SARS-CoV-2 testing strategies for outbreak mitigation in vaccinated populations

Vaccine apartheid: global cooperation and equity

Reovirus type 3 (Reo-3) can infect numerous rodent species and induces the clinical syndrome 'oily skin disease' in neonatal mice, and is a common contaminant of biological materials. The reverse transcriptase polymerase chain reaction (RT-PCR) assay has proven useful for the detection of Reo-3 in rodents and contaminated biological materials. Fluorogenic nuclease reverse transcriptase polymerase chain reaction assays (fnRT-PCR) combine RT-PCR with an internal fluorogenic hybridization probe, thereby potentially enhancing specificity and eliminating post-PCR processing. Therefore, an fnRT-PCR assay specific for Reo-3 was developed by targeting primer and probe sequences to a unique region of the Reo-3 M3 gene. The fnRT-PCR detected both strains of Reo-3 (Dearing and Abney), but did not detect Reovirus types 1 or 2, other viruses in the family Reoviridae, or other RNA viruses that naturally infect rodents. The fnRT-PCR detected less than 1 fg of target template and detected viral RNA in tissues obtained from mice experimentally infected with Reo-3. The assay also displayed comparable sensitivity when compared to the mouse antibody production test commonly used to detect viral contamination of biological materials. In conclusion, this fnRT-PCR assay offers a potentially high-throughput diagnostic assay for detecting Reo-3 RNA in infected mice and contaminated biological materials.

CEPI launches 100-day vaccine “moonshot”

Effective immunotherapeutic agents for use in cats are needed to aid in the management of intractable viral diseases, including feline infectious peritonitis (FIP) infection. The objectives of this study were to compare two different immune stimulants for antiviral activity in cats: (1) TLR 2/6-activating compound polyprenyl immunostimulant; (PI) and (2) liposome Toll-like receptor 3/9 agonist complexes (LTCs) to determine relative abilities to stimulate the induction of type I (IFN-α, IFN-β) and type II (IFN-γ) interferon immune responses in vitro and to study the effects of treatment on immune responses in healthy cats. Cytokine and cellular immune responses to PI and LTC were evaluated using peripheral blood mononuclear cells (PBMCs) from healthy cats incubated with LTC and PI at indicated concentrations using reverse transcriptase polymerase chain reaction assays and ELISA assays. The effects of the immune stimulants on inhibiting FIPV replication were assessed using a feline macrophage cell line (fcwf-4). Cytokine and cellular immune responses to PI and LTC were evaluated in blood samples from healthy cats treated with PI and LTC, using reverse transcriptase polymerase chain reaction (RT-PCR) and ELISA assays. In the in vitro studies, both compounds triggered the upregulated expression of IFN-α, IFN-γ, and IL-1β genes in cat PBMC, whereas treatment with LTC induced significantly greater expression of IFN-α and IFN-γ on Day 1 and IL-1b on Day 3. There was significant protection from FIPV-induced cytopathic effects when fcwf-4 cells were treated with conditioned medium from LTC-activated leukocytes. In the healthy cat study (in vivo), both PI and LTC increased the mRNA signal for IFN-α, IFN-γ, and IL-1β above baseline at multiple time points with statistically greater increases in the LTC group on either Day 1 (IFN-α, IFN-γ) or Day 3 (IL-1β). In addition, RANTES increased over time in cats treated with the LTC. Both LTC and PI protocols induced immune-enhancing effects, suggesting a possible clinical use for the management of chronic infectious diseases like FIP. Activating the TLR 3 and 9 pathways (LTC) induced superior broad interferon production in vitro than the activation of the TLR 2 and 6 pathways (PI).

20024 Background: Carcinoma of unknown primary (CUP) wherein metastatic disease presents without an identifiable primary tumor site represents approximately 3–5% of all cancers. Identifying the origin of the primary tumor in patients with CUP can enable rational choice of therapeutic regimens. We developed an optimized set of ten gene markers for a quantitative reverse transcriptase polymerase chain reaction (qRTPCR) assay, and demonstrated high accuracy in predicting the tissue of origin when used on with formalin-fixed, paraffin-embedded (FFPE) metastatic carcinoma samples. Methods: Twenty-three putative tissue-specific markers for lung, colon, pancreas, breast, prostate and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by qRTPCR on 205 FFPE metastatic carcinomas of known tissue origin. Next, we optimized the RNA isolation and qRTPCR methods for these ten markers, and tested the qRTPCR assay on two sets of FFPE metastatic tumors. Results: We applied the 10-gene qRTPCR assay to a set of 260 metastatic tumors of known origin, generating an overall accuracy of 78%. Furthermore we tested an independent set of 48 metastatic samples, including thirty-seven samples where either the tissue of origin was known or which initially presented as CUP but were subsequently resolved. In these 48 samples, our assay demonstrated an accuracy of 76%. Conclusions: Our results suggested that optimized ten-gene markers qRTPCR assay reliably predicts tissue of origin of metastatic carcinomas in FFPE tissues. Such assay can significantly improve the rate of tissue of origin identification for carcinoma of unknown primary. [Table: see text]

