARS Cov2 PCR tests were used. The basic idea was to combine and concentrate several samples to the maximal volume, which can be extracted with the single extraction column. Out of 16 tested pools, 12 were positive with cycle threshold (Ct) values within 0.5 and 3.01 Ct of the original individual specimens. The analysis of 112 specimens determined that 12 pools were positive, followed by identification of 6 positive individual specimens among the 112 tested. This testing was accomplished with the use of 16 extractions/PCR tests, resulting in saving of 96 reactions but adding the 40 centrifugal filters. The present study demonstrated that pool testing could detect even up to a single positive sample with Ct value as high as 34. According to the standard protocols, reagents and equipment, this pooling method can be applied easily in current clinical testing laboratories.

Laboratory organisation and management of SARS-CoV-2 infection in Niger, West Africa

Background

As the coronavirus disease 2019 (COVID-19) pandemic unfolds, laboratory services have been identified as key to its containment. This article outlines the laboratory organisation and management and control interventions in Niger.

Intervention

The capitol city of Niger, Niamey, adopted a ‘National COVID-19 Emergency Preparedness and Response Plan’ to strengthen the preparedness of the country for the detection of severe acute respiratory syndrome coronavirus-2. Laboratory training and diagnostic capacity building were supported by existing active clinical and research laboratories for more rapid and practicable responses. The National Reference Laboratory for Respiratory Viruses located at the Centre de Recherche Médicale et Sanitaire was designated as the reference centre for COVID-19 testing. The national plan for COVID-19 testing is being gradually adopted in other regions of the country in response to the rapidly evolving COVID-19 emergency and to ensure a more rapid turn-around time.

Lessons learnt

After the decentralisation of COVID-19 testing to other regions of the country, turn-around times were reduced from 48–72 h to 12–24 h. Reducing turn-around times allowed Niger to reduce the length of patients’ stays in hospitals and isolation facilities. Shortages in testing capacity must be anticipated and addressed. In an effort to reduce risk of shortages and increase availability of reagents and consumables, Niamey diversified real-time reverse transcriptase–polymerase chain reaction kits for severe acute respiratory syndrome coronavirus-2 detection.

Recommendations

Continued investment in training programmes and laboratory strategy is needed in order to strengthen Niger’s laboratory capacity against the outbreak.

Optimizing the diagnostic capacity for COVID-19 PCR testing for low resource and high demand settings: The development of information-dependent pooling protocol

Aim

To compare different pooling methods in an attempt to improve the COVID-19 PCR diagnostic capacities.

Method

We developed a novel information-dependent pooling protocol (indept), based on transmission of less informative sequential pools on to the next pooling cycle to maximize savings. We then compared it to the halving, generalized halving, splitting and hypercube protocols in a simulation study, across variety of scenarios.

Results

All five methods yielded various amount of test savings, which mostly depended on the virus prevalence in the population. In situations of low prevalence (up to 5%), indept had the best performance, requiring on average 20% of tests needed for singular testing across scenarios that were analyzed. Nevertheless, this comes at the expense of speed, with the worst-case scenario of indept protocol requiring up to twice the time needed to test the same number of samples in comparison to the hypercube protocol. In order to offset this, we developed a faster version of the protocol (indeptSp), which minimizes the number of terminal pools and manages to retain savings compared to other protocols, despite marginally longer processing times.

Conclusion

The increasing demand for more testing globally can benefit from application of pooling, especially in resource-restrained situations of the low- and middle-income countries or situations of high testing demand. Singular testing in situations of low prevalence should be systematically discouraged.