Testing at scale during the COVID-19 pandemic

Population immunity enhances the evolution of SARS-CoV-2 in Beijing revealed by wastewater genomic surveillance

This study aims to elucidate the impact of population immunity on the regional evolution of SARS-CoV-2. A total of 3701 wastewater SARS-CoV-2 concentration values and 168 wastewater whole genomes of SARS-CoV-2 were obtained in Beijing over 11 months following the implementation of the "dynamic zero-COVID" policy adjustments in December 2022. The findings indicate that the number of variant strains identified through wastewater surveillance was 2.46 times greater than that detected by clinical monitoring, with single nucleotide polymorphisms showing an increase of up to 7.14 times. This enhanced surveillance facilitates a more comprehensive analysis of regional virus evolution patterns. Following the adjustment of epidemic measure, Beijing experienced three distinct waves of epidemics, and the dominant variant transitioned directly from BA.5 in the first wave to XBB after six months in the second one. During this period, strong population immunity formed by centralized infection in over 90 % of the population blocked the outbreak of internationally prevalent and concerning variants BQ.1 and CH.1.1, resulting in a 12.5 % faster regional evolution of SARS-CoV-2 strains in Beijing compared to the international context. Subsequently, in August 2023, EG.5 became the dominant variant in the third wave, aligning with international trends. The epidemics in Beijing have caused significant positive selection pressure on SARS-CoV-2 strains, favoring those with enhanced antigenic escape mutations in spike gene. These results underscore that the extensive infection after the adjustment of epidemic prevention policies has accelerated the evolution of SARS-CoV-2 in Beijing and been conducive to antigenic escape evolution, which can effectively inform decision making for epidemic control and preemptive vaccine design.

Munich goes viral: Measuring the impact of the Oktoberfest on COVID-19 infection rates using difference-in-differences

With about 6 million visitors, the 2022 Oktoberfest in Germany has been one of the largest in-person social events following the COVID-19 pandemic. Despite high vaccination rates in Germany at that time, health authorities pointed out the high risk of getting infected at such events. Using a unique dataset, we estimate the causal impact of the Oktoberfest on the spread of infection by applying an event study design. Our results imply a significant increase in the infection rates during and after Oktoberfest, especially in the age cohorts 15-34 and 35-59. However, the case rate drops relatively quickly after Oktoberfest. We also find little to no effect of the fair on the infection rates of the remaining age cohorts below 15 and above 60 years of age. A robustness check using the hospitalization rate as dependent variable confirms those results. Our findings have important implications for regulations of large social events in times of COVID-19, when the share of vaccinated people in the population is already high.

SARS-CoV-2 Testing Behavior in Symptomatic Adults and the Role of Exposure Risk, Susceptibility and Healthcare Access in a U.S. National Cohort (2020-2023)

Background

The COVID-19 pandemic highlighted the critical role of diagnostic testing for managing transmission and reducing the risk of serious illness. This study examines SARS-CoV-2 testing behavior patterns, including at-home and laboratory tests, among adults with COVID-like symptoms from 2020-2023. We explore characteristics associated with testing frequency and assess the impact of SARS-CoV-2 exposure risk, susceptibility to COVID-19 complications, and barriers to healthcare access on frequency of testing when ill.

Methods

The CHASING COVID Cohort study comprises a diverse sample of U.S. adults, with data collected quarterly from March 2020 to December 2023. We categorized participants with COVID-like symptoms reported 2+ times (N = 3,929) as 'frequent testers' if they tested ≥ 66% of the time when symptomatic, 'occasional testers' if they tested > 33% and < 66% of the time, and 'infrequent testers' if they tested ≤ 33% of the time. Informed by the Blumenshine Pandemic Disease Framework, we examined the impact of SARS-CoV-2 exposure risk, susceptibility to COVID-19 complications if infected, and barriers to healthcare access on testing frequency using crude and adjusted log-binomial regression models.

Results

Infrequent testers were more likely to be female, Hispanic or Black/non-Hispanic, have an annual household income <$35,000, have fewer years of education, have children in the household, reside in a rural area or southern state. Testing frequency was positively correlated with COVID-19 vaccination, willingness to take antivirals, trust in public health agencies and healthcare providers for COVID-19 vaccine information. Those with more (versus less) exposure risk (aOR 1.14, 95% CI [1.01, 1.26]), COVID-19 susceptibility (aOR 1.17, 95% CI [1.05, 1.30]), no insurance (aOR 1.52, 95% CI [1.37, 1.70]), and no regular healthcare provider (aOR 1.32, 95% CI [1.19, 1.46]) were more likely to test infrequently. Those with more (versus less) exposure risk, susceptibility, and barriers to healthcare were less likely to have purchased SARS-CoV-2 at-home tests and to have requested freely available tests from covidtests.gov.

Conclusions

Initiatives to increase testing uptake should prioritize reaching those with greater risk of SARS-CoV-2 exposure, susceptibility to severe COVID-19, and for those with barriers to healthcare access.

Wastewater surveillance as a predictive tool for COVID-19: A case study in Chengdu

OBJECTIVE

This study was conducted to enhance conventional epidemiological surveillance by implementing city-wide wastewater monitoring of SARS-CoV-2 RNA. The research aimed to develop a quantitative model for estimating infection rates and to compare these predictions with clinical case data. Furthermore, this wastewater surveillance was utilized as an early warning system for potential COVID-19 outbreaks during a large international event, the Chengdu 2023 FISU Games.

METHODS

This study employed wastewater based epidemiology (WBE), utilizing samples collected twice a week from nine wastewater treatment plants that serve 66.1% of Chengdu's residents, totaling 15.2 million people. The samples were collected between January 18, 2023, and June 15, 2023, and were tested for SARS-CoV-2 RNA. A model employed back-calculation of SARS-CoV-2 infections by integrating wastewater viral load measurements with human fecal and urinary shedding rates, as well as population size estimates derived from NH4-N concentrations, utilizing Monte Carlo simulations to quantify uncertainty. The model's predictions compared with the number of registered cases identified by the Nucleic Acid Testing Platform of Chengdu during the same period. Additionally, we conducted sampling from two manholes in the wastewater pipeline, which encompassed all residents of the Chengdu 2023 FISU World University Games village, and tested for SARS-CoV-2 RNA. We also gathered data on COVID-19 cases from the symptom monitoring system between July 20 and August 11.

RESULTS

From the third week to the twenty-fourth week of 2023, the weekly median concentration of SARS-CoV-2 RNA fluctuated, starting at 16.94 copies/ml in the third week, decreasing to 1.62 copies/ml by the fifteenth week, then gradually rising to a peak of 41.27 copies/ml in the twentieth week, before ultimately declining to 8.74 copies/ml by the twenty-fourth week. During this period, the number of weekly new cases exhibited a similar trend, and the results indicated a significant correlation between the viral concentration and the number of weekly new cases (spearman's r = 0.93, P < 0.001). The quantitative wastewater surveillance model estimated that approximately 2,258,245 individuals (P5-P95: 847,869 - 3,928,127) potentially contracted COVID-19 during the epidemic wave from March 4th to June 15th, which is roughly 33 times the number of registered cases (68,190 cases) reported on the Nucleic Acid Testing Platform. Furthermore, the infection rates of SARS-CoV-2, as estimated by the model, ranged from 0.012% (P5-P95: 0.004% - 0.020%) at the lowest baseline to 3.27% (P5-P95: 1.23% - 5.69%) at the peak of the epidemic, with 15.1% (P5-P95: 5.65% - 26.2%) of individuals infected during the epidemic wave between March 4th and June 15th. Additionally, we did not observe any COVID-19 outbreaks or cluster infections at the Chengdu 2023 FISU World University Games village, and there was no significant difference in the concentrations of SARS-CoV-2 in athletes before and after check-in at the village.

CONCLUSIONS

This study demonstrates the effectiveness of wastewater surveillance as a long-term sentinel approach for monitoring SARS-CoV-2 and providing early warnings for COVID-19 outbreaks during large international events. This method significantly enhances traditional epidemiological surveillance. The quantitative wastewater surveillance model offers a reliable means of estimating the number of infected individuals, which can be instrumental in informing policy decisions.

Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis

Synthetic genetic materials, particularly those in genetically modified organisms (GMOs) deployed into complex environments, necessitate robust postmarket surveillance for continuous monitoring of both the materials and their applications throughout their lifecycle. Here, we introduce novel-coded genomic material for a blind mutation test that evaluates mutagenesis in synthetic genomic sequences without requiring direct sequence comparison. This test utilizes a Genome-Digest, which is embedded within essential genes, establishing mathematical correlation between the nucleotide sequence and codon order. This novel design allows for independent assessment of mutations by decoding the nucleotide sequence, thereby eliminating the need for reference sequences or extensive bioinformatic analysis. Furthermore, the test has the capability to analyze mixed genomic materials from a single sample and can be extended to the pooled testing of multiple samples as well. Building on this framework, we propose the 'Genome-ShockWatch' methodology. In proof-of-concept trials, it successfully detected mutations that exceeded a predefined threshold in long-read sequencing data from a yogurt sample containing Genome-Digest encoded Nissle 1917 E. coli cells and naturally occurring probiotic bacteria. Consequently, the Genome-Digest system provides a robust foundation for the routine surveillance and management of GMOs and related synthetic products, ensuring their safety and efficacy in diverse environmental contexts.

Molecular epidemiological surveillance of respiratory syncytial virus infection in Myanmar from 2019 to 2023

To evaluate genetic changes in respiratory syncytial virus (RSV) between 2019 and 2023, we analyzed RSV strains from Myanmar before and after the COVID- 19 pandemic. Real-time polymerase chain reaction (RT-PCR) positive samples from children presenting with acute respiratory infections at outpatient clinics in Yangon were sequenced to determine the genotype. Phylogenetic and molecular evolutionary analyses were conducted using the Bayesian Markov Chain Monte Carlo method to construct the time-scale Maximum Clade Credibility tree. Of 1127 samples, 104 (9.2%) RSV-A and 233 (20.7%) RSV-B were positive by RT-PCR. There was an absence of a notable epidemic in 2020, a temporal shift with a surge of RSV-A in the 2021 outbreak, a lack of expected cases in 2022 and a substantial resurgence of RSV-B in 2023. The genotype of RSV-A was mainly A.D.3 lineage through the study period, while RSV-B were B.D.4.1.1 and B.D.E.1. RSV-A showed that the same lineage persisted within Myanmar throughout the pandemic, leading to a large outbreak post-COVID. In contrast, RSV-B strains appear to have temporarily disappeared during the pandemic, but subsequently, globally circulating strains likely entered Myanmar, resulting in a major outbreak in 2023. The estimated evolutionary rate at the G-ectodomain for RSV-A was 7.76 × 10⁻³ and RSV-B was 5.67 × 10⁻³ substitutions/site/year. Strengthening genomic surveillance will likely support comparisons of circulating strains with those in other countries and facilitate the introduction of vaccines and other interventions.

Lifting of travel restrictions brings additional noise in COVID-19 surveillance through wastewater-based epidemiology in post-pandemic period

The post-pandemic world still faces ongoing COVID-19 infections, although international travel has returned to pre-pandemic conditions. Wastewater-based epidemiology (WBE) is considered an efficient tool for the population-wide surveillance of COVID-19 infections during the pandemic. However, the performance of WBE in post-pandemic era with travel restrictions lifted remains unknown. Utilizing weekly county-level wastewater surveillance data from June 2021-November 2022 for 222 counties in 49 states (covering 104 million people) in the United States of America, we retrospectively evaluated the correlations between SARS-CoV-2 RNA (CRNA) and reported cases, as well as the impacts of international air travel, demographics, socioeconomic aspects, test accessibility, epidemiological, and environmental factors on reported cases under the corresponding CRNA. The lifting of travel restrictions in June 2022, shifted the correlation between CRNA and COVID-19 incidence in the following 7-day and 14-day from 0.70 (IQR: 0.30-0.88) in June 2021-May 2022 (pandemic) to 0.01 (IQR: -0.31-0.36) in June-November 2022 (post-pandemic), and from 0.74 (IQR: 0.31-0.90) to -0.01 (IQR: -0.38-0.45), respectively. Besides, after lifting the travel restrictions, under the same CRNA, the reported case numbers were impacted by many factors, including the variations of international passengers, test accessibility, Omicron prevalence, ratio of population aged between 18 and 65, minority vulnerability, and healthcare system. This highlights the importance of demographics, infection testing, variants and socioeconomic status on the accuracy and implication of WBE to monitor COVID-19 infection status in post-pandemic era. Our findings facilitate the public health authorities to dynamically adjust their WBE-based tools/strategies to the local contexts to achieve optimal community surveillance.

Translation of COVID-19 Serology Test on Foil-Based Lateral Flow Chips: A Journey from Injection Molding to Scalable Roll-to-Roll Nanoimprint Lithography

Lateral flow tests (LFTs) had a pivotal role in combating the spread of the SARS-CoV-2 virus throughout the COVID-19 pandemic thanks to their affordability and ease of use. Most of LFT devices were based on nitrocellulose membrane strips whose industrial upscaling to billions of devices has already been extensively demonstrated. Nevertheless, the assay option in an LFT format is largely restricted to qualitative detection of the target antigens. In this research, we surveyed the potential of UV nanoimprint lithography (UV-NIL) and extrusion coating (EC) for the high-throughput production of disposable capillary-driven, foil-based tests that allow multistep assays to be implemented for quantitative readout to address the inherent lack of on-demand fluid control and sensitivity of paper-based devices. Both manufacturing technologies operate on the principle of imprinting that enables high-volume, continuous structuring of microfluidic patterns in a roll-to-roll (R2R) production scheme. To demonstrate the feasibility of R2R-fabricated foil chips in a point-of-care biosensing application, we adapted a commercial chemiluminescence multiplex test for COVID-19 antibody detection originally developed for a capillary-driven microfluidic chip manufactured with injection molding (IM). In an effort to build a complete ecosystem for the R2R manufacturing of foil chips, we also recruited additional processes to streamline chip production: R2R biofunctionalization and R2R lamination. Compared to conventional fabrication techniques for microfluidic devices, the R2R techniques highlighted in this work offer unparalleled advantages concerning improved scalability, dexterity of seamless handling, and significant cost reduction. Our preliminary evaluation indicated that the foil chips exhibited comparable performance characteristics to the original IM-fabricated devices. This early success in assay translation highlights the promise of implementing biochemical assays on R2R-manufactured foil chips. Most importantly, it underscores the potential utilization of UV-NIL and EC as an alternative to conventional technologies for the future development in vitro diagnostics (IVD) in response to emerging point-of-care testing demands.

PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance

MOTIVATION

Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g., epidemiological information), genomics is used to obtain knowledge on health pathogenic threats and insights on their evolution, to monitor pathogens spread, and to evaluate the effectiveness of countermeasures. From a decision-making policy perspective, it is essential to ensure the entire process's quality before relying on analysis results as evidence. Available workflows usually offer quality assessment tools that are primarily focused on the quality of raw NGS reads but often struggle to keep pace with new technologies and threats, and fail to provide a robust consensus on results, necessitating manual evaluation of multiple tool outputs.

RESULTS

We present PathoSeq-QC, a bioinformatics decision support workflow developed to improve the trustworthiness of genomic surveillance analyses and conclusions. Designed for SARS-CoV-2, it is suitable for any viral threat. In the specific case of SARS-CoV-2, PathoSeq-QC: (i) evaluates the quality of the raw data; (ii) assesses whether the analysed sample is composed by single or multiple lineages; (iii) produces robust variant calling results via multi-tool comparison; (iv) reports whether the produced data are in support of a recombinant virus, a novel or an already known lineage. The tool is modular, which will allow easy functionalities extension.

AVAILABILITY AND IMPLEMENTATION

PathoSeq-QC is a command-line tool written in Python and R. The code is available at https://code.europa.eu/dighealth/pathoseq-qc.

Portable molecular diagnostic platform for rapid point-of-care detection of mpox and other diseases

The World Health Organization's designation of mpox as a public health emergency of international concern in August 2024 underscores the urgent need for effective diagnostic solutions to combat this escalating threat. The rapid global spread of clade II mpox, coupled with the sustained human-to-human transmission of the more virulent clade I mpox in the Democratic Republic of Congo, highlights a critical gap in point-of-care diagnostics for this emergent disease. In response, we developed Dragonfly, a portable molecular diagnostic platform for point-of-care use that integrates power-free nucleic acid extraction (<5 minutes) with lyophilised colourimetric LAMP chemistry. The platform demonstrated an analytical limit-of-detection of 100 genome copies per reaction for monkeypox virus, effectively distinguishing it from other orthopoxviruses, herpes simplex virus, and varicella-zoster virus. Clinical validation on 164 samples, including 51 mpox-positive cases, yielded 96.1% sensitivity and 100% specificity for orthopoxviruses, and 94.1% sensitivity and 100% specificity for monkeypox virus. Here, we present a rapid, accessible, and robust point-of-care diagnostic solution for mpox, suitable for both low- and high-resource settings, addressing the global resurgence of orthopoxviruses in the context of declining smallpox immunity.