Purpose:To assess the rapid antigen test (RAT) against the gold standard reverse transcription-polymerase chain reaction (RT-PCR) to screen COVID-19 infection in asymptomatic patients undergoing ophthalmic procedures.Methods:This was a retrospective hospital-based study. Point-of-care (PoC) RAT was performed using nasopharyngeal swab, while RT-PCR for SARS-CoV-2 viral RNA was performed using both nasopharyngeal and throat swabs.Results:A total of 629 patients were tested for SARS-CoV-2 by using both RAT and RT-PCR. Only one patient had tested positive for SARS-CoV-2 with both RAT and RT-PCR, while two patients had tested positive with RT-PCR after an initial negative RAT. The positivity rate for RAT was 0.15% (1/629), and that for RT-PCR was 0.47%. Percent agreement or proportion of agreement observed between the two tests was 99.68%, while Cohen’s kappa coefficient value was 0.49. The sensitivity of RAT in comparison to RT-PCR was 33.33%, specificity was 100%, positive predictive value was 100%, and negative predictive value was 99.68%.Conclusion:The sensitivity and Cohen’s kappa coefficient in our study were low but that can be attributed to the overall low positivity rates with both RAT and RT-PCR. However, percent agreement observed between the two tests was very high. Therefore, we recommend initial screening of all the patients for COVID-19 symptoms followed by RAT before performing any ophthalmic surgical procedure to ensure the safety of the health care professionals as well as the patients.

ObjectivesCompared with reverse transcription polymerase chain reaction (RT-PCR), rapid antigen detection tests (RADTs) for SARS-CoV-2 diagnostics are faster, less expensive, but also less accurate. Performance of RADTs is context-specific and depends on disease prevalence. In this real-world study, we assessed impact of RADTs in an inpatient setting through the entire COVID-19 emergency phase. MethodsIn this matched retrospective study, data on RT-PCR and RADT laboratory diagnoses of SARS-CoV-2 made between February 2020 and May 2023 in a large hospital were analyzed. To be included in the study, samples used for both RT-PCR and RADT had to be collected on the same day. ResultsOf 278,867 RT-PCR tests available, 13,321 same-day RADTs could be matched to RT-PCR. Over the entire period, RADT sensitivity and specificity were 76.4% and 99.4%, respectively. With the observed positivity rate of 9.4%, positive and negative predictive values were 92.7% and 97.6%, respectively. Compared with the periods dominated by the Alpha and Delta variants of concern, RADT accuracy was slightly lower during the Omicron phase. ConclusionThis real-world experience demonstrates that despite suboptimal sensitivity and some variation by predominant variants of concern and positivity prevalence, the use of RADTs is useful in hospital settings. Public health implications were discussed.

A prospective clinical evaluation of the diagnostic accuracy of the SARS-CoV-2 rapid antigen test using anterior nasal samples

BackgroundEvidence of COVID-19 vaccine safety relied upon the global vaccine monitoring infrastructure due to shortened clinical development timelines and emergency use licensure. Differences in AVSS capacity between high-income countries (HICs) versus low- and middle-income countries (LMICs) were known prior to the pandemic. ObjectiveTo assess the global landscape of COVID-19 vaccine AVSS activities to identify gaps in safety evidence generation across vaccine products and populations with a focus on LMICs. MethodsA cross-sectional survey was conducted in January 2022 on AVSS activities evaluating adverse events following immunization (AEFI). Data collected included country, targeted population, COVID-19 vaccine product(s), design of surveillance/monitoring activities or study, and AEFIs to be monitored.To supplement these findings, we conducted a literature review of COVID-19 vaccine safety activities published in PubMed through January 2023. Observational activities assessing AEFI, specifically adverse events of special interest (AESI), following routine use of COVID-19 vaccines in medical practice were included; systematic reviews, benefit/risk assessments, clinical trials, and case reports/series were excluded. ResultsThe survey, completed by 34 respondents and compiled with reviews of 7 publicly available Risk Management Plans from five vaccine manufacturers, identified 79 monitoring activities in HICs, 24 in LMICs, and 9 in multiple regions. Most activities in LMICs were planned cohort event monitoring (CEM) studies (n = 18); two multi-national hospital-based sentinel surveillance studies for AESI were ongoing. Activities in LMICs evaluated multiple COVID-19 vaccine products simultaneously and were sponsored by health authorities. The literature review identified 1245 unique citations, of which 379 met inclusion criteria. The majority evaluated vaccines primarily used in high-income countries: Pfizer BioNTech (Comirnaty; n = 303), Moderna (mRNA-1273; n = 164), AstraZeneca (AZD1222; n = 126), and Janssen (Ad26.COV2.S); n = 62); 14 citations assessed vaccines used exclusively in LMICs: Sinovac (CoronaVac), Beijing CNBG (BBIBP-Corv), Bharat (Covaxin), SII (Covashield), and Gamaleya (Gam-Covid-Vac) vaccines. ConclusionsRobust safety evidence for input into benefit/risk assessments is likely unavailable for most COVID-19 vaccines used primarily in LMICs due to emphasis on cohort event monitoring methods. Goals for equitable vaccine access should be coupled with investment and support for building infrastructure and capacity for safety evidence generation to inform policy and regulatory decisions at local levels.

