Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children

Overcoming bias in estimating epidemiological parameters with realistic history-dependent disease spread dynamics

Epidemiological parameters such as the reproduction number, latent period, and infectious period provide crucial information about the spread of infectious diseases and directly inform intervention strategies. These parameters have generally been estimated by mathematical models that involve an unrealistic assumption of history-independent dynamics for simplicity. This assumes that the chance of becoming infectious during the latent period or recovering during the infectious period remains constant, whereas in reality, these chances vary over time. Here, we find that conventional approaches with this assumption cause serious bias in epidemiological parameter estimation. To address this bias, we developed a Bayesian inference method by adopting more realistic history-dependent disease dynamics. Our method more accurately and precisely estimates the reproduction number than the conventional approaches solely from confirmed cases data, which are easy to obtain through testing. It also revealed how the infectious period distribution changed throughout the COVID-19 pandemic during 2020 in South Korea. We also provide a user-friendly package, IONISE, that automates this method.

Advancing quantitative PCR with color cycle multiplex amplification

Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.

Diagnostic performance of multiplex lateral flow tests in ambulatory patients with acute respiratory illness

We assessed the performance of three different multiplex lateral flow assays manufactured by SureScreen, Microprofit and Goldsite which provide results for influenza, respiratory syncytial virus (RSV) and SARS-CoV-2. Between 4 April and 20 October 2023, 1646 patients 6 months and older presenting to an outpatient department of a hospital in Hong Kong with ≥2 symptoms or signs of an acute respiratory illness were enrolled. The point estimates for all three multiplex tests had sensitivity >80% for influenza A and SARS-CoV-2 compared to PCR, and the tests manufactured by Microprofit and Goldsite had sensitivity >84% to detect RSV. Specificity was >97% for all three tests except for the SureScreen test which had specificity 86.2% (95% CI: 83.9% to 88.3%) for influenza A. Sensitivity was lower than reported by the manufacturers, resulting in a higher risk of false negatives. The three multiplex tests performed better in patients with high viral loads.

SARS-CoV-2 Test-to-Stay in Daycare

BACKGROUND AND OBJECTIVES

Test-to-stay concepts apply serial testing of children in daycare after exposure to SARS-CoV-2 without use of quarantine. This study aims to assess the safety of a test-to-stay screening in daycare facilities.

METHODS

714 daycare facilities and approximately 50 000 children ≤6 years in Cologne, Germany participated in a SARS-CoV-2 Pool-polymerase chain reaction (PCR) screening from March 2021 to April 2022. The screening initially comprised post-exposure quarantine and was adapted to a test-to-stay approach during its course. To assess safety of the test-to-stay approach, we explored potential changes in frequencies of infections among children after the adaptation to the test-to-stay approach by applying regression discontinuity in time (RDiT) analyses. To this end, PCR-test data were linked with routinely collected data on reported infections in children and analyzed using ordinary least squares regressions.

RESULTS

219 885 Pool-PCRs and 352 305 Single-PCRs were performed. 6440 (2.93%) Pool-PCRs tested positive, and 17 208 infections in children were reported. We estimated that during a period of 30 weeks, the test-to-stay concept avoided between 7 and 20 days of quarantine per eligible daycare child. RDiT revealed a 26% reduction (Exp. Coef: 0.74, confidence interval 0.52-1.06) in infection frequency among children and indicated no significant increase attributable to the test-to-stay approach. This result was not sensitive to adjustments for 7-day incidence, season, SARS-CoV-2 variant, and socioeconomic status.

CONCLUSIONS

Our analyses provide evidence that suggest safety of the test-to-stay approach compared with quarantine measures. This approach offers a promising option to avoid use of quarantine after exposure to respiratory pathogens in daycare settings.

