Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study.

In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.

Prostate-specific antigen testing patterns and prostate cancer stage at diagnosis in older Ohio cancer patients.

BACKGROUND: Prostate cancer (PCa) screening recommendations do not support prostate-specific antigen (PSA) screening for older men. Such screening often occurs, however. It is, therefore, important to understand how frequently and among which subgroups screening occurs, and the extent of distant stage PCa diagnoses among screened older men. METHODS: Using the 2014-2016 linked Ohio Cancer Incidence Surveillance System (OCISS) and Medicare administrative database, we identified men 68 and older diagnosed with PCa and categorized their PSA testing in the three years preceding diagnosis as screening or diagnostic. We conducted multivariable logistic regression analysis to identify correlates of screening PSA and to determine whether screening PSA is independently associated with distant stage disease. RESULTS: Our study population included 3034 patients (median age: 73 years). 62.1% of PCa patients underwent at least one screening-based PSA in the three years preceding diagnosis. Older age (75-84 years: aOR [95% CI]: 0.84 [0.71, 0.99], ≥ 85: aOR: 0.27 [0.19, 0.38]), and frailty (aOR: 0.51 [0.37, 0.71]) were associated with lower screening. Screening was associated with decreased odds of distant stage disease (aOR: 0.55 [0.42, 0.71]). However, older age (75-84 years: aOR: 2.43 [1.82, 3.25], ≥ 85: aOR: 10.57 [7.05, 15.85]), frailty (aOR: 5.00 [2.78, 9.31]), and being separated or divorced (aOR: 1.64 [1.01, 2.60]) were associated with increased distant stage PCa. CONCLUSION: PSA screening in older men is common, though providers appear to curtail PSA screening as age and frailty increase. Screened older men are diagnosed at earlier stages, but the harms of screening cannot be assessed.

Implementation and Performance of a Point-of-Care COVID-19 Test Program in 4000 California Schools.

OBJECTIVE: To evaluate the feasibility and accuracy of an unprecedented COVID-19 antigen testing program in schools, which required a healthcare provider order, laboratory director, a Clinical Laboratory Improvement Amendments certificate of waiver, as well as training of school personnel. STUDY DESIGN: Descriptive report of a point-of-care, school-based antigen testing program in California from August 1st, 2021 through May 30, 2022, in which participants grades K-12 self-swabbed and school personnel performed testing. Participants included 944 009 students, personnel, and community members from 4022 California kindergarten through high schools. Outcomes measured include sensitivity and specificity (with polymerase chain reaction [PCR] as comparator) of the Abbott BinaxNOW antigen test, number of tests performed, and active infections identified. RESULTS: Of 102 022 paired PCR/antigen tests, the overall sensitivity and specificity for the antigen test was 81.2% (95% CI: 80.5%-81.8%) and 99.6% (95% CI: 99.5%-99.6%), respectively, using cycle threshold values <30. During January through March 2022, the highest prevalence period, the positive predictive value of antigen testing was 94.7% and the negative predictive value was 94.2%. Overall, 4022 school sites were enrolled and 3 987 840 million antigen tests were performed on 944 009 individuals. A total of 162 927 positive antigen tests were reported in 135 163 individuals (14.3% of persons tested). CONCLUSIONS: Rapidly implementing a school-based testing program in thousands of schools is feasible. Self-swabbing and testing by school personnel can yield accurate results. On-site COVID-19 testing is no longer necessary in schools, but this model provides a framework for future infectious disease threats.

The use of intracellular dyes to create a multiplexed flow cytometry-based red blood cell phenotyping assay.

BACKGROUND AND OBJECTIVES: Flow cytometry can be used to phenotype red blood cell antigens, allowing for high-throughput testing while using low reagent volumes. This article utilizes intracellular dyes to pre-label red blood cells to further multiplex flow cytometry-based red blood cell antigen phenotyping. MATERIALS AND METHODS: Red blood cells were pre-labelled using the intracellular dyes V450 and Oregon Green. These dyes are detected fluorescently via flow cytometry. Four combinations of intracellular staining were used to allow four patient or donor red blood cells to be analysed in a single test well. Antigen phenotyping was then performed via flow cytometry using a previously described method. RESULTS: The intracellular dyes showed uniform staining when measured in mean fluorescence intensity and allowed the red blood cells to be clearly distinguished from one another. The presence or absence of red blood cell antigens was determined with 100% accuracy. CONCLUSION: The use of intracellular dyes allowed a fourfold increase in the throughput of our previously described flow cytometry-based red blood cell antigen phenotyping method. The described method allows up to 48 patients to be simultaneously phenotyped using a single 96-well microplate. Furthermore, additional fluorescent dyes could potentially increase the throughput exponentially.

A nanogap-enhanced SERS nanotag-based lateral flow assay for ultrasensitive and simultaneous monitoring of SARS-CoV-2 S and NP antigens.