ObjectiveTo analyze the premarket purchase commitments for coronavirus disease 2019 (covid-19) vaccines from leading manufacturers to recipient countries.DesignCross sectional analysis.Data sourcesWorld Health Organization’s draft landscape of covid-19 candidate vaccines, along...

Socioeconomic status and risk of cardiovascular disease in 20 low-income, middle-income, and high-income countries: the Prospective Urban Rural Epidemiologic (PURE) study

The American Academy of Pediatrics recommends that all negative rapid diagnostic tests for Streptococcus pyogenes pharyngitis be backed up by culture, which creates a dilemma for clinicians who must make treatment decisions without complete diagnostic information at the time of visit. The use of a follow-up serial rapid antigen test instead of a follow-up culture would provide a more timely result. Two swabs were collected from children who were suspected of having S pyogenes pharyngitis. Each swab was used for a culture and an OSOM Ultra Strep A Test rapid antigen test. The gold standard of comparison was defined as the identification of S pyogenes on either of the 2 culture plates. Three diagnostic strategies were evaluated: a single rapid antigen test, a rapid antigen test with follow-up rapid antigen test (rapid-rapid), and a rapid antigen test with follow-up culture (rapid-culture). A total of 210 (23.7%) of 887 throat cultures with matched data were identified with S pyogenes. A single rapid antigen test had a sensitivity of 87.6% (95% confidence interval [CI]: 83.2%-92.1%), the sensitivity of the rapid-rapid follow-up was 91.4% (95% CI: 87.6%-95.2%), and the sensitivity of the rapid-culture follow-up was 95.7% (95% CI: 93.0%-98.5%), which was significantly higher than the others. As shown in Fig 1, when these test strategies were evaluated on a subgroup with clinical symptoms commonly associated with S pyogenes pharyngitis, the sensitivities all increased and were no longer significantly different. None of the strategies reliably exceeded a 95% sensitivity threshold. The American Academy of Pediatrics strategy for S pyogenes detection in children with pharyngitis, requiring a backup culture for those with negative antigen tests, was not exceeded by any other test strategy; however, a rapid-rapid diagnostic strategy may approximate it with the use of judicious clinical selection of patients.

IntroductionThe COVID-19 pandemic focused attention on the importance of vaccine security to national security. Demand for vaccines far exceeded supply when the first COVID-19 vaccines were released. Growing data suggest...

Rapid antigen detection tests (RADTs) are immunoassays that produce results in 15 min or less, have low sensitivity (50 %), but high specificity (95 %). We studied the clinical impact and laboratory savings of a diagnostic algorithm for influenza infection using RADTs as a first-step technique during the influenza season. From January 15th to March 31st 2014, we performed a diagnostic algorithm for influenza infection consisting of an RADT for all respiratory samples received in the laboratory. We studied all the patients with positive results for influenza infection, dividing them into two groups: Group A with a negative RADT but positive reference tests [reverse transcription polymerase chain reaction (RT-PCR) and/or culture] and Group B with an initial positive RADT. During the study period, we had a total of 1,156 patients with suspicion of influenza infection. Of them, 217 (19 %) had a positive result for influenza: 132 (11 %) had an initial negative RADT (Group A) and 85 (7 %) had a positive RADT (Group B). When comparing patients in Group A and Group B, we found significant differences, as follows: prescribed oseltamivir (67 % vs. 82 %; p = 0.02), initiation of oseltamivir before 24 h (89 % vs. 97 %; p = 0.03), antibiotics prescribed (89 % vs. 67 %; p = <0.01), intensive care unit (ICU) admissions after diagnosis (23 % vs. 14 %; p = 0.05), and need for supplementary oxygen (61 % vs. 47 %; p = 0.01). An influenza algorithm including RADTs as the first step improves the time of administration of proper antiviral therapy, reduces the use of antibiotics and ICU admissions, and decreases hospital costs.

Activity limitations, use of assistive devices, and mortality and clinical events in 25 high-income, middle-income, and low-income countries: an analysis of the PURE study