[Results of PCR Pool Testing In Primary and Special Needs Schools In Bavaria For The School Year 2021/2022: Sentinel Surveillance In Face-To-Face Teaching During The Sars-CoV-2 Pandemic]

In the school years 2019/20 and 2020/21, children were physically, psychologically, and socially stressed by school closures caused by the SARS-CoV-2 pandemic. To ensure attendance with optimal infection protection, PCR pool testing was conducted during the 2021/22 school year at Bavarian elementary schools and schools for pupils with special needs for timely detection of SARS-CoV-2 infection. This study analyzes the results of PCR pool testing over time stratified by region, school type, and age of children. The data were obtained from classes in elementary and special needs schools, involving pupils aged 6 to 11 years, who participated in the Bavaria-wide PCR pool testing from 09/20/21 to 04/08/22. Samples were collected twice weekly, consisting of PCR pool samples and individual PCR samples, which were only evaluated in case of a positive pool test. A class was considered positive if at least one individual sample from that class was positive within a calendar week (CW). A school (class) was considered to be infection-prone if three or more classes in that school (students in that class) were positive within a CW. The data included 2,430 elementary schools (339 special needs schools) with 23,021 (2,711) classes and 456,478 (29,200) children. A total of 1,157,617 pools (of which 3.37% were positive) and 724,438 individual samples (6.76% positive) were analyzed. Larger schools exhibited higher PR compared to smaller schools. From January 2022, the Omicron variant led to a massive increase in PR across Bavaria. The incidence rates per 100,000 person-weeks within the individual school samples were significantly lower than the concurrently reported age-specific and general infection incidences in the overall Bavarian population. PCR pool testing revealed relatively few positive pools, with an average of four children per one hundred pools testing positive. Schools and classes were rarely considered infection-prone, even during periods of high incidences outside of schools. The combination of PCR pool testing and hygiene measures allowed for a largely safe in-person education for pupils in primary and special needs schools in the school year 2021/22.

Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing

BACKGROUND

The challenges of rapid upscaling of testing capacity were a major lesson from the COVID-19 pandemic response. The need for process adjustments in high-throughput testing laboratories made sample pooling a challenging option to implement.

OBJECTIVE

This study aimed to evaluate whether pooling samples at source (swab pooling) was as effective as qRT-PCR testing of individuals in identifying cases of SARS-CoV-2 in real-world community testing conditions using the same high-throughput pipeline.

METHODS

Two cohorts of 10 (Pool10: 1,030 participants and 103 pools) and 6 (Pool6: 1,284 participants and 214 pools) samples per pool were tested for concordance, sensitivity, specificity, and Ct value differences with individual testing as reference.

RESULTS

Swab pooling allowed unmodified application of an existing high-throughput SARS-Cov-2 testing pipeline with only marginal loss of accuracy. For Pool10, concordance was 98.1% (95% Confidence interval: 93.3-99.8%), sensitivity was 95.7% (85.5-99.5%), and specificity was 100.0% (93.6-100.0%). For Pool6, concordance was 97.2% (94.0-99.0%), sensitivity was 97.5% (93.7-99.3%), and specificity was 96.4% (87.7-99.6%). Differences of outcomes measure between pool size were not significant. Most positive individual samples, which were not detected in pools, had very low viral concentration. If only individual samples with a viral concentration > 400 copies/ml (i.e. Ct value < 30) were considered positive, the overall sensitivity of pooling increased to 99.5%.

CONCLUSION

The study demonstrated high sensitivity and specificity by swab pooling and the immediate capability of high-throughput laboratories to implement this method making it an option in planning of rapid upscaling of laboratory capacity for future pandemics.

Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study

China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact tracing and isolation, based on 419 million travel movements among 366 Chinese cities. The study period for this model began from September 2022. The COVID-19 disease burden was evaluated, considering 8 types of underlying health conditions in the Chinese population. We identified the marginal effects between the testing speed and reduction in the epidemic duration. The findings suggest that assuming a vaccine coverage of 89%, the Omicron-like wave could be suppressed by 3-day interval population-level testing (PLT), while it would become endemic with 4-day interval PLT, and without testing, it would result in an epidemic. PLT conducted every 3 days would not only eliminate infections but also keep hospital bed occupancy at less than 29.46% (95% CI, 22.73-38.68%) of capacity for respiratory illness and ICU bed occupancy at less than 58.94% (95% CI, 45.70-76.90%) during an outbreak. Furthermore, the underlying health conditions would lead to an extra 2.35 (95% CI, 1.89-2.92) million hospital admissions and 0.16 (95% CI, 0.13-0.2) million ICU admissions. Our study provides insights into health preparedness to balance the disease burden and sustainability for a country with a population of billions.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Towards Point of Care CRISPR-Based Diagnostics: From Method to Device

Rapid, accurate, and portable on-site detection is critical in the face of public health emergencies. Infectious disease control and public health emergency policymaking can both be aided by effective and trustworthy point of care tests (POCT). A very promising POCT method appears to be the clustered regularly interspaced short palindromic repeats and associated protein (CRISPR/Cas)-based molecular diagnosis. For on-site detection, CRISPR/Cas-based detection can be combined with multiple signal sensing methods and integrated into smart devices. In this review, sensing methods for CRISPR/Cas-based diagnostics are introduced and the advanced strategies and recent advances in CRISPR/Cas-based POCT are reviewed. Finally, the future perspectives of CRISPR and POCT are summarized and prospected.

