Evaluating the effectiveness of lockdowns and restrictions during SARS-CoV-2 variant waves in the Canadian province of Nova Scotia.

Introduction: After the initial onset of the SARS-CoV-2 pandemic, the government of Canada and provincial health authorities imposed restrictive policies to limit virus transmission and mitigate disease burden. In this study, the pandemic implications in the Canadian province of Nova Scotia (NS) were evaluated as a function of the movement of people and governmental restrictions during successive SARS-CoV-2 variant waves (i.e., Alpha through Omicron). Methods: Publicly available data obtained from community mobility reports (Google), the Bank of Canada Stringency Index, the "COVID-19 Tracker" service, including cases, hospitalizations, deaths, and vaccines, population mobility trends, and governmental response data were used to relate the effectiveness of policies in controlling movement and containing multiple waves of SARS-CoV-2. Results: Our results indicate that the SARS-CoV-2 pandemic inflicted low burden in NS in the initial 2 years of the pandemic. In this period, we identified reduced mobility patterns in the population. We also observed a negative correlation between public transport (-0.78), workplace (-0.69), retail and recreation (-0.68) and governmental restrictions, indicating a tight governmental control of these movement patterns. During the initial 2 years, governmental restrictions were high and the movement of people low, characterizing a 'seek-and-destroy' approach. Following this phase, the highly transmissible Omicron (B.1.1.529) variant began circulating in NS at the end of the second year, leading to increased cases, hospitalizations, and deaths. During this Omicron period, unsustainable governmental restrictions and waning public adherence led to increased population mobility, despite increased transmissibility (26.41-fold increase) and lethality (9.62-fold increase) of the novel variant. Discussion: These findings suggest that the low initial burden caused by the SARS-CoV-2 pandemic was likely a result of enhanced restrictions to contain the movement of people and consequently, the spread of the disease. Easing public health restrictions (as measured by a decline in the BOC index) during periods of high transmissibility of circulating COVID-19 variants contributed to community spread, despite high levels of immunization in NS.

Simultaneous detection of SARS-CoV-2, influenza A, respiratory syncytial virus, and measles in wastewater by multiplex RT-qPCR.

A multiplex quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based method was designed for the simultaneous detection of influenza A, SARS-CoV-2, respiratory syncytial virus, and measles virus. The performance of the multiplex assay was compared to four monoplex assays for relative quantification using standard quantification curves. Results showed that the multiplex assay had comparable linearity and analytical sensitivity to the monoplex assays, and the quantification parameters of both assays demonstrated minimal differences. Viral reporting recommendations for the multiplex method were estimated based on the corresponding limit of quantification (LOQ) and the limit of detection at 95 % confidence interval (LOD) values for each viral target. The LOQ was determined by the lowest nominal RNA concentrations where %CV values were ≤35 %. Corresponding LOD values for each viral target were between 15 and 25 gene copies per reaction (GC/rxn), and LOQ values were within 10 to 15 GC/rxn. The detection performance of a new multiplex assay was validated in the field by collecting composite wastewater samples from a local treatment facility and passive samples from three sewer shed locations. Results indicated that the assay could accurately estimate viral loads from various sample types, with samples collected from passive samplers showing a greater range of detectable viral concentrations than composite wastewater samples. This suggests that the sensitivity of the multiplex method may be improved when paired with more sensitive sampling methods. Laboratory and field results demonstrate the robustness and sensitivity of the multiplex assay and its applicability to detect the relative abundance of four viral targets among wastewater samples. Conventional monoplex RT-qPCR assays are suitable for diagnosing viral infections. However, multiplex analysis using wastewater provides a fast and cost-effective way to monitor viral diseases in a population or environment.

The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

Comparison between Nasal and Nasopharyngeal Swabs for SARS-CoV-2 Rapid Antigen Detection in an Asymptomatic Population, and Direct Confirmation by RT-PCR from the Residual Buffer.