FEN1-Aided RPA (FARPA) Coupled with Autosampling Microfluidic Chip Enables Highly Multiplexed On-Site Pathogen Screening

A simple, rapid, low-cost, and multiplex detection platform is crucial for the diagnosis of infectious diseases, especially for on-site pathogen screening. However, current methods are difficult to satisfy the requirements for minimal instrument and multiplexed point-of-care testing (POCT). Herein, we propose a versatile and easy-to-use platform (FARPA-chip) by combining multiplex FARPA with an autosampling microfluidic chip. A pair of universal recombinase polymerase amplification (RPA) primers introduced during double-stranded cDNA (ds-cDNA) preparation are employed to amplify multiple targets, followed by amplicon-decoding with the chip, indicating no bias in amplifying different targets due to the universal RPA primers. FARPA-chip exhibits that as low as 10 copies of each target RNA in the starting sample can be sensitively detected by 12-plex detection of vector-borne viruses within 45 min and no cross-talk is observed between different targets. The feasibility of this platform is confirmed by designing a 9-plex FARPA-chip to detect 6 kinds of clinically common respiratory viruses from 16 clinical samples of nasopharyngeal swabs, and the results are completely consistent with RT-qPCR. Furthermore, by integrating quick extraction reagent, the turnaround time can be significantly decreased to <50 min, highlighting that our FARPA-chip enables a cost-effective on-site pathogen screening with a relatively high level of multiplexing. Depending on the number of chambers in the chip, the current design is theoretically capable of detecting up to 24 different pathogens, which should fulfill most clinical purposes. We believe that the proposed platform could provide an effective way for a series of healthcare-related applications in resource-limited settings.

Anti-SARS-CoV-2 nucleocapsid antibodies to detect exposure to SARS-CoV-2: results from a prospective cohort study on COVID-19 vaccination

BACKGROUND

In May 2023, the World Health Organization declared COVID-19 no longer a public health emergency. Despite successful vaccination campaigns, vaccines provide limited protection against transmission. Since general testing has been abandoned in most countries, alternative population surveillance methods to assess SARS-CoV-2 exposure are needed.

METHODS

N-antigen is a protein of the SARS-CoV-2 virus that is not present in the vaccines and hence may be a useful serological marker of infection. This study evaluated N-antigen antibodies as a marker of SARS-CoV-2 exposure in a vaccinated Swedish cohort. Serum samples were collected and analysed for N-antigen antibodies using the mesoscale system. Nonlinear mixed-effects model accounting for multiple measurements per individual was used to estimate the half-life of N-antigen antibodies.

RESULTS

A total of 3,202 participants (median age 31 years) were recruited from April 2021 to February 2022 from four vaccination centres in Skåne, Sweden. A total of 2,999 participants had at least one valid N-antigen antibody measurement. The estimated half-life of N-antigen antibodies was 59 days (95% CI: 55-64 days). The estimated 95% range of halves-lives were from 24 to 174 days. The repeated measurements of N-antigen antibody levels could accurately detect SARS-CoV-2 infection. A twofold increase had a sensitivity of 91%, whereas a 16-fold increase had a specificity of 91%, respectively. The area under the curve (AUC) for predicting infection was 0.88 [95% C.I. 0.86-0.90].

CONCLUSION

Repeated monitoring of N-antigen antibody levels may be a valuable tool for assessing SARS-CoV-2 exposure and thus aid in monitoring transmission thereby helping in guiding vaccination strategies.

Immuno-μSARS2 Chip: A Peptide-Based Microarray to Assess COVID-19 Prognosis Based on Immunological Fingerprints

A multiplexed microarray chip (Immuno-μSARS2) aiming at providing information on the prognosis of the COVID-19 has been developed. The diagnostic technology records information related to the profile of the immunological response of patients infected by the SARS-CoV-2 virus. The diagnostic technology delivers information on the avidity of the sera against 28 different peptide epitopes and 7 proteins printed on a 25 mm2 area of a glass slide. The peptide epitopes (12-15 mer) derived from structural proteins (Spike and Nucleocapsid) have been rationally designed, synthesized, and used to develop Immuno-μSARS2 as a multiplexed and high-throughput fluorescent microarray platform. The analysis of 755 human serum samples (321 from PCR+ patients; 288 from PCR- patients; 115 from prepandemic individuals and classified as hospitalized, admitted to intensive-care unit (ICU), and exitus) from three independent cohorts has shown that the chips perform with a 98% specificity and 91% sensitivity identifying RT-PCR+ patients. Computational analysis utilized to correlate the immunological signatures of the samples analyzed indicate significant prediction rates against exitus conditions with 82% accuracy, ICU admissions with 80% accuracy, and 73% accuracy over hospitalization requirement compared to asymptomatic patients' fingerprints. The miniaturized microarray chip allows simultaneous determination of 96 samples (24 samples/slide) in 90 min and requires only 10 μL of sera. The diagnostic approach presented for the first time here could have a great value in assisting clinicians in decision-making based on the information provided by the Immuno-μSARS2 regarding progression of the disease and could be easily implemented in diagnostics of other infectious diseases.

Wastewater-based epidemiology framework: Collaborative modeling for sustainable disease surveillance

Many wastewater-based epidemiology (WBE) programs are being implemented worldwide due to their usefulness in monitoring residents' health. Modeling wastewater dynamics in outbreak scenarios can provide important data for designing wastewater surveillance plans. For outbreak modeling to be effective, researchers must coordinate with public health authorities and laboratory services, using frameworks to ensure that their modeling and output data are relevant for informed decision-making. However, theoretical and institutional frameworks typically omit modeling, and the connection between theoretical frameworks and models is often unrecognized. A framework that surpasses theoretical conceptualization for promoting collaboration between actors by integrating modeling can achieve the required synchrony toward sustainable wastewater surveillance plans. First, we build on an existing theoretical framework to create a collaborative framework that integrates modeling and suggests stakeholder activities for designing WBE programs. Then, we demonstrate our framework for developing a WBE plan via a COVID-19 case study where we answer when, how often, and where to sample wastewater to detect and monitor an outbreak. We evaluate the results in space and time for three outbreak phases (early detection, peak, and tail). The modeling outputs indicate the need for different sampling strategies for these outbreak phases. Our results also quantify the differences in the likelihood of capturing viral events in wastewater between the sampling hours at different disease phases for COVID-19 and various spatial locations in the sewer network. This framework lays the foundation for sustainable WBE to improve the detection efficiency of wastewater surveillance plans.

Nanoparticles of natural product-derived medicines: Beyond the pandemic

This review explores the synergistic potential of natural products and nanotechnology for viral infections, highlighting key antiviral, immunomodulatory, and antioxidant properties to combat pandemics caused by highly infectious viruses. These pandemics often result in severe public health crises, particularly affecting vulnerable populations due to respiratory complications and increased mortality rates. A cytokine storm is initiated when an overload of pro-inflammatory cytokines and chemokines is released, leading to a systemic inflammatory response. Viral mutations and the limited availability of effective drugs, vaccines, and therapies contribute to the continuous transmission of the virus. The coronavirus disease-19 (COVID-19) pandemic has sparked renewed interest in natural product-derived antivirals. The efficacy of traditional medicines against pandemic viral infections is examined. Their antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties are highlighted. This review discusses how nanotechnology enhances the efficacy of herbal medicines in combating viral infections.

Nanobody-Based Lateral Flow Immunoassay for Rapid Antigen Detection of SARS-CoV-2 and MERS-CoV Proteins

The COVID-19 pandemic has highlighted the critical need for pathogen detection methods that offer both low detection limits and rapid results. Despite advancements in simplifying and enhancing nucleic acid amplification techniques, immunochemical methods remain the preferred methods for mass testing. These methods eliminate the need for specialized laboratories and highly skilled personnel, making home testing feasible. Here, we developed nanobody-based lateral flow assays (LFAs) for the rapid detection of SARS-CoV-2 and MERS-CoV in single and dual formats as point-of-care diagnostic tools. The developed LFAs are highly sensitive and successfully detected analytes at clinically relevant diagnostic cutoff values. Additionally, our results confirmed that the LFAs have a long shelf life and can be produced cost-effectively and with ease.