European Cohorts of patients and schools to Advance Response to Epidemics (EuCARE): a cluster randomised interventional and observational study protocol to investigate the relationship between schools and SARS-CoV-2 infection

BACKGROUND

Contradictory results were reported on the role of school closure/reopening on the overall SARS-CoV-2 transmission rate, as well as on which kind and level of mitigation measures implemented in schools may be effective in limiting its diffusion. Some recent studies were reassuring, showing that opening did not increase the community spread, although teachers and families are worried about the high class density. On the other hand, distance learning was associated with a negative impact on learning, sociability and psychological health, especially in vulnerable children. As it becomes clear that the SARS-CoV-2 pandemic will last for a long time, there is a high need for studies and solutions to support safe schools opening based on scientific evidence of harms and benefits. The Lolli-Methode (LM) is a strategy for epidemiological surveillance and early intervention aiming at SARS-CoV-2 outbreaks' reduction in schools, relying on polymerase chain reaction analysis of saliva samples.

METHODS

In this cluster randomised trial protocol, we aim to determine whether the LM is useful to support schools opening and to reduce clusters and attack rates in schools, compared with the standard of care (SoC) surveillance by public health departments. This multicenter study will enrol 440 classes (around 8800 students, teachers and other personnel) from two countries, cluster randomised to LM or SoC. The samples from the pools will be collected and tested using PCR-based techniques. Test results will be combined with questionnaires filled in by children, parents, schoolteachers, and principals, concerning ongoing mitigation measures, their perceived psychological impact and other health and socio-economic information. An ancillary observational study will be carried out to study the prevalence of SARS-CoV-2 in schools, frequencies and size of clusters and attack rates, to compare the effectiveness of the different preventive measures adopted and to evaluate psychological issues in students and teachers in relation to the pandemic's containment measures.

DISCUSSION

By the end of this study, we will have defined and characterised the applicability of the LM for SARS-CoV-2 surveillance, as well as the impact of pandemic preventive measures on children and teachers. Trial registration International Standard Randomised Controlled Trial Number: NCT05396040, 27.05.2022.

Detection of asymptomatic SARS-CoV-2 infections in daycare centers, schools, and companies for regional pandemic containment by a PCR testing laboratory cooperative between July 2021 and June 2022

As an important element in the regional containment of the COVID-19 pandemic a PCR testing laboratory with a cooperative character was founded in spring 2021 to screen for SARS-CoV-2 in the Nuremberg region, Germany. The aim was to detect asymptomatic infections in day care facilities for children, schools, and companies. The laboratory used an established RT-PCR protocol and analyzed approximately 18,500 pools of up to 25 pooled samples each from gargles or swabs ("lollipops") from up to 135 facilities between July 2021 and June 2022. Usually, the participating facilities were informed about positive pools within a few hours. Retention samples from positive pools were usually analyzed on the same day, and the results were reported to the facilities as well as the German Electronic Reporting and Information System (DEMIS). In the laboratory results, both the local incidences and the transition from the Delta- to the Omicron surge in early 2022 were well reflected. It is plausible that about 4,800 secondary infections could be prevented from the approximately 1,570 positive individual samples detected in conjunction with appropriate isolation measures. Such a PCR laboratory, which is characterized by short response times and high flexibility, can thus provide valuable services for regional surveillance of infection incidence.

SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

Background

Since the onset of the COVID-19 pandemic, children have been mentally and physically burdened, particularly due to school closures, with an associated loss of learning. Therefore, efficient testing strategies with high sensitivity are necessary to keep schools open. Apart from individual rapid antigen testing, various methods have been investigated, such as PCR-based pool-testing of nasopharyngeal swabs, gargle, or saliva samples. To date, previous validation studies have found the PCR-based saliva swab pool testing method to be an effective screening method, however, the acceptability and feasibility of a widespread implementation in the school-setting among stakeholders has not been comprehensively evaluated.