Containment measures employed during the COVID-19 pandemic included prompt recognition of cases, isolation, and contact tracing. Bilateral nasal (NA) swabs applied to a commercial antigen-based rapid diagnostic test (Ag-RDT) offer a simpler and more comfortable alternative to nasopharyngeal (NP) collection; however, little is known about the sensitivity of this method in an asymptomatic population. Participants in community-based asymptomatic testing sites were screened for SARS-CoV-2 using an Ag-RDT with NP sampling. Positive individuals returned for confirmatory molecular testing and consented to repeating the Ag-RDT using a bilateral NA swab for comparison. Residual test buffer (RTB) from Ag-RDTs was subjected to real-time reverse transcription-PCR (RT-PCR). Of 123,617 asymptomatic individuals, 197 NP Ag-RDT-positive participants were included, with 175 confirmed positive by RT-PCR. Of these cases, 154 were identified from the NA swab collection with Ag-RDT, with a sensitivity of 88.0% compared to the NP swab collection. Stratifying results by RT-PCR cycle threshold demonstrated that sensitivity of the nasal collection method varied based on the cycle threshold (CT) value of the paired RT-PCR sample. RT-PCR testing on the RTB from the Ag-RDT using NP and NA swab collections resulted in 100.0% and 98.7% sensitivity, respectively. NA swabs provide an adequate alternative to NP swab collection for use with Ag-RDT, with the recognition that the test is most sensitive in specimens with high viral loads. With the high sensitivity of RT-PCR testing on RTB from Ag-RDT, a more streamlined approach to confirmatory testing is possible without recollection or use of paired collections strategies. IMPORTANCE Nasal swabbing for SARS-CoV-2 (COVID-19) comes with many benefits but is slightly less sensitive than traditional nasopharyngeal swabbing; however, confirmatory lab-based testing could be performed directly from the residual buffer from either sample type.

Factors contributing to a coronavirus disease 2019 (COVID-19) outbreak on a mixed medical-surgical unit in a Canadian acute-care hospital.

Objective: To identify preventable factors that contribute to the cross transmission of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) to patients in healthcare facilities. Design: A case-control study was conducted among inpatients on a coronavirus disease 2019 (COVID-19) outbreak unit. Setting: This study was conducted in a medical-surgical unit of a tertiary-care hospital in Nova Scotia in May 2021. Patients: Patients hospitalized on the unit for at least 12 hours and healthcare workers (HCW) working on the unit within 2 weeks of outbreak declaration were included. Methods: Risk factors for SARS-CoV-2 infection were analyzed using simple and multiple logistic regression. Whole-genome sequencing (WGS) was performed to identify SARS-CoV-2 strain relatedness. Network analysis was used to describe patient accommodation. Results: SARS-CoV-2 infections were identified in 21 patients (29.6%) and 11 HCWs (6.6%). WGS data revealed 4 distinct clades of related sequences. Several factors likely contributed to the outbreak, including failure to identify SARS-CoV-2, a largely incomplete or unvaccinated population, and patient wandering behaviors. The most significant risk factor for SARS-CoV-2 infection was room sharing with an infectious patient, which was the only factor that remained statistically significant following multivariate analysis (odds ratio [OR], 9.2l; 95% confidence interval [CI], 2.04-41.67; P = .004). Conclusions: This outbreak likely resulted from admission of 2 patients with COVID-19, with subsequent transmissions to 17 patients and 11 staff. WGS and bioinformatics analyses were critical to identifying previously unrecognized nosocomial transmissions of SARS-CoV-2. This study supports strategies to reduce nosocomial transmissions of SARS-CoV-2, such as single-patient rooms, promotion of COVID-19 vaccination, and infection prevention and control measures including management of wandering behaviors.

Avoiding False-Positive SARS-CoV-2 Rapid Antigen Test Results with Point-of-Care Molecular Testing on Residual Test Buffer.

Antigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the coronavirus disease 2019 (COVID-19) pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend confirmation of positive Ag-RDT results with a nucleic acid amplification test (NAAT). This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular NAAT for SARS-CoV-2 detection (i.e., ID NOW), which was performed on-site at a volunteer-led asymptomatic community testing site on the residual test buffer (RTB) from positive Ag-RDTs. The ID NOW NAAT assay was performed on RTB from two Ag-RDTs: the Abbott Panbio and BTNX Rapid Response assays. Results of ID NOW were compared to real-time RT-PCR at a reference laboratory. Along with investigations into the clinical performance of ID NOW on RTB, analytical specificity was assessed with a panel of various respiratory organisms. Of the Ag-RDTs results evaluated, all 354 Ag-RDTs results characterized as true positives by RT-PCR were accurately identified with ID NOW testing of RTB. No SARS-CoV-2 detections by ID NOW were observed from 10 specimens characterized as false-positive Ag-RDTs, or from contrived specimens with various respiratory organisms. The use of on-site molecular testing on RTB provides a suitable option for rapid confirmatory testing of positive Ag-RDTs, thereby obviating the need for specimen recollection for molecular testing at local reference laboratories. IMPORTANCE During the COVID-19 pandemic, rapid antigen tests have been widely used for the detection of SARS-CoV-2. These simple devices allow rapid test results. However, false-positive results may occur. As such, individuals with positive rapid tests often must return to testing centers to have a second swab collected, which is then transported to a specialized laboratory for confirmation using molecular tests. As an alternative to requiring a repeat visit and a prolonged turn-around time for result confirmation, this project evaluated whether the leftover material from rapid antigen tests could be confirmed directly on a portable point-of-care molecular instrument. Using this approach, molecular confirmation of positive antigen tests could be performed in less than 15 min, and the results were equivalent to laboratory-based confirmation. This procedure eliminates the need for individuals to return to testing centers following a positive rapid antigen test and ensures accurate antigen test results through on-site confirmation.