Changes in the spectrum of ocular disease during the COVID-19 pandemic in late 2022 in the Hubei Province

We aimed to investigate changes in the ocular disease spectrum during the coronavirus disease-2019 (COVID-19) pandemic in late 2022 in the Hubei Province. This retrospective observational study was conducted in two parts. The first part involved collecting COVID-19-related information from residents of Hubei Province through an online questionnaire survey. The second part involved extracting electronic medical records from ophthalmology outpatient departments at two hospitals in Hubei Province during the pandemic and epidemic prevention and control periods, analyzing changes in the spectrum of ocular diseases. In the first part, 31.65% of patients with systemic symptoms of COVID-19 experienced ocular discomfort. The most common ocular symptoms were eye fatigue, ocular pain and dry eye. In the second part, 76.5% of patients who visited the ophthalmic clinic had COVID-19-related systemic symptoms during pandemic period. The proportion of patients with cornea/keratitis, glaucoma/acute angle-closure glaucoma (AACG) and vitreoretinal disease/retinal vein obstruction (RVO)/acute macular neuroretinalpathy (AMN) increased markedly during pandemic period. Additionally, the number of patients under 18 years and over 60 years decreased significantly compared to the same age groups pre- & post-pandemic. The COVID-19 pandemic has led to certain changes in the spectrum of ocular diseases, which warrants the attention of ophthalmologists.

The Crucial Role of Laboratory Medicine in Addressing Future Public Health Infectious Threats: Insights Gained from the COVID-19 Pandemic

Laboratory testing has played a pivotal role throughout the coronavirus disease 2019 (COVID-19) pandemic, exemplifying the importance of in vitro diagnostics in addressing public health threats posed by outbreaks of infectious diseases. This article aims to present key insights from our expertise, derived from evidence gathered during the COVID-19 pandemic, to inform strategies for managing future infectious challenges. Current scientific evidence underscores that patient sample testing not only allows to diagnose an acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but also supports outbreak prediction, improved control measures, anticipation of pressure on the healthcare system, mitigation of adverse clinical outcomes, and early detection of emerging SARS-CoV-2 variants. Additionally, wastewater monitoring has emerged as a powerful tool for forecasting disease burden, including both prevalence and severity. Collectively, these findings underscore the value of diagnostic testing and wastewater surveillance in guiding healthcare planning and optimizing resource allocation during the COVID-19 pandemic, offering a valid framework to be applied to future public health threats, especially to any potential outbreak of "Disease X" that may emerge in the future.

Localised wastewater SARS-CoV-2 levels linked to COVID-19 cases: A long-term multisite study in England

Wastewater-based surveillance (WBS) can monitor for the presence of human health pathogens in the population. During COVID-19, WBS was widely used to determine wastewater SARS-CoV-2 RNA concentration (concentrations) providing information on community COVID-19 cases (cases). However, studies examining the relationship between concentrations and cases tend to be localised or focussed on small-scale institutional settings. Few have examined this relationship in multiple settings, over long periods, with large sample numbers, nor attempted to quantify the relationship between concentrations and cases or detail how catchment characteristics affected these. This 18-month study (07/20-12/21) explored the correlation and quantitative relationship between concentrations and cases using censored regression. Our analysis used >94,000 wastewater samples collected from 452 diverse sampling sites (259 Sewage Treatment Works (STW) and 193 Sewer Network Sites (SNS)) covering ~65 % of the English population. Wastewater concentrations were linked to ~6 million diagnostically confirmed COVID-19 cases. High correlation coefficients were found between concentrations and cases (STW: median r = 0.66, IQR: 0.57-0.74; SNS: median r = 0.65, IQR: 0.54-0.74). The quantitative relationship (regression coefficient) between concentrations and cases was variable between catchments. Catchment and sampling characteristics (e.g. size of population and grab vs automated sampling) had significant but small effects on correlation and regression coefficients. During the last six months of the study correlation coefficients reduced and regression coefficients became highly variable between catchments. This coincided with a shift towards younger cases, a highly vaccinated population and rapid emergence of the variant Omicron. The English WBS programme was rapidly introduced at scale during COVID-19. Laboratory methods evolved and study catchments were highly diverse in size and characteristics. Despite this diversity, findings indicate that WBS provides an effective proxy for establishing COVID-19 dynamics across a wide variety of communities. While there is potential for predicting COVID-19 cases from wastewater concentration, this may be more effective at smaller scales.

Key factors determining the development of SARS-CoV-2 testing strategies in EU countries: a mixed-methods study

Background

The WHO and the European Center for Disease Prevention and Control (ECDC) advocated for extensive testing as a crucial pillar in managing the COVID-19 pandemic. Yet, public health emergency responses varied across European countries. In particular, there were differences in the national laboratory capacities and diagnostic testing strategies. This study was conducted during the pandemic to identify the key factors in developing national, SARS-CoV-2 testing strategies across a selection of European countries.

Methods

A mixed-methods study, comprising an interview phase and a survey phase, was performed. First, laboratory, policy-making and/or public health experts from different European countries were interviewed between 8 January 2021 and 19 March 2021, to review the development and implementation of national testing strategies.Second, a cross-sectional survey was conducted among ECDC National Focal Points (NFP) for Preparedness and Response and/or Microbiology between July and October 2022 to validate the interview findings.

Results

12 European experts were interviewed and identified the following key factors determining the development of the national SARS-COV-2 testing strategies in their countries: (1) changing testing goals over time, (2) the prevailing epidemiological situation, (3) testing capacities, (4) availability of reference laboratories, (5) supply and stockpiling of testing material, (6) availability of human resources and (7) quality management standards across laboratories. The experts interviewed stressed the important role of stockpile management, the existence of expert networks, as well as the centralisation of decision-making. Lastly, determining the actors responsible for the testing strategy and putting in place 'coordination, accountability and governance' proved to be pivotal.The survey outcome with 15 European NFPs demonstrated that the testing strategies generally changed over time to include a broader group of individuals. Furthermore, the actors 'Ministry of Health', 'Public health officials', 'National public health institutes' and 'National Expert and/or advisory groups' were selected as key players by survey respondents.

Conclusions

In general, the scope of the testing strategy in European countries included in this study expanded as the pandemic progressed. This study identified key factors discussed by European experts interviewed that contributed to the development of SARS-CoV-2 testing strategies across European countries.

Evaluation of wastewater surveillance results for SARS-CoV-2 at the national scale in the Slovak Republic

As the COVID-19 transits to endemicity, the frequency of clinical testing and its utility for determining lineage prevalence has declined. This situation is not unique to Slovakia but reflects a global trend, as attention shifts from COVID-19 to other post-pandemic issues and emerging global health challenges. Nevertheless, the pandemic itself has spurred advancements in monitoring the epidemiological situation. At the beginning of the pandemic, genomic surveillance was carried out through sequencing of individual COVID-19 cases. Subsequently, many countries implemented wastewater surveillance to monitor the prevalence of SARS-CoV-2 variants in the community. In the present study, we collected and analysed 1715 virus-positive samples from 64 wastewater treatment plants across Slovakia, serving 69 % of the population connected to the wastewater treatment pipelines. Here, we show that wastewater sequencing is effective in detecting the emergence of new virus lineages. Additionally, we can assume that wastewater surveillance provides results that are approximately consistent when compared with clinical testing at both national and city levels, concurrently providing information on variant lineages which have not been detected in clinical cases due to reduced clinical testing. Our study demonstrates and concludes the value of wastewater-based surveillance strategies in the Slovakia, establishing it as an important and supportive tool for monitoring public health and serving as an early warning system in times when clinical testing is either declining or unavailable.

Development of a large-scale rapid LAMP diagnostic testing platform for pandemic preparedness and outbreak response

The coronavirus disease 2019 (COVID-19) pandemic underscored the necessity for rapid and efficient diagnostic testing to mitigate outbreaks and control disease transmission. While real-time reverse transcriptase quantitative PCR (RT-qPCR) has been the gold standard due to its high sensitivity and specificity, its logistical complexities and extended turnaround times highlighted the need for alternative molecular methods and non-standard equipment and consumables not subject to supply chain pressure. Loop-mediated isothermal amplification (LAMP) offers several advantages over RT-qPCR, including faster processing time, assay flexibility and cost-effectiveness. During the pandemic, LAMP was successfully demonstrated as a viable alternative to RT-qPCR for SARS-Related Coronavirus 2 detection. However, due to a 100 to 1,000-fold increase in testing volumes, there was an imminent need for automating and scaling up existing LAMP testing workflows leveraging a robotic infrastructure, while retaining analytical performance and cost-effectiveness. In 2020, the Foundation TOMi started the "TOMi corona initiative" to develop and validate a high-throughput, end-to-end, automated, scalable single-step RNA purification, and LAMP-based COVID-19 testing system called SMART-LAMP (Scalable Molecular Automation for Rapid Testing using LAMP) that can process up to 40,000 samples per day using existing laboratory equipment infrastructure with sensitivity comparable to RT-qPCR. This system provides a rapid and scalable diagnostic solution for future pandemics, capable of processing over 40,000 samples per day. In addition, the system is designed to minimize consumable costs and reduces the overall use of plastics to align with increasingly strict sustainability goals that will be imposed over the coming years. Importantly, this system and public-private partnerships in the TOMi corona initiative has the potential to serve as a baseline to enhance pandemic preparedness and response capabilities.