Methods

In this pilot study, SARS-CoV-2 saliva swab pool testing of up to 15 swabs per pool was conducted in ten primary and special schools in Mecklenburg-Western Pomerania, Germany, over a period of one month. Thereafter, parents, teachers and school principals of the participating schools as well as the participating laboratories were surveyed about the feasibility and acceptability of this method, its large-scale implementation and challenges. Data were analyzed quantitatively and qualitatively.

Results

During the study period, 1,630 saliva swab pools were analyzed, of which 22 tested SARS-CoV-2 positive (1.3%). A total of N = 315 participants took part in the survey. Across all groups, the saliva swab pool testing method was perceived as more child-friendly (>87%), convenient (>82%), and easier (>81%) compared to rapid antigen testing by an anterior nasal swab. Over 80% of all participants favored widespread, regular use of the saliva swab method.

Conclusion

In school settings in particular, a high acceptability of the test method is crucial for a successful SARS-CoV-2 surveillance strategy. All respondents clearly preferred the saliva swab method, which can be used safely without complications in children six years of age and older. Hurdles and suggestions for improvement of an area-wide implementation were outlined.

Clinical Aspects of the Subsequent SARS-CoV-2 Waves in Children from 2020 to 2022-Data from a Local Cohort in Cologne, Germany (n = 21,635)

Almost two and a half years after the appearance of the first cases of SARS-CoV-2 in December 2019, more than 500 million people have been infected with SARS-CoV-2 and over 6 million have died of it worldwide. In terms of the pediatric cohort, it already became evident at an early stage that the infection causes milder symptoms in children and rarely runs a fatal course. Objective: This work presents data gathered over a period of over two years in patients between the age of 0 and 18 years. The aim is to provide information on the clinical aspects of the five different SARS-CoV-2 waves. Methods: Between 13 March 2020 and 22 April 2022, all nucleic acid amplification tests (NAATs) of children who received a swab for SARS-CoV-2 at our clinic were included. Data were collected on standardized questionnaires. The analysis of the data was anonymized and retrospective. Results: We investigated 21,635 NAATs, of which 1028 of the tests were positive (4.8%). The highest rate of positive results was observed in the fifth wave (541/2.292 NAATs (23.6%)). Most of the children who were hospitalized were hospitalized in wave three (22.9%). The availability of a vaccine was followed by a decrease in positive NAATs in the corresponding age group thereafter. Conclusions: These data underline the fact that children infected with SARS-CoV-2, regardless of which VOC, are often only mildly affected. Vaccinations seem to remain the key to avoid massive numbers of infected people and a potential collapse of the healthcare systems.

Implementing the Lolli-Method and pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools: a pilot project

Purpose

School closures have been used as part of lockdown strategies to contain the spread of SARS-CoV-2, adversely affecting children’s health and education. To ensure the accessibility of educational institutions without exposing society to the risk of increased transmissions, it is essential to establish SARS-CoV-2 testing strategies that are child-friendly, scalable and implementable in a daily school routine. Self-sampling using non-invasive saliva swabs combined with pooled RT-qPCR testing (Lolli-Method) has been proven to be a sensitive method for the detection of SARS-CoV-2.

Methods

We conducted a pilot project in Cologne, Germany, designed to determine the feasibility of a large-scale rollout of the Lolli-Method for testing without any additional on-site medical staff in schools. Over a period of three weeks, students from 22 schools were sampled using the Lolli-Method. At the end of the project, teachers were asked to evaluate the overall acceptance of the project.

Results

We analyzed a total of 757 pooled RT-qPCRs obtained from 8,287 individual swabs and detected 7 SARS-CoV-2 infected individuals. The Lolli-Method was shown to be a feasible and accepted testing strategy whose application is only slightly disruptive to the daily school routine.

Conclusion

Our observations suggest that the Lolli-Method in combination with pooled RT-qPCR can be implemented for SARS-CoV-2 surveillance in daily school routine, applicable on a large scale.

Supplementary Information

The online version contains supplementary material available at 10.1007/s15010-022-01865-0.

BioMateriOME: To understand microbe-material interactions within sustainable, living architectures

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.