Investigating the Sensitivity of Nasal or Throat Swabs: Combination of Both Swabs Increases the Sensitivity of SARS-CoV-2 Rapid Antigen Tests.

The COVID-19 pandemic has been hallmarked by several waves of variants of concern (VoCs), each with novel challenges. Currently, the highly transmissible Omicron VoC is predominant worldwide, and sore throat is common, among other cold-like symptoms. Anecdotes on social media have suggested that sampling one's throat can increase the sensitivity for Omicron detection by antigen-based rapid testing devices (Ag-RDTs). This work aimed to improve the local testing strategy and determine whether the sensitivity of Ag-RDTs designed for nasal sampling is altered with the use of self-administered throat swabs in self-perceived asymptomatic individuals. This investigation used a common Ag-RDT (i.e., Abbott Panbio COVID-19 Ag rapid test device) to compare three sampling sites: nasal swab, throat swab, and combined nasal/throat. All Ag-RDT results were confirmed with molecular testing from residual test buffer. Compared to reverse transcriptase PCR (RT-PCR), samples from nasal or throat swabs each detected 64.5% of SARS-CoV-2 cases; however, combining the contributions of each swab increased the positive percent agreement (PPA) with RT-PCR to 88.7%. This trend was also evident with the Rapid Response Ag-RDT (BTNX), which uses more flexible swabs than does the Panbio. When nasal swab collection was compared to paired sampling of the nose/throat using a single swab with the Panbio Ag-RDT, the PPAs were 68.4% and 81.6%, respectively. No false-positive results were observed with nasal, throat, or combined nasal/throat sampling. Self-administered throat and nasal/throat swabs both had >90% acceptability. These findings support the use of self-collected combined nasal/throat sampling for Ag-RDT-based SARS-CoV-2 detection in self-perceived asymptomatic individuals. IMPORTANCE This quality project demonstrates that combining the results of nasal and throat swabs or using a combined single swab of the throat and nares resulted in increased detection of SARS-CoV-2 using a rapid antigen test, in an asymptomatic population. Importantly, no false positives were detected, and over 90% of people were willing to perform the combination swab. These types of projects are instrumental in informing local practices to improve testing strategies. These data support the option of using a combined nasal/throat swab in our local setting to enhance the detection of Omicron.

Combined oropharyngeal/nares and nasopharyngeal swab sampling remain effective for molecular detection of SARS-CoV-2 Omicron variant.

The world has experienced several waves of SARS-CoV-2 variants of concern (VoCs) throughout the COVID-19 pandemic since the first cases in December 2019. The Omicron VoC has increased transmission, compared to its predecessors, and can present with sore throat and other cold-like symptoms. Given the predominance of throat symptoms, and previous work demonstrating better sensitivity using antigen-based rapid detection tests when a throat swab is included in the standard nasal sampling, this quality improvement project sought to ensure ongoing suitability of both combined oropharyngeal/nares (OPN) and nasopharyngeal (NP) swab sampling used throughout the pandemic. Consenting participants meeting Public Health testing criteria (mostly symptomatic or a close contact of a known case) were enrolled, and paired NP and OPN swabs were subjected to nucleic acid amplification testing (NAAT). Comparing paired specimens from 392 participants sensitivity of NP swabs was 89.1 % (95 % CI, 78.8-94.9), and that of OPN was 98.4 % (95 % CI: 90.9->99.9) (P-value 0.052). This project demonstrated that both NP and combined OPN swabs detected the Omicron variant with similar sensitivity by NAAT, supporting the continued use of either swab collection for SARS-CoV-2 molecular detection.

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

Generation of False-Positive SARS-CoV-2 Antigen Results with Testing Conditions outside Manufacturer Recommendations: A Scientific Approach to Pandemic Misinformation.