A lateral flow assay (LFA) strip based on dual 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB)-encoded satellite Fe3O4@Au (Mag@Au) SERS tags with nanogap is reported for  ultrasensitive and simultaneous diagnosis of two SARS-CoV-2 functional proteins. Composed of Fe3O4 core, satellite gold shell with nanogaps, and double-layer DTNB, the Mag@Au nanoparticles with an average size of 238 nm were designed as multifunctional tags to efficiently enrich the target SARS-CoV-2 protein from complex samples, significantly enhancing the SERS signal of the LFA strip and provide quantitative SERS detection of analyte on test lines. The developed dual DTNB-encoded satellite Mag@Au-based LFA allowed simultaneous quantification of spike (S) protein and nucleocapsid (NP) protein with detection limits of 23 pg mL-1 and 2 pg mL-1, respectively, lower than commercial ELISA kits and reported SERS-LFA detection system-based Au NPs and Fe3O4@3 nm Au MNPs. This magnetic SERS-LFA also showed high performance of multi-variant strain detection and further distinguished clinical samples of Omicron variant infection, demonstrating the potential of in situ detection of respiratory virus diseases.

Assessment of DNA/RNA Defend Pro: An Inactivating Sample Collection Buffer for Enhanced Stability, Extraction-Free PCR, and Rapid Antigen Testing of Nasopharyngeal Swab Samples.

This study comprehensively evaluated the DNA/RNA Defend Pro (DRDP) sample collection buffer, designed to inactivate and stabilize patient samples. The primary objectives were to assess DRDP's efficacy in ensuring sample stability, facilitating extraction-free polymerase chain reaction (PCR), and ensuring compatibility with rapid antigen testing (RAT). Ninety-five diagnostic nasopharyngeal swab samples tested for influenza virus (influenza A), respiratory syncytial virus (RSV A), and/or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were 10-fold diluted with DRDP and anonymized. Initial characterization and retesting of these samples using cobas Liat confirmed 88 samples as positive, validating the presence of viral targets. Results from rapid antigen testing showed lower sensitivity compared to nucleic acid amplification testing (NAAT) but maintained perfect specificity, with 40 out of 88 positive samples by cobas Liat also testing positive for RAT. Direct RT-qPCR of DRDP-diluted samples demonstrated robust compatibility, with 72 out of 88 samples positive for cobas Liat also testing positive by direct RT-qPCR. Non-concordant results could be explained by the 200-fold lower input of extraction-free NAAT. Stability testing involved incubating 31 positive samples at 4 °C, 20 °C, and 37 °C for 7 days, with extraction-free NAAT. DRDP guaranteed viral RNA stability at all temperatures for influenza A, SARS-CoV-2, and RSV A, showing stability up to 7 days at 4 °C. In conclusion, DRDP is an effective stabilizing medium compatible with direct RT-qPCR and rapid antigen testing and shows great potential for optimizing diagnostic processes, particularly in resource-limited or time-sensitive scenarios.

Prospective study of three saliva qualitative antigen testing kits for the detection of SARS-CoV-2 among mainly symptomatic patients in Japan.

INTRODUCTION: Rapid qualitative antigen testing has been widely used for the laboratory diagnosis of COVID-19 with nasopharyngeal samples. Saliva samples have been used as alternative samples, but the analytical performance of those samples for qualitative antigen testing has not been sufficiently evaluated. METHODS: A prospective observational study evaluated the analytical performance of three In Vitro Diagnostics (IVD) approved COVID-19 rapid antigen detection kits for saliva between June 2022 and July 2022 in Japan using real-time reverse transcription polymerase chain reaction (RT-qPCR) as a reference. A nasopharyngeal sample and a saliva sample were simultaneously obtained, and RT-qPCR was performed. RESULTS: In total, saliva samples and nasopharyngeal samples were collected from 471 individuals (RT-qPCR-positive, n = 145) for the analysis. Of these, 96.6% were symptomatic. The median copy numbers were 1.7 × 106 copies/mL for saliva samples and 1.2 × 108 copies/mL for nasopharyngeal samples (p < 0.001). Compared with the reference, the sensitivity and specificity were 44.8% and 99.7% for ImunoAce SARS-CoV-2 Saliva, 57.2% and 99.1% for Espline SARS-CoV-2 N, and 60.0% and 99.1% for QuickChaser Auto SARS-CoV-2, respectively. The sensitivities of all antigen testing kit were 100% for saliva samples with a high viral load (>107 copies/mL), whereas the sensitivities were <70% for high-viral-load nasopharyngeal samples (>107 copies/mL). CONCLUSION: COVID-19 rapid antigen detection kits with saliva showed high specificity, but the sensitivity varied among kits, and were also insufficient for the detection of symptomatic COVID-19 patients.

A population-based study of the trend in SARS-CoV-2 diagnostic modalities from the beginning of the pandemic to the Omicron surge in Kyoto City, Kyoto, Japan.