Optimising instructional materials for Covid-19 rapid tests for self-sampling and testing: Mapping the optimization process of manufacturer's instructions for use for self-testing RDTs intended for low-literacy contexts

Simple and easy to use kits for SARS-Cov-2 self-testing during epidemic waves are needed to optimize diagnostic capacity in low- and middle-income countries. SARS-Cov-2 self-testing kits are available, but application of these novel diagnostic technologies is less understood in low and middle-income contexts. We investigated the ability to understand and perform instructions for use (IFUs) for STANDARD Q COVID-19 Ag Test (SD Biosensor) and Panbio COVID-19 Ag Rapid Test Device (Abbott Rapid Diagnostics) for anterior nares (AN) nasal self-sampling and self-testing for COVID-19 in rural and urban Malawi. Qualitative research methods using iterative cognitive interview approach was used to investigate the ability of healthcare providers and lay community members to understand and perform a COVID-19 self-sample or self-test using the manufacturer's instructions for use. A total of 120 iterative cognitive interviews were done with healthcare providers and lay community members for self-sampling (N = 76) and self-testing (N = 44). Cognitive interviews began with the manufacturers version of instructions for use followed by subsequent iterations to refine problematic instructions. Structured interview guide and an observation checklist were used to collect data which was then coded inductively. A framework analysis approach was used to synthesize qualitative data. Study participants were generally proficient at performing a COVID-19 self-sampling and self-testing using the two COVID-19 Rapid Testing Devices. Several of design and content problems within manufacturer's instructions for use made their contextual application sub-optimal. Overall, participants experienced difficulties because of the omission of essential elements within instructions, use of short texts/phrase or lack of a word instruction, the lack of labels on where to open the package; the inconsistencies between word instructions within the instructions for use and the physical contents of the test package; the inability to digest and apply certain technical concepts and the lack of clarity in the phrasing of some text instructions. As expected, healthcare providers experienced fewer problems compared to lay community members. The refinement of these instructions greatly improved comprehension among lay community members. Self-sampling and self-testing for COVID-19 can be performed lay community members with fidelity in a scaled context if the manufacturer's instructions for use have been refined and tailored to the context. In the current study, we have used the study findings to map the optimisation process of manufacturer's IFU'S for self-testing RDT's intended for low literacy contexts including Malawi.

Implementing Individualized quality control plans and managing risk at the point-of-care for molecular diagnostics

INTRODUCTION

Faster turnaround times can lead to rapid patient treatment. Implementing a point-of-care (POC) molecular COVID-19 test requires careful planning. In the POC setting, there are numerous operators and regular monitoring of their activities is key to the successful implementation of a POC molecular test. Test errors can arise from samples, operators, reagents, the testing system, and even from the environment. These sources of error should be considered when implementing a new test.

AREAS COVERED

We outline the importance of establishing well-defined policies for staff to follow at the preanalytic, analytic and postanalytic phases of SARS-CoV-2 testing. As these factors are crucial for the accuracy and reliability of the test results. The key discussion points are from the CLSI EP23-Ed2 document on developing individualized quality control plans and medical literature search engines such as EMBASE, MEDLINE and MedlinePlus.

EXPERT OPINION

The risk management principles applied when implementing nucleic acid POC tests can identify specific control processes to help mitigate common sources of error when conducting molecular testing at the POC.

Feasibility of snapshot testing using wearable sensors to detect cardiorespiratory illness (COVID infection in India)

The COVID-19 pandemic has challenged the current paradigm of clinical and community-based disease detection. We present a multimodal wearable sensor system paired with a two-minute, movement-based activity sequence that successfully captures a snapshot of physiological data (including cardiac, respiratory, temperature, and percent oxygen saturation). We conducted a large, multi-site trial of this technology across India from June 2021 to April 2022 amidst the COVID-19 pandemic (Clinical trial registry name: International Validation of Wearable Sensor to Monitor COVID-19 Like Signs and Symptoms; NCT05334680; initial release: 04/15/2022). An Extreme Gradient Boosting algorithm was trained to discriminate between COVID-19 infected individuals (n = 295) and COVID-19 negative healthy controls (n = 172) and achieved an F1-Score of 0.80 (95% CI = [0.79, 0.81]). SHAP values were mapped to visualize feature importance and directionality, yielding engineered features from core temperature, cough, and lung sounds as highly important. The results demonstrated potential for data-driven wearable sensor technology for remote preliminary screening, highlighting a fundamental pivot from continuous to snapshot monitoring of cardiorespiratory illnesses.

Programmable and ultra-efficient Argonaute protein-mediated nucleic acid tests: A review

With the attributes of high sensitivity, single-base resolution, multiplex detection capability, and programmability upon nucleic acid recognition, Argonaute (Ago)-based biosensing assays are increasingly recognized as one of the most promising tools for precise identification and quantification of target analytes. Employed as highly specific sequence recognition elements of these robust diagnostic methods, Agos are revolutionizing how nucleic acid targets are detected. A systematic and comprehensive summary of this emerging and rapid-advancing technology is necessary to give play to the potential of Ago-based biosensing assays. The structure and function of Agos were briefly overviewed at the beginning of the work, followed by a review of the recent advancements in employing Agos sensing for detecting various targets with a comprehensive analysis such as viruses, tumor biomarkers, pathogens, mycoplasma, and parasite. The significance and benefits of these platforms were then deliberated. In addition, the authors shared subjective viewpoints on the existing challenges and offered relevant guidance for the future progress of Agos assays. Finally, the future research outlook regarding Ago-based sensing in this field was also outlined. As such, this review is expected to offer valuable information and fresh perspectives for a broader group of researchers.

Evaluation of a field deployable, high-throughput RT-LAMP device as an early warning system for COVID-19 through SARS-CoV-2 measurements in wastewater

Quantification of SARS-CoV-2 RNA copies in wastewater can be used to estimate COVID-19 prevalence in communities. While such results are important for mitigating disease spread, SARS-CoV-2 measurements require sophisticated equipment and trained personnel, for which a centralized laboratory is necessary. This significantly impacts the time to result, defeating its purpose as an early warning detection tool. The objective of this study was to evaluate a field portable device (called MINI) for detecting SARS-CoV-2 viral loads in wastewater using real-time reverse transcriptase loop-mediated isothermal amplification (real-time RT-LAMP). The device was tested using wastewater samples collected from buildings (with 430 to 1430 inhabitants) that had known COVID-19-positive cases. Results show comparable performance of RT-LAMP against reverse transcriptase polymerase chain reaction (RT-qPCR) when detecting SARS-CoV-2 copies in wastewater. Both RT-LAMP and RT-qPCR detected SARS-CoV-2 in wastewater from buildings with at least three positive individuals within a 6-day time frame prior to diagnosis. The large 96-well throughput provided by MINI provided scalability to multi-building detection. The portability of the MINI device enabled decentralized on-site detection, significantly reducing the time to result. The overall findings support the use of RT-LAMP within the MINI configuration as an early detection system for COVID-19 infection using wastewater collected at the building scale.

Yeast Surface-Displayed Quenchbody as a Novel Whole-Cell Biosensor for One-Step Detection of Influenza A (H1N1) Virus

Timely surveillance of airborne pathogens is essential to preventing the spread of infectious diseases and safeguard human health. Methods for sensitive, efficient, and cost-effective detection of airborne viruses are needed. With advances in synthetic biology, whole-cell biosensors have emerged as promising platforms for environmental monitoring and medical diagnostics. However, the current design paradigm of whole-cell biosensors is mostly based on intracellular detection of analytes that can transport across the cell membrane, which presents a critical challenge for viral pathogens and large biomolecules. To address this challenge, we developed a new type of whole-cell biosensor by expressing and displaying VHH-based quenchbody (Q-body) on the surface of the yeast Saccharomyces cerevisiae for simple one-step detection of influenza A (H1N1) virus. Seventeen VHH antibody fragments targeting the hemagglutinin protein H1N1-HA were displayed on the yeast cells and screened for the H1N1-HA binding affinity. The functionally displayed VHHs were selected to create surface-displayed Q-body biosensors. The surface-displayed Q-body exhibiting the highest quenching and dequenching efficiency was identified. The biosensor quantitatively detected H1N1-HA in a range from 0.5 to 16 μg/mL, with a half-maximal concentration of 2.60 μg/mL. The biosensor exhibited high specificity for H1N1-HA over other hemagglutinin proteins from various influenza A virus subtypes. Moreover, the biosensor succeeded in detecting the H1N1 virus at concentrations from 2.4 × 104 to 1.5 × 107 PFU/mL. The results from this study demonstrated a new whole-cell biosensor design that circumvents the need for transport of analytes into biosensor cells, enabling efficient detection of the target virus particles.