Antigen-based rapid diagnostics tests (Ag-RDTs) are useful tools for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, misleading demonstrations of the Abbott Panbio coronavirus disease 2019 (COVID-19) Ag-RDT on social media claimed that SARS-CoV-2 antigen could be detected in municipal water and food products. To offer a scientific rebuttal to pandemic misinformation and disinformation, this study explored the impact of using the Panbio SARS-CoV-2 assay with conditions falling outside manufacturer recommendations. Using Panbio, various water and food products, laboratory buffers, and SARS-CoV-2-negative clinical specimens were tested with and without manufacturer buffer. Additional experiments were conducted to assess the role of each Panbio buffer component (tricine, NaCl, pH, and Tween 20) as well as the impact of temperature (4°C, 20°C, and 45°C) and humidity (90%) on assay performance. Direct sample testing (without the kit buffer) resulted in false-positive signals resembling those obtained with SARS-CoV-2 positive controls tested under proper conditions. The likely explanation of these artifacts is nonspecific interactions between the SARS-CoV-2-specific conjugated and capture antibodies, as proteinase K treatment abrogated this phenomenon, and thermal shift assays showed pH-induced conformational changes under conditions promoting artifact formation. Omitting, altering, and reverse engineering the kit buffer all supported the importance of maintaining buffering capacity, ionic strength, and pH for accurate kit function. Interestingly, the Panbio assay could tolerate some extremes of temperature and humidity outside manufacturer claims. Our data support strict adherence to manufacturer instructions to avoid false-positive SARS-CoV-2 Ag-RDT reactions, otherwise resulting in anxiety, overuse of public health resources, and dissemination of misinformation. IMPORTANCE With the Panbio severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen test being deployed in over 120 countries worldwide, understanding conditions required for its ideal performance is critical. Recently on social media, this kit was shown to generate false positives when manufacturer recommendations were not followed. While erroneous results from improper use of a test may not be surprising to some health care professionals, understanding why false positives occur can help reduce the propagation of misinformation and provide a scientific rebuttal for these aberrant findings. This study demonstrated that the kit buffer's pH, ionic strength, and buffering capacity were critical components to ensure proper kit function and avoid generation of false-positive results. Typically, false positives arise from cross-reacting or interfering substances; however, this study demonstrated a mechanism where false positives were generated under conditions favoring nonspecific interactions between the two antibodies designed for SARS-CoV-2 antigen detection. Following the manufacturer instructions is critical for accurate test results.

Reliable detection of SARS-CoV-2 with patient-collected swabs and saline gargles: A three-headed comparison on multiple molecular platforms.

With increasing demands for SARS-CoV-2 testing, as well as the shortages for testing supplies, collection devices, and trained healthcare workers (HCWs) to collect specimens, self-collection is an attractive prospect to reduce the need for HCWs and expenditure of personal protective equipment. Apart from the traditional nasopharyngeal swab used for SARS-CoV-2 detection, alternative specimens have been validated such as a combined swabs of the oropharynx and anterior nares (OP/N), or throat samples using saline gargles. Both the alternative specimen types are amenable to self-collection. Objectives. This study aimed to compare the sensitivity of HCW-collected (OP/N) swabs, self-collected OP/N swabs, and self-collected saline gargles. Among 38 individuals previously testing positive for SARS-CoV-2 (or their close contacts), two self-collected specimen types (OP/N and saline gargles) were compared to HCW-collected OP/N swabs. SARS-CoV-2 testing was performed on three molecular assays: a laboratory-developed test (LDT), and two commercial assays on automated platforms: Cobas 6800 (Roche Diagnostics) and Panther (Hologic). The sensitivity of self-collected OP/N swabs was equivalent to healthcare worker (HCW)-collected OP/N swabs at 100.0 % [92.6%-100.0%] for all three molecular tests. The sensitivity of saline gargles was not significantly different than HCW-collected OP/N swabs, but varied slightly between instruments at 93.8 % [85.9%-93.8%] for the LDT, 96.8 % [88.6%-96.8%] for the Cobas assay, and 96.7 % [89.2%-96.9%] for the Panther assay. Overall, self-collection using OP/N swabs or saline gargles are reasonable alternatives to HCW-based collections for SARS-CoV-2 detection, and could facilitate broader surveillance strategies.

Exploring alternative swabs for use in SARS-CoV-2 detection from the oropharynx and anterior nares.

The COVID-19 pandemic has led to a worldwide shortage of nasopharyngeal swabs and universal transport media. This study evaluated a combined oropharynx/nares (OP/Na) sample collection using two readily-available non-flocked swabs, transported in phosphate-buffered saline, and demonstrates equivalent performance in SARS-CoV-2 detection compared to a previously-validated OP/Na collection kit.

A combined oropharyngeal/nares swab is a suitable alternative to nasopharyngeal swabs for the detection of SARS-CoV-2.

Given the global shortage of nasopharyngeal (NP) swabs typically used for respiratory virus detection, alternative collection methods were evaluated during the COVID-19 pandemic. This study showed that a combined oropharyngeal/nares swab is a suitable alternative to NP swabs for the detection of SARS-CoV-2, with sensitivities of 91.7% and 94.4%, respectively.

Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories.

With emergence of pandemic COVID-19, rapid and accurate diagnostic testing is essential. This study compared laboratory-developed tests (LDTs) used for the detection of SARS-CoV-2 in Canadian hospital and public health laboratories, and some commercially available real-time RT-PCR assays. Overall, analytical sensitivities were equivalent between LDTs and most commercially available methods.