BACKGROUND: The coronavirus disease 2019 (COVID-19) presents critical diagnostic challenges for managing the pandemic. We investigated the 30-month changes in COVID-19 testing modalities and functional testing sites from the early period of the pandemic to the most recent Omicron surge in 2022 in Kyoto City, Japan. METHODS: This is a retrospective-observational study using a local anonymized population database that included patients' demographic and clinical information, testing methods and facilities from January 2020 to June 2022, a total of 30 months. We computed the distribution of symptomatic presentation, testing methods, and testing facilities among cases. Differences over time were tested using chi-square tests of independence. RESULTS: During the study period, 133,115 confirmed COVID-19 cases were reported, of which 90.9% were symptomatic. Although nucleic acid amplification testing occupied 68.9% of all testing, the ratio of lateral flow devices (LFDs) rapidly increased in 2022. As the pandemic continued, the testing capability was shifted from COVID-19 designated facilities to general practitioners, who became the leading testing providers (57.3% of 99,945 tests in 2022). CONCLUSIONS: There was a dynamic shift in testing modality during the first 30 months of the pandemic in Kyoto City. General practitioners increased their role substantially as the use of LFDs spread dramatically in 2022. By comprehending and documenting the evolution of testing methods and testing locations, it is anticipated that this will contribute to the establishment of an even more efficient testing infrastructure for the next pandemic.

Equitable access to COVID-19 diagnostics: factors associated with the uptake of rapid antigen testing in Victoria, Australia, January - February 2022.

BACKGROUND: Accessible and accurate diagnostics are critical to control communicable diseases. Uptake of COVID-19 rapid antigen (RA) testing requires physical and financial access to tests, knowledge about usage, motivation, and ability to report results. We sought to understand patterns of and factors associated with RA test uptake in Victoria during a period of high caseload, RA test promotion, and difficulty accessing RA and PCR testing. We hypothesise RA test uptake is indicated by the ratio of cases diagnosed by RA test (probable) to those diagnosed using PCR (confirmed) (p:c). METHODS: Analysing case records, trends in p:c were assessed, between regions, sex, age groups, socio-economic strata and cultural diversity. Logistic regression assessed associations between case classification, and median age, postcode-level socio-economic disadvantage, and proportion overseas-born. RESULTS: We included 591,789 cases. Mean p:c was lower in socio-economically disadvantaged areas (decile 1 + 2: 0.90 vs. decile 9 + 10: 1.10), and in postcodes where the overseas-born population was above the Victorian average (0.83 vs. 1.05). Conversely, p:c was higher in younger age groups; with no difference between sexes overall. In metropolitan Melbourne, odds of RA test usage increased as socio-economic disadvantage decreased (decile 9 + 10, aOR 1.40, 95%CI 1.37-1.43, vs. decile 1 + 2; p < .001), decreased for cases from areas with a higher overseas-born population (aOR 0.85, 0.83-0.86, p < .001), and with older age. CONCLUSIONS: Reduced uptake of RA tests in Victoria is associated with socio-economic disadvantage, cultural diversity, and older age. Equitable access to COVID-19 diagnostics requires elimination of financial barriers, and greater engagement with culturally diverse and older groups. Inequitable RA test uptake may lead to case under-ascertainment, affecting resource allocation, effective control strategy development, in turn impacting COVID-19 morbidity and mortality, and could indicate relative engagement with response initiatives.

Knowledge and willingness toward SARS-CoV-2 rapid antigen testing among older adults in China: a nationwide cross-sectional study.

BACKGROUND AND AIMS: The end of the zero-COVID-19 policy placed a large number of older adults in China at increased risk of COVID-19 infection. SARS-CoV-2 rapid antigen testing (RAT) is a promising tool for scaling up testing and ensuring that patient management and public health measures can be implemented without delay. We aimed to understand the knowledge and willingness of RAT, and its correlates among older adults in China. METHODS: A nationwide cross-sectional survey on knowledge and willingness about RAT among older adults in China was conducted between January 14 and 28, 2023, shortly after the end of the zero-COVID-19 policy. An online questionnaire was used to collect information on sociodemographic characteristics, health characteristics, sources to access RAT information, and attitudes toward COVID-19 and its RAT. Logistic regression was used to assess correlates of knowledge of RAT and willingness to take RAT among older adults. RESULTS: A total of 1030 older adults (494 women and 536 men, mean age 68.7 ± 7.0 years) were recruited. 49.4% of the participants had a high level of RAT knowledge. After adjusting for sociodemographic characteristics, chronic diseases (0.70, 0.49-0.99), learning RAT from new media (5.46, 3.48-8.68) and traditional media (3.35, 2.13-5.34), and perceiving RAT as convenient (4.03, 2.80-5.85) were associated with levels of RAT knowledge. 53.3% of the participants were willing to take RAT. After adjusting for sociodemographic characteristics, learning RAT from new media (8.46, 5.26-14.0) and traditional media (1.63, 1.04-2.55), perceiving RAT as convenient (2.97, 2.10-4.22), and worrying about (re)infection with COVID-19 (2.12, 1.55-2.92) were associated with willingness to take RAT. CONCLUSION: The levels of RAT knowledge and willingness to take RAT among older adults in China may hinder the scale-up of RAT. Health education about RAT should be strengthened among older adults. Special efforts should be made to integrate traditional and new media to promote RAT among older adults, specifically, for virus susceptibility and the convenience of RAT. Given the reopening of society, our study could inform our response to future novel infectious diseases and aid in the timely scale-up of RAT.