RT-qPCR Testing and Performance Metrics in the COVID-19 Era

The COVID-19 pandemic highlighted the crucial role of diagnostic testing in managing infectious diseases, particularly through the use of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) tests. RT-qPCR has been pivotal in detecting and quantifying viral RNA, enabling the identification and management of SARS-CoV-2 infections. However, despite its widespread use, there remains a notable gap in understanding fundamental diagnostic metrics such as sensitivity and specificity among many scientists and healthcare practitioners. This gap is not merely academic; it has profound implications for interpreting test results, making public health decisions, and affecting patient outcomes. This review aims to clarify the distinctions between laboratory- and field-based metrics in the context of RT-qPCR testing for SARS-CoV-2 and summarise the global efforts that led to the development and optimisation of these tests during the pandemic. It is intended to enhance the understanding of these fundamental concepts among scientists and healthcare professionals who may not be familiar with the nuances of diagnostic test evaluation. Such knowledge is crucial for accurately interpreting test results, making informed public health decisions, and ultimately managing infectious disease outbreaks more effectively.

Weak-cooperative binding of a long single-stranded DNA chain on a surface

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.

Rapid single-tier serodiagnosis of Lyme disease

Point-of-care serological and direct antigen testing offers actionable insights for diagnosing challenging illnesses, empowering distributed health systems. Here, we report a POC-compatible serologic test for Lyme disease (LD), leveraging synthetic peptides specific to LD antibodies and a paper-based platform for rapid, and cost-effective diagnosis. Antigenic epitopes conserved across Borrelia burgdorferi genospecies, targeted by IgG and IgM antibodies, are selected to develop a multiplexed panel for detection of LD antibodies from patient sera. Multiple peptide epitopes, when combined synergistically with a machine learning-based diagnostic model achieve high sensitivity without sacrificing specificity. Blinded validation with 15 LD-positive and 15 negative samples shows 95.5% sensitivity and 100% specificity. Blind testing with the CDC's LD repository samples confirms the test accuracy, matching lab-based two-tier results, correctly differentiating between LD and look-alike diseases. This LD diagnostic test could potentially replace the cumbersome two-tier testing, improving diagnosis and enabling earlier treatment while facilitating immune monitoring and surveillance.

CRISPR-Cas12a-based ultrasensitive assay for visual detection of SARS-CoV-2 RNA

The development of ultrasensitive and visual methods is of great significance for molecular diagnosis at the point-of-care. In this study, we have integrated recombinase polymerase amplification (RPA) with the CRISPR-Cas12a system to design an ultrasensitive strategy for visual nucleic acid testing. RPA is utilized to amplify the target nucleic acid, producing amplicons that activate the single-stranded DNase property of CRISPR-Cas12a. The activated CRISPR-Cas12a then degrades the single-stranded DNA on magnetic nanoparticles (MNPs), releasing immobilized GOx from the MNPs which catalyses the chromogenic substrate. The developed method exhibits remarkable sensitivity, successfully detecting as low as 10 aM (∼6 copies per μL) of the target nucleic acid by visual colour changes in solution. The instrumental limit of detection is calculated to be 2.86 aM (∼2 copies per μL), comparable to the sensitivity of polymerase chain reaction (PCR). Importantly, this approach only requires isothermal incubation operation and does not involve costly instruments. The method has been validated by visually detecting the SARS-CoV-2 RNA gene fragment within 50 minutes. With its ultrasensitivity, simplicity of operation, and potential for integration into a point-of-care detection kit, this strategy holds great promise for nucleic acid testing in various settings.

Feasibility of wearable sensor signals and self-reported symptoms to prompt at-home testing for acute respiratory viruses in the USA (DETECT-AHEAD): a decentralised, randomised controlled trial

BACKGROUND

Early identification of an acute respiratory infection is important for reducing transmission and enabling earlier therapeutic intervention. We aimed to prospectively evaluate the feasibility of home-based diagnostic self-testing of viral pathogens in individuals prompted to do so on the basis of self-reported symptoms or individual changes in physiological parameters detected via a wearable sensor.

METHODS

DETECT-AHEAD was a prospective, decentralised, randomised controlled trial carried out in a subpopulation of an existing cohort (DETECT) of individuals enrolled in a digital-only observational study in the USA. Participants aged 18 years or older were randomly assigned (1:1:1) with a block randomisation scheme stratified by under-represented in biomedical research status. All participants were offered a wearable sensor (Fitbit Sense smartwatch). Participants in groups 1 and 2 received an at-home self-test kit (Alveo be.well) for two acute respiratory viral pathogens: SARS-CoV-2 and respiratory syncytial virus. Participants in group 1 could be alerted through the DETECT study app to take the at-home test on the basis of changes in their physiological data (as detected by our algorithm) or due to self-reported symptoms; those in group 2 were prompted via the app to self-test only due to symptoms. Group 3 served as the control group, without alerts or home testing capability. The primary endpoints, assessed on an intention-to-treat basis, were the number of acute respiratory infections presented (self-reported) and diagnosed (electronic health record), and the number of participants using at-home testing in groups 1 and 2. This trial is registered with ClinicalTrials.gov, NCT04336020.

FINDINGS

Between Sept 28 and Dec 30, 2021, 450 participants were recruited and randomly assigned to group 1 (n=149), group 2 (n=151), or group 3 (n=150). 179 (40%) participants were male, 264 (59%) were female, and seven (2%) identified as other. 232 (52%) were from populations historically under-represented in biomedical research. 118 (39%) of the 300 participants in groups 1 and 2 were prompted to self-test, with 61 (52%) successfully completing self-testing. Participants were prompted to home-test more frequently due to symptoms (41 [28%] in group 1 and 51 [34%] in group 2) than due to detected physiological changes (26 [17%] in group 1). Significantly more participants in group 1 received alerts to test than did those in group 2 (67 [45%] vs 51 [34%]; p=0·047). Of the 61 individuals who were prompted to test and successfully did so, 19 (31%) tested positive for a viral pathogen-all for SARS-CoV-2. The individuals diagnosed as positive for SARS-CoV-2 in the electronic health record were eight (5%) in group 1, four (3%) in group 2, and two (1%) in group 3, but it was difficult to confirm if they were tied to symptomatic episodes documented in the trial. There were no adverse events.

INTERPRETATION

In this direct-to-participant trial, we showed early feasibility of a decentralised programme to prompt individuals to use a viral pathogen diagnostic test based on symptoms tracked in the study app or physiological changes detected using a wearable sensor. Barriers to adequate participation and performance were also identified, which would need to be addressed before large-scale implementation.

FUNDING

Janssen Pharmaceuticals.

Colorimetric sensing for translational applications: from colorants to mechanisms

Colorimetric sensing offers instant reporting via visible signals. Versus labor-intensive and instrument-dependent detection methods, colorimetric sensors present advantages including short acquisition time, high throughput screening, low cost, portability, and a user-friendly approach. These advantages have driven substantial growth in colorimetric sensors, particularly in point-of-care (POC) diagnostics. Rapid progress in nanotechnology, materials science, microfluidics technology, biomarker discovery, digital technology, and signal pattern analysis has led to a variety of colorimetric reagents and detection mechanisms, which are fundamental to advance colorimetric sensing applications. This review first summarizes the basic components (e.g., color reagents, recognition interactions, and sampling procedures) in the design of a colorimetric sensing system. It then presents the rationale design and typical examples of POC devices, e.g., lateral flow devices, microfluidic paper-based analytical devices, and wearable sensing devices. Two highlighted colorimetric formats are discussed: combinational and activatable systems based on the sensor-array and lock-and-key mechanisms, respectively. Case discussions in colorimetric assays are organized by the analyte identities. Finally, the review presents challenges and perspectives for the design and development of colorimetric detection schemes as well as applications. The goal of this review is to provide a foundational resource for developing colorimetric systems and underscoring the colorants and mechanisms that facilitate the continuing evolution of POC sensors.

When False-Positives Arise: Troubleshooting a SARS-Coronavirus-2 (SARS-CoV-2) Detection Assay on a Semi-Automated Platform

BACKGROUND

During the COVID-19 pandemic, many molecular diagnostic laboratories performed high-throughput SARS-CoV-2 testing often with implementation of automated workflows. In parallel, vaccination campaigns resulted increasingly in specimens from fully vaccinated patients, with resultant clinical inquiries regarding positive results in this patient population. This prompted a quality improvement initiative to investigate the semi-automated testing workflow for false-positive results. The troubleshooting workflow is described and procedural improvements are outlined that serve as a resource for other molecular diagnostic laboratories that need to overcome testing anomalies in a semi-automated environment.

METHODS

This workflow utilized the MagMax-96 Viral RNA kit and the CDC 2019-nCoV RT-qPCR Panel on the Agilent Bravo Liquid-Handler (Bravo). Screening of the environment, personnel, and the mechanical performance of instrumentation using low Ct checkerboard challenges was executed to identify sources of cross-contamination. Evaluation of the assay and reporting design was conducted.

RESULTS

Specimen contamination was observed during the viral extraction process on the Bravo. Changes to the program reduced plate contamination by 50% and importantly revealed consistent hallmarks of contaminated samples. We adjusted the reporting algorithm using these indicators of false positives. False positives that were identified made up 0.11% of the 45 000+ tests conducted over the following 8 months.

CONCLUSIONS

These adjustments provided confident and quality results while maintaining turnaround time for patients and pandemic-related public health initiatives. This corrected false-positive rate is concordant with previously published studies from diagnostic laboratories utilizing automated systems and may be considered a laboratory performance standard for this type of testing.

Assessment of an in-house IgG ELISA targeting SARS-CoV-2 RBD: Applications in infected and vaccinated individuals

The study evoluated an in-house Spike Receptor Binding Domain Enzyme-Linked Immunosorbent Assay (RBD-IgG-ELISA) for detecting SARS-CoV-2 IgG antibodies in infected and vaccinated individuals. The assay demonstrated a sensitivity of 91%, specificity of 99.25%, and accuracy of 95.13%. Precision and reproducibility were highly consistent. The RBD-IgG-ELISA was able to detect 96.25% of Polymerase chain reaction (PCR) confirmed cases for SARS-CoV-2 infection, demonstrating positive and negative predictive values of 99,18% and 91,69%, respectively. In an epidemiological survey, ELISA, lateral flow immunochromatographic assay (LFIA), and electrochemiluminescence immunoassay (ECLIA) exhibited diagnostic sensitivities of 68.29%, 63.41%, and 70.73%, respectively, along with specificities of 82.93%, 80.49%, and 80.49%, respectively. Agreement between RBD-IgG-ELISA/PCR was moderate (k index 0.512). However, good agreement between different assays (RBD-IgG-ELISA/LFIA k index 0.875, RBD-IgG-ELISA/ECLIA k index 0.901). Test performance on individuals' samples were inferior due to seroconversion time and chronicity. The IgG-RBD-ELISA assay demonstrated its effectiveness in monitoring antibody levels among healthcare professionals, revealing significant differences both before and after the administration of the third vaccine dose, with heightened protection levels observed following the third dose in five Coronavirus disease (COVID-19) vaccine regimens. In conclusion, the RBD-IgG-ELISA exhibits high reproducibility, specificity, and sensitivity, making it a suitable assay validated for serosurveillance and for obtaining information about COVID-19 infections or vaccinations.

Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections

Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.

Performance of two rapid antigen tests against SARS-CoV-2 in neighborhoods of socioeconomic vulnerability from a middle-income country

BACKGROUND

As new and improved antigen-detecting rapid diagnostic tests for SARS-CoV-2 infection (Ag-RDT) continue to be developed, assessing their diagnostic performance is necessary to increase test options with accurate and rapid diagnostic capacity especially in resource-constrained settings. This study aimed to assess the performance of two Ag-RDTs in a population-based study.

METHODS

We conducted a diagnostic accuracy study in neighborhoods with high socioeconomic vulnerability in Salvador-Brazil, including individuals aged ≥12 years old who attended primary health services, between July and December 2022, with COVID-19 symptoms or who had been in contact with a confirmed case. Two Ag-RDTs were compared in parallel using reverse transcription polymerase chain reaction (RT-PCR) as reference standard, the PanbioTM COVID-19 Ag test (Abbott®) and Immuno-Rapid COVID-19 Ag (WAMA Diagnostic®). Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) were calculated.

RESULTS

For the Abbott test the sensitivity was 52.7% (95% CI: 44.3% - 61.0%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.4% (95% CI: 75.9% - 84.4%). For the WAMA test, the sensitivity was 53.4% (95% CI: 45.0% - 61.6%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.7% (95% CI: 76.2% - 84.6%). Sensitivity for the group with Cycle Threshold (CT) <24 was 82.3% (95%CI: 72.1-90.0, n = 83) for PanbioTM COVID-19 Ag test and 87.3% (95%CI: 77.9-93.8, n = 83) for Immuno-Rapid COVID-19 Ag test.

CONCLUSION

Sensitivity for both Ag-RDT was lower than reported by manufacturers. In the stratified analysis, sensitivity was higher among those with lower CT values <24. Specificity was high for both rapid antigen tests. Both Ag-RDT showed to be useful for rapid diagnostic of potential cases of COVID-19. Negative results must be assessed carefully according to clinical and epidemiological information.

An evaluation of the national testing response during the COVID-19 pandemic in England: a multistage mixed-methods study protocol

INTRODUCTION

In 2020, the UK government established a large-scale testing programme to rapidly identify individuals in England who were infected with SARS-CoV-2 and had COVID-19. This comprised part of the UK government's COVID-19 response strategy, to protect those at risk of severe COVID-19 disease and death and to reduce the burden on the health system. To assess the success of this approach, the UK Health Security Agency (UKHSA) commissioned an independent evaluation of the activities delivered by the National Health System testing programme in England. The primary purpose of this evaluation will be to capture key learnings from the roll-out of testing to different target populations via various testing services between October 2020 and March 2022 and to use these insights to formulate recommendations for future pandemic preparedness strategy. In this protocol, we detail the rationale, approach and study design.

METHODS AND ANALYSIS

The proposed study involves a stepwise mixed-methods approach, aligned with established methods for the evaluation of complex interventions in health, to retrospectively assess the combined impact of key asymptomatic and symptomatic testing services nationally. The research team will first develop a theory of change, formulated in collaboration with testing service stakeholders, to understand the causal pathways and intended and unintended outcomes of each testing service and explore contextual impacts on each testing service's intended outcomes. Insights gained will help identify indicators to evaluate how the combined aims of the testing programme were achieved, using a mixed-methods approach.

ETHICS AND DISSEMINATION

The study protocol was granted ethics approval by the UKHSA Research Ethics and Governance Group (reference NR0347). All relevant ethics guidelines will be followed throughout. Findings arising from this evaluation will be used to inform lessons learnt and recommendations for UKHSA on appropriate pandemic preparedness testing programme designs; findings will also be disseminated in peer-reviewed journals, a publicly available report to be published online and at academic conferences. The final report of findings from the evaluation will be used as part of a portfolio of evidence produced for the independent COVID-19 government inquiry in the UK.

TRANSPARENCY DECLARATION

The lead author (the manuscript's guarantor) affirms that the manuscript is an honest, accurate and transparent account of the study being reported; no important aspects of the study have been omitted, and any discrepancies from the study as planned have been explained.

Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era

BACKGROUND

The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting.

METHODS

Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2.

RESULTS

The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022.

CONCLUSION

The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.

A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva

The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.

Evaluations of modes of pooling specimens for COVID-19 screened by quantitative PCR and droplet digital PCR

Though pooling samples for SARS-CoV-2 detection has effectively met the need for rapid diagnostic and screening tests, many factors can influence the sensitivity of a pooled test. In this study, we conducted a simulation experiment to evaluate modes of pooling specimens and aimed at formulating an optimal pooling strategy. We focussed on the type of swab, their solvent adsorption ability, pool size, pooling volume, and different factors affecting the quality of preserving RNA by different virus solutions. Both quantitative PCR and digital PCR were used to evaluate the sampling performance. In addition, we determined the detection limit by sampling which is simulated from the virus of different titers and evaluated the effect of sample-storage conditions by determining the viral load after storage. We found that flocked swabs were better than fibre swabs. The RNA-preserving ability of the non-inactivating virus solution was slightly better than that of the inactivating virus solution. The optimal pooling strategy was a pool size of 10 samples in a total volume of 9 mL. Storing the collected samples at 4 °C or 25 °C for up to 48 h had little effect on the detection sensitivity. Further, we observed that our optimal pooling strategy performed equally well as the single-tube test did. In clinical applications, we recommend adopting this pooling strategy for low-risk populations to improve screening efficiency and shape future strategies for detecting and managing other respiratory pathogens, thus contributing to preparedness for future public health challenges.

Two-Step Conversion of Metal and Metal Oxide Precursor Films to 2D Transition Metal Dichalcogenides and Heterostructures

The widely studied class of two-dimensional (2D) materials known as transition metal dichalcogenides (TMDs) are now well-poised to be employed in real-world applications ranging from electronic logic and memory devices to gas and biological sensors. Several scalable thin film synthesis techniques have demonstrated nanoscale control of TMD material thickness, morphology, structure, and chemistry and correlated these properties with high-performing, application-specific device metrics. In this review, the particularly versatile two-step conversion (2SC) method of TMD film synthesis is highlighted. The 2SC technique relies on deposition of a solid metal or metal oxide precursor material, followed by a reaction with a chalcogen vapor at an elevated temperature, converting the precursor film to a crystalline TMD. Herein, the variables at each step of the 2SC process including the impact of the precursor film material and deposition technique, the influence of gas composition and temperature during conversion, as well as other factors controlling high-quality 2D TMD synthesis are considered. The specific advantages of the 2SC approach including deposition on diverse substrates, low-temperature processing, orientation control, and heterostructure synthesis, among others, are featured. Finally, emergent opportunities that take advantage of the 2SC approach are discussed to include next-generation electronics, sensing, and optoelectronic devices, as well as catalysis for energy-related applications.

Socioeconomic and Demographic Effects on SARS-CoV-2 Testing: Evidence From the State of Uttar Pradesh, India

Background The rapid global spread of SARS-CoV-2 highlighted critical challenges in healthcare systems worldwide, with differences in testing access and utilization becoming particularly evident. This study investigates the socioeconomic and demographic factors influencing SARS-CoV-2 testing service access and utilization during the second wave of the pandemic in Uttar Pradesh (UP), India. Methods The study was conducted from July to October 2023 in two districts of Uttar Pradesh (UP). These districts were chosen because one had the highest and the other the lowest SARS-CoV-2 testing rates per million population as reported from March to June 2021. The study population included consenting adult individuals with self-reported symptoms indicative of SARS-CoV-2 infection during March-June 2021. The study excluded individuals under 18 years, those who did not consent, pregnant or lactating mothers, and those with communication-impairing medical conditions. Data were collected using a structured questionnaire based on Andersen's Behavioural Model of Health Services Use. We used chi-squared tests for all categorical variables to obtain p-values and Poisson regression to identify factors influencing testing rates. Results We screened 4,595 individuals and identified 675 eligible participants for this study. Adjusted prevalence ratios derived from multiple variate Poisson regression models showed that participants in Sitapur had a 0.47 (95% CI: 0.39-0.57) times the prevalence of being tested than those in Lucknow. Furthermore, individuals from other backward castes and scheduled castes had a 1.15 (95% CI: 0.99-1.34) and 1.22 (95% CI: 0.95-1.56) times prevalence of being tested for SARS-CoV-2, respectively, when compared to the general caste population. Scheduled Tribes showed a higher prevalence of being tested, contrasting with existing literature. Households with low, middle, and high income showed a 1.46 (95% CI: 1.12-1.89), 1.52 (95% CI: 1.14-2.02), and 1.73 (95% CI: 1.23-2.45) times the prevalence of SARS-CoV-2 testing compared to those below the poverty line, respectively. Behavioral factors such as media use showed an inverse relationship with testing prevalence; individuals who did not watch TV at all had a 0.83 (95% CI: 0.70-0.99) times prevalence of being tested compared to frequent viewers, and similarly, those not using the internet on mobiles had a 0.82 (95% CI: 0.67-0.99) times prevalence than daily users. Individuals using private healthcare facilities had a 0.87 (95% CI: 0.77-0.99) times prevalence of SARS-CoV-2 testing compared to those using government facilities. Conclusions These findings highlight the importance of public health strategies that address socio-economic and behavioral disparities to ensure equitable testing access across all community groups.

Adjusting Incidence Estimates with Laboratory Test Performances: A Pragmatic Maximum Likelihood Estimation-Based Approach

Understanding the incidence of disease is often crucial for public policy decision-making, as observed during the COVID-19 pandemic. Estimating incidence is challenging, however, when the definition of incidence relies on tests that imperfectly measure disease, as in the case when assays with variable performance are used to detect the SARS-CoV-2 virus. To our knowledge, there are no pragmatic methods to address the bias introduced by the performance of labs in testing for the virus. In the setting of a longitudinal study, we developed a maximum likelihood estimation-based approach to estimate laboratory performance-adjusted incidence using the expectation-maximization algorithm. We constructed confidence intervals (CIs) using both bootstrapped-based and large-sample interval estimator approaches. We evaluated our methods through extensive simulation and applied them to a real-world study (TrackCOVID), where the primary goal was to determine the incidence of and risk factors for SARS-CoV-2 infection in the San Francisco Bay Area from July 2020 to March 2021. Our simulations demonstrated that our method converged rapidly with accurate estimates under a variety of scenarios. Bootstrapped-based CIs were comparable to the large-sample estimator CIs with a reasonable number of incident cases, shown via a simulation scenario based on the real TrackCOVID study. In more extreme simulated scenarios, the coverage of large-sample interval estimation outperformed the bootstrapped-based approach. Results from the application to the TrackCOVID study suggested that assuming perfect laboratory test performance can lead to an inaccurate inference of the incidence. Our flexible, pragmatic method can be extended to a variety of disease and study settings.

Multicolor-Assay-on-a-Chip Processed by Robotic Operation (MACpro) with Improved Diagnostic Accuracy for Field-Deployable Detection

The ability to deploy decentralized laboratories with autonomous and reliable disease diagnosis holds the potential to deliver accessible healthcare services for public safety. While microfluidic technologies provide precise manipulation of small fluid volumes with improved assay performance, their limited automation and versatility confine them to laboratories. Herein, we report the utility of multicolor assay-on-a-chip processed by robotic operation (MACpro), to address this unmet need. The MACpro platform comprises a robot-microfluidic interface and an eye-in-hand module that provides flexible yet stable actions to execute tasks in a programmable manner, such as the precise manipulation of the microfluidic chip along with different paths. Notably, MACpro shows improved detection performance by integrating the microbead-based antibody immobilization with enhanced target recognition and multicolor sensing via Cu2+-catalyzed plasmonic etching of gold nanorods for rapid and sensitive analyte quantification. Using interferon-gamma as an example, we demonstrate that MACpro completes a sample-to-answer immunoassay within 30 min and achieves a 10-fold broader dynamic range and a 10-fold lower detection limit compared to standard enzyme-linked immunosorbent assays (0.66 vs 5.2 pg/mL). MACpro extends the applications beyond traditional laboratories and presents an automated solution to expand diagnostic capacity in diverse settings.

Special Issue "Molecular and Genetic Aspects of SARS-CoV-2 Infection and COVID-19 Disease"

We are pleased to present the first and second editions of this Special Issue, titled "Molecular and Genetic Aspects of SARS-CoV-2 Infection and COVID-19 Disease", of the International Journal of Molecular Sciences [...].

A retrospective study suggests 55 days of persistence of SARS-CoV-2 during the first wave of the pandemic in Santiago de Chile

Background

As the COVID-19 pandemic persists, infections continue to surge globally. Presently, the most effective strategies to curb the disease and prevent outbreaks involve fostering immunity, promptly identifying positive cases, and ensuring their timely isolation. Notably, there are instances where the SARS-CoV-2 virus remains infectious even after patients have completed their quarantine.

Objective

Understanding viral persistence post-quarantine is crucial as it could account for localized infection outbreaks. Therefore, studying and documenting such instances is vital for shaping future public health policies.

Design

This study delves into a unique case of SARS-CoV-2 persistence in a 60-year-old female healthcare worker with a medical history of hypertension and hypothyroidism. The research spans 55 days, marking the duration between her initial and subsequent diagnosis during Chile's first COVID-19 wave, with the analysis conducted using RT-qPCR.

Results

Genomic sequencing-based phylogenetic analysis revealed that the SARS-CoV-2 detected in both Nasopharyngeal swab samples (NPSs) was consistent with the 20B clade of the Nextstrain classification, even after a 55-day interval.

Conclusion

This research underscores the need for heightened vigilance concerning cases of viral persistence. Such instances, albeit rare, might be pivotal in understanding sporadic infection outbreaks that occur post-quarantine.

Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance

Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.